Institute for Computational Biomedicine,
Department of Physiology and Biophysics,
Department of Physiology and Biophysics, Institute for Computational Biomedicine
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Reconstructing the duplication history of tandemly repeated genes.
Molecular biology and evolution Mar, 2002 | Pubmed ID: 11861887
An efficient and accurate distance based algorithm to reconstruct tandem duplication trees.
Bioinformatics (Oxford, England) , 2002 | Pubmed ID: 12385990
IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes.
Developmental and comparative immunology Oct, 2003 | Pubmed ID: 12818634
Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.
Genome biology , 2005 | Pubmed ID: 15693947
Revealing posttranscriptional regulatory elements through network-level conservation.
PLoS computational biology Dec, 2005 | Pubmed ID: 16355253
Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks.
Molecular systems biology , 2006 | Pubmed ID: 16732191
Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo.
PLoS biology May, 2007 | Pubmed ID: 17456005
Developing a systems-level understanding of gene expression.
Genome biology , 2007 | Pubmed ID: 17472736
A universal framework for regulatory element discovery across all genomes and data types.
Molecular cell Oct, 2007 | Pubmed ID: 17964271
Fastcompare: a nonalignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation.
Methods in molecular biology (Clifton, N.J.) , 2007 | Pubmed ID: 17993685
let-7 Overexpression leads to an increased fraction of cells in G2/M, direct down-regulation of Cdc34, and stabilization of Wee1 kinase in primary fibroblasts.
The Journal of biological chemistry Mar, 2009 | Pubmed ID: 19126550
The BCL6 transcriptional program features repression of multiple oncogenes in primary B cells and is deregulated in DLBCL.
Blood May, 2009 | Pubmed ID: 19307668
Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition.
Development (Cambridge, England) Jun, 2009 | Pubmed ID: 19465600
DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices.
BMC bioinformatics , 2009 | Pubmed ID: 19941641
Revealing global regulatory perturbations across human cancers.
Molecular cell Dec, 2009 | Pubmed ID: 20005852
DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma.
Blood Nov, 2010 | Pubmed ID: 20610814
EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis.
Blood Dec, 2010 | Pubmed ID: 20736451
Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite.
PLoS pathogens , 2010 | Pubmed ID: 21060817
Mutations in FLVCR1 cause posterior column ataxia and retinitis pigmentosa.
American journal of human genetics Nov, 2010 | Pubmed ID: 21070897
Large-scale discovery and characterization of protein regulatory motifs in eukaryotes.
PloS one , 2010 | Pubmed ID: 21206902
An integrated ChIP-seq analysis platform with customizable workflows.
BMC bioinformatics , 2011 | Pubmed ID: 21736739
DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation.
Blood Sep, 2011 | Pubmed ID: 21828137
Using transcriptome sequencing to identify mechanisms of drug action and resistance.
Nature chemical biology Mar, 2012 | Pubmed ID: 22327403
A panel of four miRNAs accurately differentiates malignant from benign indeterminate thyroid lesions on fine needle aspiration.
Clinical cancer research : an official journal of the American Association for Cancer Research Apr, 2012 | Pubmed ID: 22351693
Faster sequencers, larger datasets, new challenges.
Genome biology , 2012 | Pubmed ID: 22452984
Calcimimetics versus parathyroidectomy for treatment of primary hyperparathyroidism: retrospective chart analysis of a prospective database.
Annals of surgery May, 2012 | Pubmed ID: 22470074
Identification of functionally active, low frequency copy number variants at 15q21.3 and 12q21.31 associated with prostate cancer risk.
Proceedings of the National Academy of Sciences of the United States of America Apr, 2012 | Pubmed ID: 22496589
Concordant signaling pathways produced by pesticide exposure in mice correspond to pathways identified in human Parkinson's disease.
PloS one , 2012 | Pubmed ID: 22563483
Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons.
Cell Jun, 2012 | Pubmed ID: 22608085
Oncogene-mediated alterations in chromatin conformation.
Proceedings of the National Academy of Sciences of the United States of America Jun, 2012 | Pubmed ID: 22615383
Genome-wide detection of genes targeted by non-Ig somatic hypermutation in lymphoma.
PloS one , 2012 | Pubmed ID: 22808135
Oncogenic transcription factors as master regulators of chromatin topology: a new role for ERG in prostate cancer.
Cell cycle (Georgetown, Tex.) Sep, 2012 | Pubmed ID: 22918253
Efficient direct reprogramming of mature amniotic cells into endothelial cells by ETS factors and TGFβ suppression.
Cell Oct, 2012 | Pubmed ID: 23084400
Integrative epigenomic analysis identifies biomarkers and therapeutic targets in adult B-acute lymphoblastic leukemia.
Cancer discovery Nov, 2012 | Pubmed ID: 23107779
Human ESC-derived hemogenic endothelial cells undergo distinct waves of endothelial to hematopoietic transition.
Blood Jan, 2013 | Pubmed ID: 23169780
Antagonistic function of the RNA-binding protein HuR and miR-200b in post-transcriptional regulation of vascular endothelial growth factor-A expression and angiogenesis.
The Journal of biological chemistry Feb, 2013 | Pubmed ID: 23223443
Epigenetic repression of miR-31 disrupts androgen receptor homeostasis and contributes to prostate cancer progression.
Cancer research Feb, 2013 | Pubmed ID: 23233736
Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.
PLoS genetics , 2013 | Pubmed ID: 23326238
NFIB is a governor of epithelial-melanocyte stem cell behaviour in a shared niche.
Nature Mar, 2013 | Pubmed ID: 23389444
Metabolic alterations in lung cancer-associated fibroblasts correlated with increased glycolytic metabolism of the tumor.
Molecular cancer research : MCR Jun, 2013 | Pubmed ID: 23475953
Inferring chromatin-bound protein complexes from genome-wide binding assays.
Genome research Aug, 2013 | Pubmed ID: 23554462
Epigenomic alterations in localized and advanced prostate cancer.
Neoplasia (New York, N.Y.) Apr, 2013 | Pubmed ID: 23555183
Downregulation of FOXP1 is required during germinal center B-cell function.
Blood May, 2013 | Pubmed ID: 23580662
Punctuated evolution of prostate cancer genomes.
Cell Apr, 2013 | Pubmed ID: 23622249
A novel approach for characterizing microsatellite instability in cancer cells.
PloS one , 2013 | Pubmed ID: 23671654
EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation.
Cancer cell May, 2013 | Pubmed ID: 23680150
AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes.
Nature Aug, 2013 | Pubmed ID: 23803762
A stable transcription factor complex nucleated by oligomeric AML1-ETO controls leukaemogenesis.
Nature Aug, 2013 | Pubmed ID: 23812588
The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry.
Nature neuroscience Aug, 2013 | Pubmed ID: 23817550
Molecular signatures of tissue-specific microvascular endothelial cell heterogeneity in organ maintenance and regeneration.
Developmental cell Jul, 2013 | Pubmed ID: 23871589
A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters.
Cell reports Aug, 2013 | Pubmed ID: 23911289
Akt suppression of TGFβ signaling contributes to the maintenance of vascular identity in embryonic stem cell-derived endothelial cells.
Stem cells (Dayton, Ohio) Jan, 2014 | Pubmed ID: 23963623
Synergistic activation of inflammatory cytokine genes by interferon-γ-induced chromatin remodeling and toll-like receptor signaling.
Immunity Sep, 2013 | Pubmed ID: 24012417
EZH2 mutations are frequent and represent an early event in follicular lymphoma.
Blood Oct, 2013 | Pubmed ID: 24052547
Genetic regulation of vesiculogenesis and immunomodulation in Mycobacterium tuberculosis.
Proceedings of the National Academy of Sciences of the United States of America Dec, 2013 | Pubmed ID: 24248369
Molecular diagnosis of autosomal dominant polycystic kidney disease using next-generation sequencing.
The Journal of molecular diagnostics : JMD Mar, 2014 | Pubmed ID: 24374109
Double-stranded DNA in exosomes: a novel biomarker in cancer detection.
Cell research Jun, 2014 | Pubmed ID: 24710597
Histone variant H3.3 is an essential maternal factor for oocyte reprogramming.
Proceedings of the National Academy of Sciences of the United States of America May, 2014 | Pubmed ID: 24799717
Silencing of UCHL1 by CpG promoter hyper-methylation is associated with metastatic gastroenteropancreatic well-differentiated neuroendocrine (carcinoid) tumors.
Annals of surgical oncology Dec, 2014 | Pubmed ID: 24854489
DrugTargetSeqR: a genomics- and CRISPR-Cas9-based method to analyze drug targets.
Nature chemical biology Aug, 2014 | Pubmed ID: 24929528
Impact of ERBB2 mutations on in vitro sensitivity of bladder cancer to lapatinib.
Cancer biology & therapy Sep, 2014 | Pubmed ID: 24971884
Reprogramming human endothelial cells to haematopoietic cells requires vascular induction.
Nature Jul, 2014 | Pubmed ID: 25030167
Cell-cycle reprogramming for PI3K inhibition overrides a relapse-specific C481S BTK mutation revealed by longitudinal functional genomics in mantle cell lymphoma.
Cancer discovery Sep, 2014 | Pubmed ID: 25082755
Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas.
Genome biology , 2014 | Pubmed ID: 25123191
Tracing the roots of cancer evolution.
Cancer discovery Sep, 2014 | Pubmed ID: 25185189
Histone methyltransferase MMSET/NSD2 alters EZH2 binding and reprograms the myeloma epigenome through global and focal changes in H3K36 and H3K27 methylation.
PLoS genetics Sep, 2014 | Pubmed ID: 25188243
Tbx5 is required for avian and Mammalian epicardial formation and coronary vasculogenesis.
Circulation research Oct, 2014 | Pubmed ID: 25245104
Differentiation of human pluripotent stem cells to cells similar to cord-blood endothelial colony-forming cells.
Nature biotechnology Nov, 2014 | Pubmed ID: 25306246
The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer.
Nature communications , 2014 | Pubmed ID: 25415230
ELAVL1 regulates alternative splicing of eIF4E transporter to promote postnatal angiogenesis.
Proceedings of the National Academy of Sciences of the United States of America Dec, 2014 | Pubmed ID: 25422430
Dicer expression and microRNA dysregulation associate with aggressive features in thyroid cancer.
Surgery Dec, 2014 | Pubmed ID: 25456905
Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells.
Blood Feb, 2015 | Pubmed ID: 25488972
Lymphoblastic transformation of follicular lymphoma: a clinicopathologic and molecular analysis of 7 patients.
Human pathology Feb, 2015 | Pubmed ID: 25529125
ELAVL1 modulates transcriptome-wide miRNA binding in murine macrophages.
Cell reports Dec, 2014 | Pubmed ID: 25533351
Vascular niche promotes hematopoietic multipotent progenitor formation from pluripotent stem cells.
The Journal of clinical investigation Mar, 2015 | Pubmed ID: 25664855
Transcriptome analysis of individual stromal cell populations identifies stroma-tumor crosstalk in mouse lung cancer model.
Cell reports Feb, 2015 | Pubmed ID: 25704820
Selective inhibition of protein arginine methyltransferase 5 blocks initiation and maintenance of B-cell transformation.
Blood Apr, 2015 | Pubmed ID: 25742700
The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo.
Cell Apr, 2015 | Pubmed ID: 25843629
Epigenomic evolution in diffuse large B-cell lymphomas.
Nature communications , 2015 | Pubmed ID: 25891015
The chromatin Remodeler CHD8 is required for activation of progesterone receptor-dependent enhancers.
PLoS genetics Apr, 2015 | Pubmed ID: 25894978
CCMCL1: a new model of aggressive mantle cell lymphoma.
Blood Apr, 2015 | Pubmed ID: 25907904
Integrative clinical genomics of advanced prostate cancer.
Cell May, 2015 | Pubmed ID: 26000489
Identification of Reprogrammed Myeloid Cell Transcriptomes in NSCLC.
PloS one , 2015 | Pubmed ID: 26046767
A primer on precision medicine informatics.
Briefings in bioinformatics Jun, 2015 | Pubmed ID: 26048401
Mechanosensitive pannexin-1 channels mediate microvascular metastatic cell survival.
Nature cell biology Jul, 2015 | Pubmed ID: 26098574
Deficiency of UBE2T, the E2 Ubiquitin Ligase Necessary for FANCD2 and FANCI Ubiquitination, Causes FA-T Subtype of Fanconi Anemia.
Cell reports Jul, 2015 | Pubmed ID: 26119737
Use of RNA sequencing to evaluate rheumatic disease patients.
Arthritis research & therapy , 2015 | Pubmed ID: 26126608
Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.
JAMA oncology Jul, 2015 | Pubmed ID: 26181256
Obesity-dependent changes in interstitial ECM mechanics promote breast tumorigenesis.
Science translational medicine Aug, 2015 | Pubmed ID: 26290412
DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID.
Cell reports Sep, 2015 | Pubmed ID: 26365193
The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development.
Nature medicine Oct, 2015 | Pubmed ID: 26366710
Vascular Platform to Define Hematopoietic Stem Cell Factors and Enhance Regenerative Hematopoiesis.
Stem cell reports Nov, 2015 | Pubmed ID: 26441307
Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma.
Genome medicine , 2015 | Pubmed ID: 26521025
Vitamin C selectively kills KRAS and BRAF mutant colorectal cancer cells by targeting GAPDH.
Science (New York, N.Y.) Dec, 2015 | Pubmed ID: 26541605
Prediction of Genetic Interactions Using Machine Learning and Network Properties.
Frontiers in bioengineering and biotechnology , 2015 | Pubmed ID: 26579514
5' UTR m(6)A Promotes Cap-Independent Translation.
Cell Nov, 2015 | Pubmed ID: 26593424
Combinatorial targeting of nuclear export and translation of RNA inhibits aggressive B-cell lymphomas.
Blood Nov, 2015 | Pubmed ID: 26603836
Prostate-Specific Membrane Antigen Is a Potential Antiangiogenic Target in Adrenocortical Carcinoma.
The Journal of clinical endocrinology and metabolism Mar, 2016 | Pubmed ID: 26771706
Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer.
Nature medicine Mar, 2016 | Pubmed ID: 26855148
Nuclear envelope expansion is crucial for proper chromosomal segregation during a closed mitosis.
Journal of cell science Mar, 2016 | Pubmed ID: 26869222
Practical Analysis of Genome Contact Interaction Experiments.
Methods in molecular biology (Clifton, N.J.) , 2016 | Pubmed ID: 27008015
Predictive features of ligand-specific signaling through the estrogen receptor.
Molecular systems biology Apr, 2016 | Pubmed ID: 27107013
Epigenetic profiles signify cell fate plasticity in unipotent spermatogonial stem and progenitor cells.
Nature communications Apr, 2016 | Pubmed ID: 27117588
Disruption of Adipose Rab10-Dependent Insulin Signaling Causes Hepatic Insulin Resistance.
Diabetes Jun, 2016 | Pubmed ID: 27207531
A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors.
Cell reports Jun, 2016 | Pubmed ID: 27264179
Inherited DNA-Repair Gene Mutations in Men with Metastatic Prostate Cancer.
The New England journal of medicine Aug, 2016 | Pubmed ID: 27433846
Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq.
Genome medicine 07, 2016 | Pubmed ID: 27460926
Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma.
The Journal of clinical investigation Sep, 2016 | Pubmed ID: 27482887
KLF4: A new player in plasma cell development.
Cell cycle (Georgetown, Tex.) Oct, 2016 | Pubmed ID: 27485539
EZH2 and BCL6 Cooperate to Assemble CBX8-BCOR Complex to Repress Bivalent Promoters, Mediate Germinal Center Formation and Lymphomagenesis.
Cancer cell Aug, 2016 | Pubmed ID: 27505670
Deep Sequencing of T-cell Receptor DNA as a Biomarker of Clonally Expanded TILs in Breast Cancer after Immunotherapy.
Cancer immunology research Oct, 2016 | Pubmed ID: 27587469
An Epigenomic Approach to Improving Response to Neoadjuvant Cisplatin Chemotherapy in Bladder Cancer.
Biomolecules Sep, 2016 | Pubmed ID: 27598218
Discovery and clinical introduction of first-in-class imipridone ONC201.
Oncotarget Nov, 2016 | Pubmed ID: 27602582
Multi-tiered Reorganization of the Genome during B Cell Affinity Maturation Anchored by a Germinal Center-Specific Locus Control Region.
Immunity Sep, 2016 | Pubmed ID: 27637145
A Data-Driven Approach to Predicting Successes and Failures of Clinical Trials.
Cell chemical biology Oct, 2016 | Pubmed ID: 27642066
N-Myc Induces an EZH2-Mediated Transcriptional Program Driving Neuroendocrine Prostate Cancer.
Cancer cell Oct, 2016 | Pubmed ID: 27728805
CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas.
Cancer discovery Jan, 2017 | Pubmed ID: 27733359
Clonal evolution of chemotherapy-resistant urothelial carcinoma.
Nature genetics Dec, 2016 | Pubmed ID: 27749842
The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations.
Journal of the American Medical Informatics Association : JAMIA May, 2017 | Pubmed ID: 27789569
Therapeutic efficacy of the bromodomain inhibitor OTX015/MK-8628 in ALK-positive anaplastic large cell lymphoma: an alternative modality to overcome resistant phenotypes.
Oncotarget Nov, 2016 | Pubmed ID: 27793034
Systematic Discovery of Chromatin-Bound Protein Complexes from ChIP-seq Datasets.
Methods in molecular biology (Clifton, N.J.) , 2017 | Pubmed ID: 27832531
Mechanisms of Acquired Drug Resistance to the HDAC6 Selective Inhibitor Ricolinostat Reveals Rational Drug-Drug Combination with Ibrutinib.
Clinical cancer research : an official journal of the American Association for Cancer Research Dec, 2016 | Pubmed ID: 27993968
Endothelial-specific inhibition of NF-κB enhances functional haematopoiesis.
Nature communications Dec, 2016 | Pubmed ID: 28000664
Reversible methylation of m(6)Am in the 5' cap controls mRNA stability.
Nature 01, 2017 | Pubmed ID: 28002401
Role of RPL39 in Metaplastic Breast Cancer.
Journal of the National Cancer Institute Jun, 2017 | Pubmed ID: 28040796
Systems Structural Biology Analysis of Ligand Effects on ERα Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies.
Cell chemical biology Jan, 2017 | Pubmed ID: 28042045
A Computational Approach for Identifying Synergistic Drug Combinations.
PLoS computational biology Jan, 2017 | Pubmed ID: 28085880
Sox17 drives functional engraftment of endothelium converted from non-vascular cells.
Nature communications Jan, 2017 | Pubmed ID: 28091527
Regulatory elements in molecular networks.
Wiley interdisciplinary reviews. Systems biology and medicine May, 2017 | Pubmed ID: 28093886
Effective Combination Therapies for B-cell Lymphoma Predicted by a Virtual Disease Model.
Cancer research Apr, 2017 | Pubmed ID: 28130226
Melanoma genome evolution across species.
BMC genomics Feb, 2017 | Pubmed ID: 28173755
BCL6 Antagonizes NOTCH2 to Maintain Survival of Human Follicular Lymphoma Cells.
Cancer discovery May, 2017 | Pubmed ID: 28232365
Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Anti-Tumor Innate Immunity.
Cancer discovery Mar, 2017 | Pubmed ID: 28274958
Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine.
Cancer discovery May, 2017 | Pubmed ID: 28331002
Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression.
eLife Mar, 2017 | Pubmed ID: 28350298
EthSEQ: ethnicity annotation from whole exome sequencing data.
Bioinformatics (Oxford, England) Mar, 2017 | Pubmed ID: 28369222
Epigenetic Identity in AML Depends on Disruption of Non-promoter Regulatory Elements and is Affected by Antagonistic Effects of Mutations in Epigenetic Modifiers.
Cancer discovery Apr, 2017 | Pubmed ID: 28408400
Stem Cell Lineage Infidelity Drives Wound Repair and Cancer.
Cell May, 2017 | Pubmed ID: 28434617
Global miRNA expression analysis identifies novel key regulators of plasma cell differentiation and malignant plasma cell.
Nucleic acids research Apr, 2017 | Pubmed ID: 28459970
Identification of a nucleoside analog active against adenosine kinase-expressing plasma cell malignancies.
The Journal of clinical investigation May, 2017 | Pubmed ID: 28504647
An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data.
Nature communications May, 2017 | Pubmed ID: 28513628
Conversion of adult endothelium to immunocompetent haematopoietic stem cells.
Nature May, 2017 | Pubmed ID: 28514438
Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells.
Cell reports May, 2017 | Pubmed ID: 28514649
Concerted regulation of retinal pigment epithelium basement membrane and barrier function by angiocrine factors.
Nature communications May, 2017 | Pubmed ID: 28524846
Lymphatic endothelial S1P promotes mitochondrial function and survival in naive T cells.
Nature May, 2017 | Pubmed ID: 28538737
Jonathan B. Reichel1,
Jason McCormick2,
Jonathan R. Fromm3,
Olivier Elemento4,
Ethel Cesarman5,
Mikhail Roshal6
1Innovation Laboratory, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center,
2Flow-Sorting Core Facility, Weill Cornell Medical College,
3Department of Laboratory Medicine, University of Washington,
4Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medical College,
5Department of Pathology and Laboratory Medicine, Weill Cornell Medical College,
6Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
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