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SRCC-enabled publications

Below are selected publications that have utilized and acknowledged Stanford Research Computing Center's computational resources and expertise.

It is important that publications resulting from computations performed on 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, Nero) 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!

Also, check out the Goolge Scholar search for Stanford Research Computing Center acknowledgements.


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,

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, 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

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

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:

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;

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


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,

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 2020

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

Nearest Neighbor distributions: new statistical measures for cosmological clustering
Arka Banerjee, Tom Abel
Monthly Notices of the Royal Astronomical Society, 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

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

Large-Scale Labeling and Assessment of Sex Bias in Publicly Available Expression Data
Emily Flynn, Annie Chang, Russ B. Altman

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

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

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, 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 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:

Drug Response Pharmacogenetics for 200,000 UK Biobank Participants
Gregory McInnes, Russ B Altman

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, 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

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: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

GANSim: Conditional Facies Simulation Using an Improved Progressive Growing of Generative Adversarial Networks (GANs)
Suihong Song, Tapan Mukerji, Jiagen Hou
EarthArXiv 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: 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

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:  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 2020-06-22

A genotype-phenotype-fitness map reveals local modularity and global pleiotropy of adaptation
Grant Kinsler, Kerry Geiler-Samerotte, Dmitri Petrov

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

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

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

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,

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
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,
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:

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
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

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:

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

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
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

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,
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
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; 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

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 Published:18 March 2020

Beyond the Core: Who Has Larger Social Networks?
Bas Hofstra, Rense Corten, Frank van Tubergen
Social Forces, 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).

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

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

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

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

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

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

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);

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;
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

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

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


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

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

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 |

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

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

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

Practical Considerations for Continuum Models Applied to Surface Electrochemistry
Joseph Gauthier, Colin Dickens, Stefan Ringe, Karen Chan

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

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

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 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

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

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;

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;

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: 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.

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

Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships
Christopher M.Jakobson, Daniel F.Jarosz
Cell Systems, Published: May 1, 2019

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;

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

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

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

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

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

RNA design movesets and strategies from an Internet-scale videogame
Rohan Koodli, Benjamin Keep, Katherine R Coppess, Fernando Portela, Eterna Players, Rhiju Das
doi: 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

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)

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)


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

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 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

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

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

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

Convolutional models of RNA energetics
Michelle J Wu

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

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

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

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

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

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:, 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

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 -

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
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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);

Simple, direct and efficient multi-way spectral clustering
A Damle, V Minden, L Ying
Information and Inference: A Journal of the IMA, 2018

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, 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);

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.

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 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)

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)

The Scientific Filesystem
Vanessa Sochat
GigaScience, Volume 7, Issue 5, 1 May 2018, 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)

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)  

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 -

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


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

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

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)

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

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.

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

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

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

Kinetic Machine Learning Unravels Ligand-Directed Conformational Change of μ Opioid Receptor
Evan N. Feinberg, Amir Barati Farimani, Carlos Xavier Hernandez, Vijay S. Pande

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);

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

Wen Torng, Russ B. Altman
BMC Bioinformatics. 2017; 18: 302. Published online 2017 Jun 14. doi: 10.1186/s12859-017-1702-0
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.
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
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
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,

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);
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 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.
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

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


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.

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:

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:

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

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


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