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
arcasHLA: high-resolution HLA typing from RNAseq
Bioinformatics, 2020
36(1):33-40
Distinct Viral and Mutational Spectrum of Endemic Burkitt Lymphoma
PLOS Pathogens, 2005
11(10):e1005158
HLA Typing from RNA Sequencing and Applications to Cancer
Methods in Molecular Biology, 2020
2120:71-92
Network analysis of global influenza spread
PLOS Computational Biology, 2010
6(11):e1001005
Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2
bioRxiv, 2020
2020.02.10.942748
Topology of viral evolution
Proc Natl Acad Sci USA., 2013
110(46):18566-71
Patterns of evolution and host gene mimicry in influenza and other RNA viruses
PLOS Pathogens, 2008
4(6):e1000079
Quantifying pathogen surveillance using temporal genomic data
mBio, 2013
4(1):e00524-12
Viral reassortment as an information exchange between viral segments
Proc Natl Acad Sci USA., 2012
109(9):3341-6
Identifying hosts of families of viruses: a machine learning approach
PLOS One, 2011
6(12):e27631
A Structure-Informed Atlas of Human-Virus Interactions
Cell, 2019
178(6):1526-1541.e16
Frequency analysis techniques for identification of viral genetic data
mBio, 2010
1(3):e00156-10
The origin of the recent swine influenza A(H1N1) virus infecting humans
Eurosurveillance, 2009
14(17):19193
Cluster analysis of the origins of the new influenza A(H1N1) virus
Eurosurveillance, 2009
14(21):19224
Evolutionary Dynamics of Pandemic Methicillin-Sensitive Staphylococcus aureus ST398 and Its International Spread via Routes of Human Migration
mBio, 2017
8(1):e01375-16
Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system
PLOS One, 2009
4(6):e5969
Reassortment patterns in Swine influenza viruses
PLOS Currents, 2009
1: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
High-resolution Genomic Surveillance of 2014 Ebolavirus Using Shared Subclonal Variants
PLOS Currents, 2015
7:ecurrents.outbreaks.c7fd7946ba606c982668a96bcba43c90
Signs of the 2009 influenza pandemic in the New York-Presbyterian Hospital electronic health records
PLOS One, 2010
5(9):e12658
Host Dependent Evolutionary Patterns and the Origin of 2009 H1N1 Pandemic Influenza
PLOS Currents, 2010
2:RRN1147
Anomalies in the influenza virus genome database: new biology or laboratory errors?
Journal of Virology, 2008
82(17):8947-5
Evolution of the influenza a virus: some new advances
Evolutionary Bioinformatics Online, 2008
3:299-307
Next generation syndromic surveillance: molecular epidemiology, electronic health records and the pandemic Influenza A (H1N1) virus
PLOS Currents, 2009
1:RRN1012
Differences in patient age distribution between influenza A subtypes
PLOS One, 2009
4(8):e6832
Viral diversity and clonal evolution from unphased genomic data
BMC Genomics, 2014
15 Suppl 6(Suppl 6):S17
Rates of asymptomatic respiratory virus infection across age groups
Epidemiology and Infection, 2019
147:e176
Longitudinal active sampling for respiratory viral infections across age groups
Influenza and Other Respiratory Viruses, 2019
13(3):226-232
Active surveillance documents rates of clinical care seeking due to respiratory illness
Influenza and Other Respiratory Viruses, 2020
00:1–8
An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function
Immunity, 2017
47(3):450-465.e5
Cancer Genomic and Immune Characterization
Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes
Nature Communications, 2015
6:7033
Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors
Science, 2019
366(6466):714-723
Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma
Nature Medicine, 2019
25(3):462-469
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
CD8 + T-cell-Mediated Immunoediting Influences Genomic Evolution and Immune Evasion in Murine Gliomas
Clinical Cancer Research, 2020
-
Can patient selection and neoadjuvant administration resuscitate PD-1 inhibitors for glioblastoma?
Journal of Neurosurgery, 2019
1-6
Longitudinal molecular trajectories of diffuse glioma in adults
Nature, 2019
576(7785):112-120
Pan-cancer analysis identifies mutations in SUGP1 that recapitulate mutant SF3B1 splicing dysregulation
Proc Natl Acad Sci USA., 2020
117(19):10305-10312
Somatic mutations and cell identity linked by Genotyping of Transcriptomes
Nature, 2019
571(7765):355-360
GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia
Cancer Discovery, 2019
9(12):1774-1791
Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma
Somatic CLL mutations occur at multiple distinct hematopoietic maturation stages: documentation and cautionary note regarding cell fraction purity
Leukemia, 2018
32(4):1041-104
Copy number profiling across glioblastoma populations has implications for clinical trial design
Neuro-Oncology, 2018
20(10):1368-1373
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
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
Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma
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
Mutations in the RNA Splicing Factor SF3B1 Promote Tumorigenesis through MYC Stabilization
Cancer Discovery, 2020
10(6):806-821
A Novel JAK1 Mutant Breast Implant-Associated Anaplastic Large Cell Lymphoma Patient-Derived Xenograft Fostering Pre-Clinical Discoveries
Cancers (Basel), 2020
12(6):E1603
Complete Regression of Advanced Pancreatic Ductal Adenocarcinomas upon Combined Inhibition of EGFR and C-RAF
Cancer Cell, 2019
35(4):573-587.e6
Phf6 Loss Enhances HSC Self-Renewal Driving Tumor Initiation and Leukemia Stem Cell Activity in T-ALL
Cancer Discovery, 2019
9(3):436-451
The Long Noncoding RNA Paupar Modulates PAX6 Regulatory Activities to Promote Alpha Cell Development and Function
Cell Metabolism, 2019
30(6):1091-1106.e8
Disease-Causing Mutations in SF3B1 Alter Splicing by Disrupting Interaction with SUGP1
Molecular Cell, 2019
76(1):82-95.e7
Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers
Genome Biology, 2019
20(1):253
Distinct genomic profile and specific targeted drug responses in adult cerebellar glioblastoma
Neuro-Oncology, 2019
21(1):47-5
Repurposing dasatinib for diffuse large B cell lymphoma
Proc Natl Acad Sci USA., 2019
116(34):16981-16986
Blastic plasmacytoid dendritic cell neoplasm: genomics mark epigenetic dysregulation as a primary therapeutic target
Haematologica, 2019
104(4):729-737
Novel insights into the genetics and epigenetics of MALT lymphoma unveiled by next generation sequencing analyses
Haematologica, 2019
104(12):e558-e561
Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations
International Journal of Cancer, 2019
144(12):3023-3030
Secretome analysis of patient-derived GBM tumor spheres identifies midkine as a potent therapeutic target
Experimental & Molecular Medicine, 2019
51(12):1-11
Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma
Blood, 2018
131(22):2454-2465
Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukemia
Nature, 2018
553(7689):511-514
Refined karyotype-based prognostic stratification of chronic lymphocytic leukemia with a low- and very-low-risk genetic profile
Leukemia, 2018
32(2):543-546
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
Spatiotemporal genomic architecture informs precision oncology in glioblastoma
Nature Genetics, 2017
49(4):594-599
The B-cell receptor controls fitness of MYC-driven lymphoma cells via GSK3β inhibition
Nature, 2017
546(7657):302-306
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
Clinical impact of small subclones harboring NOTCH1, SF3B1 or BIRC3 mutations in chronic lymphocytic leukemia
Haematologica, 2016
101(4):e135-8
A targetable GATA2-IGF2 axis confers aggressiveness in lethal prostate cancer
Cancer Cell, 2015
27(2):223-39
A novel patient-derived tumorgraft model with TRAF1-ALK anaplastic large-cell lymphoma translocation
Leukemia, 2015
29(6):1390-401
Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities
Proc Natl Acad Sci USA., 2015
112(34):E4726-34
Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness
Blood, 2014
123(15):2378-88
Leukaemogenesis induced by an activating β-catenin mutation in osteoblasts
Nature, 2014
506(7487):240-4
FBXW7 mutations in melanoma and a new therapeutic paradigm
Journal of the National Cancer Institute, 2014
106(6):dju107
Genetics of follicular lymphoma transformation
Cell Reports, 2014
6(1):130-40
Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL
Nature Medicine, 2013
19(3):368-71
The integrated landscape of driver genomic alterations in glioblastoma
Nature Genetics, 2013
45(10):1141-9
Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia
Blood, 2013
121(8):1403-12
Genetic lesions associated with chronic lymphocytic leukemia transformation to Richter syndrome
Journal of Experimental Medicine, 2013
210(11):2273-88
Transforming fusions of FGFR and TACC genes in human glioblastoma
Science, 2012
337(6099):1231-5
Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4
Cancer Cell, 2012
21(4):504-16
BRAF mutations in hairy-cell leukemia
The New England Journal of Medicine, 2011
364(24):2305-15
Inactivating mutations of acetyltransferase genes in B-cell lymphoma
Nature, 2011
471(7337):189-95
Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation
Journal of Experimental Medicine, 2011
208(7):1389-401
An information-theoretic analysis of genetics, gender and age in cancer patients
PLOS One, 2008
3(4):e1951
