Opportunities and obstacles for deep learning in biology and medicine T Ching, DS Himmelstein, BK Beaulieu-Jones, AA Kalinin, BT Do, ... Journal of The Royal Society Interface 15 (141), 20170387, 2018 | 2084 | 2018 |
Studying and modelling dynamic biological processes using time-series gene expression data Z Bar-Joseph, A Gitter, I Simon Nature Reviews Genetics 13 (8), 552-564, 2012 | 549 | 2012 |
Network-based interpretation of diverse high-throughput datasets through the Omics Integrator software package N Tuncbag, SJC Gosline, A Kedaigle, AR Soltis, A Gitter, E Fraenkel PLoS computational biology 12 (4), e1004879, 2016 | 160 | 2016 |
DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data M Schulz, W Devanny, A Gitter, S Zhong, J Ernst, Z Bar-Joseph BMC Systems Biology 6 (1), 104, 2012 | 145 | 2012 |
Discovering pathways by orienting edges in protein interaction networks A Gitter, J Klein-Seetharaman, A Gupta, Z Bar-Joseph Nucleic acids research 39 (4), e22-e22, 2010 | 135 | 2010 |
Loss-Balanced Task Weighting to Reduce Negative Transfer in Multi-Task Learning S Liu, Y Liang, A Gitter Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence …, 2019 | 129 | 2019 |
Neural networks to learn protein sequence–function relationships from deep mutational scanning data S Gelman, SA Fahlberg, P Heinzelman, PA Romero, A Gitter Proceedings of the National Academy of Sciences 118 (48), e2104878118, 2021 | 110 | 2021 |
Backup in gene regulatory networks explains differences between binding and knockout results A Gitter, Z Siegfried, M Klutstein, O Fornes, B Oliva, I Simon, Z Bar‐Joseph Molecular Systems Biology 5 (1), 276, 2009 | 101 | 2009 |
Learning Drug Functions from Chemical Structures with Convolutional Neural Networks and Random Forests JG Meyer, S Liu, IJ Miller, JJ Coon, A Gitter Journal of Chemical Information and Modeling 59 (10), 4438-4449, 2019 | 98 | 2019 |
Network inference with Granger causality ensembles on single-cell transcriptomics A Deshpande, LF Chu, R Stewart, A Gitter Cell Reports 38 (6), 110333, 2022 | 97* | 2022 |
Linking the signaling cascades and dynamic regulatory networks controlling stress responses A Gitter, M Carmi, N Barkai, Z Bar-Joseph Genome Research 23 (2), 365-376, 2013 | 86 | 2013 |
Practical model selection for prospective virtual screening S Liu, M Alnammi, SS Ericksen, AF Voter, GE Ananiev, JL Keck, ... Journal of chemical information and modeling 59 (1), 282-293, 2018 | 68 | 2018 |
Open collaborative writing with Manubot DS Himmelstein, V Rubinetti, DR Slochower, D Hu, VS Malladi, ... PLOS Computational Biology 15 (6), e1007128, 2019 | 63 | 2019 |
Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism ZE Sychev, A Hu, TA DiMaio, A Gitter, ND Camp, WS Noble, ... PLoS pathogens 13 (3), e1006256, 2017 | 62 | 2017 |
A Network-based Approach for Predicting Missing Pathway Interactions S Navlakha, A Gitter, Z Bar-Joseph PLoS Computational Biology 8 (8), e1002640, 2012 | 43 | 2012 |
Identifying proteins controlling key disease signaling pathways A Gitter, Z Bar-Joseph Bioinformatics 29 (13), i227-i236, 2013 | 38 | 2013 |
A text-guided protein design framework S Liu, Y Li, Z Li, A Gitter, Y Zhu, J Lu, Z Xu, W Nie, A Ramanathan, C Xiao, ... arXiv preprint arXiv:2302.04611, 2023 | 35 | 2023 |
Pathogenesis, symptomatology, and transmission of SARS-CoV-2 through analysis of viral genomics and structure HM Rando, AL MacLean, AJ Lee, R Lordan, S Ray, V Bansal, AN Skelly, ... mSystems 6 (5), e00095-21, 2021 | 35 | 2021 |
Computationally efficient measure of topological redundancy of biological and social networks R Albert, B DasGupta, R Hegde, GS Sivanathan, A Gitter, G Gürsoy, ... Physical Review E 84 (3), 036117, 2011 | 32 | 2011 |
Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data AS Köksal, K Beck, DR Cronin, A McKenna, ND Camp, S Srivastava, ... Cell Reports 24 (13), 3607-3618, 2018 | 31 | 2018 |