J. Mesirov

发表

Sequencing a genome by walking with clone-end sequences (abstract): a mathematical analysis

Jill P. Mesirov, Bonnie Berger, Eric S. Lander, 2000, RECOMB '00.

Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.

J. Mesirov, E. Lander, D. Slonim, 1999, Science.

PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

M. Daly, J. Mesirov, E. Lander, 2003, Nature Genetics.

Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation.

J. Mesirov, E. Lander, D. Slonim, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Multiclass cancer diagnosis using tumor gene expression signatures

T. Poggio, J. Mesirov, E. Lander, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Hybrid system for protein secondary structure prediction.

J. Mesirov, D. Waltz, X. Zhang, 1992, Journal of molecular biology.

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

Joshua M. Korn, Christopher A. Miller, Derek Y. Chiang, 2008, Nature.

Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.

S. Gabriel, J. Mesirov, R. Wilson, 2010, Cancer cell.

Metagenes and molecular pattern discovery using matrix factorization

Pablo Tamayo, Jill P Mesirov, Todd R Golub, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction

B. Berger, S. Batzoglou, J. Mesirov, 2000 .

Protein Structure Prediction by Memory-Base Reasoning,

J. Mesirov, D. Waltz, Xiru Zhang, 1988 .

The Molecular Signatures Database (MSigDB) hallmark gene set collection.

J. Mesirov, P. Tamayo, A. Liberzon, 2015, Cell systems.

The Molecular Signatures Database Hallmark Gene Set Collection

J. Mesirov, P. Tamayo, A. Liberzon, 2015 .

The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity

Adam A. Margolin, Michael P. Morrissey, S. Gabriel, 2012, Nature.

Chemosensitivity prediction by transcriptional profiling

J. Mesirov, E. Lander, D. Slonim, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Initial sequencing and analysis of the human genome.

J. V. Moran, V. J. Pollara, D. Haussler, 2001, Nature.

Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning

Todd, J. Mesirov, E. Lander, 2002, Nature Medicine.

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Pablo Tamayo, Aravind Subramanian, Sayan Mukherjee, 2005, Proceedings of the National Academy of Sciences of the United States of America.

An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis

J. Mesirov, T. Golub, Sayan Mukherjee, 2005, Nature Genetics.

Initial sequencing and comparative analysis of the mouse genome.

Colin N. Dewey, Simon C. Potter, James A. Cuff, 2002 .

Distinct physiological states of Plasmodium falciparum in malaria-infected patients

A. Regev, J. Mesirov, E. Lander, 2007, Nature.

Automated high-dimensional flow cytometric data analysis

J. Mesirov, G. McLachlan, P. Tamayo, 2009, Proceedings of the National Academy of Sciences.

GenePattern 2.0

J. Mesirov, P. Tamayo, Jim Lerner, 2006, Nature Genetics.

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov, 2012, Briefings Bioinform..

Metagene projection for cross-platform, cross-species characterization of global transcriptional states

J. Mesirov, P. Tamayo, B. Ebert, 2007, Proceedings of the National Academy of Sciences.

Consensus Clustering: A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data

Jill P. Mesirov, Stefano Monti, Pablo Tamayo, 2003, Machine Learning.

Comprehensive molecular characterization of human colon and rectal cancer

Steven J. M. Jones, Joshua M. Stuart, Brian D. O’Connor, 2012, Nature.

Comprehensive genomic characterization of squamous cell lung cancers

Steven J. M. Jones, Joshua M. Stuart, Brian D. O’Connor, 2012, Nature.

Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer

J. Mesirov, E. Lander, P. Tamayo, 2011, Proceedings of the National Academy of Sciences.

An Efficient Implementation of the Back-propagation Algorithm on the Connection Machine CM-2

Jill P. Mesirov, David L. Waltz, Michael McKenna, 1989, NIPS.

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

Charles E. Chapple, E. Mauceli, B. Birren, 2004, Nature.

ARACHNE: a whole-genome shotgun assembler.

B. Berger, E. Mauceli, S. Batzoglou, 2002, Genome research.

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

Ben S. Wittner, B. Wittner, J. Mesirov, 2009, Nature.

Human and mouse gene structure: comparative analysis and application to exon prediction

Jill P. Mesirov, Lior Pachter, Bonnie Berger, 2000, RECOMB '00.

Portraits of breast cancer progression

Jill P. Mesirov, Gabriela Alexe, Gyan Bhanot, 2007, BMC Bioinformatics.

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

Ellen T. Gelfand, Thomas M Green, J. Mesirov, 2014, Scientific Data.

Prediction of central nervous system embryonal tumour outcome based on gene expression

T. Poggio, J. Mesirov, E. Lander, 2002, Nature.

High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates.

Gabriela Alexe, Gyan Bhanot, Charles DeLisi, 2007, Cancer research.

Comprehensive molecular portraits of human breast tumors

Steven J. M. Jones, Andrew H. Beck, Joshua F. McMichael, 2012, Nature.

Predicting relapse in patients with medulloblastoma by integrating evidence from clinical and genomic features.

J. Mesirov, P. Tamayo, M. Meyerson, 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Prediction of high-responding peptides for targeted protein assays by mass spectrometry

J. Mesirov, S. Carr, V. Fusaro, 2009, Nature Biotechnology.

Efficient mapping of mendelian traits in dogs through genome-wide association

K. Lindblad-Toh, J. Mesirov, E. Lander, 2007, Nature Genetics.

The limitations of simple gene set enrichment analysis assuming gene independence

J. Mesirov, P. Tamayo, A. Liberzon, 2011, J. Biomed. Informatics.

Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States.

Clarence K Mah, J. Mesirov, P. Tamayo, 2017, Cell systems.

Gene Set Enrichment Analysis Made Right

J. Mesirov, P. Tamayo, A. Liberzon, 2011 .

Integrative genomic analysis of medulloblastoma identifies a molecular subgroup that drives poor clinical outcome.

J. Mesirov, P. Tamayo, M. Meyerson, 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

Whole-genome sequence assembly for mammalian genomes: Arachne 2.

E. Mauceli, K. Lindblad-Toh, J. Mesirov, 2003, Genome research.

Two-dimensional, viscous, incompressible flow in complex geometries on a massively parallel processor

J. Mesirov, J. Sethian, J. Brunet, 1992 .

Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

Adam A. Margolin, Michael P. Morrissey, S. Gabriel, 2012, Nature.

Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921))

Ronald W. Davis, J. V. Moran, V. J. Pollara, 2001 .

Comment on "The Consensus Coding Sequences of Human Breast and Colorectal Cancers"

R. Tibshirani, J. Mesirov, E. Lander, 2007, Science.

Gene Expression Changes in an Animal Melanoma Model Correlate with Aggressiveness of Human Melanoma Metastases

J. Mesirov, Jean-Philippe Brunet, A. Subramanian, 2008, Molecular Cancer Research.

A unified GenomeSpace recipe to identify essential genes and associated subnetworks from Genome-Scale CRISPR-Cas9 knockout screens

Daniel E. Carlin, J. Mesirov, T. Ideker, 2018, F1000Research.

Prognostically relevant gene signatures of high-grade serous ovarian carcinoma.

K. Cibulskis, S. Gabriel, J. Mesirov, 2012, The Journal of clinical investigation.

Joint Modeling and Registration of Cell Populations in Cohorts of High-Dimensional Flow Cytometric Data

Ronald M. Levy, Sharon X. Lee, G. Nolan, 2013, PloS one.

Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups.

Colin J. Daniel, Clarence K Mah, Maxwell P. Gold, 2018, Cancer cell.

Assembly of polymorphic genomes: algorithms and application to Ciona savignyi.

Jill P Mesirov, Chad Nusbaum, Yutaka Satou, 2005, Genome research.

Cytometric profiling in multiple sclerosis uncovers patient population structure and a reduction of CD8low cells.

Pablo Tamayo, Saumyadipta Pyne, Jill P Mesirov, 2008, Brain : a journal of neurology.

Criteria for the use of omics-based predictors in clinical trials

Jill P. Mesirov, William L. Bigbee, James H. Doroshow, 2013, Nature.

Targeted Tumor-Penetrating siRNA Nanocomplexes for Credentialing the Ovarian Cancer Oncogene ID4

Jill P. Mesirov, Justin H Lo, Erkki Ruoslahti, 2012, Science Translational Medicine.

Contributing authors

J. Mesirov, Katie Dietz, Trish Abalo, 1996, The Journal of Supercomputing.

β-Catenin-Driven Cancers Require a YAP1 Transcriptional Complex for Survival and Tumorigenesis

Jill P. Mesirov, Joseph Rosenbluh, Aviad Tsherniak, 2012, Cell.

Criteria for the use of omics-based predictors in clinical trials: explanation and elaboration

Jill P Mesirov, Lisa M McShane, James H Doroshow, 2013, BMC Medicine.

Juicebox Provides a Visualization System for HiC Contact Maps with Unlimited Zoom Citation

Jill P. Mesirov, Eric S. Lander, Muhammad S. Shamim, 2016 .

MEDULLOBLASTOMA EXOME SEQUENCING UNCOVERS SUBTYPE-SPECIFIC SOMATIC MUTATIONS

Jill P. Mesirov, Petar Stojanov, Scott L. Pomeroy, 2012, Nature.

An RNA Profile Identifies Two Subsets of Multiple Sclerosis Patients Differing in Disease Activity

J. Mesirov, P. Tamayo, H. Weiner, 2012, Science Translational Medicine.

A FZD7-specific Antibody–Drug Conjugate Induces Ovarian Tumor Regression in Preclinical Models

Edwin F. Juarez, J. Mesirov, Myan Do, 2021, Molecular Cancer Therapeutics.

What does your cell really do? Model-based assessment of mammalian cells metabolic functionalities using omics data

Jill P. Mesirov, Anne Richelle, Nathan E. Lewis, 2020, bioRxiv.

A unified web platform for network-based analyses of genomic data

Ted E. Natoli, D. Thompson, N. Hacohen, 2017 .

Gene expression Comparative gene marker selection suite

J. Mesirov, G. Getz, Michael Reich, 2006 .

OTX2 Activity at Distal Regulatory Elements Shapes the Chromatin Landscape of Group 3 Medulloblastoma.

Martin J. Aryee, J. Mesirov, P. Tamayo, 2017, Cancer discovery.

DiSCoVERing Innovative Therapies for Rare Tumors: Combining Genetically Accurate Disease Models with In Silico Analysis to Identify Novel Therapeutic Targets

J. Mesirov, P. Tamayo, P. Clemons, 2016, Clinical Cancer Research.

Research in Computational Molecular Biology, 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings

Jill P. Mesirov, Satoru Miyano, Simon Kasif, 2005, RECOMB.

EPEN-18. Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma

Jesse R. Dixon, Edwin F. Juarez, James T. Robinson, 2020, Neuro-Oncology.

Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response

J. Mesirov, W. Thompson, O. Harismendy, 2021, bioRxiv.

Plasmodium falciparum gene expression measured directly from tissue during human infection

J. Mesirov, J. Daily, D. Wirth, 2014, Genome Medicine.

Data Preprocessing Data normalization , Imputation Gene Filtering PCA 85 % variation k-Level Ensemble Consensus Clustering

J. Mesirov, P. Tamayo, G. Bhanot, 2007 .

Inhibition of KRAS-driven tumorigenicity by interruption of an autocrine cytokine circuit.

Travis J Cohoon, N. Hacohen, J. Mesirov, 2014, Cancer discovery.

Carcinoma-associated fibroblast-like differentiation of human mesenchymal stem cells.

J. Mesirov, G. Alexe, D. Banerjee, 2008, Cancer research.

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

Jill P. Mesirov, Zhipeng Lu, Qiangfeng Cliff Zhang, 2016, Cell.

TORC1/2 kinase inhibition depletes glutathione and synergizes with carboplatin to suppress the growth of MYC-driven medulloblastoma.

J. Mesirov, P. Tamayo, S. Pomeroy, 2021, Cancer letters.

Systematic interrogation of 3q26 identifies TLOC1 and SKIL as cancer drivers.

J. Mesirov, P. Tamayo, W. Hahn, 2013, Cancer discovery.

Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway

Jill P. Mesirov, Dong Gao, Stuart L. Schreiber, 2017, Nature.

Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R, and GenePattern Notebook implementations of CoGAPS

J. Mesirov, P. Tamayo, Michael Reich, 2022, bioRxiv.

Transcriptional Profiling of Plasmodium falciparum Parasites from Patients with Severe Malaria Identifies Distinct Low vs. High Parasitemic Clusters

A. Regev, J. Mesirov, N. Pochet, 2012, PloS one.

Golub , Monitoring and Class Prediction by Gene Expression Molecular Classification of Cancer : Class Discovery

J. Mesirov, E. Lander, D. Slonim, 2007 .

Perturbation theory for condition $(C)$ in the calculus of variations

J. Mesirov, 1977 .

Subgroup-Enriched Pathways and Kinase Signatures in Medulloblastoma Patient-Derived Xenografts

Jessica M. Rusert, J. Mesirov, R. Wechsler-Reya, 2022, Journal of proteome research.

Developmental basis of SHH medulloblastoma heterogeneity

Maxwell P. Gold, Andrew M Masteller, J. Mesirov, 2022, bioRxiv.

CRRAO Advanced Institute of Mathematics, Statistics and Computer Science (AIMSCS)

Jill P. Mesirov, Geoffrey J. McLachlan, Sharon X. Lee, 2013 .

Sashimi plots: Quantitative visualization of RNA sequencing read alignments

Eric T. Wang, J. Mesirov, E. Wang, 2013, 1306.3466.

Inhibition of dual-specificity tyrosine phosphorylation-regulated kinase 2 perturbs 26S proteasome-addicted neoplastic progression

Edwin F. Juarez, J. Mesirov, J. Dixon, 2019, Proceedings of the National Academy of Sciences.

Gene Expression Studies May Identify Lower Risk Myelodysplastic Syndrome Patients Likely to Respond to Therapy with Ezatiostat Hydrochloride (TLK199)

J. Mesirov, P. Tamayo, O. Botvinnik, 2011 .

Inactivation of histone chaperone HIRA unmasks a link between normal embryonic development of melanoblasts and maintenance of adult melanocyte stem cells

Neil J. Fullarton, Alexander T. Wenzel, J. Mesirov, 2022, bioRxiv.

Research in Computational Molecular Biology

J. Mesirov, M. Waterman, P. Pevzner, 2008 .

The Molecular Signatures Database Revisited: Extending Support for Mouse Data

J. Mesirov, C. Bult, H. Thorvaldsdóttir, 2022, bioRxiv.

analysis Combo: a whole genome comparative browser

J. Mesirov, C. Burge, J. Galagan, 2006 .

Sequencing a genome by walking with clone-end sequences: a mathematical analysis.

B. Berger, S. Batzoglou, J. Mesirov, 1999 .

Integrative Genomics Viewer

Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov, 2011, Nature Biotechnology.

Subclass Mapping: Identifying Common Subtypes in Independent Disease Data Sets

Jill P. Mesirov, Pablo Tamayo, Todd R. Golub, 2007, PloS one.

Single-cell characterization of step-wise acquisition of carboplatin resistance in ovarian cancer

Alexander T. Wenzel, J. Mesirov, O. Harismendy, 2022, npj Systems Biology and Applications.

MOLECULAR CANCER THERAPEUTICS | TARGETING DRUG RESISTANCE KIT Cells Mediate Imatinib Resistance in Gastrointestinal Stromal Tumor

J. Mesirov, P. Tamayo, J. Sicklick, 2021 .

Characterizing genomic alterations in cancer by complementary functional associations

Gabriela Alexe, Chiara Romualdi, Pablo Tamayo, 2016, Nature Biotechnology.

Targeting an IKBKE cytokine network impairs triple-negative breast cancer growth.

Travis J Cohoon, J. Mesirov, P. Tamayo, 2014, The Journal of clinical investigation.

A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors.

J. Mesirov, P. Tamayo, W. Hahn, 2014, Cancer discovery.

MicroSCALE Screening Reveals Genetic Modifiers of Therapeutic Response in Melanoma

J. Mesirov, P. Tamayo, W. Hahn, 2012, Science Signaling.

Molecular signatures database (MSigDB) 3.0

Helga Thorvaldsdóttir, Jill P. Mesirov, Pablo Tamayo, 2011, Bioinform..

An Analytical Method for Multiclass Molecular Cancer Classification

Sayan Mukherjee, Jill P. Mesirov, Sridhar Ramaswamy, 2003, SIAM Rev..

MYC regulation of a “poor-prognosis” metastatic cancer cell state

Clifford A. Meyer, Ben S. Wittner, B. Wittner, 2010, Proceedings of the National Academy of Sciences.

Molecular classification of multiple tumor types

Sayan Mukherjee, Jill P. Mesirov, Sridhar Ramaswamy, 2001, ISMB.

Germline variants that influence the tumor immune microenvironment also drive response to immunotherapy

J. Mesirov, W. Thompson, O. Harismendy, 2021 .

Comprehensive molecular profiling of lung adenocarcinoma

Steven J. M. Jones, Christopher A. Miller, Joshua M. Stuart, 2014, Nature.

Using GenePattern for Gene Expression Analysis

Arthur Liberzon, Jill P Mesirov, Heidi Kuehn, 2008, Current protocols in bioinformatics.

Cytoscape: the network visualization tool for GenomeSpace workflows

Trey Ideker, Ted Liefeld, Jill P Mesirov, 2014, F1000Research.

Cytoscape: the network visualization tool for GenomeSpace workflows

Trey Ideker, Ted Liefeld, Jill P Mesirov, 2014, F1000Research.

The landscape of extrachromosomal circular DNA in medulloblastoma

Jesse R. Dixon, Edwin F. Juarez, Joshua T Lange, 2021, bioRxiv.

A phenotypically supervised single-cell analysis protocol to study within-cell-type heterogeneity of cultured mammalian cells

J. Mesirov, Michael Reich, H. Carter, 2021, STAR protocols.

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA , IDH 1 , EGFR , and NF 1 Citation Verhaak

Yuan Qi, Jill P. Mesirov, Li Ding, 2010 .

Lawrence Berkeley National Laboratory Lawrence Berkeley National Laboratory Title Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA , IDH 1 , EGFR , and NF 1 Permalink

S. Gabriel, J. Mesirov, R. Wilson, 2010 .

Lymphatic-preserving treatment sequencing with immune checkpoint inhibition unleashes cDC1-dependent antitumor immunity in HNSCC

J. Mesirov, S. Schokrpur, B. Fox, 2022, Nature Communications.

Cancer Vulnerabilities Unveiled by Genomic Loss

Jill P. Mesirov, Joseph Rosenbluh, Aviad Tsherniak, 2012, Cell.

Cancer Vulnerabilities Unveiled by Genomic Loss Citation

J. Mesirov, W. Hahn, R. Beroukhim, 2012 .

A resampling-based method for class discovery and visualization of gene expression microarray data

Jill P. Mesirov, Stefano Monti, Pablo Tamayo, 2003 .

application to hematopoietic differentiation Interpreting patterns of gene expression with self-organizing maps: Methods and

Jill P. Mesirov, Qing Zhu, Donna K. Slonim, 2007 .

GeNets: A unified web platform for network-based analyses of genomic data

Bang Wong, Aviv Regev, Yang Li, 2018, Nature Methods.

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.

James T. Robinson, Jill P. Mesirov, Eric S. Lander, 2016, Cell systems.

Leveraging premalignant biology for immune-based cancer prevention

J. Mesirov, T. Ideker, T. Rebbeck, 2016, Proceedings of the National Academy of Sciences.

Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation

J. Mesirov, P. Tamayo, M. Hatten, 2016, Neuron.

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

Pablo Tamayo, Arthur Liberzon, Sanchita Bhattacharya, 2016, Immunity.

Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations.

S. Gabriel, J. Mesirov, P. Tamayo, 2017, Cancer discovery.

Combo: a whole genome comparative browser

Jill P. Mesirov, Christopher B. Burge, Tamara Yu, 2006, Bioinform..

Assembly of polymorphic genomes: algorithms and application to Ciona savignyi.

B. Birren, C. Nusbaum, J. Mesirov, 2005, Genome research.

Integrative radiogenomic profiling of squamous cell lung cancer.

J. Mesirov, P. Tamayo, M. Meyerson, 2013, Cancer research.

Therapeutics , Targets , and Chemical Biology Integrative Radiogenomic Pro fi ling of Squamous Cell Lung Cancer

er, J. Mesirov, P. Tamayo, 2013 .

Inactivation of the Snf5 tumor suppressor stimulates cell cycle progression and cooperates with p53 loss in oncogenic transformation.

Pablo Tamayo, Aravind Subramanian, Jill P Mesirov, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Breast cancer stratification from analysis of micro-array data of micro-dissected specimens.

J. Mesirov, P. Tamayo, G. Bhanot, 2007, Genome informatics. International Conference on Genome Informatics.

ATARiS: Computational quantification of gene suppression phenotypes from multisample RNAi screens

Pablo Tamayo, Aviad Tsherniak, Rameen Beroukhim, 2013, Genome research.

GSEA-P: a desktop application for Gene Set Enrichment Analysis

Jill P. Mesirov, Pablo Tamayo, Aravind Subramanian, 2007, Bioinform..

A Curated Resource for Phosphosite-specific Signature Analysis*

Jill P. Mesirov, Pablo Tamayo, Hasmik Keshishian, 2018, Molecular & Cellular Proteomics.

Targeted Tumor-Penetrating siRNA Nanocomplexes for Credentialing the Ovarian Cancer Target ID4

J. Mesirov, P. Tamayo, W. Hahn, 2012 .

Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes

B. Haas, J. Mesirov, N. Pochet, 2020, JCO clinical cancer informatics.

Comprehensive molecular profiling of lung adenocarcinoma

Steven J. M. Jones, Christopher A. Miller, Joshua M. Stuart, 2014, Nature.

GeNets: a unified web platform for network-based genomic analyses

Bang Wong, Jill P. Mesirov, Aviv Regev, 2018, Nature Methods.

igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)

Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov, 2020, bioRxiv.

Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma

Jessica M. Rusert, Edwin F. Juarez, James D. Jensen, 2020, Cancer Research.

Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway

Pablo Tamayo, Justin Klekota, Jill P Mesirov, 2010, Nature Medicine.

AraPath: a knowledgebase for pathway analysis in Arabidopsis

Jill P. Mesirov, Arthur Liberzon, Jason Hennessey, 2012, Bioinform..

Comparative gene marker selection suite

Jill P. Mesirov, Stefano Monti, Gad Getz, 2006, Bioinform..

Kataegis Expression Signature in Breast Cancer Is Associated with Late Onset, Better Prognosis, and Higher HER2 Levels.

Pablo Tamayo, Jill P Mesirov, Matteo D'Antonio, 2016, Cell reports.

Integrative radiogenomic profiling of squamous cell lung cancer.

Dmitriy Sonkin, Stuart L. Schreiber, Pablo Tamayo, 2013, Cancer Research.

β-Catenin-Driven Cancers Require a YAP1 Transcriptional Complex for Survival and Tumorigenesis

J. Mesirov, W. Hahn, W. Goessling, 2013, Cell.

Comprehensivegenomiccharacterization of squamous cell lung cancers

Joshua M. Stuart, Derek Y. Chiang, A. Sivachenko, 2012 .

Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data

Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov, 2017, bioRxiv.

MicroSCALE Screening Reveals Genetic Modifiers of Therapeutic Response in Melanoma

J. Mesirov, P. Tamayo, W. Hahn, 2012, Science Signaling.

A functional landscape of resistance to ALK inhibition in lung cancer.

S. Gabriel, J. Mesirov, P. Tamayo, 2015, Cancer cell.

A Functional Landscape o f Resistance to ALK Inhibition in Lung Cancer Graphical Abstract Highlights

S. Gabriel, J. Mesirov, P. Tamayo, 2015 .

Variant Review with the Integrative Genomics Viewer.

James T. Robinson, Jill P. Mesirov, Ahmet Zehir, 2017, Cancer research.

Model-based assessment of mammalian cell metabolic functionalities using omics data

Jill P. Mesirov, Anne Richelle, Nathan E. Lewis, 2021, Cell reports methods.

A Genome-Wide siRNA Screen in Mammalian Cells for Regulators of S6 Phosphorylation

J. Mesirov, P. Tamayo, J. Avruch, 2015, PloS one.

Support Vector Machine Classification of Microarray Data

Jill P. Mesirov, Donna K. Slonim, Tomaso A. Poggio, 2001 .

Improving genome annotations using phylogenetic profile anomaly detection

Jill P. Mesirov, Tarjei S. Mikkelsen, James E. Galagan, 2005, Bioinform..

Computational Biology

Jill P. Mesirov, Donna K. Slonim, J. Mesirov, 2018, Encyclopedia of Parallel Computing.

The GenePattern Notebook Environment.

Helga Thorvaldsdóttir, Pablo Tamayo, Ted Liefeld, 2017, Cell systems.

GenePattern flow cytometry suite

Jill P. Mesirov, Yu Qian, Richard H. Scheuermann, 2013, Source Code for Biology and Medicine.

An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data.

J. Mesirov, Clarence K. Mah, Thorin Tabor, 2018, F1000Research.

An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data

Edwin F. Juarez, Clarence K Mah, Alexander T Wenzel, 2018, F1000Research.

Quantitative visualization of alternative exon expression from RNA-seq data

Eric T. Wang, J. Mesirov, E. Wang, 2015, Bioinform..

Integrated Genomic Analysis of the 8q24 Amplification in Endometrial Cancers Identifies ATAD2 as Essential to MYC-Dependent Cancers

J. Mesirov, P. Tamayo, R. Beroukhim, 2013, PloS one.

GeneCluster 2.0: an advanced toolset for bioarray analysis

Jill P. Mesirov, Pablo Tamayo, Michael Reich, 2004, Bioinform..

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

Pablo Tamayo, Aviad Tsherniak, Ted Liefeld, 2014, Scientific Data.

Control of Huntington's Disease-Associated Phenotypes by the Striatum-Enriched Transcription Factor Foxp2.

J. Mesirov, Adrian M Heilbut, E. Kolaczyk, 2017, Cell reports.

Responses to Bacteria, Virus, and Malaria Distinguish the Etiology of Pediatric Clinical Pneumonia.

J. Mesirov, S. Carr, Q. Bassat, 2016, American journal of respiratory and critical care medicine.

Transcriptional Categorization of the Etiology of Pneumonia Syndrome in Pediatric Patients in Malaria-Endemic Areas

J. Mesirov, Q. Bassat, M. Gillette, 2016, The Journal of infectious diseases.

Study of protein sequence comparison metrics on the connection machine CM-2

Jill P. Mesirov, Eric S. Lander, Washington Taylor, 1989, Proceedings Supercomputing Vol.II: Science and Applications.

Pten Deficiency Leads To Proteasome Addiction, A Novel Vulnerability In Glioblastoma.

J. Mesirov, F. Furnari, K. Vuori, 2021, Neuro-oncology.

Parallel approaches to short range molecular dynamics simulations

Jill P. Mesirov, Pablo Tamayo, Bruce M. Boghosian, 1991, Proceedings of the 1991 ACM/IEEE Conference on Supercomputing (Supercomputing '91).

Class prediction and discovery using gene expression data

Jill P. Mesirov, Donna K. Slonim, Eric S. Lander, 2000, RECOMB '00.

Estimating Dataset Size Requirements for Classifying DNA Microarray Data

Sayan Mukherjee, Jill P. Mesirov, Colin Campbell, 2003, J. Comput. Biol..

A method for downstream analysis of gene set enrichment results facilitates the biological interpretation of vaccine efficacy studies

J. Mesirov, P. Tamayo, W. Haining, 2016, bioRxiv.

An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays

Clarence K Mah, Jill P Mesirov, Lukas Chavez, 2018, F1000Research.

Ovarian Cancer Oncogene Targeted Tumor-Penetrating siRNA Nanocomplexes for Credentialing the

J. Mesirov, P. Tamayo, W. Hahn, 2012 .

3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma

Jesse R. Dixon, Edwin F. Juarez, J. Mesirov, 2023, Nature communications.

Molecular adaptations of striatal spiny projection neurons during levodopa-induced dyskinesia

P. Greengard, J. Mesirov, D. Surmeier, 2014, Proceedings of the National Academy of Sciences.

Accessible Reproducible Research

Jill P Mesirov, J. Mesirov, 2010, Science.

Sashimi plots: Quantitative visualization of alternative isoform expression from RNA-seq data

Eric T. Wang, J. Mesirov, E. Wang, 2014, bioRxiv.

Location of Gastrointestinal Stromal Tumor (GIST) in the Stomach Predicts Tumor Mutation Profile and Drug Sensitivity

J. Mesirov, S. Horgan, J. Sicklick, 2021, Clinical Cancer Research.

Gene signatures related to B‐cell proliferation predict influenza vaccine‐induced antibody response

Pablo Tamayo, Jill P Mesirov, Bali Pulendran, 2014, European journal of immunology.

An optimal hypercube direct N-body solver on the Connection Machine

Jill P. Mesirov, Alan Edelman, Jean-Philippe Brunet, 1990, Proceedings SUPERCOMPUTING '90.

Computing turbulent flow in complex geometries on a massively parallel processor

Jill P. Mesirov, James A. Sethian, Adam Greenberg, 1991, Proceedings of the 1991 ACM/IEEE Conference on Supercomputing (Supercomputing '91).

A parallel implementation of the random vortex method

Jill P. Mesirov, James A. Sethian, Adam Greenberg, 1991 .

Consensus Clustering: A Resampling-Based Method for Class Discovery and Visualization of Gene Expression Microarray Data

J. Mesirov, T. Golub, P. Tamayo, 2003, Machine Learning.

Comprehensive molecular portraits of human breast tumours

Steven J. M. Jones, Joshua F. McMichael, Joshua M. Stuart, 2013 .

Research in Computational Molecular Biology, 12th Annual International Conference, RECOMB 2008, Singapore, March 30 - April 2, 2008. Proceedings

Martin Vingron, Limsoon Wong, J. Mesirov, 2008, Annual International Conference on Research in Computational Molecular Biology.

A genomic data viewer for iPad

J. Mesirov, H. Thorvaldsdóttir, James T. Robinson, 2015, Genome Biology.

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

Amy E. Hawkins, J. Mesirov, L. Fulton, 2009 .

Tool Juicebox Provides a Visua lization System for HiC Contact Maps with Unlimited Zoom Graphical

Neva C. Durand, J. Mesirov, E. Lander, 2022 .

Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis

Daniel J. Blankenberg, J. Mesirov, H. Thorvaldsdóttir, 2023, bioRxiv.

Research in Computational Molecular Biology: 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings (Lecture ... Science / Lecture Notes in Bioinformatics)

J. Mesirov, P. Pevzner, S. Kasif, 2005 .

Portraits of breast cancer progression

J. Mesirov, P. Tamayo, G. Bhanot, 2007, BMC Bioinform..

Prediction of response to therapy with ezatiostat in lower risk myelodysplastic syndrome

J. Mesirov, P. Tamayo, O. Botvinnik, 2012, Journal of Hematology & Oncology.

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

James T. Robinson, Jill P. Mesirov, Anton Nekrutenko, 2015, Nature Methods.

Mathematical foundations of elasticity

T. R. Hughes, M. Golubitsky, J. Mesirov, 1982 .

The GPCR–Gαs–PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure

Alexander T. Wenzel, J. Mesirov, E. Ruppin, 2023, Nature Immunology.

Data driven linear algebraic methods for analysis of molecular pathways : application to disease progression in shock / trauma

M. Sriram Iyengar, David W. Mercer, Mary F. McGuire, 2012 .

GeneCruiser: a web service for the annotation of microarray data

Jill P. Mesirov, Pablo Tamayo, Ted Liefeld, 2005, Bioinform..

Molecular signatures database (MSigDB) 3.0

J. Mesirov, P. Tamayo, A. Subramanian, 2011, Bioinform..

KITlow Cells Mediate Imatinib Resistance in Gastrointestinal Stromal Tumor

Alexander T. Wenzel, J. Mesirov, P. Tamayo, 2021, Molecular Cancer Therapeutics.

Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States.

John G Doench, J. Mesirov, P. Tamayo, 2017, Cell systems.

Comprehensive genomic characterization of squamous cell lung cancers

Joshua M. Stuart, Brian D. O’Connor, Charles J. Vaske, 2012, Nature.

Inhibition of KRAS-driven tumorigenicity by interruption of an autocrine cytokine circuit.

N. Hacohen, J. Mesirov, P. Tamayo, 2014, Cancer discovery.

An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data

J. Mesirov, Clarence K. Mah, Thorin Tabor, 2018, F1000Research.

GeNets: A unified web platform for network-based analyses of genomic data

N. Hacohen, A. Regev, J. Mesirov, 2018 .

Integrative radiogenomic profiling of squamous cell lung cancer.

J. Mesirov, P. Tamayo, M. Meyerson, 2013, Cancer research.

Open Peer Review Invited Referee Responses Cytoscape: the Network Visualization Tool for Genomespace

J. Mesirov, T. Ideker, Michael Reich, 2022 .

Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response

J. Mesirov, O. Harismendy, H. Carter, 2023, Nature communications.

Computational biology

J. Mesirov, Donna K. Slonim, 1999, Computing in Science & Engineering.

Mathematical approaches to biomolecular structure and dynamics

Jill P. Mesirov, Klaus Schulten, De Witt L. Sumners, 1996 .

From the Cover: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

J. Mesirov, E. Lander, T. Golub, 2005 .

Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS

J. Mesirov, Michael Reich, L. Goff, 2023, Nature Protocols.

Extending support for mouse data in the Molecular Signatures Database (MSigDB)

J. Mesirov, C. Bult, H. Thorvaldsdóttir, 2023, Nature Methods.

Continued fraction expansions of rational expressions with irreducible denominators in characteristic 2

Jill P. Mesirov, Melvin M. Sweet, J. Mesirov, 1987 .

Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma

Jesse R. Dixon, J. Mesirov, V. Bafna, 2023, Nature Genetics.

Lawrence Berkeley Laboratory

J. Mesirov, J. Sethian, A. Greenberg, 2009 .

Integrative radiogenomic profiling of squamous cell lung cancer

J. Mesirov, M. Meyerson, Drew J. Adams, 2013 .

Title: Integrative Radiogenomic Profiling of Squamous Cell Lung Cancer

J. Mesirov, M. Meyerson, P. Hammerman, 2022 .

A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression

Helga Thorvaldsdóttir, Trey Ideker, Jill Mesirov, 2017, F1000Research.

GeNets: A unified web platform for network-based analyses of genomic data

Ted E. Natoli, N. Hacohen, A. Regev, 2018, Nature methods.