Author details

Full Name

Jeremy L Muhlich

Affiliation

ORCID

Career Start Year

2008

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37547011	Addressing persistent challenges in digital image analysis of cancerous tissues.	bioRxiv	2023
36170403	Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data.	IEEE Trans Vis Comput Graph	2023
37961235	Quality Control for Single Cell Analysis of High-plex Tissue Profiles using CyLinter.		2023
36700386	Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance.		2023
34750536	Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data.	Nature Biomedical Engineering	2022
35972352	Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR.		2022
34606456	Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data.		2022
34824477	MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging.	Nat Methods	2022
33554860	shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data.	eLife	2021
33822482	A Simple Method for Creating a High-Content Microscope for Imaging Multiplexed Tissue Microarrays.	Curr Protoc	2021
33113355	Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells.	Cell Syst	2020
33768192	Minerva: a light-weight, narrative image browser for multiplexed tissue images.		2020
32898474	SYLARAS: A Platform for the Statistical Analysis and Visual Display of Systemic Immunoprofiling Data and Its Application to Glioblastoma.		2020
30649541	A Systems Toxicology Approach for the Prediction of Kidney Toxicity and Its Mechanisms In Vitro.	Toxicol Sci	2019
31848351	Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer.	Sci Data	2019
29199020	The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.	Cell Syst	2018
29065900	GRcalculator: an online tool for calculating and mining dose-response data.	BMC Cancer	2017
29175850	From word models to executable models of signaling networks using automated assembly.	Mol Syst Biol	2017
26260164	A Quantitative Approach to Screen for Nephrotoxic Compounds In Vitro.	J Am Soc Nephrol	2016
24655548	Analysis of growth factor signaling in genetically diverse breast cancer lines.	BMC Biol	2014
24906883	LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.	Nucleic Acids Res	2014
24518066	Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS).	J Biomol Screen	2014
23423320	Programming biological models in Python using PySB.	Molecular Systems Biology	2013
23385484	Properties of cell death models calibrated and compared using Bayesian approaches.	Molecular Systems Biology	2013
21516115	Adaptive informatics for multifactorial and high-content biological data.	Nature Methods	2011
20482787	Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities.	BMC Bioinformatics	2010
19343194	Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling.	PLoS Comput Biol	2009
18218655	Flexible informatics for linking experimental data to mathematical models via DataRail.	Bioinformatics	2008
17947324	ChemBank: a small-molecule screening and cheminformatics resource database.	Nucleic Acids Res	2008