SRCC Acknowledged Publications

Below are some selected publications that have utilized and acknowledged Stanford Research Computing Center's computational resources and expertise. For a comprehensive listing check out the Google Scholar search for Stanford Research Computing Center acknowledgements. 

It is important that publications resulting from computations performed on our systems such as Sherlock, Farmshare or SCG acknowledge this. The following wording is suggested for your Acknowledgements section:

"Some of the computing for this project was performed on the Sherlock (or XStream, Farmshare, PHS, ICME) cluster. We would like to thank Stanford University and the Stanford Research Computing Center for providing computational resources and support that contributed to these research results."

Thank you!

2023

Phage-inclusive profiling of human gut microbiomes with Phanta
Yishay Pinto, Meenakshi Chakraborty, Navami Jain & Ami S. Bhatt
Nature Biotechnology (2023) Published: 25 May 2023

Narcolepsy risk loci outline role of T cell autoimmunity and infectious triggers in narcolepsy
Hanna M. Ollila, Eilon Sharon, Ling Lin, Nasa Sinnott-Armstrong, Aditya Ambati, Selina M. Yogeshwar, Ryan P. Hillary, Otto Jolanki, Juliette Faraco, Mali Einen, Guo Luo, Jing Zhang, Fang Han, Han Yan, Xiao Song Dong, Jing Li, Jun Zhang, Seung-Chul Hong, Tae Won Kim, Yves Dauvilliers, Lucie Barateau, Gert Jan Lammers, Rolf Fronczek, Geert Mayer, Emmanuel J. Mignot, et al.
Nature Communications volume 14, Article number: 2709 (2023)

Quantifying bias introduced by sample collection in relative and absolute microbiome measurements
Dylan G. Maghini, Mai Dvorak, Alex Dahlen, Morgan Roos, Scott Kuersten & Ami S. Bhatt    
Nature Biotechnology (2023) Published: 27 April 2023

Supercritical fluids behave as complex networks
Filip Simeski & Matthias Ihme    
Nature Communications volume 14, Article number: 1996 (2023) Published: 10 April 2023

EHR foundation models improve robustness in the presence of temporal distribution shift
Lin Lawrence Guo, Ethan Steinberg, Scott Lanyon Fleming, Jose Posada, Joshua Lemmon, Stephen R. Pfohl, Nigam Shah, Jason Fries & Lillian Sung    
Nature Scientific Reports volume 13, Article number: 3767 (2023)

Predictors of Myocardial Ischemia in Patients with Kawasaki Disease: Insights from Patient-Specific Simulations of Coronary Hemodynamics
Karthik Menon, Jongmin Seo, Ryuji Fukazawa, Shunichi Ogawa, Andrew M. Kahn, Jane C. Burns & Alison L. Marsden     
Journal of Cardiovascular Translational Research (2023) Published: 20 March 2023

An optimized reporter of the transcription factor hypoxia-inducible factor 1α reveals complex HIF-1α activation dynamics in single cells
Stevan Jeknić Takamasa Kudo Joanna J. Song  Markus W. Covert
Journal of Biological Chemistry

Geometric frustration of Jahn–Teller order in the infinite-layer lattice
Woo Jin Kim, Michelle A. Smeaton, Chunjing Jia, Berit H. Goodge, Byeong-Gwan Cho, Kyuho Lee, Motoki Osada, Daniel Jost, Anton V. Ievlev, Brian Moritz, Lena F. Kourkoutis, Thomas P. Devereaux & Harold Y. Hwang
Nature Published: 22 February 2023

Charachterization of spatially mapped volumetric molecular ultrasound signals for predicting response to anti-vascular therapy
Cody A. Keller, Shaya Zarkesh, Jianhua Zhou, Amelie M. Lutz, Dimitre Hristov, Aya Kamaya & Ahmed El Kaffas
Nature Scientific Reports volume 13, Article number: 1686 (2023)

Tracer-field cross-correlations with k-nearest neighbour distributions
Arka Banerjee, Tom Abel
Monthly Notices of the Royal Astronomical Society, Volume 519, Issue 4, March 2023, Pages 4856–4868

svMorph: Interactive Geometry-Editing Tools for Virtual Patient-Specific Vascular Anatomies
Jonathan Pham, Sofia Wyetzner, Martin R. Pfaller, David W. Parker, Doug L. James, Alison L. Marsden
J Biomech Eng. Mar 2023, 145(3): 031001 

Covariance matrices for variance-suppressed simulations
Tony Zhang, Chia-Hsun Chuang, Risa H Wechsler, Shadab Alam, Joseph DeRose, Yu Feng, Francisco-Shu Kitaura, Marcos Pellejero-Ibanez, Sergio Rodríguez-Torres, Chun-Hao To, Gustavo Yepes, Cheng Zhao
Monthly Notices of the Royal Astronomical Society, Volume 518, Issue 3, January 2023
Pages 3737–3745

2022

Practical synthesis of the therapeutic leads tigilanol tiglate and its analogues
Paul A. Wender, Zachary O. Gentry, David J. Fanelli, Quang H. Luu-Nguyen, Owen D. McAteer & Edward Njoo
Nature Chemistry (2022)

Investigating the electronic structure of high explosives with X‑ray Raman spectroscopy
Oscar A. Paredes‑Mellone, Michael H. Nielsen, John Vinson, Konmeng Moua, K. Dean Skoien, Dimosthenis Sokaras & Trevor M. Willey
Nature, Scientific Reports volume 12, Article number: 19460 (2022)

MYC oncogene elicits tumorigenesis associated with embryonic, ribosomal biogenesis, and tissue-lineage dedifferentiation gene expression changes
Delaney K. Sullivan, Anja Deutzmann, Josiah Yarbrough, Maya S. Krishnan, Arvin M. Gouw, David I. Bellovin, Stacey J. Adam, Daniel F. Liefwalker, Renumathy Dhanasekaran & Dean W. Felsher
Oncogene volume 41, pages 4960–4970 (2022)

Uncovering translation roadblocks during the development of a synthetic tRNA
Arjun Prabhakar, Natalie Krahn, Jingji Zhang, Oscar Vargas-Rodriguez, Miri Krupkin, Ziao Fu, Francisco J Acosta-Reyes, Xueliang Ge, Junhong Choi, Ana Crnković, Måns Ehrenberg, Elisabetta Viani Puglisi, Dieter Söll, Joseph Puglisi
Nucleic Acids Research, Volume 50, Issue 18, 14 October 2022, Pages 10201–10211

RNA secondary structure packages evaluated and improved by high-throughput experiments
Hannah K. Wayment-Steele, Wipapat Kladwang, Alexandra I. Strom, Jeehyung Lee, Adrien Treuille, Alex Becka, Eterna Participants & Rhiju Das
Nature Methods volume 19, pages 1234–1242 (2022) Published: 03 October 2022

A comparison of approaches to improve worst-case predictive model performance over patient subpopulations
Stephen R. Pfohl, Haoran Zhang, Yizhe Xu, Agata Foryciarz, Marzyeh Ghassemi & Nigam H. Shah
Scientific Reports volume 12, Article number: 3254 (2022)

Hierarchical Orthogonal Factorization: Sparse Least Squares Problems
Abeynaya Gnanasekaran & Eric Darve
Journal of Scientific Computing volume 91, Article number: 50 (2022)

Thermodynamics of correlated electrons in a magnetic field
Jixun K. Ding, Wen O. Wang, Brian Moritz, Yoni Schattner, Edwin W. Huang & Thomas P. Devereaux
Nature Communications Physics volume 5, Article number: 204 (2022)
Published: 10 August 2022

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks
Jacob W. Freimer, Oren Shaked, Sahin Naqvi, Nasa Sinnott-Armstrong, Arwa Kathiria, Christian M. Garrido, Amy F. Chen, Jessica T. Cortez, William J. Greenleaf, Jonathan K. Pritchard & Alexander Marson
Nature Genetics volume 54, pages 1133–1144 (2022)
Published: 11 July 2022

Inhibition of calcium-triggered secretion by hydrocarbon-stapled peptides
Ying Lai, Giorgio Fois, Jose R. Flores, Michael J. Tuvim, Qiangjun Zhou, Kailu Yang, Jeremy Leitz, John Peters, Yunxiang Zhang, Richard A. Pfuetzner, Luis Esquivies, Philip Jones, Manfred Frick, Burton F. Dickey & Axel T. Brunger
Nature volume 603, pages 949–956 (2022) Published: 23 March 2022

Molecularly defined circuits for cardiovascular and cardiopulmonary control
Avin Veerakumar, Andrea R. Yung, Yin Liu & Mark A. Krasnow    
Nature (2022) Published: 01 June 2022

A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site
Chu Zheng, Yuezhi Mao, Jacek Kozuch, Austin O. Atsango, Zhe Ji, Thomas E. Markland & Steven G. Boxer    
Nature Chemistry (2022) Published: 05 May 2022

DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide
Nicolas Altemose, Annie Maslan, Owen K. Smith, Kousik Sundararajan, Rachel R. Brown, Reet Mishra, Angela M. Detweiler, Norma Neff, Karen H. Miga, Aaron F. Straight & Aaron Streets   
Nature Methods volume 19, pages 711–723 (2022)
Published: 08 April 2022

Structure-Based Evolution of G Protein-Biased μ-Opioid Receptor Agonists
Dr. Haoqing Wang, Florian Hetzer, Dr. Weijiao Huang, Dr. Qianhui Qu, Dr. Justin Meyerowitz, Dr. Jonas Kaindl, Dr. Harald Hübner, Prof. Dr. Georgios Skiniotis, Prof. Dr. Brian K. Kobilka, Prof. Dr. Peter Gmeiner
Angewandte Chemie International Edition First published: 06 April 2022 https://doi.org/10.1002/anie.202200269

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements
Savannah J Hoyt, Jessica M Storer, Gabrielle A Hartley, Patrick G S Grady, Ariel Gershman, Leonardo G de Lima, Charles Limouse, Reza Halabian, Luke Wojenski, Matias Rodriguez, Nicolas Altemose, Arang Rhie, Leighton J Core, Jennifer L Gerton, Wojciech Makalowski, Daniel Olson, Jeb Rosen, Arian F A Smit, Aaron F Straight, Mitchell R Vollger, Travis J Wheeler, Michael C Schatz, Evan E Eichler, Adam M Phillippy, Winston Timp, Karen H Migia, Rachel J O'Neill  
Science, 1 Apr 2022 Vol 376, Issue 6588
DOI: 10.1126/science.abk3112

Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing
Sneha D. Goenka, John E. Gorzynski, Kishwar Shafin, Dianna G. Fisk, Trevor Pesout, Tanner D. Jensen, Jean Monlong, Pi-Chuan Chang, Gunjan Baid, Jonathan A. Bernstein, Jeffrey W. Christle, Karen P. Dalton, Daniel R. Garalde, Megan E. Grove, Joseph Guillory, Alexey Kolesnikov, Maria Nattestad, Maura R. Z. Ruzhnikov, Mehrzad Samadi, Ankit Sethia, Elizabeth Spiteri, Christopher J. Wright, Katherine Xiong, Tong Zhu, Miten Jain, Fritz J. Sedlazeck, Andrew Carroll, Benedict Paten & Euan A. Ashley    
Nature Biotechnology Published: 28 March 2022

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Kathrin Leppek, Gun Woo Byeon, Wipapat Kladwang, Hannah K. Wayment-Steele, Craig H. Kerr, Adele F. Xu, Do Soon Kim, Ved V. Topkar, Christian Choe, Daphna Rothschild, Gerald C. Tiu, Roger Wellington-Oguri, Kotaro Fujii, Eesha Sharma, Andrew M. Watkins, John J. Nicol, Jonathan Romano, Bojan Tunguz, Fernando Diaz, Hui Cai, Pengbo Guo, Jiewei Wu, Fanyu Meng, Shuai Shi, Eterna Participants, Philip R. Dormitzer, Alicia Solórzano, Maria Barna & Rhiju Das
Nature Communications volume 13, Article number: 1536 (2022) Published: 22 March 2022

Development of a polygenic risk score to improve detection of peripheral artery disease
Fudi Wang, Ilies Ghanzouri, Nicholas J Leeper, Philip S Tsao, Elsie Gyang Ross
Vascular Medicine, First Published March 14, 2022 https://doi.org/10.1177/1358863X211067564

Multiple causal variants underlie genetic associations in humans
Nathan S. Abell, Marianne K. DeGorter, Michael J. Gloudemans, Emily Greenwald, Kevin S. Smith, Zihuai He and Stephen B. Montgomery
Science • 17 Mar 2022 • Vol 375, Issue 6586 • pp. 1247-1254 • DOI: 10.1126/science.abj5117

fastISM: performant in silico saturation mutagenesis for convolutional neural networks
Surag Nair, Avanti Shrikumar, Jacob Schreiber, Anshul Kundaje
Bioinformatics, Volume 38, Issue 9, 1 May 2022, Pages 2397–2403, https://doi.org/10.1093/bioinformatics/btac135
Published: 03 March 2022

Vernier template synthesis of molecular knots
Zoe Ashbridge Elisabeth Kreidt Lucian Pirvu Fredrik Schaufelberger Joakim Halldin Stenlid Frank Abild-Pedersenand David A. Leig
Science  3 Mar 2022  Vol 375, Issue 6584  pp. 1035-1041  DOI: 10.1126/science.abm9247

TDP-43 represses cryptic exon inclusion in the FTD–ALS gene UNC13A
X. Rosa Ma, Mercedes Prudencio, …Aaron D. Gitler    
Nature volume 603, pages 124–130 (2022)

A comparison of approaches to improve worst-case predictive model performance over patient subpopulations
Stephen R. Pfohl, Haoran Zhang, Yizhe Xu, Agata Foryciarz, Marzyeh Ghassemi & Nigam H. Shah     
Nature Scientific Reports volume 12, Article number: 3254 (2022)
Published: 28 February 2022

Cost-Effectiveness Analysis and Microsimulation of Serial Multiparametric Magnetic Resonance Imaging in Active Surveillance of Localized Prostate Cancer
Christopher J. Magnani, Tina Hernandez-Boussard, Laurence C. Baker, Jeremy D. Goldhaber-Fiebert and James D. Brooks
Journal of Urology 25 Feb 2022
https://doi.org/10.1097/JU.0000000000002490

Net benefit, calibration, threshold selection, and training objectives for algorithmic fairness in healthcare
Stephen R. Pfohl, Yizhe Xu, Agata Foryciarz, Nikolaos Ignatiadis, Julian Genkins, Nigam H. Shah
arXiv:2202.01906, Submitted on 3 Feb 2022

Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins
Brian L. Hie, Kevin K. Yang, Peter S.Kim
Cell Systems 3 February 2022 https://doi.org/10.1016/j.cels.2022.01.003

Born-Infeld (BI) for AI: Energy-Conserving Descent (ECD) for Optimization
G. Bruno De Luca, Eva Silverstein
arXiv:2201.11137 Submitted on 26 Jan 2022

Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay
Anna N. Rasmussen, Christopher A. Francis
Microbial Ecology Research Article 25 January 2022

Confidence intervals for the Cox model test error from cross-validation
MW Sun, R Tibshirani
arXiv preprint arXiv:2201.10770, 2022

Electrophysiological foundations of the human default-mode network revealed by intracranial-EEG recordings during resting-state and cognition
Anup Das, Carlo de los Angeles, Vinod Menon
NeuroImage https://doi.org/10.1016/j.neuroimage.2022.118927  Available online 21 January 2022

Deep Learning–Based Retrofitting and Seismic Risk Assessment of Road Networks
Rodrigo Silva-Lopez, S.M.ASCE; Jack W. Baker, M.ASCE; and Alan Poulos, S.M.ASCE
Journal of Computing in Civil Engineering Volume 36 Issue 2 - March 2022

Gendered knowledge in fields and academic careers
Lanu Kim, Daniel Scott Smith, Bas Hofstra, Daniel A. McFarland
Research Policy Volume 51, Issue 1, January 2022

2021

Sensitivity Analysis of Gas-Surface Modeling in Nonequilibrium Flows
Jacob T. Needels, Umran Duzel, Kyle M. Hanquist and Juan J. Alonso
AIAA 2022-1636 Published Online:29 Dec 2021 https://doi.org/10.2514/6.2022-1636

Earth as a transducer for axion dark-matter detection
Ariel Arza, Michael A. Fedderke, Peter W. Graham, Derek F. Jackson Kimball, Saarik Kalia
arXiv:2112.09620 Submitted on 17 Dec 2021

Covariance matrices for variance-suppressed simulations
Tony Zhang, Chia-Hsun Chuang, Risa H. Wechsler, Shadab Alam, Joseph DeRose, Yu Feng, Francisco-Shu Kitaura, Marcos Pellejero-Ibanez, Sergio Rodríguez-Torres, Chun-Hao To, Gustavo Yepes, Cheng Zhao
arXiv:2112.10845 Submitted on 20 Dec 2021

Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics
Linta Reji, Emily L. Cardarelli, Kristin Boye, John R. Bargar & Christopher A. Francis    
DOI https://doi.org/10.1038/s41396-021-01167-7 The ISME Journal (2021)

Midlatitude Error Growth in Atmospheric GCMs: The Role of Eddy Growth Rate
Aditi Sheshadri, Marshall Borrus, Mark Yoder, Thomas Robinson
First published: 29 November 2021 https://doi.org/10.1029/2021GL096126

Priors on red galaxy stochasticity from hybrid effective field theory
Nickolas Kokron, Joseph DeRose, Shi-Fan Chen, Martin White, Risa H. Wechsler
arXiv:2112.00012 Submitted on 30 Nov 2021

A Performance-Based Approach to Quantify Atmospheric River Flood Risk
Corinne Bowers, Katherine A. Serafin, and Jack Baker
https://doi.org/10.5194/nhess-2021-337

COMAP Early Science: V. Constraints and Forecasts at z∼3
Dongwoo T. Chung, Patrick C. Breysse, Kieran A. Cleary, Håvard T. Ihle, Hamsa Padmanabhan, Marta B. Silva, J. Richard Bond, Jowita Borowska, Morgan Catha, Sarah E. Church, Delaney A. Dunne, Hans Kristian Eriksen, Marie Kristine Foss, Todd Gaier, Joshua Ott Gundersen, Stuart E. Harper, Andrew I. Harris, Brandon Hensley, Richard Hobbs, Laura C. Keating, Junhan Kim, James W. Lamb, Charles R. Lawrence, Jonas Gahr Sturtzel Lunde, Norman Murray, Timothy J. Pearson, Liju Philip, Maren Rasmussen, Anthony C. S. Readhead, Thomas J. Rennie, Nils-Ole Stutzer, Bade D. Uzgil, Marco P. Viero, Duncan J. Watts, Risa H. Wechsler, Ingunn Kathrine Wehus, David P. Woody
arXiv:2111.05931  last revised 12 Nov 2021 (this version, v2)

Automated generation of 0D and 1D reduced-order models of patient-specific blood flow
Martin R. Pfaller, Jonathan Pham, Aekaansh Verma, Nathan M. Wilson, David W. Parker, Weiguang Yang, Alison L. Marsden
arXiv:2111.04878 Submitted on 8 Nov 2021

Why Have the Observed High-frequency QPOs Not Been Produced by (MHD) Computer Simulations of Black Hole Accretion Disks?
Robert V. Wagoner and Celia R. Tandon
Res. Notes AAS 5 274 Published November 2021

Modeling Potential-Dependent Electrochemical Activation Barriers: Revisiting the Alkaline Hydrogen Evolution Reaction
Jiang Li, Joakim Halldin Stenlid, Thomas Ludwig, Philomena Schlexer Lamoureux, and Frank Abild-Pedersen
J. Am. Chem. Soc. 2021, Publication Date:November 9, 2021 https://doi.org/10.1021/jacs.1c07276

A language-matching model to improve equity and efficiency of COVID-19 contact tracing
Lisa Lu, Benjamin Anderson, Raymond Ha, Alexis D’Agostino, Sarah L. Rudman, Derek Ouyang, and Daniel E. Ho
PNAS October 26, 2021 118 (43) e2109443118; https://doi.org/10.1073/pnas.2109443118

Quantifying the Severity of Adverse Drug Reactions Using Social Media: Network Analysis
Adam Lavertu,  Tymor Hamamsy,   Russ B Altman
J Med Internet Res 2021;23(10):e27714 Published on 21.10.2021 in Vol 23, No 10 (2021): October

Improved detection of disease-associated gut microbes using 16S sequence-based biomarkers
Brianna S. Chrisman, Kelley M. Paskov, Nate Stockham, Jae-Yoon Jung, Maya Varma, Peter Y. Washington, Christine Tataru, Shoko Iwai, Todd Z. DeSantis, Maude David & Dennis P. Wall
BMC Bioinformatics volume 22, Article number: 509 (2021)

Platelet transcriptome identifies progressive markers and potential therapeutic targets in chronic myeloproliferative neoplasms
Zhu Shen, Wenfei Du, Cecelia Perkins, Lenn Fechter, Vanita Natu, Holden Maecker, Jesse Rowley, Jason Gotlib, James Zehnder, Anandi Krishnan
Cell Reports Medicine, Volume 2, Issue 10, 19 October 2021, 100425

Decreasing Phanerozoic extinction intensity as a consequence of Earth surface oxygenation and metazoan ecophysiology
Richard G. Stockey, Alexandre Pohl, Andy Ridgwell, Seth Finnegan and Erik A. Sperling
 PNAS October 12, 2021 118 (41) e2101900118; https://doi.org/10.1073/pnas.2101900118

Nonaqueous Solvent Adsorption on Transition Metal Surfaces with Density Functional Theory: Interaction of N,N-Dimethylformamide (DMF), Tetrahydrofuran (THF), and Dimethyl Sulfoxide (DMSO) with Ag, Cu, Pt, Rh, and Re Surfaces
Thomas Ludwig, Aayush R. Singh, and Jens K. Nørskov
J. Phys. Chem. C 202 Publication Date:October 4, 2021 https://doi.org/10.1021/acs.jpcc.1c05724

First Constraints on Dark Photon Dark Matter with Superconducting Nanowire Detectors in an Optical Haloscope
Jeff Chiles, Ilya Charaev, Robert Lasenby, Masha Baryakhtar, Junwu Huang, Alexana Roshko, George Burton, Marco Colangelo, Ken Van Tilburg, Asimina Arvanitaki, Sae Woo Nam, Karl K. Berggren
arXiv:2110.01582 Submitted on 4 Oct 2021

An optimized ATAC-seq protocol for genome-wide mapping of active regulatory elements in primary mouse cortical neurons
Maya Maor-Nof, Zohar Shipony, Georgi K. Marinov, William J. Greenleaf, Aaron D. Gitler
STAR Protocols, Cell Press https://doi.org/10.1016/j.xpro.2021.100854  30 September 2021

Computational simulation-derived hemodynamic and biomechanical properties of the pulmonary arterial tree early in the course of ventricular septal defects
Melody L. Dong, Ingrid S. Lan, Weiguang Yang, Marlene Rabinovitch, Jeffrey A. Feinstein & Alison L. Marsden    
Biomechanics and Modeling in Mechanobiology (2021) Published: 28 September 2021

The Effects of Dark Matter and Baryonic Physics on the Milky Way Subhalo Population in the Presence of the Large Magellanic Cloud
Ethan O. Nadler, Arka Banerjee, Susmita Adhikari, Yao-Yuan Mao, Risa H. Wechsler
Cosmology and Nongalactic Astrophysics arXiv:2109.12120 Submitted on 24 Sep 2021

The three-spin intermediate at the O–O cleavage and proton-pumping junction in heme–Cu oxidases
Anex Jose, Andrew W. Schaefer, Antonio C. Roveda Jr., Wesley J. Transue, Sylvia K. Choi, Ziqiao Ding, Robert B. Gennis and Edward I. Solomon
Science 10 Sep 2021 Vol 373, Issue 6560  pp. 1225-1229 DOI: 10.1126/science.abh3209

Modular Synthesis of Fully Degradable Imine-Based Semiconducting p-Type and n-Type Polymers
Helen Tran, Shayla Nikzad, Jerika A. Chiong, Nathaniel J. Schuster, Amnahir E. Peña-Alcántara, Vivian R. Feig, Yu-Qing Zheng, and Zhenan Bao
Chem. Mater. 2021 Publication Date:September 10, 2021 https://doi.org/10.1021/acs.chemmater.1c02258

A markerless platform for ambulatory systems neuroscience
Michael P. Silvernagel, Alissa S. Ling, Paul Nuyujukian
Science Robotics 8 Sep 2021 Vol 6, Issue 58 DOI: 10.1126/scirobotics.abj7045

A comparison of approaches to improve worst-case predictive model performance over patient subpopulations
Stephen R. Pfohl, Haoran Zhang, Yizhe Xu, Agata Foryciarz, Marzyeh Ghassemi, Nigam H. Shah
Submitted on 27 Aug 2021 arXiv:2108.12250

Two new hybrid populations expand the swordtail hybridization model system
Daniel L. Powell, Ben Moran, Bernard Kim, Shreya M. Banerjee, Stepfanie M. Aguillon, Paola Fascinetto-Zago, Quinn Langdon, Molly Schumer
Evolution, published: 30 August 2021 https://doi.org/10.1111/evo.14337

Electric field orientations in solution and enzyme active site revealed by a two-directional vibrational probe
Chu Zheng, Yuezhi Mao, Jacek Kozuch, Austin O. Atsango, Zhe Ji, Thomas E. Markland and Steven G. Boxer
ChemRxiv DOI 10.33774/chemrxiv-2021-578vg

Paley-like graphs for the Ramsey number r(C4,Kt)
Yuval Wigderson
arXiv:2108.08753 Submitted on 19 Aug 2021

Beware of Fake νs: The Effect of Massive Neutrinos on the Non-Linear Evolution of Cosmic Structure
Adrian E. Bayer, Arka Banerjee, Uros Seljak
Submitted on 9 Aug 2021 arXiv:2108.04215

Quantifying the effect of precipitation on landslide hazard in urbanized and non-urbanized areas
Elizabeth C. Johnston, Frances V. Davenport, Lijing Wang, Jef K. Caers, Suresh Muthukrishnan, Marshall Burke, Noah S. Diffenbaugh
First published: 09 August 2021 https://doi.org/10.1029/2021GL094038

Light bending and X-ray echoes from behind a supermassive black hole
D. R. Wilkins, L. C. Gallo, E. Costantini, W. N. Brandt & R. D. Blandford    
Nature volume 595, pages 657–660 (2021) Published: 28 July 2021

Using machine learning to analyze physical causes of climate change: A case study of U.S. Midwest extreme precipitation
Frances V. Davenport, Noah S. Diffenbaugh
Geophysical Research Letters  First published: 21 July 2021 https://doi.org/10.1029/2021GL093787

Modeling Nearest Neighbor distributions of biased tracers using Hybrid Effective Field Theory
Arka Banerjee, Nickolas Kokron, Tom Abel
Submitted on 21 Jul 2021 arXiv:2107.10287

A Design Strategy for Intrinsically Stretchable High-Performance Polymer Semiconductors: Incorporating Conjugated Rigid Fused-Rings with Bulky Side Groups
Deyu Liu, Jaewan Mun, Gan Chen, Nathaniel J. Schuster, Weichen Wang, Yu Zheng, Shayla Nikzad, Jian-Cheng Lai, Yilei Wu, Donglai Zhong, Yangju Lin, Yusheng Lei, Yuelang Chen, Sangah Gam, Jong Won Chung, Youngjun Yun, Jeffrey B.-H. Tok, and Zhenan Bao
Journal of the American Chemical Society July 21, 2021 https://doi.org/10.1021/jacs.1c04984

Single-cell transcriptomic profiling reveals distinct mechanical responses between normal and diseased tendon progenitor cells
Chris Still, Wen-Teh Chang, Seth L.Sherman, Kyle R. Sochacki, Jason L. Dragoo, Lei S. Qi
Cell Reports Medicine Volume 2, Issue 7, 20 July 2021

Warming up cold inflation
William DeRocco, Peter W. Graham, Saarik Kalia
Submitted on 15 Jul 2021 arXiv:2107.07517

On the Periodicity of Cardiovascular Fluid Dynamics Simulations
Martin R. Pfaller, Jonathan Pham, Nathan M. Wilson, David W. Parker & Alison L. Marsden    
Annals of Biomedical Engineering (2021) Published: 24 June 2021

Native mass spectrometry analyses of chaperonin complex TRiC/CCT reveal subunit N-terminal processing and re-association patterns
Miranda P. Collier, Karen Betancourt Moreira, Kathy H. Li, Yu-Chan Chen, Daniel Itzhak, Rahul Samant, Alexander Leitner, Alma Burlingame & Judith Frydman     
Nature Scientific Reports volume 11, Article number: 13084 (2021)

Genetic risk for subjective reports of insomnia associate only weakly with polygraphic measures of insomnia in 2,770 adults
Jonathan Foldager, MS, Paul E. Peppard, PhD, Erika W. Hagen, PhD, MS, Katie L. Stone, PhD, Daniel S. Evans, PhD, MPH, Gregory J. Tranah, PhD, MS, Helge Sørensen, PhD, Poul Jennum, MD, DMSc , Emmanuel Mignot, MD, PhD , Logan Schneider, MD
Journal of Clinical Sleep Medicine, Published Online:June 21, 2021 https://doi.org/10.5664/jcsm.9468

A metabolic regulon reveals early and late acting enzymes in neuroactive Lycopodium alkaloid biosynthesis
Ryan S. Nett, Yaereen Dho, Yun-Yee Low, and Elizabeth S. Sattely
PNAS June 15, 2021 118 (24) e2102949118; https://doi.org/10.1073/pnas.2102949118

Neural Collapse Under MSE Loss: Proximity to and Dynamics on the Central Path
X.Y. Han, Vardan Papyan, David L. Donoho
arXiv:2106.02073 Submitted on 3 Jun 2021

Computational fluid dynamics simulations to predict false lumen enlargement after surgical repair of Type-A aortic dissection
Rohan Shad, Sandra Kong, Robyn Fong, Nicolas Quach, Patpilai Kasinpila, Cayley Bowles, Anson Lee, William Hiesinger
Seminars in Thoracic and Cardiovascular Surgery,  3 June 2021 https://doi.org/10.1053/j.semtcvs.2021.05.012

The Earth as a transducer for dark-photon dark-matter detection
Michael A. Fedderke, Peter W. Graham, Derek F. Jackson Kimball, Saarik Kalia
arXiv:2106.00022 31 May 2021

Dark Energy Survey Year 3 results: cosmology from combined galaxy clustering and lensing -- validation on cosmological simulations
J. DeRose, R. H. Wechsler, M. R. Becker, E. S. Rykoff, S. Pandey, N. MacCrann, A. Amon, J. Myles, E. Krause, D. Gruen, B. Jain, M. A. Troxel, J. Prat, A. Alarcon, C. Sánchez, J. Blazek, M. Crocce, G. Giannini, M. Gatti, G. M. Bernstein, J. Zuntz, S. Dodelson, X. Fang, O. Friedrich, L. F. Secco, J. Elvin-Poole, S. Everett, F. Menanteau, R. Miquel, J. J. Mohr et al.
arXiv:2105.13547 28 May 2021

Metabolic tradeoffs control biodiversity gradients through geological time
Thomas H. Boag, William Gearty, Richard G. Stockey
Current Biology, Published: May 6, 2021 https://doi.org/10.1016/j.cub.2021.04.021

High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs
Betty Ha, Kevin P. Larsen, Jingji Zhang, Ziao Fu, Elizabeth Montabana, Lynnette N. Jackson, Dong-Hua Chen & Elisabetta Viani Puglisi
Nature Communications volume 12, Article number: 2500 (2021) Published: 04 May 2021

Anomalously warm weather and acute care visits in patients with multiple sclerosis: A retrospective study of privately insured individuals in the US
Holly Elser, Robbie M. Parks, Nuriel Moghavem, Mathew V. Kiang, Nina Bozinov, Victor W. Henderson, David H. Rehkopf,  Joan A. Casey
PLOS Published: April 26, 2021 https://doi.org/10.1371/journal.pmed.1003580

A model of spectral line broadening in signal forecasts for line-intensity mapping experiments
Dongwoo T. Chung, Patrick C. Breysse, Håvard Tveit Ihle, Hamsa Padmanabhan, Marta B. Silva, J. Richard Bond, Jowita Borowska, Kieran A. Cleary, Hans Kristian Eriksen, Marie Kristine Foss, Joshua Ott Gundersen, Laura C. Keating, Jonas Gahr Sturtzel Lunde, Nils-Ole Stutzer, Marco P. Viero, Duncan J. Watts, Ingunn Kathrine Wehus
Submitted on 22 Apr 2021 arXiv:2104.11171

Universal two-component dynamics in supercritical fluids
Peihao Sun, J. B. Hastings, Daisuke Ishikawa, Alfred Q. R. Baron, Giulio Monaco
arXiv:2104.07732 Submitted on 15 Apr 2021

Coordinated Reset Vibrotactile Stimulation Induces Sustained Cumulative Benefits in Parkinson's
 Kristina J. Pfeifer, Justus A. Kromer, Alexander J. Cook, Traci Hornbeck, Erika A. Lim, Bruce J. P. Mortimer, Adam S. Fogarty, Summer S. Han, Rohit Dhall, Casey H. Halpern and Peter A. Tass
Front. Physiol., Published: 06 April 2021doi: 10.3389/fphys.2021.624317

The Structure of the Oscillon: The Dynamics of Attractive Self-Interaction
David Cyncynates, Tudor Giurgica-Tiron
Submitted on 5 Apr 2021 arXiv:2104.02069

Ontology-driven weak supervision for clinical entity classification in electronic health records
Jason A. Fries, Ethan Steinberg, Saelig Khattar, Scott L. Fleming, Jose Posada, Alison Callahan & Nigam H. Shah    
Nature Communications volume 12, Article number: 2017 (2021)

De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures
Ramya Rangan, Andrew M Watkins, Jose Chacon, Rachael Kretsch, Wipapat Kladwang, Ivan N Zheludev, Jill Townley, Mats Rynge, Gregory Thain, Rhiju Das
Nucleic Acids Research, gkab119, https://doi.org/10.1093/nar/gkab119 Published: 08 March 2021

How Did Absentee Voting Affect the 2020 U.S.Election?
Jesse Yoder, Cassandra Handan-Nader, Andrew Myers, Tobias Nowacki, Daniel M. Thompson, Jennifer A. Wu, Chenoa Yorgason, and Andrew B. Hall
Democracy & Polarization Lab, Stanford University March 5, 2021

Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics
Marc Jan Bonder, Craig Smail, Michael J. Gloudemans, Laure Frésard, David Jakubosky, Matteo D’Antonio, Xin Li, Nicole M. Ferraro, Ivan Carcamo-Orive, Bogdan Mirauta, Daniel D. Seaton, Na Cai, Dara Vakili, Danilo Horta, Chunli Zhao, Diane B. Zastrow, Devon E. Bonner, HipSci Consortium, iPSCORE consortium, Undiagnosed Diseases Network, PhLiPS consortium, Matthew T. Wheeler, Helena Kilpinen, Joshua W. Knowles, Erin N. Smith, Kelly A. Frazer, Stephen B. Montgomery & Oliver Stegle
Nature Genetics volume 53, pages 313–321(2021) Published: 04 March 2021

An automated optimization strategy to design collimator geometry for small field radiation therapy systems
Jinghui Wang, Lei Wang, Peter G Maxim and Billy W Loo Jr
Physics in Medicine & Biology 3 March 2021

Beyond the Core: Who Has Larger Social Networks?
Bas Hofstra, Rense Corten, Frank van Tubergen
Social Forces, Volume 99, Issue 3, March 2021, Pages 1274–1305, https://doi.org/10.1093/sf/soaa031

Constraints on Dark Matter Properties from Observations of Milky Way Satellite Galaxies
E. O. Nadler et al. (DES Collaboration)
Phys. Rev. Lett. 126, 091101 – Published 1 March 2021

Predicting post-operative right ventricular failure using video-based deep learning
Rohan Shad, Nicolas Quach, Robyn Fong, Patpilai Kasinpila, Cayley Bowles, Miguel Castro, Ashrith Guha, Eddie Suarez, Stefan Jovinge, Sangjin Lee, Theodore Boeve, Myriam Amsallem, Xiu Tang, Francois Haddad, Yasuhiro Shudo, Y. Joseph Woo, Jeffrey Teuteberg, John P. Cunningham, Curt P. Langlotz, William Hiesinger
arXiv:2103.00364 Submitted on 28 Feb 2021

Quantitative Hemodynamics in Aortic Dissection: Comparing in vitro MRI with FSI Simulation in a Compliant Model
Judith Zimmermann, Kathrin Baeumler, Michael Loecher, Tyler E. Cork, Fikunwa O. Kolawole, Kyle Gifford, Alison L. Marsden, Dominik Fleischmann, Daniel B. Ennis
arXiv:2102.13213 Submitted on 25 Feb 2021

Peroxo Species Formed in the Bulk of Silicate Cathodes
Zhenlian Chen, Bjoern Schwarz, Xianhui Zhang, Wenqiang Du, Lirong Zheng,  Ailing Tian, Ying Zhang,  Zhiyong Zhang,  Xiao Cheng Zeng, Zhifeng Zhang, Liyuan Huai, Jinlei Wu, Helmut Ehrenberg, Deyu Wang, Jun Li
Angewandte Chemie. First published: 23 February 2021 https://doi.org/10.1002/ange.202100730

Gifsplanation via Latent Shift: A Simple Autoencoder Approach to Progressive Exaggeration on Chest X-rays
Joseph Paul Cohen, Rupert Brooks, Sovann En, Evan Zucker, Anuj Pareek, Matthew P. Lungren, Akshay Chaudhari
arXiv:2102.09475, Submitted on 18 Feb 2021

Postselection-Free Entanglement Dynamics via Spacetime Duality
Matteo Ippoliti and Vedika Khemani
Phys. Rev. Lett. 126, 060501 – Published 9 February 2021

Cosmological cross-correlations and nearest neighbor distributions
Arka Banerjee, Tom Abel
arXiv:2102.01184, Submitted on 1 Feb 2021

The SAGA Survey. II. Building a Statistical Sample of Satellite Systems around Milky Way–like Galaxies
Yao-Yuan Mao1, Marla Geha, Risa H. Wechsler, Benjamin Weiner, Erik J. Tollerud, Ethan O. Nadler, and Nitya Kallivayalil
Published February 1, 2021 The Astrophysical Journal, Volume 907, Number 2

The Genetic Architecture of Variation in the Sexually Selected Sword Ornament and Its Evolution in Hybrid Populations
Daniel L. Powel, Cheyenne Payne, Shreya M.Banerjee, Mackenzie Keegan, Elizaveta Bashkirova, Rong feng Cui, Peter Andolfatto, Gil G. Rosenthal, Molly Schumer
Current Biology, https://doi.org/10.1016/j.cub.2020.12.049 Published: January 28, 2021

Limits on wCDM from the EFTofLSS with the PyBird code
Guido D'Amicoa, Leonardo Senatore and Pierre Zhang
Journal of Cosmology and Astroparticle Physics, Volume 2021, January 2021

The cosmology dependence of galaxy clustering and lensing from a hybrid N-body-perturbation theory model
Nickolas Kokron, Joseph DeRose, Shi-Fan Chen, Martin White, Risa H. Wechsler
arXiv:2101.11014 Submitted on 26 Jan 2021

p53 is a central regulator driving neurodegeneration caused by C9orf72 poly(PR)
Maya Maor-Nof, Zohar Shipony, Rodrigo Lopez-Gonzalez, Lisa Nakayama, Yong-Jie Zhang, Julien Couthouis, Jacob A. Blum, Patricia A. Castruita, Gabriel R. Linares, Kai Ruan, Gokul Ramaswami, David J. Simon, Aviv Nof, Manuel Santana, Kyuho Han, Nasa Sinnott-Armstrong, Michael C. Bassik, Daniel H. Geschwind, Marc Tessier-Lavigne, Laura D. Attardi, Thomas E. Lloyd, Justin K. Ichida, Fen-Biao Gao, William J. Greenleaf, Jennifer S. Yokoyama, Leonard Petrucelli, Aaron D. Gitler
Cell, Published: January 21, 2021 https://doi.org/10.1016/j.cell.2020.12.025

DES Y1 results: Splitting growth and geometry to test ΛCDM
J. Muir et al. (DES Collaboration)
Phys. Rev. D 103, 023528 – Published 21 January 2021

Spectral properties and enhanced superconductivity in renormalized Migdal-Eliashberg theory
Benjamin Nosarzewski, Michael Schüler, and Thomas P. Devereaux
Phys. Rev. B 103, 024520 – Published 20 January 2021

Deep learning predicts postsurgical recurrence of hepatocellular carcinoma from digital histopathologic images
Yamashita Rikiya; Long, Jin; Saleem Atif; Rubin, Daniel L; Shen, Jeanne
Scientific Reports (Nature Publisher Group); London Vol. 11, Iss. 1,  (2021). DOI:10.1038/s41598-021-81506-y

Genetics of 35 blood and urine biomarkers in the UK Biobank
Nasa Sinnott-Armstrong, Yosuke Tanigawa, David Amar, Nina Mars, Christian Benner, Matthew Aguirre, Guhan Ram Venkataraman, Michael Wainberg, Hanna M. Ollila, Tuomo Kiiskinen, Aki S. Havulinna, James P. Pirruccello, Junyang Qian, Anna Shcherbina, FinnGen, Fatima Rodriguez, Themistocles L. Assimes, Vineeta Agarwala, Robert Tibshirani, Trevor Hastie, Samuli Ripatti, Jonathan K. Pritchard, Mark J. Daly & Manuel A. Rivas    
Nature Genetics volume 53, pages185–194(2021) Published: 18 January 2021

Kleine Levin syndrome is associated with birth difficulties and genetic variants in the TRANK1 gene loci
Aditya Ambati, Ryan Hillary, Smaranda Leu-Semenescu, Hanna M. Ollila, Ling Lin, Emmanuel During, Neal Farber, Thomas J Rico, Juliette Faraco, Eileen Leary, Andrea Goldstein-Piekarski, Yu-Shu Huang, Fang Han, Yakov Sivan, Michel Lecendreux, Pauline Dodet, Makoto Honda, Natan Gadoth, Sona Nevsimalova, Fabio Pizza, Takashi Kanbayashi, Rosa Peraita Adrados, Guy Leschziner, Rosa Hasan, Francesca Canellas, Kazuhiko Kume, Makrina Daniilidou, Patrice Bourgin, David Rye, José L Vicario, Birgit Högl, Seung Chul Hong, Guiseppe Plazzi, Geert Mayer, Anne Marie Landtblom, Yves Dauvilliers, Isabelle Arnulf, Emmanuel Mignot
Medrxiv doi: https://doi.org/10.1101/2021.01.08.20249006

Contribution of historical precipitation change to US flood damages
Frances V. Davenport, Marshall Burke, and Noah S. Diffenbaugh
PNAS January 26, 2021 118 (4) e2017524118; https://doi.org/10.1073/pnas.2017524118

Nearest neighbour distributions: New statistical measures for cosmological clustering
Arka Banerjee, Tom Abel
Monthly Notices of the Royal Astronomical Society, Volume 500, Issue 4, February 2021, Pages 5479–5499

Correlation-assisted quantized charge pumping
Jacob A. Marks, Michael Schüler, Jan C. Budich, and Thomas P. Devereaux
Phys. Rev. B 103, 035112 – Published 11 January 2021

Deep learning model for the prediction of microsatellite instability in colorectal cancer: a diagnostic study
Rikiya Yamashita MD, Jin Long PhD, Prof Teri Longacre MD, Lan Peng MD, Prof Gerald Berry MD, Brock Martin MD, Prof John Higgins MD, Prof Daniel L Rubin MD, Jeanne Shen MD
The Lancet, Oncology, Volume 22, Issue 1, January 2021, Pages 132-141

2020

The Binary–Host Connection: Astrophysics of Gravitational-Wave Binaries from Host Galaxy Properties
Susmita Adhikari, Maya Fishbach, Daniel E. Holz, Risa H. Wechsler and Zhanpei Fanig
The Astrophysical Journal, Volume 905, Number 1 Published December 8, 2020

ATOM3D: Tasks On Molecules in Three Dimensions
Raphael J.L. Townshend, Martin Vögele, Patricia Suriana, Alexander Derry, Alexander Powers, Yianni Laloudakis, Sidhika Balachandar, Brandon Anderson, Stephan Eismann, Risi Kondor, Russ B. Altman, Ron O. Dror
arXiv:2012.04035 Submitted on 7 Dec 2020

Language models are an effective representation learning technique for electronic health record data
Ethan Steinberg, Ken Jung, Jason A.Fries, Conor K.Corbin, Stephen R.Pfohl, Nigam H. Shah
Journal of Biomedical Informatics, https://doi.org/10.1016/j.jbi.2020.103637

Biomimetic six-axis robots replicate human cardiac papillary muscle motion: pioneering the next generation of biomechanical heart simulator technology
Annabel M. Imbrie-Moore, Matthew H. Park, Michael J. Paulsen, Mark Sellke, Rohun Kulkami, Hanjay Wang, Yuanjia Zhu, Justin M. Farry, Alexandra T. Bourdillon, Christine Callinan, Haley J. Lucian, Camille E. Hironaka, Daniela Deschamps and Y. Joseph Woo
Journal of the Royal Society Interface, Published:02 December 2020https://doi.org/10.1098/rsif.2020.0614

Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation
Grant Kinsler, Kerry Geiler-Samerotte, Dmitri A Petrov
eLife 2020;9:e61271 doi: 10.7554/eLife.61271

Searching for Dwarf Galaxies in Gaia DR2 Phase-Space Data Using Wavelet Transforms
Elise Darragh-Ford, Ethan O. Nadler, Sean McLaughlin, Risa H. Wechsler
arXiv:2012.00099

Nearest Neighbor distributions: new statistical measures for cosmological clustering
Arka Banerjee, Tom Abel
Monthly Notices of the Royal Astronomical Society, staa3604, https://doi.org/10.1093/mnras/staa3604 Published: 20 November 2020

Function-Oriented Synthesis: Design, Synthesis, and Evaluation of Highly Simplified Bryostatin Analogues
Paul A. Wender, Jack L. Sloane, Quang H. Luu-Nguyen, Yasuyuki Ogawa, Akira J. Shimizu, Steven M. Ryckbosch, Jefferson H. Tyler, and Clayton Hardman
J. Org. Chem. November 17, 2020

Identification of highly selective covalent inhibitors
Shiyu Chen, Scott Lovell, Sumin Lee, Matthias Fellner, Peter D. Mace & Matthew Bogyo
Nature Biotechnology (2020) 16 November 2020

Two-component dynamics and the liquid-like to gas-like crossover in supercritical water
Peihao Sun, J. B. Hastings, Daisuke Ishikawa, Alfred Q. R. Baron, Giulio Monaco
arXiv:2008.06811 13 Nov 2020

Atomistic Insight into Cation Effects on Binding Energies in Cu-Catalyzed Carbon Dioxide Reduction
Thomas Ludwig, Joseph A. Gauthier, Colin F. Dickens, Kristopher S. Brown, Stefan Ringe, Karen Chan, and Jens K. Nørskov
J. Phys. Chem. Publication Date: November 3, 2020

Acetonitrile Transition Metal Interfaces from First Principles
Thomas Ludwig, Aayush R. Singh, and Jens K. Nørskov
J. Phys. Chem. Lett. 2020, 11, XXX, 9802–9811 Publication Date:November 5, 2020

Toward Force Estimation in Robot-Assisted Surgery using Deep Learning with Vision and Robot State
Zonghe Chua, Anthony M. Jarc, Allison M. Okamura
Submitted on 4 Nov 2020, arXiv:2011.02112 [cs.RO]

Postselection-free entanglement dynamics via spacetime duality
M Ippoliti, V Khemani
arXiv:2010.15840, Submitted on 29 Oct 2020

A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank
Junyang Qian, Yosuke Tanigawa, Wenfei Du, Matthew Aguirre, Chris Chang, Robert Tibshirani,Manuel A. Rivas, Trevor Hastie
PLOS, Published: October 23, 2020 https://doi.org/10.1371/journal.pgen.1009141

Estimating publication bias in meta‐analyses of peer‐reviewed studies: A meta‐meta‐analysis across disciplines and journal tiers
Maya B. Mathur, Tyler J. VanderWeele
First published: 27 October 2020 https://doi.org/10.1002/jrsm.1464

Large-Scale Labeling and Assessment of Sex Bias in Publicly Available Expression Data
Emily Flynn, Annie Chang, Russ B. Altman
doi: https://doi.org/10.1101/2020.10.26.356287

SynCity: Using open data to create a synthetic city of hourly building energy estimates by integrating data-driven and physics-based methods
Jonathan Roth, Amory Martin, Clayton Miller, Rishee K. Jain
Applied Energy Volume 280, 15 December 2020

Motion Correction of 3D Dynamic Contrast-Enhanced Ultrasound Imaging without Anatomical Bmode Images
Jia-Shu Chen, Maged Goubran Ph.D., Gaeun Kim, Jurgen K. Willmann M.D., Michael Zeineh M.D., Ph.D., Dimitre Hristov Ph.D., Ahmed El Kaffas Ph.D
Submitted on 5 Oct 2020 arXiv:2010.01721

Prevalence of neural collapse during the terminal phase of deep learning training
Vardan Papyan, X. Y. Han, and David L. Donoho
PNAS October 6, 2020 117 (40) 24652-24663

Carbonate-promoted C–H carboxylation of electron-rich heteroarenes
Tyler M. Porter and Matthew W. Kanan
Chem. Sci., 2020, 11, 11936-11944 DOI: 10.1039/D0SC04548A Accepted 5th October 2020

Dark Energy Survey Year 1 Results: Cosmological Constraints from Cluster Abundances, Weak Lensing, and Galaxy Correlations
C. To, E. Krause, E. Rozo, H. Wu, D. Gruen, R. H. Wechsler, T. F. Eifler, E. S. Rykoff, M. Costanzi, M. R. Becker, G. M. Bernstein, J. Blazek, S. Bocquet, S. L. Bridle, R. Cawthon, A. Choi, M. Crocce, C. Davis, J. DeRose, A. et al.
Submitted on 2 Oct 2020 arXiv:2010.01138

Skyrmion Superconductivity: DMRG evidence for a topological route to superconductivity
Shubhayu Chatterjee, Matteo Ippoliti, Michael P. Zaletel
arXiv:2010.01144 Submitted on 2 Oct 2020

Critical role of the sign structure in the doped Mott insulator: Luther-Emery versus Fermi-liquid-like state in quasi-one-dimensional ladders
Hong-Chen Jiang, Shuai Chen, and Zheng-Yu Weng
Phys. Rev. B 102, 104512 – Published 25 September 2020

A note on the accuracy of the generalized‐ alpha scheme for the incompressible Navier‐Stokes equations
Ju Liu, Ingrid S. Lan, Oguz Z. Tikenogullari, Alison L. Marsden
Numerical Methods in Engineering, First published: 23 September 2020 https://doi.org/10.1002/nme.6550

Sex-specific genetic effects across biomarkers
Emily Flynn, Yosuke Tanigawa, Fatima Rodriguez, Russ B. Altman, Nasa Sinnott-Armstrong & Manuel A. Rivas    
European Journal of Human Genetics volume 29, pages154–163(2021)
Published: 01 September 2020

Hubbard ladders at small U revisited
Yuval Gannot, Yi-Fan Jiang, and Steven A. Kivelson
Phys. Rev. B 102, 115136 – Published 16 September 2020

Effect of Hetero-Aromaticity on Adsorption of Pyrazine on the Ge(100)-2×1 Surface    
Tania E. Sandoval, Fabian Pieck, Ralf Tonner, and Stacey F. Bent
J. Phys. Chem. C  2020 September 9, 2020

Enhancing associative memory recall and storage capacity using confocal cavity QED
Brendan P. Marsh, Yudan Guo, Ronen M. Kroeze, Sarang Gopalakrishnan, Surya Ganguli, Jonathan Keeling, Benjamin L. Lev
arXiv:2009.01227v1 Submitted on 2 Sep 2020

Multi-task deep learning for cardiac rhythm detection in wearable devices
Jessica Torres-Soto & Euan A. Ashley    
Nature Partner Journals, npj Digital Medicine volume 3, Article number: 116 (2020)

Age-related loss of neural stem cell O-GlcNAc promotes a glial fate switch through STAT3 activation
Charles W. White III, Xuelai Fan, Jason C. Maynard, V, Elizabeth G. Wheatley, Gregor Bieri, Julien Couthouis, Alma L. Burlingame, and Saul A. Villeda
PNAS first published August 26, 2020 https://doi.org/10.1073/pnas.2007439117

Quantum Algorithmfor a Convergent Series of Approximations towards the Exact Solution of the Lowest Eigenstates of a Hamiltonian
Zhiyong Zhang
arXiv preprint arXiv:2009.03537, 2020

Returning radiation in strong gravity around black holes: reverberation from the accretion disc
D R Wilkins, J A García, T Dauser, A C Fabian
Monthly Notices of the Royal Astronomical Society, Volume 498, Issue 3, November 2020, Pages 3302–3319, https://doi.org/10.1093/mnras/staa2566 Published: 24 August 2020

Absentee Voting Is Popular During COVID-19 But Does Not Change Turnout or Partisan Rates of Voting
Jesse Yoder, Cassandra Handan-Nader, Andrew Myers,Tobias Nowacki, Daniel M. Thompson, Jennifer A. Wu,Chenoa Yorgason, and Andrew B. Hall
Democracy & Polarization Lab, Stanford University August 22, 2020

Combination of cluster number counts and two-point correlations: Validation on Mock Dark Energy Survey
C. To, E. Krause, E. Rozo, H. Wu, D. Gruen, J. DeRose, E. S. Rykoff, R. H. Wechsler, M. R. Becker, M. Costanzi, T. Eifler, M. E. S. Pereira, N. Kokron (DES Collaboration)
Submitted on 25 Aug 2020 arXiv:2008.10757

Theoretical basis for stabilizing messenger RNA through secondary structure design
Hannah K. Wayment-Steele, Do Soon Kim, Christian A. Choe, John J. Nicol, Roger Wellington-Oguri, R. Andres Parra Sperberg, Po-Ssu Huang, Eterna Participants, Rhiju Das
https://doi.org/10.1101/2020.08.22.262931 August 24, 2020

LPA and APOE are associated with statin selection in the UK Biobank
Adam Lavertu, Gregory McInnes, Yosuke Tanigawa, Russ B Altman, Manuel A. Rivas
 August 29, 2020 doi: https://doi.org/10.1101/2020.08.28.272765

Drug Response Pharmacogenetics for 200,000 UK Biobank Participants
Gregory McInnes, Russ B Altman
doi: https://doi.org/10.1101/2020.08.09.243311

Probing galaxy evolution in massive clusters using ACT and DES: splashback as a cosmic clock
Susmita Adhikari, Tae-hyeon Shin, Bhuvnesh Jain, Matt Hilton, Eric Baxter, Chihway Chang, Risa H. Wechsler, Nick Battaglia, Marcelle Soares-Santos, Eric Suchyta et al
arXiv:2008.11663  26 Aug 2020

The SAGA Survey. II. Building a Statistical Sample of Satellite Systems around Milky Way-like Galaxies
Yao-Yuan Mao, Marla Geha, Risa H. Wechsler, Benjamin Weiner, Erik J. Tollerud, Ethan O. Nadler, Nitya Kallivayalil                         
arXiv:2008.12783 28 Aug 2020

Automatic sleep stage classification with deep residual networks in a mixed-cohort setting
Alexander Neergaard Olesen, Poul Jørgen Jennum, Emmanuel Mignot, Helge Bjarup Dissing Sorensen
Sleep, Volume 44, Issue 1, January 2021, zsaa161, https://doi.org/10.1093/sleep/zsaa161 Published: 26 August 2020

Trove: Ontology-driven weak supervision for medical entity classification
Jason A. Fries, Ethan Steinberg, Saelig Khattar, Scott L. Fleming, Jose Posada, Alison Callahan, Nigam H. Shah
arXiv:2008.01972 [Submitted on 5 Aug 2020]

2D Conductive Ni-HAB as a Catalyst for the Electrochemical Oxygen Reduction Reaction
Jihye Park, Zhihua Chen, Raul A. Flores, Gustaf Wallenestrom, Ambarish Kulkarni, Jens K. Nørskov, Thomas F. Jaramillo, and Zhenan Bao
ACS Appl. Mater. Interfaces 2020
August 4, 2020 https://doi.org/10.1021/acsami.0c09323

Second Order Accurate Hierarchical Approximate Factorization of Sparse SPD Matrices
Bazyli Klockiewicz, Léopold Cambier, Ryan Humble, Hamdi Tchelepi, Eric Darve
arXiv:2007.00789  4 Aug 2020

Knockout of reactive astrocyte activating factors slows disease progression in an ALS mouse model
Kevin A. Guttenplan, Maya K. Weigel, Drew I. Adler, Julien Couthouis, Shane A. Liddelow, Aaron D. Gitler & Ben A. Barres    
Nature Communications volume 11, Article number: 3753 (2020)

Milky Way Satellite Census. III. Constraints on Dark Matter Properties fromObservations of Milky Way Satellite Galaxies
E. O. Nadler, A. Drlica-Wagner, K. Bechtol, S. Mau, R. H. Wechsler, V. Gluscevic, K. Boddy, A. B. Pace, et al.
arXiv.org  arXiv:2008.00022 Submitted on 31 Jul 2020

Reduced Thermal Conductivity of Supported and Encased Monolayer and Bilayer MoS2
Alexander Joseph Gabourie1, Saurabh Vinayak Suryavanshi, Amir Barati Farimani and Eric Pop
2D Materials IOP Science,  Accepted Manuscript online 10 July 2020

Methods for Model Calibration under High Uncertainty: Modeling Cholera in Bangladesh
Theresa Ryckman, Stephen Luby, Douglas K. Owens, Eran Bendavid, Jeremy D. Goldhaber-Fiebert
Medical Decision Making, First Published July 8, 2020
https://doi.org/10.1177/0272989X20938683

GANSim: Conditional Facies Simulation Using an Improved Progressive Growing of Generative Adversarial Networks (GANs)
Suihong Song, Tapan Mukerji, Jiagen Hou
EarthArXiv https://doi.org/10.31223/osf.io/fm24b 2020-07-05

Decoding spoken English phonemes from intracortical electrode arrays in dorsal precentral gyrus
Guy H. Wilson, Sergey D. Stavisky, Francis R. Willett, Donald T. Avansino, Jessica N. Kelemen, Leigh R. Hochberg, Jaimie M. Henderson, Shaul Druckmann, Krishna V. Shenoy
doi: https://doi.org/10.1101/2020.06.30.180935 July 01, 2020

An Empirical Characterization of Fair Machine Learning For Clinical Risk Prediction
Stephen R. Pfohl, Agata Foryciarz, Nigam H. Shah
Submitted on 20 Jul 2020 arXiv:2007.10306

Visualizing Energy Transfer at Buried Interfaces in Layered Materials Using Picosecond X‐Rays
Clara Nyby, Aditya Sood, Peter Zalden, Alexander J. Gabourie, Philipp Muscher, Daniel Rhodes, Ehren Mannebach, Jeff Corbett, Apurva Mehta, Eric Pop, Tony F. Heinz, Aaron M. Lindenberg
First published: 30 June 2020
Advanced Functional Materials  https://doi.org/10.1002/adfm.202002282

RedMaPPer: Evolution and Mass Dependence of the Conditional Luminosity Functions of Red Galaxies in Galaxy Clusters
Chun-Hao To1, Rachel M. Reddick1, Eduardo Rozo, Eli Rykoff and Risa H. Wechsler                 
Published June 29, 2020 The Astrophysical Journal, Volume 897, Number 1

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures
Kalli Kappel, Kaiming Zhang, Zhaoming Su, Andrew M. Watkins, Wipapat Kladwang, Shanshan Li, Grigore Pintilie, Ved V. Topkar, Ramya Rangan, Ivan N. Zheludev, Joseph D. Yesselman, Wah Chiu & Rhiju Das    
Nature Methods volume 17, pages699–707(2020)

Weighing neutrinos with the halo environment
Arka Banerjeea, Emanuele Castorinad, Francisco Villaescusa-Navarrof, Travis Courtg, and Matteo Vieli
Journal of Cosmology and Astroparticle Physics, Volume 2020, June 2020

Pervasive additive and non-additive effects within the HLA region contribute to disease risk in the UK Biobank
Guhan Ram Venkataraman, Julia Eve Olivieri, Christopher DeBoever, Yosuke Tanigawa, Johanne Marie Justesen, Alexander Dilthey, Manuel A. Rivas
doi: https://doi.org/10.1101/2020.05.28.119669  June 12, 2020

Active Learning Accelerated Discovery of Stable Iridium Oxide Polymorphs for the Oxygen Evolution Reaction
Raul A. Flores, Christopher Paolucci, Kirsten T. Winther, Ankit Jain, Jose Antonio Garrido Torres, Muratahan Aykol, Joseph Montoya, Jens K. Nørskov, Michal Bajdich, and Thomas Bligaard
Chem. Mater. 2020, 32, 13, 5854–5863 Publication Date:June 18, 2020

A single-cell atlas of the peripheral immune response in patients with severe COVID-19
Aaron J. Wilk, Arjun Rustagi, Nancy Q. Zhao, Jonasel Roque, Giovanny J. Martínez-Colón, Julia L. McKechnie, Geoffrey T. Ivison, Thanmayi Ranganath, Rosemary Vergara, Taylor Hollis, Laura J. Simpson, Philip Grant, Aruna Subramanian, Angela J. Rogers & Catherine A. Blish     
Nature Medicine, Published: 08 June 2020

Geological Facies Modeling Based on Progressive Growing of Generative Adversarial Networks (GANs)
Suihong Song, Tapan Mukerji and Jiagen Hou
EarthArXiv https://doi.org/10.31223/osf.io/ycufs 2020-06-22

A genotype-phenotype-fitness map reveals local modularity and global pleiotropy of adaptation
Grant Kinsler, Kerry Geiler-Samerotte, Dmitri Petrov
doi: https://doi.org/10.1101/2020.06.25.172197

Controlling arsenic mobilization during managed aquifer recharge: The role of sediment heterogeneity
Sarah Fakhreddine, Henning Prommer, Steven M. Gorelick, Jason Dadakis, and Scott Fendorf
Environ. Sci. Technol. Publication Date:June 9, 2020
https://doi.org/10.1021/acs.est.0c00794

Stabilization of extensive fine-scale diversity by ecologically driven spatiotemporal chaos
Michael T. Pearce, Atish Agarwala, and Daniel S. Fisher
PNAS first published June 9, 2020
https://doi.org/10.1073/pnas.1915313117

Pharmacogenetics at scale: An analysis of the UK Biobank
Greg McInnes, Adam Lavertu, Katrin Sangkuhl, Teri E. Klein, Michelle Whirl-Carrillo, Russ B. Altman
doi: https://doi.org/10.1101/2020.05.30.125583

Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription
Kevin P. Larsen, Junhong Choi, Lynnette N. Jackson, Kalli Kappel, Jingji Zhang, Betty Ha, Dong-Hua Chen, Elisabetta Viani Puglisi
Journal of Molecular Biology
Accepted 1 June 2020, https://doi.org/10.1016/j.jmb.2020.06.003

Efficient cosmological analysis of the SDSS/BOSS data from the Effective Field Theory of Large-Scale Structure
Thomas Colasa, Guido d'Amicoa, Leonardo Senatorea, Pierre Zhange and Florian Beutlerh
 Journal of Cosmology and Astroparticle Physics, Volume 2020, June 2020

RNA secondary structure packages ranked and improved by high-throughput experiments
Hannah K. Wayment-Steele, Wipapat Kladwang, Eterna Participants, Rhiju Das
doi: https://doi.org/10.1101/2020.05.29.124511
Posted May 31, 2020

A memory of eS25 loss drives resistance phenotypes
Alex G Johnson, Ryan A Flynn, Christopher P Lapointe, Yaw Shin Ooi, Michael L Zhao, Christopher M Richards, Wenjie Qiao, Shizuka B Yamada, Julien Couthouis, Aaron D Gitler, Jan E Carette, Joseph D Puglisi
Nucleic Acids Research, https://doi.org/10.1093/nar/gkaa444
Published: 28 May 2020

Extracting chemical reactions from text using Snorkel
Emily K. Mallory, Matthieu de Rochemonteix, Alex Ratner, Ambika Acharya, Chris Re, Roselie A. Bright & Russ B. Altman    
BMC Bioinformatics volume 21, Article number: 217 (2020)
Published: 27 May 2020

De novo 3D models of SARS-CoV-2 RNA elements and small-molecule-binding RNAs to guide drug discovery
Ramya Rangan, Andrew M. Watkins, Wipapat Kladwang, Rhiju Das
Posted April 15, 2020. doi: https://doi.org/10.1101/2020.04.14.041962

Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage
Linta Reji & Christopher A. Francis     
The ISME Journal (2020) Published: 13 May 2020

Structural topology optimization of tall buildings for dynamic seismic excitation using modal decomposition
Amory Martina, Gregory G. Deierlein
https://doi.org/10.1016/j.engstruct.2020.110717
Engineering Structures Volume 216, 1 August 2020, 110717

A radiomics approach to artificial intelligence in echocardiography: Predicting post-operative right ventricular failure
Rohan Shad, Nicolas Quach, Robyn Fong, Curt P. Langlotz, Sandra Kong, Patpilai Kasinpila, Myriam Amsallem, Francois Haddad, Yasuhiro Shudo, Y. Joseph Woo, Jeffrey Teuteberg, William Hiesinger
doi: https://doi.org/10.1101/2020.05.05.20092494

Short- and long-read metagenomics of South African gut microbiomes reveal a transitional composition and novel taxa
Fiona B. Tamburini, Dylan Maghini, Ovokeraye H. Oduaran, Ryan Brewster, Michaella R. Hulley, Venesa Sahibdeen, Shane A. Norris, Stephen Tollman, Kathleen Kahn, Ryan G. Wagner, Alisha N. Wade, Floidy Wafawanaka, Xavier Gómez-Olivé, Rhian Twine, Zané Lombard, Scott Hazelhurst, Ami S. Bhatt
Posted May 19, 2020. doi: https://doi.org/10.1101/2020.05.18.099820

Use of Patient-Specific Computational Models for Optimization of Aortic Insufficiency after Implantation of Left Ventricular Assist Device
Patpilai Kasinpila MD, Sandra Kong, Robyn Fong BS, Rohan Shad MD, Alexander Kaiser PhD, Alison Marsden PhD, Joseph Woo MD, William Hiesinger MD
The Journal of Thoracic and Cardiovascular Surgery Available online 15 May 2020
https://doi.org/10.1016/j.jtcvs.2020.04.164

Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection
Nikhil Ram-Mohan, Simone A. Thair, Ulrike M. Litzenburger, Steven Cogill, Nadya Andini, Xi Yang, Howard Y. Chang, Samuel Yang
doi: https://doi.org/10.1101/2020.04.28.066829
bioRxiv Posted April 30, 2020

The Diversity–Innovation Paradox in Science
Bas Hofstra, Vivek V. Kulkarni, Sebastian Munoz-Najar Galvez, Bryan He, Dan Jurafsky, and Daniel A. McFarland
PNAS April 28, 2020 117 (17) 9284-9291; first published April 14, 2020 https://doi.org/10.1073/pnas.1915378117

Blinding multiprobe cosmological experiments
J Muir, G M Bernstein, D Huterer, F Elsner, E Krause, A Roodman, S Allam, J Annis, S Avila, K Bechtol, E Bertin, D Brooks, E Buckley-Geer, D L Burke, A Carnero Rosell, M Carrasco Kind, J Carretero, R Cawthon, M Costanzi, L N da Costa, J De Vicente, S Desai, J P Dietrich, P Doel, T F Eifler, S Everett, P Fosalba, J Frieman, J García-Bellido, D W Gerdes, D Gruen, R A Gruendl, J Gschwend, W G Hartley, D L Hollowood, D J James, M Jarvis, K Kuehn, N Kuropatkin, O Lahav, M March, J L Marshall, P Melchior, F Menanteau, R Miquel, R L C Ogando, A Palmese, F Paz-Chinchón, A A Plazas, A K Romer, E Sanchez, V Scarpine, M Schubnell, S Serrano, I Sevilla-Noarbe, M Smith, E Suchyta, G Tarle, D Thomas, M A Troxel, A R Walker, J Weller, W Wester, J Zuntz
Monthly Notices of the Royal Astronomical Society, Volume 494, Issue 3, May 2020, Pages 4454–4470, https://doi.org/10.1093/mnras/staa965
Published: 15 April 2020

Milky Way Satellite Census. II. Galaxy–Halo Connection Constraints Including the Impact of the Large Magellanic Cloud
E. O. Nadler1, R. H. Wechsler, K. Bechtol, Y.-Y. Mao, G. Green, A. Drlica-Wagner, M. McNanna, S. Mau A. B. Pace1, J. D. Simon et.al.
Published 2020 April 15
The Astrophysical Journal, Volume 893, Number 1

Hierarchy of energy scales in an O(3) symmetric antiferromagnetic quantum critical metal: A Monte Carlo study
Carsten Bauer, Yoni Schattner, Simon Trebst, and Erez Berg
Phys. Rev. Research 2, 023008 – Published 6 April 2020

Minkowski functionals for phase behavior under confinement
Arnout M P Boelens, Hamdi A Tchelepi
Submitted on 3 Apr 2020 arXiv:2004.01344

Integration of Tobacco Treatment Services into Cancer Care at Stanford
Kathleen Gali, Brittany Pike, Matthew S Kendra, Cindy Tran, Priya Fielding-Singh, Kayla Jimenez, Rachelle Mirkin, Judith J Prochaska
Int. J. Environ. Res. Public Health 2020, 17(6), 2101; https://doi.org/10.3390/ijerph17062101 Published: 22 March 2020

Initial Review and Analysis of COVID-19 Host Genetics and Associated Phenotypes
Yosuke Tanigawa and Manuel Rivas
Received: 23 March 2020 / Approved: 24 March 2020 / Online: 24 March 2020 (08:36:20 CET)

Deep Quantum Geometry of Matrices
Xizhi Han  and Sean A. Hartnoll
Phys. Rev. X 10, 011069 – Published 23 March 2020

A molecular cell atlas of the human lung from single cell RNA sequencing
Kyle J. Travaglini, Ahmad N. Nabhan, Lolita Penland, Rahul Sinha, Astrid Gillich, Rene V. Sit, Stephen Chang, Stephanie D. Conley, Yasuo Mori, Jun Seita, Gerald J. Berry, Joseph B. Shrager, Ross J. Metzger, Christin S. Kuo, Norma Neff, Irving L. Weissman, Stephen R. Quake, Mark A. Krasnow
doi: https://doi.org/10.1101/742320

The impact of the fiducial cosmology assumption on BAO distance scale measurements
Paul Carter, Florian Beutler, Will J Percival, Joseph DeRose, Risa H Wechsler, Cheng Zhao
Monthly Notices of the Royal Astronomical Society, Volume 494, Issue 2, May 2020, Pages 2076–2089
https://doi.org/10.1093/mnras/staa761 Published:18 March 2020

Beyond the Core: Who Has Larger Social Networks?
Bas Hofstra, Rense Corten, Frank van Tubergen
Social Forces, soaa031, https://doi.org/10.1093/sf/soaa031 Published:22 April 2020

Spatial Characterization of Tumor Perfusion Properties from 3D DCE-US Perfusion Maps are Early Predictors of Cancer Treatment Response
Ahmed El Kaffas, Assaf, Hoogi Zhou, Jianhua Durot, Isabelle Wang, Huaijun, Jarrett Rosenberg,  Albert tseng, Hersh Sagreiya, Alireza  Akhbardeh, Daniel L. Rubin,  Aya  Kamaya, Dimitre Hristov & Jürgen K. Willmann                
Scientific Reports (Nature Publisher Group); London Vol. 10, Iss. 1,  (2020).
DOI:10.1038/s41598-020-63810-1

TeraChem Cloud: A High-Performance Computing Service for Scalable Distributed GPU-Accelerated Electronic Structure Calculations
Stefan Seritan, Keiran Thompson and Todd J. Martínez
J. Chem. Inf. Model. April 8, 2020 https://doi.org/10.1021/acs.jcim.9b01152

Inpainting Galactic Foreground Intensity and Polarization maps using Convolutional Neural Network
Giuseppe Puglisi, Xiran Bai
Submitted on 30 Mar 2020 arXiv:2003.13691

A new paradigm for accelerating clinical data science at Stanford Medicine
Somalee Datta, Jose Posada, Garrick Olson, Wencheng Li, Ciaran O'Reilly, Deepa Balraj, Joseph Mesterhazy, Joseph Pallas, Priyamvada Desai, Nigam Shah
arXiv:2003.10534 (Submitted on 17 Mar 2020)

Early warning signals of malaria resurgence in Kericho, Kenya
Mallory J. Harris, Simon I. Hay and John M. Drake
Biology Letters, The Royal Society
Published:18 March 2020 https://doi.org/10.1098/rsbl.2019.0713

Implications of the fractional charge of hydroxide at the electrochemical interface
Joseph A. Gauthier, Leanne D. Chen, Michal Bajdich and  Karen Chan
Phys. Chem. Chem. Phys., 2020, Advance Article
https://doi.org/10.1039/D0CP00115E

Lateral Variations of Shear‐Wave Velocity in the D″ Layer Beneath the Indian‐Eurasian Plate Collision Zone
Guohui Li Ling Bai Jeroen Ritsema
First published: 12 March 2020
https://doi.org/10.1029/2019GL086856

Engineered Fluorescent E. coli Lysogens Allow Live-Cell Imaging of Functional Prophage Induction Triggered inside Macrophages
Katie Bodner, Arin L.Melkonian, Angela I.M. Barth, Takamasa Kudo, Yu Tanouchi, Markus W.Covert
Cell Systems, Published: March 18, 2020
https://doi.org/10.1016/j.cels.2020.02.006

A mathematical model of ctDNA shedding predicts tumor detection size
Stefano Avanzini, David M. Kurtz, Jacob J. Chabon, Sharon Seiko Hori, Sanjiv Sam Gambhir, Ash A. Alizadeh, Maximilian Diehn, Johannes G. Reiter
doi: https://doi.org/10.1101/2020.02.12.946228

Excited state charge distribution and bond expansion of ferrous complexes observed with femtosecond valence-to-core x-ray emission spectroscopy
Kathryn Ledbetter, Marco E. Reinharu, Kristjan Kunnus, Alessandro Gallo, Alexander Britz, Elisa Biasin, James M. Glownia, Silke Nelson, Tim B. Van Driel, Clemens Weninger, Diana B. Zederkof, Kristoffer Haldrup, Amy A. Cordones, Kelly J. Gaffney, Dimosthenis Sokaras and Roberto Alonso-Mori                                 
J. Chem. Phys. 152, 074203 (2020); https://doi.org/10.1063/1.5139441

Possible superconductivity with Bogoliubov Fermi surface in lightly doped Kagome U(1) spin liquid
Yi-Fan Jiang, Hong Yao, Fan Yang
Submitted on 5 Mar 2020 arXiv:2003.0285

Detective quantum efficiency of photon-counting CdTe and Si detectors for computed tomography: a simulation study
Mats Persson, Adam Wang, Norbert J. Pelc               
Submitted on 1 Mar 2020 arXiv:2003.00390

Wind Turbine Performance in Very Large Wind Farms: Betz Analysis Revisited
Jacob R. West and Sanjiva K. Lele
Energies 2020, 13(5), 1078; https://doi.org/10.3390/en13051078
Published: 1 March 2020

Enhanced Menshutkin SN2 Reactivity in Mesoporous Silica: The Influence of Surface Catalysis and Confinement
Steven A. Yamada, Samantha T. Hung, Weizhen Sun, Ling Zhao, and Michael D. Fayer
J. Am. Chem. Soc. 2020, 142, 12, 5636–5648 Publication Date:February 20, 2020
https://doi.org/10.1021/jacs.9b12666

Effects of the Dopant Site on the Absorption Properties of CsPb1–xMxI2Br (M = Ge, Sn, Sr, and Cu): A First-Principles Investigation
Yanan Liang, Li Guan, Xiaofang Xu, Shichuang Han, Jianxin Guo, Jianglong Wang, Xiaobo Chen Zhiyong Zhang, Xu Li
J. Phys. Chem. C 2020, 124, 11, 6028-6037
Publication Date:February 24, 2020 https://doi.org/10.1021/acs.jpcc.9b08246

Signatures of self-interacting dark matter on cluster density profile and subhalo distributions
Arka Banerjee, Susmita Adhikari, Neal Dalal, Surhud More and Andrey Kravtsov
Journal of Cosmology and Astroparticle Physics, Volume 2020, February 2020

Topological superconductivity in the doped chiral spin liquid on the triangular lattice
Yi-Fan Jiang, Hong-Chen Jiang
arXiv:2002.04686 Submitted on 11 Feb 2020

Causal Inference in Genetic Trio Studies
Stephen Bates, Matteo Sesia, Chiara Sabatti, Emmanuel Candes
arXiv:2002.09644 (Submitted on 22 Feb 2020)

DC Hall coefficient of the strongly correlated Hubbard model
Wen O. Wang, Jixun K. Ding, Brian Moritz, Edwin W. Huang, Thomas P. Devereaux
arXiv:2002.12289 Submitted on 27 Feb 2020

Variations and expression features of CYP2D6 contribute to schizophrenia risk
Liang Ma, Anna Shcherbina & Sundari Chetty    
Molecular Psychiatry (2020) Published: 11 February 2020

Genome-wide synthetic lethal CRISPR screen identifies FIS1 as a genetic interactor of ALS-linked C9ORF72
Noori Chai, Michael S.,Haney, Julien Couthouis, David W. Morgens, Alyssa Benjamin, Kathryn Wu, James Ousey, Shirleen Fang, Sarah Finer, Michael C. Bassik and Aaron D.Gitler
Brain Research Volume 1728, 1 February 2020, 146601

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention    
Jessica A. Grembi, Lan H. Nguyen, Thomas D. Haggerty, Christopher D. Gardner, Susan P. Holmes & Julie Parsonnet    
Nature Scientific Reports volume 10, Article number: 1405 (2020)

Fluid–structure interaction simulations of patient-specific aortic dissection
Kathrin Bäumler, Vijay Vedula, Anna M. Sailer, Jongmin Seo, Peter Chiu, Gabriel Mistelbauer, Frandics P. Chan, Michael P. Fischbein, Alison L. Marsden & Dominik Fleischmann    
Biomechanics and Modeling in Mechanobiology (2020) Published: 28 January 2020

A note on the accuracy of the generalized-α scheme for the incompressible Navier-Stokes equations
Ju Liu, Ingrid S. Lan, Oguz Z. Tikenogullari, Alison L. Marsden
 arXiv:2002.01098 (Submitted on 4 Feb 2020)

Signatures of Velocity-Dependent Dark Matter Self-Interactions in Milky Way-mass Halos
Ethan O. Nadler, Arka Banerjee, Susmita Adhikari, Yao-Yuan Mao, Risa H. Wechsler
arXiv:2001.08754 (Submitted on 23 Jan 2020)

Chromatin accessibility dynamics in a model of human forebrain development
Alexandro E. Trevino, Nasa Sinnott-Armstrong, Jimena Andersen, Se-Jin Yoon, Nina Huber, Jonathan K. Pritchard, Howard Y. Chang, William J. Greenleaf, Sergiu P. Pașca
Science  24 Jan 2020: Vol. 367, Issue 6476, eaay1645

Polygenic prediction and GWAS of depression, PTSD, and suicidal ideation/self-harm in a Peruvian cohort
Hanyang Shen, Bizu Gelaye, Hailiang Huang, Marta B. Rondon, Sixto Sanchez & Laramie E. Duncan    
Nature, Neuropsychopharmacology (2020)

Pairing and non-Fermi liquid behavior in partially flat-band systems: Beyond nesting physics
Sharareh Sayyad, Edwin W. Huang, Motoharu Kitatani, Mohammad-Sadegh Vaezi, Zohar Nussinov, Abolhassan Vaezi, and Hideo Aoki
Phys. Rev. B 101, 014501 – Published 6 January 2020

Language Models Are An Effective Patient Representation Learning Technique For Electronic Health Record Data
Ethan Steinberg, Ken Jung, Jason A. Fries, Conor K. Corbin, Stephen R. Pfohl, Nigam H. Shah
arXiv:2001.05295 (Submitted on 6 Jan 2020)

The cascade unzipping of ladderane reveals dynamic effects in mechanochemistry
Zhixing Chen, Xiaolei Zhu, Jinghui Yang, Jaron A. M. Mercer, Noah Z. Burns, Todd J. Martinez & Yan Xia    
Nature Chemistry volume 12, pages302–309(2020) Published: 06 January 2020

The binary-host connection: astrophysics of gravitational wave binaries from their host galaxy properties
Susmita Adhikari, Maya Fishbach, Daniel E. Holz, Risa H. Wechsler, Zhanpei Fang
 arXiv:2001.01025 (Submitted on 4 Jan 2020)

Parallelization of the inverse fast multipole method with an application to boundary element method
Toru Takahashi, Chao Chen, Eric Darve
Computer Physics Communications Volume 247, February 2020
https://doi.org/10.1016/j.cpc.2019.106975

2019

Higher N-point function data analysis techniques for heavy particle production and WMAP results
Moritz Münchmeyer and Kendrick M. Smith
Phys. Rev. D 100, 123511 – Published 6 December 2019

Evolution and Diversity of Assembly-Line Polyketide Synthases
Aleksandra Nivina, Kai P. Yuet, Jake Hsu, Chaitan Khosla
Chem. Rev. 2019
Publication Date :December 15, 2019

Strange metallicity in the doped Hubbard model
Edwin W. Huang, Ryan Sheppard, Brian Moritz, Thomas P. Devereaux
Science  22 Nov 2019:Vol. 366, Issue 6468, pp. 987-990
DOI: 10.1126/science.aau7063

Phase-field investigation of the stages in radial growth of core–shell Ge/Ge1−xSnx nanowires
Yanming Wang, Andrew C. Meng, Paul C. McIntyre and Wei Cai                          
Nanoscale, 2019, 11, 21974-21980
DOI: 10.1039/C9NR07587A (Paper)

Unified Approach to Implicit and Explicit Solvent Simulations of Electrochemical Reaction Energetics
Joseph A. Gauthier, Colin F. Dickens, Hendrik H. Heeneni, Sudarshan Vijay, Stefan Ringe, Karen Chan
J. Chem. Theory Comput. 2019, 15, 12, 6895-6906
https://doi.org/10.1021/acs.jctc.9b00717

Variations in the Intensity and Spatial Extent of Tropical Cyclone Precipitation
Danielle Touma, Samantha Stevenson, Suzana J. Camargo, Daniel E. Horton, Noah S. Diffenbaugh
Geophysical Research Letters, First published: 18 October 2019
https://doi.org/10.1029/2019GL083452

Angle-resolved photoemission spectroscopy of a Fermi–Hubbard system
Peter T. Brown, Elmer Guardado-Sanchez, Benjamin M. Spar, Edwin W. Huang, Thomas P. Devereaux & Waseem S. Bakr
Nature Physics volume 16, pages26–31(2020)

Superconductivity in the doped Hubbard model and its interplay with next-nearest hopping t′
Hong-Chen Jiang, Thomas P. Devereaux
Science  27 Sep 2019: Vol. 365, Issue 6460, pp. 1424-1428
DOI: 10.1126/science.aal5304

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements
Josh Tycko, Michael Wainberg, Georgi K. Marinov, Oana Ursu, Gaelen T. Hess, Braeden K. Ego, Aradhana, Amy Li, Alisa Truong, Alexandro E. Trevino, Kaitlyn Spees, David Yao, Irene M. Kaplow, Peyton G. Greenside, David W. Morgens, Douglas H. Phanstiel, Michael P. Snyder, Lacramioara Bintu, William J. Greenleaf, Anshul Kundaje & Michael C. Bassik
Nature Communications volume 10, Article number: 4063 (2019)
Published: 06 September 2019

Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
Joseph W. Foley, Chunfang Zhu, Philippe Jolivet, Shirley X. Zhu, Peipei Lu, Michael J. Meaney and Robert B. West            
Genome Res. 2019. 29: 1816-1825

Modeling Environmental DNA Transport in the Coastal Ocean Using Lagrangian Particle Tracking
Elizabeth A. Andruszkiewicz, Jeffrey R. Koseff, Oliver B. Fringer, Nicholas T. Ouellette, Anna B. Lowe, Christopher A. Edwards and Alexandria B. Boehm
Frontiers in Marine Science, 07 August 2019 | https://doi.org/10.3389/fmars.2019.00477

Transition Metal Arsenide Catalysts for the Hydrogen Evolution Reaction
Joseph A. Gauthier, Laurie A. King, Faith Tucker Stults, Raul A. Flores, Jakob Kibsgaard, Yagya N. Regmi, Karen Chan and Thomas F. Jaramillo
J. Phys. Chem. C20191233924007-24012
Publication Date:September 24, 2019 https://doi.org/10.1021/acs.jpcc.9b05738

Impact of Number Representation for High-Order Implicit Large-Eddy Simulations
F. D. Witherden and A. Jameson
American Institute of Aeronautics and Astronautics Journal
Published Online:17 Sep 2019 https://doi.org/10.2514/1.J058434

Migration and Informal Insurance
C Meghir, AM Mobarak, CD Mommaerts, M Morten
July 2019 National Bureau of Economic Research Working Paper  - nber.org

Practical Considerations for Continuum Models Applied to Surface Electrochemistry
Joseph Gauthier, Colin Dickens, Stefan Ringe, Karen Chan
https://doi.org/10.26434/chemrxiv.8188454.v1

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding
Morteza Roodgar, Afshin Babveyh, Lan Huong, Wenyu Zhou, Rahul Sinha, Hayan Lee, John B. Hanks, Mohan Avula, Lihua Jiang, Hoyong Lee, Giltae Song, Hassan Chaib, Irv L. Weissman, Serafim Batzoglou, Susan Holmes, David G. Smith, Joseph L. Mankowski, Stefan Prost, Michael P. Snyder
doi: https://doi.org/10.1101/635045

Measuring Group Differences in High‐Dimensional Choices: Method and Application to Congressional Speech
Matthew Gentzkow, Jesse M. Shapiro, Matt Taddy
First published: 25 July 2019 https://doi.org/10.3982/ECTA16566

Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts
Surag Nair, Daniel S Kim, Jacob Perricone, Anshul Kundaje
Bioinformatics, Volume 35, Issue 14, July 2019, Pages i108–i116  
https://doi.org/10.1093/bioinformatics/btz352 Published: 05 July 2019

Transcription factor networks in aged naïve CD4 T cells bias lineage differentiation
Bin Hu, Guangjin Li, Zhongde Ye, Claire E. Gustafson, Lu Tian, Cornelia M. Weyand, Jörg J. Goronzy
First published: 01 July 2019 https://doi.org/10.1111/acel.12957

Quantitative evidence for early metastatic seeding in colorectal cancer
Zheng Hu, Jie Ding, Zhicheng Ma, Ruping Sun, Jose A. Seoane, J. Scott Shaffer, Carlos J. Suarez, Anna S. Berghoff, Chiara Cremolini, Alfredo Falcone, Fotios Loupakis, Peter Birner, Matthias Preusser, Heinz-Josef Lenz & Christina Curtis   
Nature Genetics volume 51, pages1113–1122 (2019)

Enhanced correlations and superconductivity in weakly interacting partially flat-band systems: A determinantal quantum Monte Carlo study
Edwin W. Huang, Mohammad-Sadegh Vaezi, Zohar Nussinov, and Abolhassan Vaezi
Phys. Rev. B 99, 235128 – Published 13 June 2019

Practical Considerations for Continuum Models Applied to Surface Electrochemistry
Joseph A. Gauthier, Colin F. Dickens, Stefan Ringe, Karen Chan
ChemRxiv https://doi.org/10.26434/chemrxiv.8188454.v1

Early Changes in CT Perfusion Parameters: Primary Renal Carcinoma Versus Metastases After Treatment with Targeted Therapy
Alice C. Fan, Vandana Sundaram, Aya Kino, Heiko Schmiedeskamp, Thomas J. Metzner and Aya Kamaya
Cancers 2019, 11(5), 608; https://doi.org/10.3390/cancers11050608

Surface Photovoltage-Induced Ultralow Work Function Material for Thermionic Energy Converters
Peter Schindler, Daniel C. Riley, Igor Bargatin, Kunal Sahasrabuddhe, Jared W. Schwede, Steven Sun, Piero Pianetta, Zhi-Xun Shen, Roger T. Howe, and Nicholas A. Melosh
ACS Energy Letters 2019 4 (10), 2436-2443
DOI: 10.1021/acsenergylett.9b01214

Pseudogap crossover in the electron-phonon system
I. Esterlis, S. A. Kivelson, and D. J. Scalapino
Phys. Rev. B 99, 174516 – Published 24 May 2019

Global warming has increased global economic inequality
Noah S. Diffenbaugh and Marshall Burke
PNAS May 14, 2019 116 (20) 9808-9813; https://doi.org/10.1073/pnas.1816020116

Uncovering the structure of self-regulation through data-driven ontology discovery
Ian W. Eisenberg, Patrick G. Bissett, A. Zeynep Enkavi, Jamie Li, David P. MacKinnon, Lisa A. Marsch & Russell A. Poldrack
Nature Communications 10, Article number: 2319 (2019)

Global analysis of epigenetic heterogeneity identifies divergent drivers of esophageal squamous cell carcinoma
Wei Cao, Hayan Lee, Wei Wu, Aubhishek Zaman, Sean McCorkle, Ming Yan, Justin Chen, Qinghe Xing, Nasa Sinnott-Armstrong, Hongen Xu, M.Reza Sailani, Wenxue Tang, Yuanbo Cui, Jia liu, Hongyan Guan, Pengju Lv, Xiaoyan Sun, Lei Sun, Pengli Han, Yanan Lou, Jing Chang, Jinwu Wang, Yuchi Gao, Jiancheng Guo, Gundolf Schenk, Alan Hunter Shain, Fred G. Biddle, Eric Collisson, Michael Snyder, Trever G. Bivona
doi: https://doi.org/10.1101/641357 Posted May 18, 2019

Towards a Flexible Deep Learning Method for Automatic Detection of Clinically Relevant Multi-Modal Events in the Polysomnogram
Alexander Neergaard Olesen, Stanislas Chambon, Valentin Thorey, Poul Jennum, Emmanuel Mignot, Helge B. D. Sorensen
arXiv:1905.08059 (Submitted on 16 May 2019)

Transplantation of donor grafts with defined ratio of conventional and regulatory T cells in HLA-matched recipients
Everett H. Meyer, Ginna Laport, Bryan J. Xie, Kate MacDonald, Kartoosh Heydari, Bita Sahaf, Sai-Wen Tang, Jeanette Baker, Randall Armstrong, Keri Tate, Cynthia Tadisco, Sally Arai, Laura Johnston, Robert Lowsky, Lori Muffly, Andrew R. Rezvani, Judith Shizuru, Wen-Kai Weng, Kevin Sheehan, David Miklos, and Robert S. Negrin
Published in Volume 4, Issue 10 on May 16, 2019 JCI Insight. 2019;4(10):e127244. https://doi.org/10.1172/jci.insight.127244

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding
Morteza Roodgar, Afshin Babveyh,Lan Huong, Wenyu Zhou, Rahul Sinha, Hayan Lee, John B. Hanks, Mohan Avula, Lihua Jiang, Hoyong Lee, Giltae Song, Hassan Chaib, Irv L. Weissman, Serafim Batzoglou, Susan Holmes, David G. Smith, Joseph L. Mankowski, Stefan Prost, Michael P. Snyder
doi: https://doi.org/10.1101/635045

Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships
Christopher M.Jakobson, Daniel F.Jarosz
Cell Systems, Published: May 1, 2019 https://doi.org/10.1016/j.cels.2019.04.002

Blind tests of RNA–protein binding affinity prediction
Kalli Kappel, Inga Jarmoskaite, Pavanapuresan P. Vaidyanathan, William J. Greenleaf, Daniel Herschlag, and Rhiju Das
PNAS April 23, 2019 116 (17) 8336-8341; https://doi.org/10.1073/pnas.1819047116

Robust mouse tracking in complex environments using neural networks
Brian Q. Geuther, Sean P. Deats, Kai J. Fox, Steve A. Murray, Robert E. Braun, Jacqueline K. White, Elissa J. Chesler, Cathleen M. Lutz & Vivek Kumar    
Nature Communications, Biology volume 2, Article number: 124 (2019)

Pervasive function and evidence for selection across standing genetic variation in S. cerevisiae
Christopher M. Jakobson, Richard She & Daniel F. Jarosz   
Nature Communications Volume 10, Article number: 1222 (2019)

Predicting gait adaptations due to ankle plantarflexor muscle weakness and contracture using physics-based musculoskeletal simulations
Carmichael F. Ong, Thomas Geijtenbeek, Jennifer L. Hicks, Scott L. Delp
doi: https://doi.org/10.1101/597294

Efficient construction of generalized master equation memory kernels for multi-state systems from nonadiabatic quantum-classical dynamics
William C. Pfalzgraff, Andrés Montoya Castillo, Aaron Kelly, Thomas E. Markland
(Submitted on 22 Mar 2019)

Pairing and non-Fermi liquid behavior in partially flat-band systems
Sharareh Sayyad, Edwin W. Huang, Motoharu Kitatani, Mohammad-Sadegh Vaezi, Zohar Nussinov, Abolhassan Vaezi, Hideo Aoki
Submitted on 23 Mar 2019, last revised 29 Mar 2019

Uncertainty quantification of simulated biomechanical stimuli in coronary artery bypass grafts
Justin S. Trana, Daniele E. Schiavazzi, Andrew M. Kahn, Alison L. Marsden
Computer Methods in Applied Mechanics and Engineering, Volume 345, 1 March 2019, Pages 402-428
https://doi.org/10.1016/j.cma.2018.10.024

A functional subset of CD8+ T cells during chronic exhaustion is defined by SIRPα expression
Lara M. Myers, Michal Caspi Tal, Laughing Bear Torrez Dulgeroff, Aaron B. Carmody, Ronald J. Messer, Gunsagar Gulati, Ying Ying Yiu, Matthew M. Staron, Cesar Lopez Angel, Rahul Sinha, Maxim Markovic, Edward A. Pham, Benjamin Fram, Aijaz Ahmed, Aaron M. Newman, Jeffrey S. Glenn, Mark M. Davis, Susan M. Kaech, Irving L. Weissman & Kim J. Hasenkrug
Nature Communications Volume 10, Article number: 794 (2019)

Non-invasive machine learning estimation of effort differentiates sleep-disordered breathing pathology
Umaer Hanif, Logan D Schneider, Lotte Trap, Eileen B Leary, Hyatt Moore IV, Christian Guilleminault, Poul Jennum, Helge B D Sorensen, and Emmanuel J M Mignot
Published 26 February 2019, Institute of Physics and Engineering in Medicine
Physiological Measurement, Volume 40, Number 2

Thermal transport in MoS2 from molecular dynamics using different empirical potentials
Ke Xu, Alexander J. Gabourie, Arsalan Hashemi, Zheyong Fan, Ning Wei, Amir Barati Farimani, Hannu-Pekka Komsa, Arkady V. Krasheninnikov, Eric Pop, and Tapio Ala-Nissila
Phys. Rev. B 99, 054303 – Published 11 February 2019

Super-geometric electron focusing on the hexagonal Fermi surface of PdCoO2
Maja D. Bachmann, Aaron L. Sharpe, Arthur W. Barnard, Carsten Putzke, Markus König, Seunghyun Khim, David Goldhaber-Gordon, Andrew P. Mackenzie, Philip J. W. Moll
arXiv:1902.03769

Imidazole and 1-Methylimidazole Hydrogen Bonding and Non-Hydrogen Bonding Liquid Dynamics: Ultrafast IR Experiments
Jae Yoon Shin, Yong-Lei Wang, Steven A. Yamada, Samantha Ting Hung, and Michael D. Fayer
J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.8b11299
Publication Date (Web): February 6, 2019

Sub-Femtosecond Stark Control of Molecular Photoexcitation with Near Single-Cycle Pulses
Benoit Mignolet, Basile F. E. Curchod, Francoise Remacle and Todd J. Martínez            
J. Phys. Chem. Lett., 2019, 10, pp 742–747
DOI: 10.1021/acs.jpclett.8b03814 Publication Date (Web): January 29, 2019

Intradomain Interactions in an NMDA Receptor Fragment Mediate N-Glycan Processing and Conformational Sampling
Ganesh P. Subedi, Anton V. Sinitskiy, Jacob T. Roberts, Kashyap R. Patel, Vijay S.Pande, Adam W. Barb
Structure, Volume 27, Issue 1, 2 January 2019, Pages 55-65.e3

Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level
Miriam V. Gutschow, John C. Mason, Keara M. Lane, Inbal Maayan, Jacob J. Hughey, Bryce T. Bajar, Debha N. Amatya, Sean D. Valle, and Markus W. Covert
Molecular Biology of the Cell Vol. 30, No. 2
Published Online:14 Jan 2019 https://doi.org/10.1091/mbc.E18-07-0423

Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking
Kalli Kappel, Rhiju Das
Structure, Volume 27, Issue 1, 2 January 2019, Pages 140-151.e5
https://doi.org/10.1016/j.str.2018.10.001

RNA design movesets and strategies from an Internet-scale videogame
Rohan Koodli, Benjamin Keep, Katherine R Coppess, Fernando Portela, Eterna Players, Rhiju Das
doi: https://doi.org/10.1101/326736 Posted January 15, 2019

Modeling of radiation-induced defect recovery in 3C-SiC under high field bias conditions
Ricardo Peterson, Debbie Senesky
Computational Materials Science, Volume 161, 15 April 2019, Pages 10-15
https://doi.org/10.1016/j.commatsci.2019.01.016

Globally Constructed Adaptive Local Basis Set for Spectral Projectors of Second Order Differential Operators
Yingzhou Li and Lin Lin
Multiscale Model. Simul., 17(1), 92–116. (25 pages)
https://doi.org/10.1137/17M1140236

fMRIPrep: a robust preprocessing pipeline for functional MRI
Oscar Esteban, Christopher J. Markiewicz, Ross W. Blair, Craig A. Moodie, A. Ilkay Isik, Asier Erramuzpe, James D. Kent, Mathias Goncalves, Elizabeth DuPre, Madeleine Snyder, Hiroyuki Oya, Satrajit S. Ghosh, Jessey Wright, Joke Durnez, Russell A. Poldrack & Krzysztof J. Gorgolewski     
Nature Methods volume 16, pages111–116 (2019)

Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation
Zhongyue Yang, Rimsha Mehmood, Mengyi Wang, Helena W. Qi, Adam H. Steeves and Heather J. Kulik
React. Chem. Eng., 2019, Advance Article DOI: 10.1039/C8RE00213D (Paper)

The unWISE Catalog: Two Billion Infrared Sources from Five Years of WISE Imaging
Edward F. Schlafly, Aaron M. Meisner, Gregory M. Green
 arXiv:1901.03337 (Submitted on 10 Jan 2019)

An Algebraic Sparsified Nested Dissection Algorithm Using Low-Rank Approximations
Léopold Cambier, Chao Chen, Erik G Boman, Sivasankaran Rajamanickam, Raymond S. Tuminaro, Eric Darve
arXiv:1901.02971 (Submitted on 9 Jan 2019)

Thermal Boundary Conductance of Two-Dimensional MoS2 Interfaces
Saurabh V. Suryavanshi, Alexander J. Gabourie, Amir Barati Farimani, Eric Pop
arXiv:1901.02447 (Submitted on 8 Jan 2019)

The Buzzard Flock: Dark Energy Survey Synthetic Sky Catalogs
Joseph DeRose, Risa H. Wechsler, Matthew R. Becker, Michael T. Busha, Eli S. Rykoff, Niall MacCrann, Brandon Erickson, August E. Evrard, Andrey Kravtsov, Daniel Gruen, Sahar Allam, Santiago Avila, Sarah Bridle, David Brooks, Elizabeth Buckley-Geer, Aurelio Carnero Rosell, Matias Carrasco Kind, Jorge Carretero, Francisco J. Castander, Ross Cawthon, Martin Crocce, Luiz N. da Costa, Christopher Davis, Juan De Vicente, Jörg P. Dietrich, Peter Doel, Alex Drlica-Wagner, Pablo Fosalba, Josh Frieman, Juan Garcia-Bellido, Gaston Gutierrez, Will G. Hartley, Devon L. Hollowood, Ben Hoyle, David J. James, Elisabeth Krause, Kyler Kuehn, Nikolay Kuropatkin, Marcos Lima, Marcio A. G. Maia, Felipe Menanteau, Christopher J. Miller, Ramon Miquel, Ricardo L. C. Ogando, Andrés Plazas Malagón, A. Kathy Romer, Eusebio Sanchez, Rafe Schindler, Santiago Serrano, Ignacio Sevilla-Noarbe, Mathew Smith, Eric Suchyta, Molly E. C. Swanson, Gregory Tarle, Vinu Vikram
arXiv:1901.02401 (Submitted on 8 Jan 2019)

2018

Automated design of collective variables using supervised machine learning featured
Mohammad M. Sultan and Vijay S. Pande
J. Chem. Phys. 149, 094106 (2018); https://doi.org/10.1063/1.5029972

Exploiting graphical processing units to enable quantum chemistry calculation of large solvated molecules with conductor‐like polarizable continuum models
Fang Liu, David M. Sanchez, Heather J. Kulik, Todd J. Martínez
https://doi.org/10.1002/qua.25760 First published: 11 October 2018

Biochat: a database for natural language processing of Gene Expression Omnibus data
Bohdan B Khomtchouk, Vsevolod Dyomkin, Kasra A Vand, Themistocles Assimes, Or Gozani
doi: https://doi.org/10.1101/480020

PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development
Jennifer L. Wilson, Rebecca Racz, Tianyun Liu, Oluseyi Adeniyi, Jielin Sun, Anuradha Ramamoorthy, Michael Pacanowski, Russ Altman
PLOS Published: December 7, 2018
https://doi.org/10.1371/journal.pcbi.1006614

Challenges in Modeling Electrochemical Reaction Energetics with Polarizable Continuum Models
Joseph A. Gauthier, Stefan Ringe, Colin F. Dickens, Alejandro J. Garza, Alexis T. Bell, Martin Head-Gordon, Jens K. Nørskov, Karen Chan
ACS Catal. 2019, 9, 2, 920-931
Publication Date:November 28, 2018
https://doi.org/10.1021/acscatal.8b02793

Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level
Miriam V. Gutschow, John C. Mason, Keara M. Lane, Inbal Maayan, Jacob J. Hughey, Bryce T. Bajar, Debha N. Amatya, Sean D., Valle, Markus W. Covert
Molecular Biology of the Cell Published Online: 21 Nov 2018
https://doi.org/10.1091/mbc.E18-07-0423

Convolutional models of RNA energetics
Michelle J Wu
doi: https://doi.org/10.1101/470740

Searching for Subsecond Stellar Variability with Wide-field Star Trails and Deep Learning
David Thomas and Steven M. Kahn
The Astrophysical Journal, Volume 868, Number 1, Published 2018 November 16

A global test of ecoregions
Jeffrey R. Smith, Andrew D. Letten, Po-Ju Ke, Christopher B. Anderson, J. Nicholas Hendershot, Manpreet K. Dhami, Glade A. Dlott, Tess N. Grainger, Meghan E. Howard, Beth M. L. Morrison, Devin Routh, Priscilla A. San Juan, Harold A. Mooney, Erin A. Mordecai, Thomas W. Crowther & Gretchen C. Daily
Nature Ecology & Evolution,  Published: 05 November 2018
DOI https://doi.org/10.1038/s41559-018-0709-x

An energetic reformulation of kinetic rate laws enables scalable parameter estimation for biochemical networks
John C. Mason, Markus W. Covert
Journal of Theoretical Biology, 24 October 2018
DOI https://doi.org/10.1016/j.jtbi.2018.10.041

Spectroscopic Signature of Oxidized Oxygen States in Peroxides
Zengqing Zhuo, Chaitanya Das Pemmaraju, John Vinson, Chunjing Jia, Brian Moritz, Ilkyu Lee, Shawn Sallis, Qinghao Li, Jinpeng Wu, Kehua Dai, Yi-De Chuang, Zahid Hussain, Feng Pan, Thomas P. Devereaux, and Wanli Yang
J. Phys. Chem. Lett.
DOI 10.1021/acs.jpclett.8b02757 Publication Date (Web): October 16, 2018

Three-dimensional collective charge excitations in electron-doped copper oxide superconductors
M. Hepting, L. Chaix, E. W. Huang, R. Fumagalli, Y. Y. Peng, B. Moritz, K. Kummer, N. B. Brookes, W. C. Lee, M. Hashimoto, T. Sarkar, J.-F. He, C. R. Rotundu, Y. S. Lee, R. L. Greene, L. Braicovich, G. Ghiringhelli, Z. X. Shen, T. P. Devereaux & W. S. Lee     
Nature volume 563, pages374–378 (2018)
Published: 31 October 2018
DOI https://doi.org/10.1038/s41586-018-0648-3

A Predictive Model for Postembolization Syndrome after Transarterial Hepatic Chemoembolization of Hepatocellular Carcinoma
Mohamed H. Khalaf, Vandana Sundaram, Mohammed Ahmed AbdelRazek Mohammed, Rajesh Shah, Ankaj Khosla, Katherine Jackson, Manisha Desai, Nishita Kothary     
Published Online: Oct 9 2018 https://doi.org/10.1148/radiol.2018180257

Probing the Electron Accepting Orbitals of Ni-Centered Hydrogen Evolution Catalysts with Noninnocent Ligands by Ni L-Edge and S K-Edge X-ray Absorption
Sergey Koroidov, Kiryong Hong, Kasper S. Kjaer, Lin Li, Kristjan Kunnus, Marco Reinhard, Robert W. Hartsock, Das Amit, Richard Eisenberg, C. Das Pemmaraju, Kelly J. Gaffney, and Amy A. Cordones
Inorg. Chem., Article ASAP DOI: 10.1021/acs.inorgchem.8b01497
Publication Date (Web): October 11, 2018

Data-driven human transcriptomic modules determined by independent component analysis
Weizhuang Zhou and Russ B. Altman
BMC Bioinformatics 201819:327 Published: 17 September 2018
https://doi.org/10.1186/s12859-018-2338-4

Landscape of stimulation-responsive chromatin across diverse human immune cells
Diego Calderon, Michelle L.T. Nguyen, Anja Mezger, Arwa Kathiria, Vinh Nguyen, Ninnia Lescano, Beijing Wu, John Trombetta, Jessica V. Ribado, David A. Knowles, Ziyue Gao, Audrey V. Parent, Trevor D. Burt, Mark S. Anderson, Lindsey A. Criswell, William J. Greenleaf, Alexander Marson, Jonathan K. Pritchard
doi: https://doi.org/10.1101/409722, Posted September 5, 2018.

A parallel direct cut algorithm for high-order overset methods with application to a spinning golf ball
J. Crabill, F.D. Witherden, A. Jameson
Journal of Computational Physics, 2018 - Elsevier
https://doi.org/10.1016/j.jcp.2018.05.036

Deep Neural Network Computes Electron Densities and Energies of a Large Set of Organic Molecules Faster than Density Functional Theory (DFT)
Anton V. Sinitskiy, Vijay S. Pande
arXiv preprint arXiv:1809.02723, 2018 - arxiv.org

Analyzing interferometric observations of strong gravitational lenses with recurrent and convolutional neural networks
Warren R. Morningstar, Yashar D. Hezaveh, Laurence Perreault Levasseur, Roger D. Blandford, Philip J. Marshall, Patrick Putzky, Risa H. Wechsler
arXiv:1808.00011 (Submitted on 31 Jul 2018)

Imaging CF3I conical intersection and photodissociation dynamics with ultrafast electron diffraction
Jie Yang, Xiaolei Zhu, Thomas J. A. Wolf, Zheng Li, J. Pedro F. Nunes, Ryan Coffee, James P. Cryan, Markus Gühr, Kareem Hegazy, Tony F. Heinz, Keith Jobe, Renkai Li, Xiaozhe Shen, Theodore Veccione, Stephen Weathersby, Kyle J. Wilkin, Charles Yoneda, Qiang Zheng, Todd J. Martinez, Martin Centurion, Xijie Wang
Science  06 Jul 2018: Vol. 361, Issue 6397, pp. 64-67
DOI: 10.1126/science.aat0049

Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water
Tim J. Zuehlsdorff1, Joseph A. Napoli, Joel M. Milanese, Thomas E. Markland, and Christine M. Isborn
The Journal of Chemical Physics 149, 024107 (2018); https://doi.org/10.1063/1.5025517

Simple, direct and efficient multi-way spectral clustering
A Damle, V Minden, L Ying
Information and Inference: A Journal of the IMA, 2018
https://doi.org/10.1093/imaiai/iay008

Bioimpedance and New‐Onset Heart Failure: A Longitudinal Study of >500 000 Individuals From the General Population
Daniel Lindholm, Eri Fukaya, Nicholas J. Leeper, Erik Ingelsson
Journal of the American Heart Association. 2018;7:e008970,
https://doi.org/10.1161/JAHA.118.008970 Originally published June 29, 2018

Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers
Surl-Hee Ahn, Jay W. Grate, and Eric F. Darve
The Journal of Chemical Physics 149, 072330 (2018); https://doi.org/10.1063/1.5024552

Direct Methane to Methanol: The Selectivity–Conversion Limit and Design Strategies
Allegra A. Latimer, Arvin Kakekhani, Ambarish R. Kulkarni, and Jens K. Nørskov
ACS Catal., 2018, 8, pp 6894–6907
DOI: 10.1021/acscatal.8b00220 Publication Date (Web): June 29, 2018

AIM: An Abstraction for Improving Machine Learning Prediction
V Stodden, X Wu, V Sochat
2018 IEEE Data Science Workshops, June 2018, DOI: 10.1109/DSW.2018.8439914

Efficient Threshold Selection for Multivariate Total Variation Denoising  
Sylvain Sardy & Hatef Monajemi       
Journal of Computational and Graphical Statistics
10 May 2018 DOI: 10.1080/10618600.2018.1476251

MRI to MGMT: predicting methylation status in glioblastoma patients using convolutional recurrent neural networks
Han L, Kamdar MR.
Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing.
2018;23:331-342.

Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins
Po-Nan Li, Jonathan Herrmann, Bradley B. Tolar, Frédéric Poitevin, Rasika Ramdasi, John R. Bargar, David A. Stahl, Grant J. Jensen,
Christopher A. Francis, Soichi Wakatsuki, Henry van den Bedem
The ISME Journal https://doi.org/10.1038/s41396-018-0191-0 Accepted: 14 April 201

Biological Insights Into Muscular Strength: Genetic Findings in the UK Biobank
Emmi Tikkanen, Stefan Gustafsson, David Amar, Anna Shcherbina, Daryl Waggott, Euan A. Ashley & Erik Ingelsson
Nature Scientific Reports volume 8, Article number: 6451 (2018)
doi:10.1038/s41598-018-24735-y

Architecture of an HIV-1 reverse transcriptase initiation complex
Kevin P. Larsen, Yamuna Kalyani Mathiharan, Kalli Kappel, Aaron T. Coey, Dong-Hua Chen, Daniel Barrero, Lauren Madigan, Joseph D. Puglisi, Georgios Skiniotis & Elisabetta Viani Puglisi
Nature volume 557, pages118–122 (2018)
doi:10.1038/s41586-018-0055-9

The Scientific Filesystem
Vanessa Sochat
GigaScience, Volume 7, Issue 5, 1 May 2018, giy023,
https://doi.org/10.1093/gigascience/giy023

Breakdown of the Migdal-Eliashberg theory: A determinant quantum Monte Carlo study
I. Esterlis, B. Nosarzewski, E. W. Huang, B. Moritz, T. P. Devereaux, D. J. Scalapino, and S. A. Kivelson
Phys. Rev. B 97, 140501(R) – Published 2 April 2018

CRISPR–Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity
Nicholas J. Kramer, Michael S. Haney, David W. Morgens, Ana Jovičić, Julien Couthouis, Amy Li, James Ousey, Rosanna Ma, Gregor Bieri, C. Kimberly Tsui, Yingxiao Shi, Nicholas T. Hertz, Marc Tessier-Lavigne, Justin K. Ichida, Michael C. Bassik & Aaron D. Gitler
Nature Genetics (2018)
doi:10.1038/s41588-018-0070-7

Bad metallic transport in a modified Hubbard model
Connie H. Mousatov, Ilya Esterlis, Sean A. Hartnoll
arXiv:1803.08054, 2018 (Submitted on 21 Mar 2018)

Cholesterol enhances influenza binding avidity by controlling nanoscale receptor clustering
I. N. Goronzy, R. J. Rawle, S. G. Boxer and P. M. Kasson
DOI: 10.1039/C7SC03236F Chem. Sci., 2018, 9, 2340-2347

Natural Gradient Deep Q-learning
Ethan Knight, Osher Lerner
arXiv:1803.07482 [cs.LG] (Submitted on 20 Mar 2018)

Machine Learning Harnesses Molecular Dynamics to Discover New μ Opioid Chemotypes
Evan N. Feinberg, Amir Barati Farimani, Rajendra Uprety, Amanda Hunkele, Gavril W. Pasternak, Susruta Majumdar, Vijay S. Pande
arXiv:1803.04479 [q-bio.BM] (Submitted on 12 Mar 2018)

Using Deep Learning for Segmentation and Counting within Microscopy Data
Carlos X. Hernández, Mohammad M. Sultan, Vijay S. Pande
arXiv:1802.10548 [cs.CV] (Submitted on 28 Feb 2018)

Decision functions from supervised machine learning algorithms as collective variables for accelerating molecular simulations
Mohammad M. Sultan, Vijay S. Pande
arXiv:1802.10510 [stat.ML] (Submitted on 28 Feb 2018)

Sterically controlled mechanochemistry under hydrostatic pressure
Hao Yan, Fan Yang, Ding Pan, Yu Lin, J. Nathan Hohman, Diego Solis-Ibarra, Fei Hua Li, Jeremy E. P. Dahl, Robert M. K. Carlson,Boryslav A. Tkachenko, Andrey A. Fokin, Peter R. Schreiner, Giulia Galli, Wendy L. Mao, Zhi-Xun Shen & Nicholas A. Melosh
Nature volume 554, pages 505–510 (22 February 2018)  
DOI:10.1038/nature25765

Comparing fully general relativistic and Newtonian calculations of structure formation
William E. East, Radosław Wojtak, and Tom Abel
Phys. Rev. D 97, 043509 – Published 13 February 2018

Intermolecular correlations are necessary to explain diffuse scattering from protein crystals
A Peck, F Poitevin, TJ Lane
IUCrJ, 2018 - scripts.iucr.org

Unprecedented climate events: Historical changes, aspirational targets, and national commitments
Noah S. Diffenbaugh, Deepti Singh, and Justin S. Mankin
Science Advances  14 Feb 2018:
Vol. 4, no. 2, eaao3354
DOI: 10.1126/sciadv.aao3354

Transferable neural networks for enhanced sampling of protein dynamics  
Mohammad M. Sultan, Hannah K. Wayment-Steele, Vijay S. Pande
eprint arXiv:1801.00636 Publication Date:01/02/2018

Reducing Noise in Cosmological N-body Simulations with Neutrinos
Arka Banerjee, Devon Powell, Tom Abel, Francisco Villaescusa-Navarro
arXiv:1801.03906  Submitted 11 Jan 2018

2017

Local estrogen axis in the human bone microenvironment regulates estrogen receptor-positive breast cancer cells
Derek F. Amanatullah, John S. Tamaresis, Pauline Chu, Michael H. Bachmann, Nhat M. Hoang, Deborah Collyar, Aaron T. Mayer, Robert B. West, William J. Maloney, Christopher H. Contag & Bonnie L. King     
Breast Cancer Research volume 19, Article number: 121 (2017)

Comprehensive computational design of ordered peptide macrocycles
Parisa Hosseinzadeh, Gaurav Bhardwaj, Vikram Khipple Mulligan, Matthew D. Shortridge, Timothy W. Craven, Fátima Pardo-Avila, Stephen A. Rettie, David E. Kim, Daniel-Adriano Silva, Yehia M. Ibrahim, Ian K. Webb, John R. Cort, Joshua N. Adkins, Gabriele Varani, David Baker
Science  15 Dec 2017:
Vol. 358, Issue 6369, pp. 1461-1466
DOI: 10.1126/science.aap7577

Towards understanding feedback from supermassive black holes using convolutional neural networks
Stanislav Fort
arXiv:1712.00523

Variational Encoding of Complex Dynamics
Carlos X. Hernández, Hannah K. Wayment-Steele, Mohammad M. Sultan, Brooke E. Husic, Vijay S. Pande
arXiv:1711.08576v2

Numerical evidence of fluctuating stripes in the normal state of high-Tc cuprate superconductors
Edwin W. Huang, Christian B. Mendl, Shenxiu Liu, Steve Johnston, Hong-Chen Jiang, Brian Moritz, Thomas P. Devereaux
Science  01 Dec 2017: Vol. 358, Issue 6367, pp. 1161-1164
DOI: 10.1126/science.aak9546

Comparing Fully General Relativistic and Newtonian Calculations of Structure Formation
William E. East, Radosław Wojtak, Tom Abel
(Submitted on 17 Nov 2017) https://arxiv.org/abs/1711.06681

Structural sensitivity in HIV modeling: A case study of vaccination
Cora L. Bernard Margaret L. Brandeau
Infectious Disease Modelling, Volume 2, Issue 4, November 2017, Pages 399-411
https://doi.org/10.1016/j.idm.2017.08.002

Photoactivated Molecular Layer Deposition through Iodo−Ene Coupling Chemistry
Mie Lillethorup , David S. Bergsman , Tania E. Sandoval , and Stacey F. Bent
Chem. Mater., 2017, 29 (23), pp 9897–9906
DOI: 10.1021/acs.chemmater.7b01780 Publication Date (Web): November 12, 2017

Timeslice experiments for understanding regional climate projections: applications to the tropical hydrological cycle and European winter circulation
Chadwick, R., Douville, H. & Skinner, C.B.
Clim Dyn (2017) 49: 3011.
https://doi.org/10.1007/s00382-016-3488-6

Ultrafast Intersystem Crossing in Acetylacetone via Femtosecond X-ray Transient Absorption at the Carbon K-Edge
Aditi Bhattacherjee, Chaitanya Das Pemmaraju, Kirsten Schnorr, Andrew R. Attar, and Stephen R. Leone
J. Am. Chem. Soc., 2017, 139 (46), pp 16576–16583
DOI: 10.1021/jacs.7b07532

Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers
Vanessa V. Sochat, Cameron J. Prybol, Gregory M. Kurtzer
PLoS One. 2017 Nov 29;12(11):e0188511. doi: 10.1371/journal.pone.0188511. eCollection 2017.

Simulated Dynamics of Glycans on Ligand-Binding Domain of NMDA Receptors Reveals Strong Dynamic Coupling between Glycans and Protein Core
Anton V. Sinitskiy and Vijay S. Pande
J. Chem. Theory Comput.,DOI: 10.1021/acs.jctc.7b00817  October 11, 2017

The DECam Plane Survey: Optical photometry of two billion objects in the southern Galactic plane
E. F. Schlafly, G. M. Green, D. Lang, T. Daylan, D. P. Finkbeiner, A. Lee, A. M. Meisner, D. Schlegel, F. Valdes
(Submitted on 3 Oct 2017) arXiv:1710.01309

MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites
Oscar Esteban, Daniel Birman, Marie Schaer, Oluwasanmi O. Koyejo, Russell A. Poldrack, Krzysztof J. Gorgolewski
PLOS Published: September 25, 2017 https://doi.org/10.1371/journal.pone.0184661

Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site
Lu Wang, Stephen D. Fried, and Thomas E. Markland
J. Phys. Chem. B, 2017, 121 (42), pp 9807–9815
DOI: 10.1021/acs.jpcb.7b06985 Publication Date (Web): September 15, 2017

Stripe order from the perspective of the Hubbard model
Edwin W. Huang, Christian B. Mendl, Hong-Chen Jiang, Brian Moritz, Thomas P. Devereaux
Submitted on 7 Sep 2017, arXiv:1709.02398

Bioimpedance and new onset heart failure: A longitudinal study of ~500,000 individuals from the general population
Daniel Lindholm, Eri Fukaya, Nicholas J. Leeper, Erik Ingelsson
doi: https://doi.org/10.1101/183483

Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems
Mohammad M. Sultan and Vijay S. Pande
J. Phys. Chem. B, Article ASAP
DOI: 10.1021/acs.jpcb.7b06896

Impact of Hydrogen Bonding on the Dynamics and Structure of Protic Ionic Liquid/Water Binary Mixtures
Heather E. Bailey, Yong-Lei Wang , and Michael D. Fayer
J. Phys. Chem. B, 2017, 121 (36), pp 8564–8576
DOI: 10.1021/acs.jpcb.7b06376

Decoding the spectroscopic features and timescales of aqueous proton defects
Joseph A. Napoli, Ondrej Marsalek, and Thomas E. Markland
arXiv:1709.05740

Kinetic Machine Learning Unravels Ligand-Directed Conformational Change of μ Opioid Receptor
Evan N. Feinberg, Amir Barati Farimani, Carlos Xavier Hernandez, Vijay S. Pande
doi: https://doi.org/10.1101/170886

Fast automated analysis of strong gravitational lenses with convolutional neural networks
Yashar D. Hezaveh, Laurence Perreault Levasseur & Philip J. Marshall
Nature 548, 555–557 (31 August 2017) doi:10.1038/nature23463

Analytical gradients for tensor hyper-contracted MP2 and SOS-MP2 on graphical processing units
Chenchen Song and Todd J. Martínez
The Journal of Chemical Physics 147, 161723 (2017); https://doi.org/10.1063/1.4997997

Mechanochemical unzipping of insulating polyladderene to semiconducting polyacetylene
Zhixing Chen, Jaron A. M. Mercer, Xiaolei Zhu, Joseph A. H. Romaniuk, Raphael Pfattner, Lynette Cegelski, Todd J. Martinez, Noah Z. Burns, Yan Xia,
Science  04 Aug 2017:Vol. 357, Issue 6350, pp. 475-479
DOI: 10.1126/science.aan2797

Ab Initio Simulations of a Supernova-driven Galactic Dynamo in an Isolated Disk Galaxy
Iryna Butsky, Jonathan Zrake, Ji-hoon Kim, Hung-I Yang, and Tom Abel
The Astrophysical Journal, Volume 843, Number 2, Published 2017 July 12

Is Multitask Deep Learning Practical for Pharma?
Bharath Ramsundar, Bowen Liu, Zhenqin Wu, Andreas Verras, Matthew Tudor, Robert P. Sheridan, and Vijay Pande
J. Chem. Inf. Model., 2017, 57 (8), pp 2068–2076
DOI: 10.1021/acs.jcim.7b00146 Publication Date (Web): July 10, 2017

3D Deep Convolutional Neural Networks for Amino Acid Environment Similarity Analysis
Wen Torng, Russ B. Altman
BMC Bioinformatics. 2017; 18: 302. Published online 2017 Jun 14. doi: 10.1186/s12859-017-1702-0

ERAD defects and the HFE-H63D variant are associated with increased risk of liver damages in Alpha 1-Antitrypsin Deficiency
Philippe Joly, Hélène Vignaud, Julie Di Martino, Mathias Ruiz, Roman Garin, Lioara Restier, Abdelouahed Belmalih, Christelle Marchal, Christophe Cullin, Benoit Arveiler, Patricia Fergelot, Aaron D. Gitler, Alain Lachaux, Julien Couthouis, Marion Bouchecareilh
PLoS One. 2017; 12(6): e0179369. Published online 2017 Jun 15. doi: 10.1371/journal.pone.0179369

Decrease of d-wave pairing strength in spite of the persistence of magnetic excitations in the overdoped Hubbard model
Edwin W. Huang, Douglas J. Scalapino, Thomas A. Maier, Brian Moritz, Thomas P. Devereaux
(Submitted on 10 May 2017) arXiv:1705.03949

α-CASSCF: An Efficient, Empirical Correction for SA-CASSCF To Closely Approximate MS-CASPT2 Potential Energy Surfaces
James W. Snyder Jr., Robert M. Parrish, and Todd J. Martínez
J. Phys. Chem. Lett., 2017, 8 (11), pp 2432–2437
DOI: 10.1021/acs.jpclett.7b00940 Publication Date (Web): May 17, 2017

Computing Localized Representations of the Kohn--Sham Subspace Via Randomization and Refinement
Anil Damle, Lin Lin, and Lexing Ying
SIAM J. Sci. Comput., 39(6), B1178–B1198.
https://doi.org/10.1137/16M1098589

A geographically-diverse collection of 418 human gut microbiome pathway genome databases
Aria S. Hahn, Tomer Altman,Kishori M. Konwar, Niels W. Hanson, Dongjae Kim, David A. Relman, David L. Dill and Steven J. Hallam
doi:10.1038/sdata.2017.35 Published online: 11 April 2017

Unravelling the influence of quantum proton delocalization on electronic charge transfer through the hydrogen bond
Christoph Schran Ondrej Marsalek Thomas E.Markland
Accepted 10 April 2017
https://doi.org/10.1016/j.cplett.2017.04.034

Low Data Drug Discovery with One-Shot Learning
Han Altae-Tran, Bharath Ramsundar, Aneesh S. Pappu, Vijay Pande
ACS Cent Sci. 2017 Apr 26; 3(4): 283–293. Published online 2017 Apr 3. doi: 10.1021/acscentsci.6b00367

Computationally Discovered Potentiating Role of Glycans on NMDA Receptors
Anton V. Sinitskiy, Nathaniel H. Stanley, David H. Hackos, Jesse E. Hanson, Benjamin D. Sellers, Vijay S. Pande
Sci Rep. 2017; 7: 44578. Published online 2017 Apr 5. doi: 10.1038/srep44578

Phase Field Model for Morphological Transition in Nanowire Vapor–Liquid–Solid Growth
Yanming Wang, Paul C. McIntyre, and Wei Cai
Cryst. Growth Des., 2017, 17 (4), pp 2211–2217
DOI: 10.1021/acs.cgd.7b00197

Superradiant Instability and Backreaction of Massive Vector Fields around Kerr Black Holes
William E. East and Frans Pretorius
Phys. Rev. Lett. 119, 041101 – Published 24 July 2017

Statistical algorithms improve accuracy of gene fusion detection 
Gillian Hsieh Rob Bierman Linda Szabo Alex Gia Lee Donald E. FreemanNathaniel Watson E. Alejandro Sweet-Cordero Julia Salzman
Nucleic Acids Research, Volume 45, Issue 13, 27 July 2017, Pages e126, https://doi.org/10.1093/nar/gkx453

Topology-optimized metasurfaces: impact of initial geometric layout
Jianji Yang and Jonathan A. Fan
Opt. Lett. 42, 3161-3164 (2017)

Previous Models of Diffuse Scattering From Protein Crystals Do Not Explain Experimental Observations
Ariana Peck, Frédéric Poitevin, Thomas J. Lane

Application of the inverse fast multipole method as a preconditioner in a 3D Helmholtz boundary element method
T Takahashi, P Coulier, E Darve
Journal of Computational Physics, 2017 - Elsevier

Intertwined order in a frustrated four-leg t−J cylinder
John F. Dodaro, Hong-Chen Jiang, and Steven A. Kivelson
Phys. Rev. B 95, 155116 – Published 12 April 2017

Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity
Joseph Gomes, Bharath Ramsundar, Evan N. Feinberg, Vijay S. Pande
(Submitted on 30 Mar 2017) arXiv:1703.10603

A direct-compatible formulation of the coupled perturbed complete active space self-consistent field equations on graphical processing units
James W. Snyder Jr. B. Scott Fales, Edward G. Hohenstein, Benjamin G. Levine, and Todd J. Martínez
The Journal of Chemical Physics 146, 174113 (2017); https://doi.org/10.1063/1.4979844

Seasonally fluctuating selection can maintain polymorphism at many loci via segregation lift
Meike J. Wittmann, Alan O. Bergland, Marcus W. Feldman, Paul S. Schmidt, and Dmitri A. Petrov
PNAS,  March 8, 2017 doi: 10.1073/pnas.1702994114

MoleculeNet: A Benchmark for Molecular Machine Learning
Zhenqin Wu, Bharath Ramsundar, Evan N. Feinberg, Joseph Gomes, Caleb Geniesse, Aneesh S. Pappu, Karl Leswing, Vijay Pande
(Submitted on 2 Mar 2017) arXiv:1703.00564

Quantum Dynamics and Spectroscopy of Ab Initio Liquid Water: The Interplay of Nuclear and Electronic Quantum Effects
Ondrej Marsalek and Thomas E. Markland
J. Phys. Chem. Lett., 2017, 8 (7), pp 1545–1551
DOI: 10.1021/acs.jpclett.7b00391 Publication Date (Web): March 15, 2017

The Role of Plant CO2 Physiological Forcing in Shaping Future Daily-Scale Precipitation
Christopher B. Skinner and Christopher J. Poulsen, Robin Chadwick, Noah S. Diffenbaugh, Richard P. Fiorella
https://doi.org/10.1175/JCLI-D-16-0603.1 Published 9 March 2017

Fast Spatial Gaussian Process Maximum Likelihood Estimation via Skeletonization Factorizations
Victor Minden, Anil Damle, Kenneth L. Ho, and Lexing Ying
Multiscale Model. Simul., 15(4), 1584–1611.
https://doi.org/10.1137/17M1116477

Electrostatic Control of Regioselectivity in Au(I)-Catalyzed Hydroarylation
Vivian M. Lau, William C. Pfalzgraff, Thomas E. Markland, and Matthew W. Kanan
J. Am. Chem. Soc., 2017, 139 (11), pp 4035–4041
DOI: 10.1021/jacs.6b11971 Publication Date (Web): February 22, 2017

Sparsity/Undersampling Tradeoffs in Anisotropic Undersampling, with Applications in MR Imaging/Spectroscopy
Hatef Monajemi, David L. Donoho
(Submitted on 10 Feb 2017) arXiv:1702.03062

Spacetime dynamics of a Higgs vacuum instability during inflation
WE East, J Kearney, B Shakya, H Yoo, KM Zurek
Physical Review D, 2017 - APS

2016

Au–Ge MEAM potential fitted to the binary phase diagram
Yanming Wang, Adriano Santana and Wei Cai
Published 23 December 2016 Modelling and Simulation in Materials Science and Engineering, Volume 25, Number 2

Reverse time migration for microseismic sources using the geometric mean as an imaging condition
Nori Nakata and Gregory C. Beroza (2016) GEOPHYSICS, 81(2), KS51-KS60.
https://doi.org/10.1190/geo2015-0278.1

Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity
Chenchen Song and Todd J. Martínez
The Journal of Chemical Physics 144, 174111 (2016); doi: http://dx.doi.org/10.1063/1.4948438

Massively Parallel Computation of Accurate Densities for N-body Dark Matter Simulations using the Phase-Space-Element Method
Ralf Kaehler

Communication: A difference density picture for the self-consistent field ansatz
Robert M. Parrish, Fang Liu and Todd J. Martínez
The Journal of Chemical Physics 144, 131101 (2016); doi: http://dx.doi.org/10.1063/1.4945277

Electronic pair binding and Hund's rule violations in doped C60
Hong-Chen Jiang and Steven Kivelson
Phys. Rev. B 93, 165406 – Published 5 April 2016

Eco-evolutionary buffering: rapid evolution facilitates regional coexistence of species engaged in local priority effects
Meike J. Wittmann, Tadashi Fukami
doi: https://doi.org/10.1101/040659

Freely decaying turbulence in force-free electrodynamics
Jonathan Zrake, William E. East
Published 2016 January 22

2015

Breast Cancer Cell Colonization of the Human Bone Marrow Adipose Tissue Niche 1
Zach S. Templeton, Wen-Rong Lie, Weiqi Wang, Yael Rosenberg-Hasson, Rajiv V.Alluri, John S. Tamaresis, Michael H. Bachmann, Kitty Lee, William J. Maloney, Christopher H. Contag, Bonnie L.King
Neoplasia Volume 17, Issue 12, December 2015, Pages 849-861 December 2015

Spontaneous Decay of Periodic Magnetostatic Equilibria
William E. East, Jonathan Zrake, Yajie Yuan, and Roger D. Blandford
Phys. Rev. Lett. 115, 095002 – Published 28 August 2015