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Author Details

Mariano J Alvarez
Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center
2000
55
29
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36374194OncoLoop: A Network-Based Precision Cancer Medicine Framework.Cancer Discov2023
37061969A Transcriptome-Based Precision Oncology Platform for Patient-Therapy Alignment in a Diverse Set of Treatment-Resistant Malignancies.Cancer Discov2023
36585452Network-based assessment of HDAC6 activity predicts preclinical and clinical responses to the HDAC6 inhibitor ricolinostat in breast cancer.Nat Cancer2023
34728525A Phase II Study of the Efficacy and Safety of Oral Selinexor in Recurrent Glioblastoma.Clin Cancer Res2022
35854100A model for network-based identification and pharmacological targeting of aberrant, replication-permissive transcriptional programs induced by viral infection.Commun Biol2022
36083100A Patient-to-Model-to-Patient (PMP) Cancer Drug Discovery Protocol for Identifying and Validating Therapeutic Agents Targeting Tumor Regulatory Architecture.Curr Protoc2022
35132404A Model for Network-Based Identification and Pharmacological Targeting of Aberrant, Replication-Permissive Transcriptional Programs Induced by Viral Infection.Res Sq2022
33434495A modular master regulator landscape controls cancer transcriptional identity.Cell2021
34323164A 2:1 randomized, open-label, phase II study of selinexor vs. physician's choice in older patients with relapsed or refractory acute myeloid leukemia.Leuk Lymphoma2021
34341990Fimepinostat (CUDC-907) in patients with relapsed/refractory diffuse large B cell and high-grade B-cell lymphoma: report of a phase 2 trial and exploratory biomarker analyses.Br J Haematol2021
32511361The Host Cell ViroCheckpoint: Identification and Pharmacologic Targeting of Novel Mechanistic Determinants of Coronavirus-Mediated Hijacked Cell States.bioRxiv2020
33149111Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow.Nat Commun2020
30996079Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state.Sci Transl Med2019
31548719Reply to 'H-STS, L-STS and KRJ-I are not authentic GEPNET cell lines'.Nat Genet2019
29510988Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma.Cancer Discov2018
29915428A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors.Nat Genet2018
30232459Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer.Nat Commun2018
29662057Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm.Nat Commun2018
27977008The recurrent architecture of tumour initiation, progression and drug sensitivity.Nat Rev Cancer2017
29023443Systematic, network-based characterization of therapeutic target inhibitors.PLoS Comput Biol2017
28813674An Integrated Systems Biology Approach Identifies TRIM25 as a Key Determinant of Breast Cancer Metastasis.Cell Rep2017
28740083PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens.Nat Commun2017
27153732Detection and removal of spatial bias in multiwell assays.Bioinformatics2016
27799065A case study of an integrative genomic and experimental therapeutic approach for rare tumors: identification of vulnerabilities in a pediatric poorly differentiated carcinoma.Genome Med2016
27322546Functional characterization of somatic mutations in cancer using network-based inference of protein activity.Nat Genet2016
27518566Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks.Cell2016
25336442Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency.Stem Cells2015
26248315SPARC Controls Melanoma Cell Plasticity through Rac1.PLoS One2015
26338767DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes.Bioinformatics2015
26227964Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers.Genes Dev2015
26146077The Regulatory Machinery of Neurodegeneration in In Vitro Models of Amyotrophic Lateral Sclerosis.Cell Rep2015
26214373Identification of neurodegenerative factors using translatome-regulatory network analysis.Nat Neurosci2015
25886852Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks.Genome Biol2015
25608936A systems approach to drug discovery in Alzheimer's disease.Neurotherapeutics2015
24823640Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy.Cancer Cell2014
25419740A community computational challenge to predict the activity of pairs of compounds.Nat Biotechnol2014
25303533Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks.Cell2014
23178486STK38 is a critical upstream regulator of MYC's oncogenic activity in human B-cell lymphoma.Oncogene2013
23671412Improving breast cancer survival analysis through competition-based multidimensional modeling.PLoS Comput Biol2013
21985558PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis.Plant J2012
22308355Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis.Proc Natl Acad Sci U S A2012
21862554Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling.Development2011
20032975The transcriptional network for mesenchymal transformation of brain tumours.Nature2010
20531406A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.Mol Syst Biol2010
19965633Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells.Blood2010
19209707Dissecting the interface between signaling and transcriptional regulation in human B cells.Pac Symp Biocomput2009
20042104Correlating measurements across samples improves accuracy of large-scale expression profile experiments.Genome Biol2009
19741643Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.Nat Biotechnol2009
19187043A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature.Plant J2009
17349040Model based analysis of real-time PCR data from DNA binding dye protocols.BMC Bioinformatics2007
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Collaborators

Andrea Califano
Columbia University
Co-authored papers 47
Presha Rajbhandari
Columbia University
Co-authored papers 5
Kai Wang
Pfizer Inc.
Co-authored papers 5
Celine Lefebvre
The Scripps Research Institute
Co-authored papers 5
Brygida Bisikirska
Columbia University
Co-authored papers 5
Pavel Sumazin
Baylor College of Medicine
Co-authored papers 4
Riccardo Dalla-Favera
Institute for Cancer Genetics, Columbia University
Co-authored papers 4
Wei Keat Lim
Regeneron Pharmaceuticals
Co-authored papers 4
Katia Basso
Institute for Cancer Genetics, Columbia University
Co-authored papers 4
Alexander Lachmann
Co-authored papers 3
Kenneth Aldape
National Cancer Institute
Co-authored papers 3
Gustavo Stolovitzky
IBM T.J. Watson Research Center
Co-authored papers 3
Adam A Margolin
Icahn School of Medicine
Co-authored papers 3
Michael E Berens
Co-authored papers 2
Dawn L Hershman
Co-authored papers 2
Mukesh Bansal
Co-authored papers 2
Katherine D Crew
Columbia University Irving Medical Center
Co-authored papers 2
Anna Lasorella
Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami
Co-authored papers 2
Manjunath Kustagi
Columbia University
Co-authored papers 2
Hanina Hibshoosh
Co-authored papers 2
Antonio Iavarone
Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami
Co-authored papers 2
Stuart L Schreiber
Broad Institute
Co-authored papers 1
Stephen H Friend
University of Oxford
Co-authored papers 1
Sahil Seth
The University of Texas MD Anderson Cancer Center
Co-authored papers 1
Nevan J Krogan (CM4AI)
University of California San Francisco
Co-authored papers 1
Stacey J Adam
Foundation for the National Institutes of Health
Co-authored papers 1
Pieter Mestdagh
Co-authored papers 1
Evan Y Snyder
Sanford Burnham Prebys Medical Discovery Institute
Co-authored papers 1
Guy M McKhann
New York Presbyterian Hospital, Columbia University Medical Center
Co-authored papers 1
James C Costello
University of Colorado Anschutz Medical Campus
Co-authored papers 1
Release 1.2