User profiles for Jeremy Muhlich
Jeremy L MuhlichDirector 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
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 …
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
For the Library of Integrated Network-based Cellular Signatures (LINCS) project many gene
expression signatures using the L1000 technology have been produced. The L1000 …
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 …
environment developed through a collaboration between the Chemical Biology Program and …
[HTML][HTML] MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging
Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible
in a preserved spatial context. However, reproducible analysis of large multichannel …
in a preserved spatial context. However, reproducible analysis of large multichannel …
Programming biological models in Python using PySB
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 …
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 …
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
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 …
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
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 …
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
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 …
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
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 …
visualization of large biological specimens, particularly human and animal tissues. Recent …