Flexible informatics for linking experimental data to mathematical models via DataRail. - Julio Saez-Rodriguez; Arthur Goldsipe; Jeremy Muhlich; Leonidas G. Alexopoulos; Bjorn Millard; Douglas A. Lauffenburger; Peter K. Sorger (Bioinform., 2008)

ChemBank: a small-molecule screening and cheminformatics resource database. - Kathleen Petri Seiler; Gregory A. George; Mary Pat Happ; Nicole E. Bodycombe; Hyman A. Carrinski; Stephanie Norton; Steve Brudz; John P. Sullivan; Jeremy Muhlich; Martin Serrano; Paul Ferraiolo; Nicola J. Tolliday; et al. (Nucleic Acids Res., 2008)

Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling. - Bree B. Aldridge; Julio Saez-Rodriguez; Jeremy Muhlich; Peter K. Sorger; Douglas A. Lauffenburger (PLoS Comput. Biol., 2009)

Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities. - Andrew N. Tolopko; John P. Sullivan; Sean D. Erickson; David Wrobel; Su L. Chiang; Katrina Rudnicki; Stewart Rudnicki; Jennifer Nale; Laura M. Selfors; Dara Greenhouse; Jeremy Muhlich; Caroline E. Shamu (BMC Bioinform., 2010)

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. - Qiaonan Duan; Corey Flynn; Mario Niepel; Marc Hafner; Jeremy Muhlich; Nicolas F. Fernandez; Andrew D. Rouillard; Christopher M. Tan; Edward Y. Chen; Todd R. Golub; Peter K. Sorger; Aravind Subramanian; et al. (Nucleic Acids Res., 2014)

Minerva: a light-weight, narrative image browser for multiplexed tissue images. - John Hoffer; Rumana Rashid; Jeremy Muhlich; Yu-An Chen; Douglas Russell; Juha Ruokonen; Robert Krüger; Hanspeter Pfister; Sandro Santagata; Peter K. Sorger (J. Open Source Softw., 2020)

piNET: a versatile web platform for downstream analysis and visualization of proteomics data. - Behrouz Shamsaei; Szymon Chojnacki; Marcin Pilarczyk; Mehdi Fazel-Najafabadi; Wen Niu; Chuming Chen; Karen Ross; Andrea Matlock; Jeremy Muhlich; Somchai Chutipongtanate; Jie Zheng 001; John Turner; et al. (Nucleic Acids Res., 2020)

Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR. - Jeremy Muhlich; Yu-An Chen; Clarence Han-Wei Yapp; Douglas Russell; Sandro Santagata; Peter K. Sorger (Bioinform., 2022)

Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data. - Jared Jessup; Robert Krüger; Simon Warchol; John Hoffer; Jeremy Muhlich; Cecily C. Ritch; Giorgio Gaglia; Shannon Coy; Yu-An Chen; Jia-Ren Lin; Sandro Santagata; Peter K. Sorger; et al. (IEEE Trans. Vis. Comput. Graph., 2022)

Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data. - Simon Warchol; Robert Krüger; Ajit Johnson Nirmal; Giorgio Gaglia; Jared Jessup; Cecily C. Ritch; John Hoffer; Jeremy Muhlich; Megan L. Burger; Tyler Jacks; Sandro Santagata; Peter K. Sorger; et al. (IEEE Trans. Vis. Comput. Graph., 2023)

psudo: Exploring Multi-Channel Biomedical Image Data with Spatially and Perceptually Optimized Pseudocoloring. - Simon Warchol; Jakob Troidl; Jeremy Muhlich; Robert Krüger; John Hoffer; Tica Lin; Johanna Beyer; Elena L. Glassman; Peter K. Sorger; Hanspeter Pfister (Comput. Graph. Forum, 2024)