Categories

• team 159
• Associated Scientist 9
• Associate 39
• Intern 17
• Postdoctoral Researcher 31
• Graduate Students 1
• Staff Engineer 11
• Undergraduate Students and Interns 4
• Graduate Student 14
• Staff Scientist 19
• Software Engineer 2
• Operations and Administration 7
• Principal Investigator 1
• Undergraduate Student 2
• papers 125
• paper 125
• portals 5
• portal 5
• recognitions 5
• misc 4
• home 1
• tools 1
• tool 1
• events 3
• positions 5
• position 5
• projects 11
• project 11

team

• Grace Zou
• Benny Zhitomirsky
• Thomas Zhang
• Qing Zhang
• Xingli Yu
• Keren Yizhak
• Estelle Yao
• Xuan Zhao
• Xiaomeng Sun
• Ting Wu
• Timothy Wood
• Sam Wiseman
• Johann Wenckstern
• Jakob Weiss
• Douglas Voet
• Gabriela Virdzekova
• Michael Vinyard
• Johanna van Vliet
• Samantha Van Seters
• Eliezer (Eli) Van Allen
• Junko Tsuji
• Grace Tiao
• Amaro Taylor-Weiner
• Keira Sweetnam
• James Stuart
• Nicolas Stransky
• Kai Stewart
• Chip Stewart
• Oliver Spiro
• Nick Sontha
• Ron Solan
• Sachet Shukla
• Kristy Schlueter-Kuck
• Constantijn Scharlee
• Eddie Salinas
• Gordon Saksena
• Jessica Rosenblum
• Daniel Rosebrock
• Whijae Roh
• Esther Rheinbay
• Arvind Ravi
• Alex Ramos
• Alvin Qin
• Chuhan (Joyce) Qi
• Oliver Priebe
• Kavya Prasad
• Amber Pospistle
• Kiara Pontious
• Paz Polak
• Romanos Sklavenitis-Pistofidis
• Petar Stojanov
• Chandra Pedamallu
• Chidimma Nzerem
• Michael Noble
• Nicole Lu
• Vasuki Narasimha Swamy
• Oz Mordechai
• Graydon Moorhead
• Mendy Miller
• Conor Messer
• David Merrell
• Arielle Medford
• Aaron McKenna
• Nick Maus
• Yosef Maruvka
• Liz Martin
• Jialin Ma
• Kate Lu
• Sara López-Tamargo
• Xavi Loinaz
• Dimitry Livitz
• Julia Liu
• Natalie Lipieta
• Ziao Lin
• Lee Lichtenstein
• Liang Li
• Ruitong Li
• Matt Leventhal
• Ignaty Leshchiner
• Liza Leshchiner
• David Lehotzky
• David Lee
• Mike Lawrence
• Erik Landolsi
• Dan-Avi Landau
• Kirsten Kübler
• Antonia Kowalewski
• Binyamin Knisbacher
• Serene King
• Sungjae Kim
• Jaegil Kim
• Adam Kiezun
• Khrystofor Khokhlov
• Marcin Kaszkowiak
• Negin Karisani
• Mike Kanare
• Atanas Kamburov
• Shaw Kagawa
• Connor Johnson
• Raquel Jacobs
• Elizabeth Hopkins
• Mark Holton
• Julian Hess
• David Heiman
• Nick Haradhvala
• Megan Hanna
• Johan Gustafsson
• Anay Gupta
• Aaron Graubert
• Alex Gorelick
• Gad Getz
• Alyssa George
• Yifat Geffen
• Diego Garay
• Sam Freeman
• Ruslana Frazer
• Danielle Firer
• Juan Carlos Fernandez del Castillo
• Jideofor Ezike
• Zachary Everton
• Chris Etienne
• Pınar Özden Eser
• Ammar Elawad
• Liudmila Elagina
• Andrew Dunford
• Yotam Drier
• Olivia Dias
• David DeLuca
• Veda Dayananda
• Brian Danysh
• Simona Dalin
• Johnathan Dagan
• Tim Coorens
• Kristian Cibulskis
• Claudia Chu
• Maisha Chowdhury
• Abhishek Choudhary
• Justin Chen
• Guang Chen
• Justin Cha
• Scott Carter
• Eleonora Calabretta
• Rebecca Peyser Boiarsky
• Chet Birger
• Caleb Beroukhim
• Jessica Berberi
• Rotem Ben-Hamo
• Saveliy Belkin
• Alex Barbera
• Yousef Badran
• Alex Azizi
• Audrey Li
• Monica Arniella
• Michelle Aranha
• Shankara Anand
• A.b Almasri
• Jean-Baptiste Alberge
• Yo Akiyama
• Francois Aguet

Associated Scientist

• Yosef Maruvka
• Ignaty Leshchiner
• Erik Landolsi
• Kirsten Kübler
• Julian Hess
• Tim Coorens
• Abhishek Choudhary
• Jean-Baptiste Alberge
• Francois Aguet

Associate

• Grace Zou
• Thomas Zhang
• Qing Zhang
• Ting Wu
• Timothy Wood
• Jakob Weiss
• Grace Tiao
• Kai Stewart
• Oliver Spiro
• Nick Sontha
• Ron Solan
• Daniel Rosebrock
• Oliver Priebe
• Kavya Prasad
• Chidimma Nzerem
• Graydon Moorhead
• Conor Messer
• Liz Martin
• Xavi Loinaz
• Dimitry Livitz
• Liang Li
• Matt Leventhal
• Shaw Kagawa
• Connor Johnson
• Elizabeth Hopkins
• Mark Holton
• Aaron Graubert
• Alyssa George
• Danielle Firer
• Juan Carlos Fernandez del Castillo
• Liudmila Elagina
• Andrew Dunford
• Claudia Chu
• Maisha Chowdhury
• Guang Chen
• Alex Barbera
• Monica Arniella
• Shankara Anand
• Yo Akiyama

Intern

• Johann Wenckstern
• Johanna van Vliet
• Keira Sweetnam
• James Stuart
• Amber Pospistle
• Nick Maus
• Sara López-Tamargo
• Julia Liu
• Natalie Lipieta
• Anay Gupta
• Diego Garay
• Zachary Everton
• Olivia Dias
• Veda Dayananda
• Johnathan Dagan
• Caleb Beroukhim
• A.b Almasri

Postdoctoral Researcher

• Benny Zhitomirsky
• Keren Yizhak
• Xuan Zhao
• Xiaomeng Sun
• Gabriela Virdzekova
• Eliezer (Eli) Van Allen
• Sachet Shukla
• Whijae Roh
• Esther Rheinbay
• Arvind Ravi
• Paz Polak
• Romanos Sklavenitis-Pistofidis
• Petar Stojanov
• Oz Mordechai
• Arielle Medford
• David Lee
• Dan-Avi Landau
• Binyamin Knisbacher
• Sungjae Kim
• Khrystofor Khokhlov
• Negin Karisani
• Atanas Kamburov
• Johan Gustafsson
• Alex Gorelick
• Yotam Drier
• Simona Dalin
• Eleonora Calabretta
• Rotem Ben-Hamo
• Yousef Badran
• Alex Azizi
• Michelle Aranha

Graduate Students

• Audrey Li

Staff Engineer

• Sam Wiseman
• Samantha Van Seters
• Eddie Salinas
• Gordon Saksena
• Michael Noble
• Aaron McKenna
• Jialin Ma
• David Heiman
• Ruslana Frazer
• Chet Birger
• Saveliy Belkin

Undergraduate Students and Interns

• Jessica Rosenblum
• Ammar Elawad
• Justin Chen
• Jessica Berberi

Graduate Student

• Xingli Yu
• Estelle Yao
• Michael Vinyard
• Amaro Taylor-Weiner
• Constantijn Scharlee
• Nicole Lu
• Ziao Lin
• Ruitong Li
• Antonia Kowalewski
• Marcin Kaszkowiak
• Sam Freeman
• Jideofor Ezike
• Chris Etienne
• Rebecca Peyser Boiarsky

Staff Scientist

• Junko Tsuji
• Nicolas Stransky
• Chip Stewart
• Kristy Schlueter-Kuck
• Alex Ramos
• Alvin Qin
• Chandra Pedamallu
• Vasuki Narasimha Swamy
• David Merrell
• Lee Lichtenstein
• Liza Leshchiner
• David Lehotzky
• Mike Lawrence
• Jaegil Kim
• Nick Haradhvala
• Yifat Geffen
• Pınar Özden Eser
• David DeLuca
• Scott Carter

Software Engineer

• Douglas Voet
• Kristian Cibulskis

Operations and Administration

• Kiara Pontious
• Mendy Miller
• Serene King
• Mike Kanare
• Raquel Jacobs
• Megan Hanna
• Brian Danysh

Principal Investigator

• Gad Getz

Undergraduate Student

• Chuhan (Joyce) Qi
• Kate Lu

papers

• Tamoxifen induces PI3K activation in uterine cancer
• SWIFT-seq enables comprehensive single-cell transcriptomic profiling of circulating tumor cells in multiple myeloma and its precursors
• Genomic landscape of multiple myeloma and its precursor conditions
• Generation of a biliary tract cancer cell line atlas identifies molecular subtypes and therapeutic targets
• Large-scale dependency and drug screens characterize the therapeutic vulnerabilities of Multiple Myeloma with 1q
• Single-cell RNA sequencing defines distinct disease subtypes and reveals hypo-responsiveness to interferon in asymptomatic Waldenstrom's Macroglobulinemia
• DLBclass: A Probabilistic Molecular Classifier to Guide Clinical Investigation and Practice in DLBCL
• Deeper evaluation of a single-cell foundation model
• Developmental mosaicism underlying EGFR-mutant lung cancer presenting with multiple primary tumors
• AnnoMate: Exploring and annotating integrated molecular data through custom interactive visualizations
• Systematic identification of minor histocompatibility antigens predicts outcomes of allogeneic hematopoietic cell transplantation
• Clinical Outcomes and Evolution of Clonal Hematopoiesis in Patients with Newly Diagnosed Multiple Myeloma
• Pan-cancer proteogenomics connects oncogenic drivers to functional states
• Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation
• Protogenomic data and resources for pan-cancer analysis
• Genetic events associated with venetoclax resistance in CLL identified by whole-exome sequencing of patient samples
• Inferring early genetic progression in cancers with unobtainable premalignant disease
• Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer
• Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome
• MinimuMM-seq: Genome sequencing of circulating tumor cells for minimally invasive molecular characterization of multiple myeloma pathology
• Single Cell Characterization of Myeloma and its Precursor Conditions Reveals Transcriptional Signatures of Early Tumorigenesis
• Immune biomarkers of response to immunotherapy in patients with high-risk smoldering myeloma
• Pirtobrutinib Targets BTK C481S in Ibrutinib-Resistant CLL but Second-Site BTK Mutations Lead to Resistance
• Clinical Efficacy and Whole Exome Sequencing of Liquid Biopsies in a Phase IB/II study of Bazedoxifene and Palbociclib in Hormone Receptor-Positive Breast Cancer
• Distinct cellular dynamics associated with response to CAR-T therapy for refractory B-cell lymphoma
• Tangent normalization for somatic copy-number inference in cancer genome analysis
• High-resolution profiling of lung adenocarcinoma identifies expression subtypes with specific biomarkers and clinically relevant vulnerabilities
• Molecular map of chronic lymphocytic leukemia and its impact on outcome
• Genetic subtypes of smoldering multiple myeloma are associated with distinct pathogenic phenotypes and clinical outcomes
• Prevalence of monoclonal gammopathies and clinical outcomes in a high-risk US population screened by mass spectrometry: a multicentre cohort study
• Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma
• ZBTB33 is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing
• Parallel Genomic Alterations of Antigen and Payload Targets mediate Polyclonal Acquired Clinical Resistance to Sacituzumab Govitecan in Triple-Negative Breast Cancer
• Inflammatory stromal cells in the myeloma microenvironment
• Radiation-related genomic profile of papillary thyroid cancer after the Chernobyl accident
• Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
• Single-cell RNA sequencing: one step closer to the clinic
• RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts
• The Lipogenic Regulator SREBP2 Induces Transferrin in Circulating Melanoma Cells and Suppresses Ferroptosis
• DNA polymerase and mismatch repair exert distinct microsatellite instability signatures in normal and malignant human cells
• Identification of Somatically Acquired BRCA1/2 Mutations by cfDNA Analysis in Patients with Metastatic Breast Cancer
• Genomic Profiling of Smoldering Multiple Myeloma Identifies Patients at a High Risk of Disease Progression
• Predicting and affecting response to cancer therapy based on pathway-level biomarkers
• Clonal hematopoiesis is associated with adverse outcomes in multiple myeloma patients undergoing transplant
• Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
• Single-cell RNA sequencing reveals compromised immune microenvironment in precursor stages of multiple myeloma
• The repertoire of mutational signatures in human cancer
• Pan-cancer analysis of whole genomes
• The evolutionary history of 2,658 cancers
• Genomic analyses of PMBL reveal new drivers and mechanisms of sensitivity to PD-1 blockade
• Genomic analyses of flow-sorted Hodgkin Reed-Sternberg cells reveal complementary mechanisms of immune evasion
• Scaling computational genomics to millions of individuals with GPUs
• Passenger Hotspot Mutations in Cancer
• Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers
• RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues
• The Cancer Genome Atlas Expression Subtypes Stratify Response to Checkpoint Inhibition in Advanced Urothelial Cancer and Identify a Subset of Patients with High Survival Probability
• Growth dynamics in naturally progressing chronic lymphocytic leukaemia
• Comprehensive analysis of tumour initiation, spatial and temporal progression under multiple lines of treatment
• Tumor mutational landscape is a record of the pre-malignant state
• Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma
• Comment on "DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification"
• Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma
• DeTiN: overcoming tumor-in-normal contamination
• Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair
• Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes
• NetSig: network-based discovery from cancer genomes
• Analysis of ITGB2 rare germ line variants in chronic lymphocytic leukemia
• Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors
• Comprehensive molecular characterization of muscle invasive bladder cancer
• Resolving the phylogenetic origin of glioblastoma via multifocal genomic analysis of pre-treatment and treatment-resistant autopsy specimens
• Analysis of somatic microsatellite indels identifies driver events in human tumors
• A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer
• Recurrent and functional regulatory mutations in breast cancer
• Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias
• Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors
• Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair
• Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution
• Mutations driving CLL and their evolution in progression and relapse
• Comprehensive assessment of cancer missense mutation clustering in protein structures
• Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets
• Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes
• Oncotator: cancer variant annotation tool
• Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma
• Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia
• Integrated genomic characterization of papillary thyroid cancer
• The genomic landscape of pediatric Ewing sarcoma
• Assessing the clinical utility of cancer genomic and proteomic data across tumor types
• Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine
• Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer
• PRADA: pipeline for RNA sequencing data analysis
• Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing
• Discovery and saturation analysis of cancer genes across 21 tumour types
• Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy
• Exome sequencing identifies BRAF mutations in papillary craniopharyngiomas
• Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asian patients
• Pan-cancer patterns of somatic copy number alteration
• KDM4A lysine demethylase induces site-specific copy gain and rereplication of regions amplified in tumors
• An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers
• Mutational heterogeneity in cancer and the search for new cancer-associated genes
• Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation
• Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
• Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity
• Evolution and impact of subclonal mutations in chronic lymphocytic leukemia
• Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability
• A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers
• Sequence analysis of mutations and translocations across breast cancer subtypes
• Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer
• Melanoma genome sequencing reveals frequent PREX2 mutations
• Absolute quantification of somatic DNA alterations in human cancer
• RNA-SeQC: RNA-seq metrics for quality control and process optimization
• Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing
• SF3B1 and other novel cancer genes in chronic lymphocytic leukemia
• Accurate estimation of homologue-specific DNA concentration-ratios in cancer samples allows long-range haplotyping
• ContEst: estimating cross-contamination of human samples in next-generation sequencing data
• Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion
• GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
• Initial genome sequencing and analysis of multiple myeloma
• Advances in understanding cancer genomes through second-generation sequencing
• The landscape of somatic copy-number alteration across human cancers
• High-resolution mapping of copy-number alterations with massively parallel sequencing
• Somatic mutations affect key pathways in lung adenocarcinoma
• Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma
• Characterizing the cancer genome in lung adenocarcinoma
• Comment on "The consensus coding sequences of human breast and colorectal cancers"
• MicroRNA expression profiles classify human cancers

paper

• Tamoxifen induces PI3K activation in uterine cancer
• SWIFT-seq enables comprehensive single-cell transcriptomic profiling of circulating tumor cells in multiple myeloma and its precursors
• Genomic landscape of multiple myeloma and its precursor conditions
• Generation of a biliary tract cancer cell line atlas identifies molecular subtypes and therapeutic targets
• Large-scale dependency and drug screens characterize the therapeutic vulnerabilities of Multiple Myeloma with 1q
• Single-cell RNA sequencing defines distinct disease subtypes and reveals hypo-responsiveness to interferon in asymptomatic Waldenstrom's Macroglobulinemia
• DLBclass: A Probabilistic Molecular Classifier to Guide Clinical Investigation and Practice in DLBCL
• Deeper evaluation of a single-cell foundation model
• Developmental mosaicism underlying EGFR-mutant lung cancer presenting with multiple primary tumors
• AnnoMate: Exploring and annotating integrated molecular data through custom interactive visualizations
• Systematic identification of minor histocompatibility antigens predicts outcomes of allogeneic hematopoietic cell transplantation
• Clinical Outcomes and Evolution of Clonal Hematopoiesis in Patients with Newly Diagnosed Multiple Myeloma
• Pan-cancer proteogenomics connects oncogenic drivers to functional states
• Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation
• Protogenomic data and resources for pan-cancer analysis
• Genetic events associated with venetoclax resistance in CLL identified by whole-exome sequencing of patient samples
• Inferring early genetic progression in cancers with unobtainable premalignant disease
• Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer
• Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome
• MinimuMM-seq: Genome sequencing of circulating tumor cells for minimally invasive molecular characterization of multiple myeloma pathology
• Single Cell Characterization of Myeloma and its Precursor Conditions Reveals Transcriptional Signatures of Early Tumorigenesis
• Immune biomarkers of response to immunotherapy in patients with high-risk smoldering myeloma
• Pirtobrutinib Targets BTK C481S in Ibrutinib-Resistant CLL but Second-Site BTK Mutations Lead to Resistance
• Clinical Efficacy and Whole Exome Sequencing of Liquid Biopsies in a Phase IB/II study of Bazedoxifene and Palbociclib in Hormone Receptor-Positive Breast Cancer
• Distinct cellular dynamics associated with response to CAR-T therapy for refractory B-cell lymphoma
• Tangent normalization for somatic copy-number inference in cancer genome analysis
• High-resolution profiling of lung adenocarcinoma identifies expression subtypes with specific biomarkers and clinically relevant vulnerabilities
• Molecular map of chronic lymphocytic leukemia and its impact on outcome
• Genetic subtypes of smoldering multiple myeloma are associated with distinct pathogenic phenotypes and clinical outcomes
• Prevalence of monoclonal gammopathies and clinical outcomes in a high-risk US population screened by mass spectrometry: a multicentre cohort study
• Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma
• ZBTB33 is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing
• Parallel Genomic Alterations of Antigen and Payload Targets mediate Polyclonal Acquired Clinical Resistance to Sacituzumab Govitecan in Triple-Negative Breast Cancer
• Inflammatory stromal cells in the myeloma microenvironment
• Radiation-related genomic profile of papillary thyroid cancer after the Chernobyl accident
• Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
• Single-cell RNA sequencing: one step closer to the clinic
• RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts
• The Lipogenic Regulator SREBP2 Induces Transferrin in Circulating Melanoma Cells and Suppresses Ferroptosis
• DNA polymerase and mismatch repair exert distinct microsatellite instability signatures in normal and malignant human cells
• Identification of Somatically Acquired BRCA1/2 Mutations by cfDNA Analysis in Patients with Metastatic Breast Cancer
• Genomic Profiling of Smoldering Multiple Myeloma Identifies Patients at a High Risk of Disease Progression
• Predicting and affecting response to cancer therapy based on pathway-level biomarkers
• Clonal hematopoiesis is associated with adverse outcomes in multiple myeloma patients undergoing transplant
• Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
• Single-cell RNA sequencing reveals compromised immune microenvironment in precursor stages of multiple myeloma
• The repertoire of mutational signatures in human cancer
• Pan-cancer analysis of whole genomes
• The evolutionary history of 2,658 cancers
• Genomic analyses of PMBL reveal new drivers and mechanisms of sensitivity to PD-1 blockade
• Genomic analyses of flow-sorted Hodgkin Reed-Sternberg cells reveal complementary mechanisms of immune evasion
• Scaling computational genomics to millions of individuals with GPUs
• Passenger Hotspot Mutations in Cancer
• Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers
• RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues
• The Cancer Genome Atlas Expression Subtypes Stratify Response to Checkpoint Inhibition in Advanced Urothelial Cancer and Identify a Subset of Patients with High Survival Probability
• Growth dynamics in naturally progressing chronic lymphocytic leukaemia
• Comprehensive analysis of tumour initiation, spatial and temporal progression under multiple lines of treatment
• Tumor mutational landscape is a record of the pre-malignant state
• Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma
• Comment on "DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification"
• Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma
• DeTiN: overcoming tumor-in-normal contamination
• Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair
• Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes
• NetSig: network-based discovery from cancer genomes
• Analysis of ITGB2 rare germ line variants in chronic lymphocytic leukemia
• Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors
• Comprehensive molecular characterization of muscle invasive bladder cancer
• Resolving the phylogenetic origin of glioblastoma via multifocal genomic analysis of pre-treatment and treatment-resistant autopsy specimens
• Analysis of somatic microsatellite indels identifies driver events in human tumors
• A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer
• Recurrent and functional regulatory mutations in breast cancer
• Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias
• Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors
• Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair
• Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution
• Mutations driving CLL and their evolution in progression and relapse
• Comprehensive assessment of cancer missense mutation clustering in protein structures
• Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets
• Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes
• Oncotator: cancer variant annotation tool
• Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma
• Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia
• Integrated genomic characterization of papillary thyroid cancer
• The genomic landscape of pediatric Ewing sarcoma
• Assessing the clinical utility of cancer genomic and proteomic data across tumor types
• Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine
• Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer
• PRADA: pipeline for RNA sequencing data analysis
• Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing
• Discovery and saturation analysis of cancer genes across 21 tumour types
• Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy
• Exome sequencing identifies BRAF mutations in papillary craniopharyngiomas
• Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asian patients
• Pan-cancer patterns of somatic copy number alteration
• KDM4A lysine demethylase induces site-specific copy gain and rereplication of regions amplified in tumors
• An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers
• Mutational heterogeneity in cancer and the search for new cancer-associated genes
• Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation
• Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
• Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity
• Evolution and impact of subclonal mutations in chronic lymphocytic leukemia
• Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability
• A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers
• Sequence analysis of mutations and translocations across breast cancer subtypes
• Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer
• Melanoma genome sequencing reveals frequent PREX2 mutations
• Absolute quantification of somatic DNA alterations in human cancer
• RNA-SeQC: RNA-seq metrics for quality control and process optimization
• Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing
• SF3B1 and other novel cancer genes in chronic lymphocytic leukemia
• Accurate estimation of homologue-specific DNA concentration-ratios in cancer samples allows long-range haplotyping
• ContEst: estimating cross-contamination of human samples in next-generation sequencing data
• Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion
• GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
• Initial genome sequencing and analysis of multiple myeloma
• Advances in understanding cancer genomes through second-generation sequencing
• The landscape of somatic copy-number alteration across human cancers
• High-resolution mapping of copy-number alterations with massively parallel sequencing
• Somatic mutations affect key pathways in lung adenocarcinoma
• Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma
• Characterizing the cancer genome in lung adenocarcinoma
• Comment on "The consensus coding sequences of human breast and colorectal cancers"
• MicroRNA expression profiles classify human cancers

portals

• Getz Lab Project Portal
• CLL-map Portal
• FireBrowse
• Tumor Portal
• GTExPortal

portal

• Getz Lab Project Portal
• CLL-map Portal
• FireBrowse
• Tumor Portal
• GTExPortal

recognitions

• Precision Medicine World Conference (PMWC) Luminary Award (2023)
• Paul C. Zemecnik Chair in Oncology at the MGH Cancer Center (2013 - present)
• 2020 AACR Team Science Awards: TCGA Pilot Project Team
• 2020 AACR Team Science Awards: TCGA Current Project Team
• 2017 Paul Marks Prize for Cancer Research

misc

• The Getz Lab
• Donate
• Contact
• About

home

• The Getz Lab

tools

• DeTin

tool

• DeTin

events

• Fall 2022 Lab Picnic
• 2021 Lab Holiday Party
• Fall 2021 Lab Picnic

positions

• Postdoctoral Associate
• Senior Research Associate
• Postdoctoral Fellow
• Postdoctoral Associate
• Associate Computational Biologist II

position

• Postdoctoral Associate
• Senior Research Associate
• Postdoctoral Fellow
• Postdoctoral Associate
• Associate Computational Biologist II

projects

• Comprehensive landscape of Chernobyl-associated papillary thyroid cancers
• Proteogenomic Analysis
• Single-cell analysis of the tumor microenvironment
• Development of tools for the detection and characterization of immune responses in cancer
• Drivers of Resistance
• Pre-cancer to cancer transition and cancer cell-of-origin
• Heterogeneity and clonal evolution of cancer
• Advances in mutational signatures
• Driver discovery in non-coding regions of the genome
• Detecting cancer-associated genes
• Characterizing the cancer genome

project

• Comprehensive landscape of Chernobyl-associated papillary thyroid cancers
• Proteogenomic Analysis
• Single-cell analysis of the tumor microenvironment
• Development of tools for the detection and characterization of immune responses in cancer
• Drivers of Resistance
• Pre-cancer to cancer transition and cancer cell-of-origin
• Heterogeneity and clonal evolution of cancer
• Advances in mutational signatures
• Driver discovery in non-coding regions of the genome
• Detecting cancer-associated genes
• Characterizing the cancer genome