| The human tumor atlas network: charting tumor transitions across space and time at single-cell resolution O Rozenblatt-Rosen, A Regev, P Oberdoerffer, T Nawy, A Hupalowska, ... Cell 181 (2), 236-249, 2020 | 472 | 2020 |
| The library of integrated network-based cellular signatures NIH program: system-level cataloging of human cells response to perturbations AB Keenan, SL Jenkins, KM Jagodnik, S Koplev, E He, D Torre, Z Wang, ... Cell systems 6 (1), 13-24, 2018 | 443 | 2018 |
| ChemBank : a small-molecule screening and cheminformatics resource database KP Seiler, GA George, MP Happ, NE Bodycombe, HA Carrinski, S Norton, ... Nucleic acids research 36 (suppl_1), D351-D359, 2007 | 357 | 2007 |
| LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures Q Duan, C Flynn, M Niepel, M Hafner, JL Muhlich, NF Fernandez, ... Nucleic acids research 42 (W1), W449-W460, 2014 | 346 | 2014 |
| Programming biological models in Python using PySB CF Lopez, JL Muhlich, JA Bachman, PK Sorger Molecular systems biology 9 (1), 646, 2013 | 282 | 2013 |
| Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling BB Aldridge, J Saez-Rodriguez, JL Muhlich, PK Sorger, DA Lauffenburger PLoS computational biology 5 (4), e1000340, 2009 | 216 | 2009 |
| From word models to executable models of signaling networks using automated assembly BM Gyori, JA Bachman, K Subramanian, JL Muhlich, L Galescu, ... Molecular systems biology 13 (11), 954, 2017 | 183 | 2017 |
| MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging D Schapiro, A Sokolov, C Yapp, YA Chen, JL Muhlich, J Hess, ... Nature methods 19 (3), 311-315, 2022 | 177 | 2022 |
| A quantitative approach to screen for nephrotoxic compounds in vitro M Adler, S Ramm, M Hafner, JL Muhlich, EM Gottwald, E Weber, A Jaklic, ... Journal of the American Society of Nephrology 27 (4), 1015-1028, 2016 | 139 | 2016 |
| GRcalculator: an online tool for calculating and mining dose–response data NA Clark, M Hafner, M Kouril, EH Williams, JL Muhlich, M Pilarczyk, ... BMC cancer 17, 1-11, 2017 | 109 | 2017 |
| Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR JL Muhlich, YA Chen, C Yapp, D Russell, S Santagata, PK Sorger Bioinformatics 38 (19), 4613-4621, 2022 | 108 | 2022 |
| Properties of cell death models calibrated and compared using Bayesian approaches H Eydgahi, WW Chen, JL Muhlich, D Vitkup, JN Tsitsiklis, PK Sorger Molecular systems biology 9 (1), 644, 2013 | 108 | 2013 |
| Receptor-driven ERK pulses reconfigure MAPK signaling and enable persistence of drug-adapted BRAF-mutant melanoma cells L Gerosa, C Chidley, F Fröhlich, G Sanchez, SK Lim, J Muhlich, JY Chen, ... Cell systems 11 (5), 478-494. e9, 2020 | 107 | 2020 |
| Flexible informatics for linking experimental data to mathematical models via DataRail J Saez-Rodriguez, A Goldsipe, J Muhlich, LG Alexopoulos, B Millard, ... Bioinformatics 24 (6), 840-847, 2008 | 94 | 2008 |
| Metadata standard and data exchange specifications to describe, model, and integrate complex and diverse high-throughput screening data from the library of integrated network … UD Vempati, C Chung, C Mader, A Koleti, N Datar, D Vidović, D Wrobel, ... Journal of biomolecular screening 19 (5), 803-816, 2014 | 87 | 2014 |
| Adaptive informatics for multifactorial and high-content biological data BL Millard, M Niepel, MP Menden, JL Muhlich, PK Sorger Nature methods 8 (6), 487-492, 2011 | 81 | 2011 |
| shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data K Shimada, JA Bachman, JL Muhlich, TJ Mitchison Elife 10, e57116, 2021 | 78 | 2021 |
| MITI minimum information guidelines for highly multiplexed tissue images D Schapiro, C Yapp, A Sokolov, SM Reynolds, YA Chen, D Sudar, Y Xie, ... Nature methods 19 (3), 262-267, 2022 | 56 | 2022 |
| Analysis of growth factor signaling in genetically diverse breast cancer lines M Niepel, M Hafner, EA Pace, M Chung, DH Chai, L Zhou, JL Muhlich, ... BMC biology 12, 1-13, 2014 | 56 | 2014 |
| Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer R Rashid, G Gaglia, YA Chen, JR Lin, Z Du, Z Maliga, D Schapiro, C Yapp, ... Scientific data 6 (1), 323, 2019 | 52 | 2019 |
