Publications by authors named "Jeremy Muhlich"

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Spatially-resolved Embedding Analysis with Linked Imaging Data.
Simon Warchol, Grace Guo, Johannes Knittel, Dan Freeman, Usha Bhalla, Jeremy L Muhlich

IEEE Trans Vis Comput Graph· December 2025

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SEAL : Spatially-resolved Embedding Analysis with Linked Imaging Data.
Simon Warchol, Grace Guo, Johannes Knittel, Dan Freeman, Usha Bhalla, Jeremy L Muhlich

bioRxiv· July 2025

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Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma.
Tanjina Kader, Jia-Ren Lin, Clemens B Hug, Shannon Coy, Yu-An Chen, Jeremy L Muhlich

Cancer Discov· June 2025

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Addressing persistent challenges in digital image analysis of cancer tissue: resources developed from a hackathon.
Sandhya Prabhakaran, Clarence Yapp, Gregory J Baker, Johanna Beyer, Young Hwan Chang, Jeremy Muhlich

Mol Oncol· June 2025

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Sharing data from the Human Tumor Atlas Network through standards, infrastructure and community engagement.
Ino de Bruijn, Milen Nikolov, Clarisse Lau, Ashley Clayton, David L Gibbs, Jeremy Muhlich

Nat Methods· April 2025

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Quality control for single-cell analysis of high-plex tissue profiles using CyLinter.
Gregory J Baker, Edward Novikov, Ziyuan Zhao, Tuulia Vallius, Janae A Davis, Jeremy L Muhlich

Nat Methods· December 2024

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An estrogen receptor signaling transcriptional program linked to immune evasion in human hormone receptor-positive breast cancer.
Kenichi Shimada, Daniel E Michaud, Yvonne Xiaoyong Cui, Kelly Zheng, Jonathan Goldberg, Jeremy L Muhlich

bioRxiv· November 2024

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Integrating spatial profiles and cancer genomics to identify immune-infiltrated mismatch repair proficient colorectal cancers.
Jeremiah Wala, Ino de Bruijn, Shannon Coy, Andréanne Gagné, Sabrina Chan, Jeremy Muhlich

bioRxiv· September 2024

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Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma.
Tanjina Kader, Jia-Ren Lin, Clemens Hug, Shannon Coy, Yu-An Chen, Jeremy Muhlich

bioRxiv· September 2024

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psudo: Exploring Multi-Channel Biomedical Image Data with Spatially and Perceptually Optimized Pseudocoloring.
Simon Warchol, Jakob Troidl, Jeremy Muhlich, Robert Krueger, John Hoffer

bioRxiv· June 2024

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Sharing Data from the Human Tumor Atlas Network through Standards, Infrastructure, and Community Engagement.
Ino de Bruijn, Milen Nikolov, Clarisse Lau, Ashley Clayton, David L Gibbs, Jeremy Muhlich

bioRxiv· June 2024

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Quality Control for Single Cell Analysis of High-plex Tissue Profiles using CyLinter.
Gregory J Baker, Edward Novikov, Ziyuan Zhao, Tuulia Vallius, Janae A Davis, Jeremy L Muhlich

bioRxiv· March 2024

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Addressing persistent challenges in digital image analysis of cancerous tissues.
Sandhya Prabhakaran, Clarence Yapp, Gregory J Baker, Johanna Beyer, Young Hwan Chang, Jeremy Muhlich

bioRxiv· July 2023

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Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance.
Fabian Fröhlich, Luca Gerosa, Jeremy Muhlich, Peter K Sorger

Mol Syst Biol· February 2023

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Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data.
Simon Warchol, Robert Krueger, Ajit Johnson Nirmal, Giorgio Gaglia, Jared Jessup, Jeremy Muhlich

IEEE Trans Vis Comput Graph· January 2023

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Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR.
Jeremy L Muhlich, Yu-An Chen, Clarence Yapp, Douglas Russell, Sandro Santagata

Bioinformatics· September 2022

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Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data.
Rumana Rashid, Yu-An Chen, John Hoffer, Jeremy L Muhlich, Jia-Ren Lin

Nat Biomed Eng· May 2022

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MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging.
Denis Schapiro, Artem Sokolov, Clarence Yapp, Yu-An Chen, Jeremy L Muhlich

Nat Methods· March 2022

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MITI minimum information guidelines for highly multiplexed tissue images.
Denis Schapiro, Clarence Yapp, Artem Sokolov, Sheila M Reynolds, Yu-An Chen, Jeremy Muhlich

Nat Methods· March 2022

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Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data.
Jared Jessup, Robert Krueger, Simon Warchol, John Hoffer, Jeremy Muhlich

IEEE Trans Vis Comput Graph· January 2022

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A Simple Method for Creating a High-Content Microscope for Imaging Multiplexed Tissue Microarrays.
Shabnam Abtahi, Neal R Gliksman, John F Heneghan, Steven P Nilsen, Jeremy L Muhlich

Curr Protoc· April 2021

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shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data.
Kenichi Shimada, John A Bachman, Jeremy L Muhlich, Timothy J Mitchison

Elife· February 2021

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Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells.
Luca Gerosa, Christopher Chidley, Fabian Fröhlich, Gabriela Sanchez, Sang Kyun Lim, Jeremy Muhlich

Cell Syst· November 2020

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SYLARAS: A Platform for the Statistical Analysis and Visual Display of Systemic Immunoprofiling Data and Its Application to Glioblastoma.
Gregory J Baker, Jeremy L Muhlich, Sucheendra K Palaniappan, Jodene K Moore, Stephanie H Davis

Cell Syst· September 2020

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piNET: a versatile web platform for downstream analysis and visualization of proteomics data.
Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Najafabadi, Wen Niu, Jeremy Muhlich

Nucleic Acids Res· July 2020

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