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
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
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
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.org > cs > 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
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
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
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)
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
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
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:
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)
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Practical Considerations for Continuum Models Applied to Surface Electrochemistry
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Early Changes in CT Perfusion Parameters: Primary Renal Carcinoma Versus Metastases After Treatment with Targeted Therapy
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Global warming has increased global economic inequality
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Global analysis of epigenetic heterogeneity identifies divergent drivers of esophageal squamous cell carcinoma
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Towards a Flexible Deep Learning Method for Automatic Detection of Clinically Relevant Multi-Modal Events in the Polysomnogram
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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
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Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding
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Cell Systems, Published: May 1, 2019 https://doi.org/10.1016/j.cels.2019.04.002
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Robust mouse tracking in complex environments using neural networks
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Uncertainty quantification of simulated biomechanical stimuli in coronary artery bypass grafts
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Non-invasive machine learning estimation of effort differentiates sleep-disordered breathing pathology
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Physiological Measurement, Volume 40, Number 2
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Super-geometric electron focusing on the hexagonal Fermi surface of PdCoO2
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Imidazole and 1-Methylimidazole Hydrogen Bonding and Non-Hydrogen Bonding Liquid Dynamics: Ultrafast IR Experiments
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Sub-Femtosecond Stark Control of Molecular Photoexcitation with Near Single-Cycle Pulses
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Intradomain Interactions in an NMDA Receptor Fragment Mediate N-Glycan Processing and Conformational Sampling
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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
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Structure, Volume 27, Issue 1, 2 January 2019, Pages 140-151.e5
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RNA design movesets and strategies from an Internet-scale videogame
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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
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Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation
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The unWISE Catalog: Two Billion Infrared Sources from Five Years of WISE Imaging
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An Algebraic Sparsified Nested Dissection Algorithm Using Low-Rank Approximations
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Thermal Boundary Conductance of Two-Dimensional MoS2 Interfaces
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Machine Learning Harnesses Molecular Dynamics to Discover New μ Opioid Chemotypes
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Reducing Noise in Cosmological N-body Simulations with Neutrinos
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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
Edwin W. Huang, Douglas J. Scalapino, Thomas A. Maier, Brian Moritz, Thomas P. Devereaux
(Submitted on 10 May 2017) arXiv:1705.03949
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
Anil Damle, Lin Lin, and Lexing Ying
SIAM J. Sci. Comput., 39(6), B1178–B1198.
https://doi.org/10.1137/16M1098589
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
Christoph Schran Ondrej Marsalek Thomas E.Markland
Accepted 10 April 2017
https://doi.org/10.1016/j.cplett.2017.04.034
Yanming Wang, Paul C. McIntyre, and Wei Cai
Cryst. Growth Des., 2017, 17 (4), pp 2211–2217
DOI: 10.1021/acs.cgd.7b00197
William E. East and Frans Pretorius
Phys. Rev. Lett. 119, 041101 – Published 24 July 2017
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
Joseph Gomes, Bharath Ramsundar, Evan N. Feinberg, Vijay S. Pande
(Submitted on 30 Mar 2017) arXiv:1703.10603
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
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
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
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
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
Victor Minden, Anil Damle, Kenneth L. Ho, and Lexing Ying
Multiscale Model. Simul., 15(4), 1584–1611.
https://doi.org/10.1137/17M1116477
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
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
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
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
