Proteome-wide copy-number estimation from transcriptomics.
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Mol Syst Biol. 2024; online ahead of print.
Multivariate analysis of metabolic state vulnerabilities across diverse cancer contexts reveals synthetically lethal associations.
Cara Abecunas, Audrey D Kidd, Ying Jiang, Hui Zong, Mohammad Fallahi-Sichani.
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Hsu J, Nguyen KT, Bujnowska M, Janes KA, Fallahi-Sichani M.
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A genetic mosaic mouse model illuminates the pre-malignant progression of basal-like breast cancer.
Jianhao Zeng, Shambhavi Singh, Ying Jiang, Eli Casarez, Kristen A. Atkins, Kevin A. Janes, Hui Zong.
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Nucleocytoplasmic transport of active HER2 causes fractional escape from the DCIS-like state.
Lixin Wang, B. Bishal Paudel, R. Anthony McKnight, Kevin A. Janes.
Nature Communications. 2023; 14(1):2110.
Opa1 and Drp1 reciprocally regulate cristae morphology, ETC function, and NAD+ regeneration in KRas-mutant lung adenocarcinoma.
Dane T. Sessions, Kee-Beom Kim, Jennifer A. Kashatus, Nikolas Churchill, Kwon-Sik Park, Marty W. Mayo, Hiromi Sesaki, David F. Kashatus.
Cell Reports. 2022; 41(11):111818.
KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data.
Crowl S, Jordan B, Ma C, Naegle KM.
Nature Communications. 2022; 13:4283.
A reaction-diffusion model predicts the intracellular length scale over which EGFR-initiated GAB1-SHP2 complexes persist.
Myers PJ, Furcht CM, Deen WM, Lazzara MJ.
bioRxiv. 2021; 2021.11.08.467801.
Modeling the complete kinetics of coxsackievirus B3 reveals human determinants of host-cell feedback.
Lopacinski AB, Sweatt AJ, Smolko CM, Gray-Gaillard E, Borgman CA, Shah M, Janes KA.
Cell Syst. 2021; 2021;12(4):304-23 e13.
Radon Cumulative Distribution Transform Subspace Modeling for Image Classification.
Shifat-E-Rabbi M, Yin X, Rubaiyat AHM, Li S, Kolouri S, Aldroubi A, Nichols JM, Rohde GK.
Journal of Mathematical Imaging and Vision. 2021; 63(9):1185-203.
Mechanistic models of microbial community metabolism.
Dillard LR, Payne DD, Papin JA.
Mol Omics. 2021; 2021;17(3):365-75.
Identifying functional metabolic shifts in heart failure with the integration of omics data and a heart-specific, genome-scale model.
Dougherty BV, Rawls KD, Kolling GL, Vinnakota KC, Wallqvist A, Papin JA.
Cell Rep. 2021; 34(10):108836.
Epigenetic modulation reveals differentiation state specificity of oncogene addiction.
Khaliq M, Manikkam M, Martinez ED, Fallahi-Sichani M.
Nat Commun. 2021; 12(1):1536.
Data-Driven Computational Modeling Identifies Determinants of Glioblastoma Response to SHP2 Inhibition.
Day EK, Zhong Q, Purow B, Lazzara MJ.
Cancer Res. 2021; 81(8):2056-70.
Premalignant oligodendrocyte precursor cells stall in a heterogeneous state of replication stress prior to gliomagenesis.
Sutcliffe MD, Galvao RP, Wang L, Kim J, Rosenfeld LK, Singh S, Zong H, Janes KA.
Cancer Res. 2021; 81(7):1868-1882.
KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions.
Xue B, Jordan B, Rizvi S, Naegle KM.
PLoS Comput Biol. 2021; 17(2):e1008681.
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PLoS Comput Biol. 2021; 17(9):e1009379.
Mito Hacker: a set of tools to enable high-throughput analysis of mitochondrial network morphology.
Rohani A, Kashatus JA, Sessions DT, Sharmin S, Kashatus DF.
Sci Rep. 2020; 10(1):18941.
A linear optimal transportation framework for quantifying and visualizing variations in sets of images.
Wang W, Slepcev D, Basu S, Ozolek JA, Rohde GK.
Int J Comput Vis. 2020; 101(2):254-69.
Enabling early detection of osteoarthritis from presymptomatic cartilage texture maps via transport- based learning.
Kundu S, Ashinsky BG, Bouhrara M, Dam EB, Demehri S, Shifat-E-Rabbi M, Spencer RG, Urish KL, Rohde GK.
Proceedings of the National Academy of Sciences. 2020; 117(40):24709.
New analysis pipeline for high-throughput domain-peptide affinity experiments improves SH2 interaction data.
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J Biol Chem. 2020; 295(32):11346-63.
Medusa: Software to build and analyze ensembles of genome- scale metabolic network reconstructions.
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PLoS Comput Biol. 2020; 16(4):e1007847.
Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments.
Jenior ML, Moutinho TJ, Jr., Dougherty BV, Papin JA.
PLoS Comput Biol. 2020; 16(4):e1007099.
Sporadic activation of an oxidative stress-dependent NRF2-p53 signaling network in breast epithelial spheroids and premalignancies.
Pereira EJ, Burns JS, Lee CY, Marohl T, Calderon D, Wang L, Atkins KA, Wang CC, Janes KA.
Sci Signal. 2020; 13(627):eaba4200.
Glioblastoma Cell Resistance to EGFR and MET Inhibition Can Be Overcome via Blockade of FGFR-SPRY2 Bypass Signaling.
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Cell Rep. 2020; 30(10):3383-96 e7.
Phenotype-based probabilistic analysis of heterogeneous responses to cancer drugs and their combination efficacy.
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PLoS Comput Biol. 2020; 16(2):e1007688.
Cell Image Classification: A Comparative Overview.
Shifat ERM, Yin X, Fitzgerald CE, Rohde GK.
Cytometry Part A : the journal of the International Society for Analytical Cytology. 2020; 97(4):347-62.
Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning.
Medlock GL, Papin JA.
Cell Syst. 2020; 10(1):109-19 e3.
Robust latent-variable interpretation of in vivo regression models by nested resampling.
Caulk AW, Janes KA.
Sci Rep. 2019; 9(1):19671.
The inner centromere is a biomolecular condensate scaffolded by the chromosomal passenger complex.
Trivedi P, Palomba F, Niedzialkowska E, Digman MA, Gratton E, Stukenberg PT.
Nat Cell Biol. 2019; 21(9):1127-37.
Drp1 Promotes KRas-Driven Metabolic Changes to Drive Pancreatic Tumor Growth.
Nagdas S, Kashatus JA, Nascimento A, Hussain SS, Trainor RE, Pollock SR, Adair SJ, Michaels AD, Sesaki H, Stelow EB, Bauer TW, Kashatus DF.
Cell Rep. 2019; 28(7):1845-59 e5.
Mechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats.
Pannala VR, Vinnakota KC, Rawls KD, Estes SK, O'Brien TP, Printz RL, Papin JA, Reifman J, Shiota M, Young JD, Wallqvist A.
Toxicol Appl Pharmacol. 2019; 372:19-32.
In situ 10-cell RNA sequencing in tissue and tumor biopsy samples.
Singh S, Wang L, Schaff DL, Sutcliffe MD, Koeppel AF, Kim J, Onengut-Gumuscu S, Park KS, Zong H, Janes KA.
Sci Rep. 2019; 9(1):4836.
Genome-Scale Characterization of Toxicity-Induced Metabolic Alterations in Primary Hepatocytes.
Rawls KD, Blais EM, Dougherty BV, Vinnakota KC, Pannala VR, Wallqvist A, Kolling GL, Papin JA.
Toxicol Sci. 2019; 172(2):279-91.
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Shah A, Melhuish TA, Fox TE, Frierson HF, Jr., Wotton D.
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Surve SV, Myers PJ, Clayton SA, Watkins SC, Lazzara MJ, Sorkin A.
Mol Biol Cell. 2018; mbcE18080512.
Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota.
Medlock GL, Carey MA, McDuffie DG, Mundy MB, Giallourou N, Swann JR, Kolling GL, Papin JA.
Cell Syst. 2018; 7(3):245-57 e7.
Combined c-Met/Trk Inhibition Overcomes Resistance to CDK4/6 Inhibitors in Glioblastoma.
Olmez I, Zhang Y, Manigat L, Benamar M, Brenneman B, Nakano I, Godlewski J, Bronisz A, Lee J, Abbas T, Abounader R, Purow B.
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Identification of Drivers of Aneuploidy in Breast Tumors.
Pfister K, Pipka JL, Chiang C, Liu Y, Clark RA, Keller R, Skoglund P, Guertin MJ, Hall IM, Stukenberg PT.
Cell Rep. 2018; 23(9):2758-69.
Automated brightfield morphometry of 3D organoid populations by OrganoSeg.
Borten MA, Bajikar SS, Sasaki N, Clevers H, Janes KA.
Sci Rep. 2018; 8(1):5319.
OpenEnsembles: A Python Resource for Ensemble Clustering.
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CD47 Blockade as an Adjuvant Immunotherapy for Resectable Pancreatic Cancer.
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The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.
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, Schurer SC, Vasiliauskas J, Pilarczyk M, Shamsaei.
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Tumor-Suppressor Inactivation of GDF11 Occurs by Precursor Sequestration in Triple-Negative Breast Cancer.
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Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions.
Blais EM, Rawls KD, Dougherty BV, Li ZI, Kolling GL, Ye P, Wallqvist A, Papin JA.
Nat Commun. 2017; 8:14250.
Ensemble clustering of phosphoproteomic data identifies differences in protein interactions and cell-cell junction integrity of HER2- overexpressing cells.
Schaberg KE, Shirure VS, Worley EA, George SC, Naegle KM.
Integr Biol (Camb). 2017; 9(6):539-47.
Epithelium-Stroma Classification via Convolutional Neural Networks and Unsupervised Domain Adaptation in Histopathological Images.
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Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA.
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PLoS Comput Biol. 2017; 13(3):e1005413.
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Detecting and segmenting cell nuclei in two-dimensional microscopy images.
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Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging.
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Curr Protoc Chem Biol. 2016; 8(4):251-64.
Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota.
Biggs MB, Medlock GL, Moutinho TJ, Lees HJ, Swann JR, Kolling GL, Papin JA.
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TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors.
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Adjuvant Trametinib Delays the Outgrowth of Occult Pancreatic Cancer in a Mouse Model of Patient-Derived Liver Metastasis.
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Different Epidermal Growth Factor Receptor (EGFR) Agonists Produce Unique Signatures for the Recruitment of Downstream Signaling Proteins.
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A Centromere-Signaling Network Underlies the Coordination among Mitotic Events.
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The Radon Cumulative Distribution Transform and Its Application to Image Classification.
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Reproducible Analysis of Post-Translational Modifications in Proteomes– Application to Human Mutations.
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Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules.
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Sprouty2 Drives Drug Resistance and Proliferation in Glioblastoma.
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Mitochondrial control by DRP1 in brain tumor initiating cells.
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Nat Neurosci. 2015; 18(4):501-10.
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Mol Cell. 2015; 57(3):537-51.
Systematic analysis of BRAF(V600E) melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis.
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Mol Syst Biol. 2015; 11(3):797.
Localizing and extracting filament distributions from microscopy images.
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Identifying Determinants of EGFR-Targeted Therapeutic Biochemical Efficacy Using Computational Modeling.
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Diversity in Dimerization Topologies Enables Differential Control of Receptor Tyrosine Kinase Phosphorylation Dynamics.
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Detecting and visualizing cell phenotype differences from microscopy images using transport-based morphometry.
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Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles.
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Proc Natl Acad Sci U S A. 2014; 111(5):E626-35.
Differential parsing of EGFR endocytic flux among parallel internalization pathways in lung cancer cells with EGFR-activating mutations.
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MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data.
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Simultaneous profiling of 194 distinct receptor transcripts in human cells.
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Regulation of EGFR trafficking and cell signaling by Sprouty2 and MIG6 in lung cancer cells.
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A flexible and robust approach for segmenting cell nuclei from 2D microscopy images using supervised learning and template matching.
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Stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors and cultured cells.
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Computational analysis of the regulation of EGFR by protein tyrosine phosphatases.
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Toward the virtual cell: automated approaches to building models of subcellular organization “learned” from microscopy images.
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Intersection of FOXO- and RUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis and tumor progression.
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Proc Natl Acad Sci U S A. 2011; 108(40):E803-12.
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Mosaic analysis with double markers reveals tumor cell of origin in glioma.
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Cell. 2011; 146(2):209-21.
TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.
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BMC Syst Biol. 2011; 5:147.
Functional integration of a metabolic network model and expression data without arbitrary thresholding.
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Bioinformatics. 2010; 27(4):541-7.
An optimal transportation approach for nuclear structure-based pathology.
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IEEE Trans Med Imaging. 2010; 30(3):621-31.
Histone H3 Thr-3 phosphorylation by Haspin positions Aurora B at centromeres in mitosis.
Wang F, Dai J, Daum JR, Niedzialkowska E, Banerjee B, Stukenberg PT, Gorbsky GJ, Higgins JM.
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Identifying single-cell molecular programs by stochastic profiling.
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Nat Methods. 2010; 7(4):311-7.
A generative model of microtubule distributions, and indirect estimation of its parameters from fluorescence microscopy images.
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Cytometry Part A : the journal of the International Society for Analytical Cytology. 2010; 77(5):457-66.
Detection and classification of thyroid follicular lesions based on nuclear structure from histopathology images.
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Cytometry Part A : the journal of the International Society for Analytical Cytology. 2010; 77(5):485-94.
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IEEE Trans Image Process. 2009; 18(2):333-45.
microRNA-7 inhibits the epidermal growth factor receptor and the Akt pathway and is down- regulated in glioblastoma.
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Combined CDK4/6 and mTOR Inhibition Is Synergistic against Glioblastoma via Multiple Mechanisms.
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Cell Rep.. 2024; Sep 20;43(10):114775.
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A genetic mosaic mouse model illuminates the pre-malignant progression of basal-like breast cancer.
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Nature Communications. 2023; 14(1):2110.
Opa1 and Drp1 reciprocally regulate cristae morphology, ETC function, and NAD+ regeneration in KRas-mutant lung adenocarcinoma.
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