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OUR EXPERTISE

Leading expertise in Computational Biology,

Mathematical Modeling, and Machine Learning

Strength across key roles: 

Clinicians, Scientists, and Programmers

A celebrated scientific tradition, as demonstrated by numerous, peer-reviewed publications in high-impact journals authored by our team members

PUBLICATIONS 

Publications from our team members

Pathogen and Immune Characterization

Geographic dependence, surveillance, and origins of the 2009 influenza A (H1N1) virus

The New England Journal of Medicine, 2009

361(2):115-9

doi: 10.1056/NEJMp0904572

arcasHLA: high-resolution HLA typing from RNAseq

Bioinformatics, 2020

36(1):33-40

doi: 10.1093/bioinformatics/btz474

Distinct Viral and Mutational Spectrum of Endemic Burkitt Lymphoma

PLOS Pathogens, 2005

11(10):e1005158

doi: 10.1371/journal.ppat.1005158

HLA Typing from RNA Sequencing and Applications to Cancer

Methods in Molecular Biology, 2020

2120:71-92

doi: 10.1007/978-1-0716-0327-7_5

Network analysis of global influenza spread

PLOS Computational Biology, 2010

6(11):e1001005

doi: 10.1371/journal.pcbi.1001005

Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2

bioRxiv, 2020

2020.02.10.942748

doi: 10.1101/2020.02.10.942748

Topology of viral evolution

Proc Natl Acad Sci USA., 2013

110(46):18566-71

doi: 10.1073/pnas.1313480110

Patterns of evolution and host gene mimicry in influenza and other RNA viruses

PLOS Pathogens, 2008

4(6):e1000079

doi: 10.1371/journal.ppat.1000079

Quantifying pathogen surveillance using temporal genomic data

mBio, 2013

4(1):e00524-12

doi: 10.1128/mBio.00524-12

Viral reassortment as an information exchange between viral segments

Proc Natl Acad Sci USA., 2012

109(9):3341-6

doi: 10.1073/pnas.1113300109

Identifying hosts of families of viruses: a machine learning approach

PLOS One, 2011

6(12):e27631

doi: 10.1371/journal.pone.0027631

A Structure-Informed Atlas of Human-Virus Interactions

Cell, 2019

178(6):1526-1541.e16

doi: 10.1016/j.cell.2019.08.005

Frequency analysis techniques for identification of viral genetic data

mBio, 2010

1(3):e00156-10

doi: 10.1128/mBio.00156-10

The origin of the recent swine influenza A(H1N1) virus infecting humans

Eurosurveillance, 2009

14(17):19193

https://pubmed.ncbi.nlm.nih.gov/19422769/

Cluster analysis of the origins of the new influenza A(H1N1) virus

Eurosurveillance, 2009

14(21):19224

doi: 10.2807/ese.14.21.19224-en

Evolutionary Dynamics of Pandemic Methicillin-Sensitive Staphylococcus aureus ST398 and Its International Spread via Routes of Human Migration

mBio, 2017

8(1):e01375-16

doi: 10.1128/mBio.01375-16

Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system

PLOS One, 2009

4(6):e5969

doi: 10.1371/journal.pone.0005969

Reassortment patterns in Swine influenza viruses

PLOS Currents, 2009

1:RRN1008

doi: 10.1371/currents.RRN1008

The Contribution of the PB1-F2 Protein to the Fitness of Influenza A Viruses and its Recent Evolution in the 2009 Influenza A (H1N1) Pandemic Virus

PLOS Currents, 2009

1:RRN1006

doi: 10.1371/currents.RRN1006

High-resolution Genomic Surveillance of 2014 Ebolavirus Using Shared Subclonal Variants

PLOS Currents, 2015

7:ecurrents.outbreaks.c7fd7946ba606c982668a96bcba43c90

doi: 10.1371/currents.outbreaks.c7fd7946ba606c982668a96bcba43c90

Signs of the 2009 influenza pandemic in the New York-Presbyterian Hospital electronic health records

PLOS One, 2010

5(9):e12658

doi: 10.1371/journal.pone.0012658

Host Dependent Evolutionary Patterns and the Origin of 2009 H1N1 Pandemic Influenza

PLOS Currents, 2010

2:RRN1147

doi: 10.1371/currents.RRN1147

Anomalies in the influenza virus genome database: new biology or laboratory errors?

Journal of Virology, 2008

82(17):8947-5

doi: 10.1128/JVI.00101-08

Evolution of the influenza a virus: some new advances

Evolutionary Bioinformatics Online, 2008

3:299-307

https://pubmed.ncbi.nlm.nih.gov/19430605/

Next generation syndromic surveillance: molecular epidemiology, electronic health records and the pandemic Influenza A (H1N1) virus

PLOS Currents, 2009

1:RRN1012

doi: 10.1371/currents.rrn1012

Differences in patient age distribution between influenza A subtypes

PLOS One, 2009

4(8):e6832

doi: 10.1371/journal.pone.0006832

Viral diversity and clonal evolution from unphased genomic data

BMC Genomics, 2014

15 Suppl 6(Suppl 6):S17

doi: 10.1186/1471-2164-15-S6-S17

Rates of asymptomatic respiratory virus infection across age groups

Epidemiology and Infection, 2019

147:e176

doi: 10.1017/S0950268819000505

Longitudinal active sampling for respiratory viral infections across age groups

Influenza and Other Respiratory Viruses, 2019

13(3):226-232

doi: 10.1111/irv.12629

Active surveillance documents rates of clinical care seeking due to respiratory illness

Influenza and Other Respiratory Viruses, 2020

00:1–8

doi: 10.1111/irv.12753

An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function

Immunity, 2017

47(3):450-465.e5

doi: 10.1016/j.immuni.2017.08.010

Cancer Genomic and Immune Characterization

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Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes

Nature Communications, 2015

6:7033

doi: 10.1038/ncomms8033

Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors

Science, 2019

366(6466):714-723

doi: 10.1126/science.aaw9032

Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma

Nature Medicine, 2019

25(3):462-469

doi: 10.1038/s41591-019-0349-y

Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary Melanoma

Cancer Research, 2020

80(5):1078-1087

doi: 10.1158/0008-5472.CAN-19-2039

CD8 + T-cell-Mediated Immunoediting Influences Genomic Evolution and Immune Evasion in Murine Gliomas

Clinical Cancer Research, 2020

-

doi: 10.1158/1078-0432.CCR-19-3104

Can patient selection and neoadjuvant administration resuscitate PD-1 inhibitors for glioblastoma?

Journal of Neurosurgery, 2019

1-6

doi: 10.3171/2019.9.JNS192523

Longitudinal molecular trajectories of diffuse glioma in adults

Nature, 2019

576(7785):112-120

doi: 10.1038/s41586-019-1775-1

Pan-cancer analysis identifies mutations in SUGP1 that recapitulate mutant SF3B1 splicing dysregulation

Proc Natl Acad Sci USA., 2020

117(19):10305-10312

doi: 10.1073/pnas.1922622117

Somatic mutations and cell identity linked by Genotyping of Transcriptomes

Nature, 2019

571(7765):355-360

doi: 10.1038/s41586-019-1367-0

GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia

Cancer Discovery, 2019

9(12):1774-1791

doi: 10.1158/2159-8290.CD-19-0471

Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma

Gut, 2019

68(3):499-511

doi: 10.1136/gutjnl-2017-314353

Somatic CLL mutations occur at multiple distinct hematopoietic maturation stages: documentation and cautionary note regarding cell fraction purity

Leukemia, 2018

32(4):1041-104

doi: 10.1038/leu.2017.343

Copy number profiling across glioblastoma populations has implications for clinical trial design

Neuro-Oncology, 2018

20(10):1368-1373

doi: 10.1093/neuonc/noy108

Restoration of Replication Fork Stability in BRCA1- and BRCA2-Deficient Cells by Inactivation of SNF2-Family Fork Remodelers

Molecular Cell, 2017

68(2):414-430.e8

doi: 10.1016/j.molcel.2017.09.036

Activating mutations and translocations in the guanine exchange factor VAV1 in peripheral T-cell lymphomas

Proc Natl Acad Sci USA., 2017

114(4):764-769

doi: 10.1073/pnas.1608839114

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

Cell, 2016

164(3):550-63

doi: 10.1016/j.cell.2015.12.028

Clonal evolution of glioblastoma under therapy

Nature Genetics, 2016

48(7):768-76

doi: 10.1038/ng.3590

Identification of a new subclass of ALK-negative ALCL expressing aberrant levels of ERBB4 transcripts

Blood, 2016

127(2):221-32

doi: 10.1182/blood-2014-12-614503

The genetics of nodal marginal zone lymphoma

Blood, 2016

128(10):1362-73

doi: 10.1182/blood-2016-02-696757

Identification of a new subclass of ALK-negative ALCL expressing aberrant levels of ERBB4 transcripts

Cancer Cell, 2015

27(4):516-32

doi: 10.1016/j.ccell.2015.03.006

Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas

Nature Genetics, 2014

46(2):166-70

doi: 10.1038/ng.2873

Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia

Blood, 2014

123(14):2139-47

doi: 10.1182/blood-2013-11-539726

GAB2 induces tumor angiogenesis in NRAS-driven melanoma

Oncogene, 2013

32(31):3627-37

doi: 10.1038/onc.2012.367

Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia

Nature Medicine, 2012

18(2):298-301

doi: 10.1038/nm.2651

Mutations of NOTCH1 are an independent predictor of survival in chronic lymphocytic leukemia

Blood, 2012

119(2):521-9

doi: 10.1182/blood-2011-09-379966

Analysis of the coding genome of diffuse large B-cell lymphoma

Nature Genetics, 2011

43(9):830-7

doi: 10.1038/ng.892

Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia

Blood, 2014

123(14):2139-47

doi: 10.1182/blood-2013-11-539726

Whole-exome sequencing identifies somatic mutations of BCOR in acute myeloid leukemia with normal karyotype

Blood, 2011

118(23):6153-63

doi: 10.1182/blood-2011-07-365320

Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness

Blood, 2011

118(26):6904-8

doi: 10.1182/blood-2011-08-373159

PHF6 mutations in T-cell acute lymphoblastic leukemia

Nature Genetics, 2010

42(4):338-42

doi: 10.1038/ng.542

Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy

Nature Genetics, 2018

50(10):1399-1411

10.1038/s41588-018-0209-6

Mutations in the RNA Splicing Factor SF3B1 Promote Tumorigenesis through MYC Stabilization

Cancer Discovery, 2020

10(6):806-821

10.1158/2159-8290.CD-19-1330

A Novel JAK1 Mutant Breast Implant-Associated Anaplastic Large Cell Lymphoma Patient-Derived Xenograft Fostering Pre-Clinical Discoveries

Cancers (Basel), 2020

12(6):E1603

doi: 10.3390/cancers12061603

Complete Regression of Advanced Pancreatic Ductal Adenocarcinomas upon Combined Inhibition of EGFR and C-RAF

Cancer Cell, 2019

35(4):573-587.e6

doi: 10.1016/j.ccell.2019.03.002

Phf6 Loss Enhances HSC Self-Renewal Driving Tumor Initiation and Leukemia Stem Cell Activity in T-ALL

Cancer Discovery, 2019

9(3):436-451

doi: 10.1158/2159-8290.CD-18-1005

The Long Noncoding RNA Paupar Modulates PAX6 Regulatory Activities to Promote Alpha Cell Development and Function

Cell Metabolism, 2019

30(6):1091-1106.e8

doi: 10.1016/j.cmet.2019.09.013

Disease-Causing Mutations in SF3B1 Alter Splicing by Disrupting Interaction with SUGP1

Molecular Cell, 2019

76(1):82-95.e7

doi: 10.1016/j.molcel.2019.07.017

Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers

Genome Biology, 2019

20(1):253

doi: 10.1186/s13059-019-1848-3

Distinct genomic profile and specific targeted drug responses in adult cerebellar glioblastoma

Neuro-Oncology, 2019

21(1):47-5

doi: 10.1093/neuonc/noy123

Repurposing dasatinib for diffuse large B cell lymphoma

Proc Natl Acad Sci USA., 2019

116(34):16981-16986

doi: 10.1073/pnas.1905239116

Blastic plasmacytoid dendritic cell neoplasm: genomics mark epigenetic dysregulation as a primary therapeutic target

Haematologica, 2019

104(4):729-737

doi: 10.3324/haematol.2018.202093

Novel insights into the genetics and epigenetics of MALT lymphoma unveiled by next generation sequencing analyses

Haematologica, 2019

104(12):e558-e561

doi: 10.3324/haematol.2018.214957

Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations

International Journal of Cancer, 2019

144(12):3023-3030

doi: 10.1002/ijc.32054

Secretome analysis of patient-derived GBM tumor spheres identifies midkine as a potent therapeutic target

Experimental & Molecular Medicine, 2019

51(12):1-11

doi: 10.1038/s12276-019-0351-y

Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma

Blood, 2018

131(22):2454-2465

doi: 10.1182/blood-2017-11-814913

Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukemia

Nature, 2018

553(7689):511-514

doi: 10.1038/nature25186

Refined karyotype-based prognostic stratification of chronic lymphocytic leukemia with a low- and very-low-risk genetic profile

Leukemia, 2018

32(2):543-546

doi: 10.1038/leu.2017.292

Saa3 is a key mediator of the protumorigenic properties of cancer-associated fibroblasts in pancreatic tumors

Proc Natl Acad Sci USA., 2018

115(6):E1147-E1156

doi: 10.1073/pnas.1717802115

Spatiotemporal genomic architecture informs precision oncology in glioblastoma

Nature Genetics, 2017

49(4):594-599

doi: 10.1038/ng.3806

The B-cell receptor controls fitness of MYC-driven lymphoma cells via GSK3β inhibition

Nature, 2017

546(7657):302-306

doi: 10.1038/nature22353

Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia

Proc Natl Acad Sci USA., 2016

113(40):11306-11311

doi: 10.1073/pnas.1608420113

Clinical impact of small subclones harboring NOTCH1, SF3B1 or BIRC3 mutations in chronic lymphocytic leukemia

Haematologica, 2016

101(4):e135-8

doi: 10.3324/haematol.2015.136051

A targetable GATA2-IGF2 axis confers aggressiveness in lethal prostate cancer

Cancer Cell, 2015

27(2):223-39

doi: 10.1016/j.ccell.2014.11.013

A novel patient-derived tumorgraft model with TRAF1-ALK anaplastic large-cell lymphoma translocation

Leukemia, 2015

29(6):1390-401

doi: 10.1038/leu.2014.347

Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities

Proc Natl Acad Sci USA., 2015

112(34):E4726-34

doi: 10.1073/pnas.1514105112

Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness

Blood, 2014

123(15):2378-88

doi: 10.1182/blood-2013-10-534271

Leukaemogenesis induced by an activating β-catenin mutation in osteoblasts

Nature, 2014

506(7487):240-4

doi: 10.1038/nature12883

FBXW7 mutations in melanoma and a new therapeutic paradigm

Journal of the National Cancer Institute, 2014

106(6):dju107

doi: 10.1093/jnci/dju107

Genetics of follicular lymphoma transformation

Cell Reports, 2014

6(1):130-40

doi: 10.1016/j.celrep.2013.12.027

Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL

Nature Medicine, 2013

19(3):368-71

doi: 10.1038/nm.3078

The integrated landscape of driver genomic alterations in glioblastoma

Nature Genetics, 2013

45(10):1141-9

doi: 10.1038/ng.2734

Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia

Blood, 2013

121(8):1403-12

doi: 10.1182/blood-2012-09-458265

Genetic lesions associated with chronic lymphocytic leukemia transformation to Richter syndrome

Journal of Experimental Medicine, 2013

210(11):2273-88

doi: 10.1084/jem.20131448

Transforming fusions of FGFR and TACC genes in human glioblastoma

Science, 2012

337(6099):1231-5

doi: 10.1126/science.1220834

Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4

Cancer Cell, 2012

21(4):504-16

doi: 10.1016/j.ccr.2012.02.007

BRAF mutations in hairy-cell leukemia

The New England Journal of Medicine, 2011

364(24):2305-15

doi: 10.1056/NEJMoa1014209

Inactivating mutations of acetyltransferase genes in B-cell lymphoma

Nature, 2011

471(7337):189-95

doi: 10.1038/nature09730

Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation

Journal of Experimental Medicine, 2011

208(7):1389-401

doi: 10.1084/jem.20110921

An information-theoretic analysis of genetics, gender and age in cancer patients

PLOS One, 2008

3(4):e1951

doi: 10.1371/journal.pone.0001951