| Using neural networks for reducing the dimensions of single-cell RNA-Seq data C Lin, S Jain, H Kim, Z Bar-Joseph Nucleic acids research 45 (17), e156-e156, 2017 | 207 | 2017 |
| Transcriptional regulatory model of fibrosis progression in the human lung JE McDonough, F Ahangari, Q Li, S Jain, SE Verleden, J Herazo-Maya, ... JCI insight 4 (22), 2019 | 123 | 2019 |
| What made you do this? understanding black-box decisions with sufficient input subsets B Carter, J Mueller, S Jain, D Gifford The 22nd International Conference on Artificial Intelligence and Statistics …, 2019 | 74* | 2019 |
| Large neighborhood search for dial-a-ride problems S Jain, P Van Hentenryck International Conference on Principles and Practice of Constraint …, 2011 | 64 | 2011 |
| Computationally optimized SARS-CoV-2 MHC class I and II vaccine formulations predicted to target human haplotype distributions G Liu, B Carter, T Bricken, S Jain, M Viard, M Carrington, DK Gifford Cell systems 11 (2), 131-144. e6, 2020 | 63 | 2020 |
| Multi-lingual evaluation of code generation models B Athiwaratkun, SK Gouda, Z Wang, X Li, Y Tian, M Tan, WU Ahmad, ... arXiv preprint arXiv:2210.14868, 2022 | 58 | 2022 |
| Maximizing overall diversity for improved uncertainty estimates in deep ensembles S Jain, G Liu, J Mueller, D Gifford Proceedings of the AAAI conference on artificial intelligence 34 (04), 4264-4271, 2020 | 54 | 2020 |
| Overinterpretation reveals image classification model pathologies B Carter, S Jain, JW Mueller, D Gifford Advances in Neural Information Processing Systems 34, 15395-15407, 2021 | 51 | 2021 |
| Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men NJ Venkatachari, S Jain, L Walker, S Bivalkar-Mehla, A Chattopadhyay, ... AIDS 31 (5), 623-633, 2017 | 19 | 2017 |
| Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch NJ Venkatachari, JM Zerbato, S Jain, AE Mancini, A Chattopadhyay, ... Retrovirology 12, 1-22, 2015 | 19 | 2015 |
| Baishakhi Ray, Parminder Bhatia, Sudipta Sengupta, Dan Roth, and Bing Xiang B Athiwaratkun, SK Gouda, Z Wang, X Li, Y Tian, M Tan, WU Ahmad, ... Multi-lingual evaluation of code generation models, 2022 | 18 | 2022 |
| Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu S Jain, A Gitter, Z Bar-Joseph PLoS computational biology 10 (12), 2014 | 18 | 2014 |
| Reconstructing the temporal progression of HIV-1 immune response pathways S Jain, J Arrais, NJ Venkatachari, V Ayyavoo, Z Bar-Joseph Bioinformatics 32 (12), i253-i261, 2016 | 15 | 2016 |
| A complete multi-valued SAT solver S Jain, E O’Mahony, M Sellmann Principles and Practice of Constraint Programming–CP 2010: 16th …, 2010 | 12 | 2010 |
| Machine learning optimization of peptides for presentation by class II MHCs Z Dai, BD Huisman, H Zeng, B Carter, S Jain, ME Birnbaum, DK Gifford Bioinformatics 37 (19), 3160-3167, 2021 | 11 | 2021 |
| Remission of Crohn’s disease after cord blood transplantation for leukocyte adhesion deficiency type 1 S Jain, P Gozdziak, A Morgan, RK Burt Bone marrow transplantation 48 (7), 1006-1007, 2013 | 10 | 2013 |
| Self-consistency for open-ended generations S Jain, X Ma, A Deoras, B Xiang arXiv preprint arXiv:2307.06857, 2023 | 5 | 2023 |
| Parallel heuristics for tsp on mapreduce S Jain, M Mallozzi Brown University, 2010 | 5 | 2010 |
| Kidney Precision Medicine Project Kpmp; Nephrotic Syndrome Study Network (NEPTUNE): Single cell transcriptomics identifies focal segmental glomerulosclerosis remission … R Menon, EA Otto, P Hoover, S Eddy, L Mariani, B Godfrey, CC Berthier, ... JCI Insight 5 (e133267), 10.1172, 2020 | 4 | 2020 |
| Code-Aware Prompting: A study of Coverage Guided Test Generation in Regression Setting using LLM G Ryan, S Jain, M Shang, S Wang, X Ma, MK Ramanathan, B Ray arXiv preprint arXiv:2402.00097, 2024 | 3 | 2024 |
Ziv Bar-JosephProfessor of Computational Biology and Machine Learning, School of Computer Science, Carnegie Mellon UniversityVerified email at andrew.cmu.edu
