Harvard Catalyst Profiles

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Jeremy Muhlich, B.A.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Fröhlich F, Gerosa L, Muhlich J, Sorger PK. Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance. Mol Syst Biol. 2023 02 10; 19(2):e10988. PMID: 36700386; PMCID: PMC9912026.
    Citations: 1     Fields:    Translation:HumansCells
  2. Muhlich JL, Chen YA, Yapp C, Russell D, Santagata S, Sorger PK. Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR. Bioinformatics. 2022 09 30; 38(19):4613-4621. PMID: 35972352; PMCID: PMC9525007.
    Citations: 4     Fields:    Translation:HumansAnimals
  3. Warchol S, Krueger R, Nirmal AJ, Gaglia G, Jessup J, Ritch CC, Hoffer J, Muhlich J, Burger ML, Jacks T, Santagata S, Sorger PK, Pfister H. Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data. IEEE Trans Vis Comput Graph. 2022 Sep 28; PP. PMID: 36170403.
    Citations:    Fields:    
  4. Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA, Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. MITI minimum information guidelines for highly multiplexed tissue images. Nat Methods. 2022 03; 19(3):262-267. PMID: 35277708; PMCID: PMC9009186.
    Citations: 6     Fields:    
  5. Jessup J, Krueger R, Warchol S, Hoffer J, Muhlich J, Ritch CC, Gaglia G, Coy S, Chen YA, Lin JR, Santagata S, Sorger PK, Pfister H. Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data. IEEE Trans Vis Comput Graph. 2022 01; 28(1):259-269. PMID: 34606456; PMCID: PMC8805697.
    Citations: 1     Fields:    Translation:Humans
  6. Schapiro D, Sokolov A, Yapp C, Chen YA, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin JR, Maliga Z, Jacobson CA, Hodgman MW, Ruokonen J, Farhi SL, Abbondanza D, McKinley ET, Persson D, Betts C, Sivagnanam S, Regev A, Goecks J, Coffey RJ, Coussens LM, Santagata S, Sorger PK. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods. 2022 03; 19(3):311-315. PMID: 34824477; PMCID: PMC8916956.
    Citations: 11     Fields:    Translation:Humans
  7. Rashid R, Chen YA, Hoffer J, Muhlich JL, Lin JR, Krueger R, Pfister H, Mitchell R, Santagata S, Sorger PK. Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data. Nat Biomed Eng. 2022 05; 6(5):515-526. PMID: 34750536; PMCID: PMC9079188.
    Citations: 3     Fields:    
  8. Abtahi S, Gliksman NR, Heneghan JF, Nilsen SP, Muhlich JL, Copeland J, Rozbicki E, Allan C, Dudeja PK, Turner JR. A Simple Method for Creating a High-Content Microscope for Imaging Multiplexed Tissue Microarrays. Curr Protoc. 2021 Apr; 1(4):e68. PMID: 33822482; PMCID: PMC8103673.
    Citations:    Fields:    
  9. Shimada K, Bachman JA, Muhlich JL, Mitchison TJ. shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data. Elife. 2021 02 08; 10. PMID: 33554860; PMCID: PMC7924953.
    Citations: 7     Fields:    Translation:HumansCells
  10. Gerosa L, Chidley C, Fröhlich F, Sanchez G, Lim SK, Muhlich J, Chen JY, Vallabhaneni S, Baker GJ, Schapiro D, Atanasova MI, Chylek LA, Shi T, Yi L, Nicora CD, Claas A, Ng TSC, Kohler RH, Lauffenburger DA, Weissleder R, Miller MA, Qian WJ, Wiley HS, Sorger PK. Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells. Cell Syst. 2020 11 18; 11(5):478-494.e9. PMID: 33113355.
    Citations: 17     Fields:    Translation:HumansCells
  11. Hoffer J, Rashid R, Muhlich JL, Chen YA, Russell DPW, Ruokonen J, Krueger R, Pfister H, Santagata S, Sorger PK. Minerva: a light-weight, narrative image browser for multiplexed tissue images. J Open Source Softw. 2020; 5(54). PMID: 33768192.
    Citations: 5     
  12. Baker GJ, Muhlich JL, Palaniappan SK, Moore JK, Davis SH, Santagata S, Sorger PK. SYLARAS: A Platform for the Statistical Analysis and Visual Display of Systemic Immunoprofiling Data and Its Application to Glioblastoma. Cell Syst. 2020 09 23; 11(3):272-285.e9. PMID: 32898474.
    Citations: 3     Fields:    Translation:HumansAnimals
  13. Shamsaei B, Chojnacki S, Pilarczyk M, Najafabadi M, Niu W, Chen C, Ross K, Matlock A, Muhlich J, Chutipongtanate S, Zheng J, Turner J, Vidovic D, Jaffe J, MacCoss M, Wu C, Pillai A, Ma'ayan A, Schürer S, Kouril M, Medvedovic M, Meller J. piNET: a versatile web platform for downstream analysis and visualization of proteomics data. Nucleic Acids Res. 2020 07 02; 48(W1):W85-W93. PMID: 32469073.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  14. Rashid R, Gaglia G, Chen YA, Lin JR, Du Z, Maliga Z, Schapiro D, Yapp C, Muhlich J, Sokolov A, Sorger P, Santagata S. Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer. Sci Data. 2019 12 17; 6(1):323. PMID: 31848351.
    Citations: 18     Fields:    Translation:Humans
  15. Ramm S, Todorov P, Chandrasekaran V, Dohlman A, Monteiro MB, Pavkovic M, Muhlich J, Shankaran H, Chen WW, Mettetal JT, Vaidya VS. A Systems Toxicology Approach for the Prediction of Kidney Toxicity and Its Mechanisms In Vitro. Toxicol Sci. 2019 05 01; 169(1):54-69. PMID: 30649541; PMCID: PMC6484891.
    Citations: 3     Fields:    Translation:HumansCells
  16. Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma'ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, Kaye J, Osterloh J, Haston K, Kalra J, Finkbiener S, Li J, Milani P, Adam M, Escalante-Chong R, Sachs K, Lenail A, Ramamoorthy D, Fraenkel E, Daigle G, Hussain U, Coye A, Rothstein J, Sareen D, Ornelas L, Banuelos M, Mandefro B, Ho R, Svendsen CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin JR, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Syst. 2018 01 24; 6(1):13-24. PMID: 29199020.
    Citations: 145     Fields:    Translation:HumansCells
  17. Gyori BM, Bachman JA, Subramanian K, Muhlich JL, Galescu L, Sorger PK. From word models to executable models of signaling networks using automated assembly. Mol Syst Biol. 2017 11 24; 13(11):954. PMID: 29175850.
    Citations: 43     Fields:    Translation:HumansCells
  18. Clark NA, Hafner M, Kouril M, Williams EH, Muhlich JL, Pilarczyk M, Niepel M, Sorger PK, Medvedovic M. GRcalculator: an online tool for calculating and mining dose-response data. BMC Cancer. 2017 Oct 24; 17(1):698. PMID: 29065900; PMCID: PMC5655815.
    Citations: 22     Fields:    Translation:HumansAnimalsCells
  19. Adler M, Ramm S, Hafner M, Muhlich JL, Gottwald EM, Weber E, Jaklic A, Ajay AK, Svoboda D, Auerbach S, Kelly EJ, Himmelfarb J, Vaidya VS. A Quantitative Approach to Screen for Nephrotoxic Compounds In Vitro. J Am Soc Nephrol. 2016 Apr; 27(4):1015-28. PMID: 26260164; PMCID: PMC4814182.
    Citations: 38     Fields:    Translation:HumansCells
  20. Duan Q, Flynn C, Niepel M, Hafner M, Muhlich JL, Fernandez NF, Rouillard AD, Tan CM, Chen EY, Golub TR, Sorger PK, Subramanian A, Ma'ayan A. LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W449-60. PMID: 24906883.
    Citations: 122     Fields:    Translation:HumansCells
  21. Niepel M, Hafner M, Pace EA, Chung M, Chai DH, Zhou L, Muhlich JL, Schoeberl B, Sorger PK. Analysis of growth factor signaling in genetically diverse breast cancer lines. BMC Biol. 2014 Mar 21; 12:20. PMID: 24655548.
    Citations: 24     Fields:    Translation:HumansCells
  22. Vempati UD, Chung C, Mader C, Koleti A, Datar N, Vidovic D, Wrobel D, Erickson S, Muhlich JL, Berriz G, Benes CH, Subramanian A, Pillai A, Shamu CE, Schürer SC. 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 Jun; 19(5):803-16. PMID: 24518066.
    Citations: 43     Fields:    Translation:HumansCells
  23. Eydgahi H, Chen WW, Muhlich JL, Vitkup D, Tsitsiklis JN, Sorger PK. Properties of cell death models calibrated and compared using Bayesian approaches. Mol Syst Biol. 2013; 9:644. PMID: 23385484.
    Citations: 42     Fields:    
  24. Lopez CF, Muhlich JL, Bachman JA, Sorger PK. Programming biological models in Python using PySB. Mol Syst Biol. 2013; 9:646. PMID: 23423320.
    Citations: 82     Fields:    Translation:Cells
  25. Millard BL, Niepel M, Menden MP, Muhlich JL, Sorger PK. Adaptive informatics for multifactorial and high-content biological data. Nat Methods. 2011 Jun; 8(6):487-93. PMID: 21516115.
    Citations: 29     Fields:    Translation:HumansCells
  26. Tolopko AN, Sullivan JP, Erickson SD, Wrobel D, Chiang SL, Rudnicki K, Rudnicki S, Nale J, Selfors LM, Greenhouse D, Muhlich JL, Shamu CE. Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities. BMC Bioinformatics. 2010 May 18; 11:260. PMID: 20482787.
    Citations: 15     Fields:    
  27. Aldridge BB, Saez-Rodriguez J, Muhlich JL, Sorger PK, Lauffenburger DA. Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput Biol. 2009 Apr; 5(4):e1000340. PMID: 19343194.
    Citations: 69     Fields:    Translation:HumansCells
  28. Saez-Rodriguez J, Goldsipe A, Muhlich J, Alexopoulos LG, Millard B, Lauffenburger DA, Sorger PK. Flexible informatics for linking experimental data to mathematical models via DataRail. Bioinformatics. 2008 Mar 15; 24(6):840-7. PMID: 18218655.
    Citations: 29     Fields:    
  29. Seiler KP, George GA, Happ MP, Bodycombe NE, Carrinski HA, Norton S, Brudz S, Sullivan JP, Muhlich J, Serrano M, Ferraiolo P, Tolliday NJ, Schreiber SL, Clemons PA. ChemBank: a small-molecule screening and cheminformatics resource database. Nucleic Acids Res. 2008 Jan; 36(Database issue):D351-9. PMID: 17947324.
    Citations: 121     Fields:    Translation:Cells
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© 2023 President and Fellows of Harvard College
Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.