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
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)
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
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
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
Causal Inference in Genetic Trio Studies
Stephen Bates, Matteo Sesia, Chiara Sabatti, Emmanuel Candes
arXiv:2002.09644 (Submitted on 22 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 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
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
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
Signatures of Self-Interacting dark matter on cluster density profile and subhalo distributions
Arka Banerjee, Susmita Adhikari, Neal Dalal, Surhud More, Andrey Kravtsov
arXiv:1906.12026 (Submitted on 28 Jun 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
ChemRxiv https://doi.org/10.26434/chemrxiv.8188454.v1
The Impact of the Fiducial Cosmology Assumption on BAO Cosmological Parameter Inference
Paul Carter, Florian Beutler, Will J. Percival, Joseph DeRose, Risa H. Wechsler, Cheng Zhao
arXiv:1906.03035 (Submitted on 7 Jun 2019)
Early Changes in CT Perfusion Parameters: Primary Renal Carcinoma Versus Metastases After Treatment with Targeted Therapy
Alice C. Fan, Vandana Sundaram, Aya Kino, Heiko Schmiedeskamp, Thomas J. Metzner and Aya Kamaya
Cancers 2019, 11(5), 608; https://doi.org/10.3390/cancers11050608
Surface Photovoltage-Induced Ultralow Work Function Material for Thermionic Energy Converters
Peter Schindler, Daniel C. Riley, Igor Bargatin, Kunal Sahasrabuddhe, Jared W. Schwede, Steven Sun, Piero Pianetta, Zhi-Xun Shen, Roger T. Howe, and Nicholas A. Melosh
ACS Energy Letters 2019 4 (10), 2436-2443
DOI: 10.1021/acsenergylett.9b01214
Pseudogap crossover in the electron-phonon system
I. Esterlis, S. A. Kivelson, and D. J. Scalapino
Phys. Rev. B 99, 174516 – Published 24 May 2019
Global warming has increased global economic inequality
Noah S. Diffenbaugh and Marshall Burke
PNAS May 14, 2019 116 (20) 9808-9813; https://doi.org/10.1073/pnas.1816020116
Uncovering the structure of self-regulation through data-driven ontology discovery
Ian W. Eisenberg, Patrick G. Bissett, A. Zeynep Enkavi, Jamie Li, David P. MacKinnon, Lisa A. Marsch & Russell A. Poldrack
Nature Communications 10, Article number: 2319 (2019)
Global analysis of epigenetic heterogeneity identifies divergent drivers of esophageal squamous cell carcinoma
Wei Cao, Hayan Lee, Wei Wu, Aubhishek Zaman, Sean McCorkle, Ming Yan, Justin Chen, Qinghe Xing, Nasa Sinnott-Armstrong, Hongen Xu, M.Reza Sailani, Wenxue Tang, Yuanbo Cui, Jia liu, Hongyan Guan, Pengju Lv, Xiaoyan Sun, Lei Sun, Pengli Han, Yanan Lou, Jing Chang, Jinwu Wang, Yuchi Gao, Jiancheng Guo, Gundolf Schenk, Alan Hunter Shain, Fred G. Biddle, Eric Collisson, Michael Snyder, Trever G. Bivona
doi: https://doi.org/10.1101/641357 Posted May 18, 2019
Towards a Flexible Deep Learning Method for Automatic Detection of Clinically Relevant Multi-Modal Events in the Polysomnogram
Alexander Neergaard Olesen, Stanislas Chambon, Valentin Thorey, Poul Jennum, Emmanuel Mignot, Helge B. D. Sorensen
arXiv:1905.08059 (Submitted on 16 May 2019)
Transplantation of donor grafts with defined ratio of conventional and regulatory T cells in HLA-matched recipients
Everett H. Meyer, Ginna Laport, Bryan J. Xie, Kate MacDonald, Kartoosh Heydari, Bita Sahaf, Sai-Wen Tang, Jeanette Baker, Randall Armstrong, Keri Tate, Cynthia Tadisco, Sally Arai, Laura Johnston, Robert Lowsky, Lori Muffly, Andrew R. Rezvani, Judith Shizuru, Wen-Kai Weng, Kevin Sheehan, David Miklos, and Robert S. Negrin
Published in Volume 4, Issue 10 on May 16, 2019 JCI Insight. 2019;4(10):e127244. https://doi.org/10.1172/jci.insight.127244
Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding
Morteza Roodgar, Afshin Babveyh,Lan Huong, Wenyu Zhou, Rahul Sinha, Hayan Lee, John B. Hanks, Mohan Avula, Lihua Jiang, Hoyong Lee, Giltae Song, Hassan Chaib, Irv L. Weissman, Serafim Batzoglou, Susan Holmes, David G. Smith, Joseph L. Mankowski, Stefan Prost, Michael P. Snyder
doi: https://doi.org/10.1101/635045
Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships
Christopher M.Jakobson, Daniel F.Jarosz
Cell Systems, Published: May 1, 2019 https://doi.org/10.1016/j.cels.2019.04.002
Blind tests of RNA–protein binding affinity prediction
Kalli Kappel, Inga Jarmoskaite, Pavanapuresan P. Vaidyanathan, William J. Greenleaf, Daniel Herschlag, and Rhiju Das
PNAS April 23, 2019 116 (17) 8336-8341; https://doi.org/10.1073/pnas.1819047116
Robust mouse tracking in complex environments using neural networks
Brian Q. Geuther, Sean P. Deats, Kai J. Fox, Steve A. Murray, Robert E. Braun, Jacqueline K. White, Elissa J. Chesler, Cathleen M. Lutz & Vivek Kumar
Nature Communications, Biology volume 2, Article number: 124 (2019)
Pervasive function and evidence for selection across standing genetic variation in S. cerevisiae
Christopher M. Jakobson, Richard She & Daniel F. Jarosz
Nature Communications Volume 10, Article number: 1222 (2019)
Predicting gait adaptations due to ankle plantarflexor muscle weakness and contracture using physics-based musculoskeletal simulations
Carmichael F. Ong, Thomas Geijtenbeek, Jennifer L. Hicks, Scott L. Delp
doi: https://doi.org/10.1101/597294
Efficient construction of generalized master equation memory kernels for multi-state systems from nonadiabatic quantum-classical dynamics
William C. Pfalzgraff, Andrés Montoya Castillo, Aaron Kelly, Thomas E. Markland
(Submitted on 22 Mar 2019)
Pairing and non-Fermi liquid behavior in partially flat-band systems
Sharareh Sayyad, Edwin W. Huang, Motoharu Kitatani, Mohammad-Sadegh Vaezi, Zohar Nussinov, Abolhassan Vaezi, Hideo Aoki
Submitted on 23 Mar 2019, last revised 29 Mar 2019
Uncertainty quantification of simulated biomechanical stimuli in coronary artery bypass grafts
Justin S. Trana, Daniele E. Schiavazzi, Andrew M. Kahn, Alison L. Marsden
Computer Methods in Applied Mechanics and Engineering, Volume 345, 1 March 2019, Pages 402-428
https://doi.org/10.1016/j.cma.2018.10.024
A functional subset of CD8+ T cells during chronic exhaustion is defined by SIRPα expression
Lara M. Myers, Michal Caspi Tal, Laughing Bear Torrez Dulgeroff, Aaron B. Carmody, Ronald J. Messer, Gunsagar Gulati, Ying Ying Yiu, Matthew M. Staron, Cesar Lopez Angel, Rahul Sinha, Maxim Markovic, Edward A. Pham, Benjamin Fram, Aijaz Ahmed, Aaron M. Newman, Jeffrey S. Glenn, Mark M. Davis, Susan M. Kaech, Irving L. Weissman & Kim J. Hasenkrug
Nature Communications Volume 10, Article number: 794 (2019)
Non-invasive machine learning estimation of effort differentiates sleep-disordered breathing pathology
Umaer Hanif, Logan D Schneider, Lotte Trap, Eileen B Leary, Hyatt Moore IV, Christian Guilleminault, Poul Jennum, Helge B D Sorensen, and Emmanuel J M Mignot
Published 26 February 2019, Institute of Physics and Engineering in Medicine
Physiological Measurement, Volume 40, Number 2
Thermal transport in MoS2 from molecular dynamics using different empirical potentials
Ke Xu, Alexander J. Gabourie, Arsalan Hashemi, Zheyong Fan, Ning Wei, Amir Barati Farimani, Hannu-Pekka Komsa, Arkady V. Krasheninnikov, Eric Pop, and Tapio Ala-Nissila
Phys. Rev. B 99, 054303 – Published 11 February 2019
Super-geometric electron focusing on the hexagonal Fermi surface of PdCoO2
Maja D. Bachmann, Aaron L. Sharpe, Arthur W. Barnard, Carsten Putzke, Markus König, Seunghyun Khim, David Goldhaber-Gordon, Andrew P. Mackenzie, Philip J. W. Moll
arXiv:1902.03769
Imidazole and 1-Methylimidazole Hydrogen Bonding and Non-Hydrogen Bonding Liquid Dynamics: Ultrafast IR Experiments
Jae Yoon Shin, Yong-Lei Wang, Steven A. Yamada, Samantha Ting Hung, and Michael D. Fayer
J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.8b11299
Publication Date (Web): February 6, 2019
Sub-Femtosecond Stark Control of Molecular Photoexcitation with Near Single-Cycle Pulses
Benoit Mignolet, Basile F. E. Curchod, Francoise Remacle and Todd J. Martínez
J. Phys. Chem. Lett., 2019, 10, pp 742–747
DOI: 10.1021/acs.jpclett.8b03814 Publication Date (Web): January 29, 2019
Intradomain Interactions in an NMDA Receptor Fragment Mediate N-Glycan Processing and Conformational Sampling
Ganesh P. Subedi, Anton V. Sinitskiy, Jacob T. Roberts, Kashyap R. Patel, Vijay S.Pande, Adam W. Barb
Structure, Volume 27, Issue 1, 2 January 2019, Pages 55-65.e3
Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level
Miriam V. Gutschow, John C. Mason, Keara M. Lane, Inbal Maayan, Jacob J. Hughey, Bryce T. Bajar, Debha N. Amatya, Sean D. Valle, and Markus W. Covert
Molecular Biology of the Cell Vol. 30, No. 2
Published Online:14 Jan 2019 https://doi.org/10.1091/mbc.E18-07-0423
Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking
Kalli Kappel, Rhiju Das
Structure, Volume 27, Issue 1, 2 January 2019, Pages 140-151.e5
https://doi.org/10.1016/j.str.2018.10.001
RNA design movesets and strategies from an Internet-scale videogame
Rohan Koodli, Benjamin Keep, Katherine R Coppess, Fernando Portela, Eterna Players, Rhiju Das
doi: https://doi.org/10.1101/326736 Posted January 15, 2019
Modeling of radiation-induced defect recovery in 3C-SiC under high field bias conditions
Ricardo Peterson, Debbie Senesky
Computational Materials Science, Volume 161, 15 April 2019, Pages 10-15
https://doi.org/10.1016/j.commatsci.2019.01.016
Globally Constructed Adaptive Local Basis Set for Spectral Projectors of Second Order Differential Operators
Yingzhou Li and Lin Lin
Multiscale Model. Simul., 17(1), 92–116. (25 pages)
https://doi.org/10.1137/17M1140236
fMRIPrep: a robust preprocessing pipeline for functional MRI
Oscar Esteban, Christopher J. Markiewicz, Ross W. Blair, Craig A. Moodie, A. Ilkay Isik, Asier Erramuzpe, James D. Kent, Mathias Goncalves, Elizabeth DuPre, Madeleine Snyder, Hiroyuki Oya, Satrajit S. Ghosh, Jessey Wright, Joke Durnez, Russell A. Poldrack & Krzysztof J. Gorgolewski
Nature Methods volume 16, pages111–116 (2019)
Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation
Zhongyue Yang, Rimsha Mehmood, Mengyi Wang, Helena W. Qi, Adam H. Steeves and Heather J. Kulik
React. Chem. Eng., 2019, Advance Article DOI: 10.1039/C8RE00213D (Paper)
The unWISE Catalog: Two Billion Infrared Sources from Five Years of WISE Imaging
Edward F. Schlafly, Aaron M. Meisner, Gregory M. Green
arXiv:1901.03337 (Submitted on 10 Jan 2019)
An Algebraic Sparsified Nested Dissection Algorithm Using Low-Rank Approximations
Léopold Cambier, Chao Chen, Erik G Boman, Sivasankaran Rajamanickam, Raymond S. Tuminaro, Eric Darve
arXiv:1901.02971 (Submitted on 9 Jan 2019)
Thermal Boundary Conductance of Two-Dimensional MoS2 Interfaces
Saurabh V. Suryavanshi, Alexander J. Gabourie, Amir Barati Farimani, Eric Pop
arXiv:1901.02447 (Submitted on 8 Jan 2019)
The Buzzard Flock: Dark Energy Survey Synthetic Sky Catalogs
Joseph DeRose, Risa H. Wechsler, Matthew R. Becker, Michael T. Busha, Eli S. Rykoff, Niall MacCrann, Brandon Erickson, August E. Evrard, Andrey Kravtsov, Daniel Gruen, Sahar Allam, Santiago Avila, Sarah Bridle, David Brooks, Elizabeth Buckley-Geer, Aurelio Carnero Rosell, Matias Carrasco Kind, Jorge Carretero, Francisco J. Castander, Ross Cawthon, Martin Crocce, Luiz N. da Costa, Christopher Davis, Juan De Vicente, Jörg P. Dietrich, Peter Doel, Alex Drlica-Wagner, Pablo Fosalba, Josh Frieman, Juan Garcia-Bellido, Gaston Gutierrez, Will G. Hartley, Devon L. Hollowood, Ben Hoyle, David J. James, Elisabeth Krause, Kyler Kuehn, Nikolay Kuropatkin, Marcos Lima, Marcio A. G. Maia, Felipe Menanteau, Christopher J. Miller, Ramon Miquel, Ricardo L. C. Ogando, Andrés Plazas Malagón, A. Kathy Romer, Eusebio Sanchez, Rafe Schindler, Santiago Serrano, Ignacio Sevilla-Noarbe, Mathew Smith, Eric Suchyta, Molly E. C. Swanson, Gregory Tarle, Vinu Vikram
arXiv:1901.02401 (Submitted on 8 Jan 2019)
2018
Automated design of collective variables using supervised machine learning featured
Mohammad M. Sultan and Vijay S. Pande
J. Chem. Phys. 149, 094106 (2018); https://doi.org/10.1063/1.5029972
Exploiting graphical processing units to enable quantum chemistry calculation of large solvated molecules with conductor‐like polarizable continuum models
Fang Liu, David M. Sanchez, Heather J. Kulik, Todd J. Martínez
https://doi.org/10.1002/qua.25760 First published: 11 October 2018
Biochat: a database for natural language processing of Gene Expression Omnibus data
Bohdan B Khomtchouk, Vsevolod Dyomkin, Kasra A Vand, Themistocles Assimes, Or Gozani
doi: https://doi.org/10.1101/480020
PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development
Jennifer L. Wilson, Rebecca Racz, Tianyun Liu, Oluseyi Adeniyi, Jielin Sun, Anuradha Ramamoorthy, Michael Pacanowski, Russ Altman
PLOS Published: December 7, 2018
https://doi.org/10.1371/journal.pcbi.1006614
Challenges in Modeling Electrochemical Reaction Energetics with Polarizable Continuum Models
Joseph A. Gauthier, Stefan Ringe, Colin F. Dickens, Alejandro J. Garza, Alexis T. Bell, Martin Head-Gordon, Jens K. Nørskov, Karen Chan
ACS Catal. 2019, 9, 2, 920-931
Publication Date:November 28, 2018
https://doi.org/10.1021/acscatal.8b02793
Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level
Miriam V. Gutschow, John C. Mason, Keara M. Lane, Inbal Maayan, Jacob J. Hughey, Bryce T. Bajar, Debha N. Amatya, Sean D., Valle, Markus W. Covert
Molecular Biology of the Cell Published Online: 21 Nov 2018
https://doi.org/10.1091/mbc.E18-07-0423
Convolutional models of RNA energetics
Michelle J Wu
doi: https://doi.org/10.1101/470740
Searching for Subsecond Stellar Variability with Wide-field Star Trails and Deep Learning
David Thomas and Steven M. Kahn
The Astrophysical Journal, Volume 868, Number 1, Published 2018 November 16
A global test of ecoregions
Jeffrey R. Smith, Andrew D. Letten, Po-Ju Ke, Christopher B. Anderson, J. Nicholas Hendershot, Manpreet K. Dhami, Glade A. Dlott, Tess N. Grainger, Meghan E. Howard, Beth M. L. Morrison, Devin Routh, Priscilla A. San Juan, Harold A. Mooney, Erin A. Mordecai, Thomas W. Crowther & Gretchen C. Daily
Nature Ecology & Evolution, Published: 05 November 2018
DOI https://doi.org/10.1038/s41559-018-0709-x
An energetic reformulation of kinetic rate laws enables scalable parameter estimation for biochemical networks
John C. Mason, Markus W. Covert
Journal of Theoretical Biology, 24 October 2018
DOI https://doi.org/10.1016/j.jtbi.2018.10.041
Spectroscopic Signature of Oxidized Oxygen States in Peroxides
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Analyzing interferometric observations of strong gravitational lenses with recurrent and convolutional neural networks
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CRISPR–Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity
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arXiv:1803.08054, 2018 (Submitted on 21 Mar 2018)
Cholesterol enhances influenza binding avidity by controlling nanoscale receptor clustering
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Natural Gradient Deep Q-learning
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Machine Learning Harnesses Molecular Dynamics to Discover New μ Opioid Chemotypes
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Using Deep Learning for Segmentation and Counting within Microscopy Data
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Decision functions from supervised machine learning algorithms as collective variables for accelerating molecular simulations
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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
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IUCrJ, 2018 - scripts.iucr.org
Unprecedented climate events: Historical changes, aspirational targets, and national commitments
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eprint arXiv:1801.00636 Publication Date:01/02/2018
Reducing Noise in Cosmological N-body Simulations with Neutrinos
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Comprehensive computational design of ordered peptide macrocycles
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Towards understanding feedback from supermassive black holes using convolutional neural networks
Stanislav Fort
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Variational Encoding of Complex Dynamics
Carlos X. Hernández, Hannah K. Wayment-Steele, Mohammad M. Sultan, Brooke E. Husic, Vijay S. Pande
arXiv:1711.08576v2
Numerical evidence of fluctuating stripes in the normal state of high-Tc cuprate superconductors
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Comparing Fully General Relativistic and Newtonian Calculations of Structure Formation
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(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
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Photoactivated Molecular Layer Deposition through Iodo−Ene Coupling Chemistry
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Timeslice experiments for understanding regional climate projections: applications to the tropical hydrological cycle and European winter circulation
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Ultrafast Intersystem Crossing in Acetylacetone via Femtosecond X-ray Transient Absorption at the Carbon K-Edge
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Simulated Dynamics of Glycans on Ligand-Binding Domain of NMDA Receptors Reveals Strong Dynamic Coupling between Glycans and Protein Core
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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
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MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites
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Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site
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Stripe order from the perspective of the Hubbard model
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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
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Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems
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Impact of Hydrogen Bonding on the Dynamics and Structure of Protic Ionic Liquid/Water Binary Mixtures
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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
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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
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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
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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
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Anil Damle, Lin Lin, and Lexing Ying
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Christoph Schran Ondrej Marsalek Thomas E.Markland
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Yanming Wang, Paul C. McIntyre, and Wei Cai
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William E. East and Frans Pretorius
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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
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Christopher B. Skinner and Christopher J. Poulsen, Robin Chadwick, Noah S. Diffenbaugh, Richard P. Fiorella
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Victor Minden, Anil Damle, Kenneth L. Ho, and Lexing Ying
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J. Am. Chem. Soc., 2017, 139 (11), pp 4035–4041
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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
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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
