User profiles for Jeremy Muhlich

Jeremy L Muhlich

Director of Software Engineering, Harvard Medical School Laboratory of Systems …
Verified email at hms.harvard.edu
Cited by 3266

[PDF][PDF] The library of integrated network-based cellular signatures NIH program: system-level cataloging of human cells response to perturbations

…, M Hafner, NS Gray, JR Lin, CE Mills, JL Muhlich… - Cell systems, 2018 - cell.com
The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common
Fund program that catalogs how human cells globally respond to chemical, genetic, and …

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures

…, C Flynn, M Niepel, M Hafner, JL Muhlich… - Nucleic acids …, 2014 - academic.oup.com
For the Library of Integrated Network-based Cellular Signatures (LINCS) project many gene
expression signatures using the L1000 technology have been produced. The L1000 …

ChemBank : a small-molecule screening and cheminformatics resource database

…, S Norton, S Brudz, JP Sullivan, J Muhlich… - Nucleic acids …, 2007 - academic.oup.com
ChemBank ( http://chembank.broad.harvard.edu/ ) is a public, web-based informatics
environment developed through a collaboration between the Chemical Biology Program and …

[HTML][HTML] MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging

D Schapiro, A Sokolov, C Yapp, YA Chen, JL Muhlich… - Nature …, 2022 - nature.com
Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible
in a preserved spatial context. However, reproducible analysis of large multichannel …

Programming biological models in Python using PySB

CF Lopez, JL Muhlich, JA Bachman… - Molecular systems …, 2013 - embopress.org
Mathematical equations are fundamental to modeling biological networks, but as networks
get large and revisions frequent, it becomes difficult to manage equations directly or to …

[HTML][HTML] Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling

…, J Saez-Rodriguez, JL Muhlich… - PLoS computational …, 2009 - journals.plos.org
When modeling cell signaling networks, a balance must be struck between mechanistic detail
and ease of interpretation. In this paper we apply a fuzzy logic framework to the analysis of …

From word models to executable models of signaling networks using automated assembly

…, JA Bachman, K Subramanian, JL Muhlich… - Molecular systems …, 2017 - embopress.org
Word models (natural language descriptions of molecular mechanisms) are a common currency
in spoken and written communication in biomedicine but are of limited use in predicting …

[PDF][PDF] Receptor-driven ERK pulses reconfigure MAPK signaling and enable persistence of drug-adapted BRAF-mutant melanoma cells

…, C Chidley, F Fröhlich, G Sanchez, SK Lim, J Muhlich… - Cell systems, 2020 - cell.com
Targeted inhibition of oncogenic pathways can be highly effective in halting the rapid
growth of tumors but often leads to the emergence of slowly dividing persister cells, which …

A quantitative approach to screen for nephrotoxic compounds in vitro

M Adler, S Ramm, M Hafner, JL Muhlich… - Journal of the …, 2016 - journals.lww.com
Nephrotoxicity due to drugs and environmental chemicals accounts for significant patient
mortality and morbidity, but there is no high throughput in vitro method for predictive …

Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR

JL Muhlich, YA Chen, C Yapp, D Russell… - …, 2022 - academic.oup.com
Motivation Stitching microscope images into a mosaic is an essential step in the analysis and
visualization of large biological specimens, particularly human and animal tissues. Recent …