Jeremy L Muhlich
Jeremy L Muhlich
Director of Software Engineering, Harvard Medical School Laboratory of Systems Pharmacology
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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
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
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
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
Programming biological models in Python using PySB
CF Lopez, JL Muhlich, JA Bachman, PK Sorger
Molecular systems biology 9 (1), 646, 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
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
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
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
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
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
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
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
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
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
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
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
Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities
AN Tolopko, JP Sullivan, SD Erickson, D Wrobel, SL Chiang, K Rudnicki, ...
BMC bioinformatics 11, 1-14, 2010
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
piNET: a versatile web platform for downstream analysis and visualization of proteomics data
B Shamsaei, S Chojnacki, M Pilarczyk, M Najafabadi, W Niu, C Chen, ...
Nucleic acids research 48 (W1), W85-W93, 2020
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