Author details

Full Name

Mariano J Alvarez

Affiliation

Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center

ORCID

Career Start Year

2000

Papers

H Index

Expertise

CM4AI Collaborator

Trey Ideker (CM4AI)

PMID	Paper Title	Journal Title	Published Year
36374194	OncoLoop: A Network-Based Precision Cancer Medicine Framework.	Cancer Discov	2023
37061969	A Transcriptome-Based Precision Oncology Platform for Patient-Therapy Alignment in a Diverse Set of Treatment-Resistant Malignancies.	Cancer Discov	2023
36585452	Network-based assessment of HDAC6 activity predicts preclinical and clinical responses to the HDAC6 inhibitor ricolinostat in breast cancer.	Nat Cancer	2023
34728525	A Phase II Study of the Efficacy and Safety of Oral Selinexor in Recurrent Glioblastoma.	Clin Cancer Res	2022
35854100	A model for network-based identification and pharmacological targeting of aberrant, replication-permissive transcriptional programs induced by viral infection.	Commun Biol	2022
36083100	A Patient-to-Model-to-Patient (PMP) Cancer Drug Discovery Protocol for Identifying and Validating Therapeutic Agents Targeting Tumor Regulatory Architecture.	Curr Protoc	2022
35132404	A Model for Network-Based Identification and Pharmacological Targeting of Aberrant, Replication-Permissive Transcriptional Programs Induced by Viral Infection.	Res Sq	2022
33434495	A modular master regulator landscape controls cancer transcriptional identity.	Cell	2021
34323164	A 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 Lymphoma	2021
34341990	Fimepinostat (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 Haematol	2021
32511361	The Host Cell ViroCheckpoint: Identification and Pharmacologic Targeting of Novel Mechanistic Determinants of Coronavirus-Mediated Hijacked Cell States.	bioRxiv	2020
33149111	Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow.	Nat Commun	2020
30996079	Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state.	Sci Transl Med	2019
31548719	Reply to 'H-STS, L-STS and KRJ-I are not authentic GEPNET cell lines'.	Nat Genet	2019
29510988	Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma.	Cancer Discov	2018
29915428	A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors.	Nat Genet	2018
30232459	Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer.	Nat Commun	2018
29662057	Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm.	Nat Commun	2018
27977008	The recurrent architecture of tumour initiation, progression and drug sensitivity.	Nat Rev Cancer	2017
29023443	Systematic, network-based characterization of therapeutic target inhibitors.	PLoS Comput Biol	2017
28813674	An Integrated Systems Biology Approach Identifies TRIM25 as a Key Determinant of Breast Cancer Metastasis.	Cell Rep	2017
28740083	PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens.	Nat Commun	2017
27153732	Detection and removal of spatial bias in multiwell assays.	Bioinformatics	2016
27799065	A case study of an integrative genomic and experimental therapeutic approach for rare tumors: identification of vulnerabilities in a pediatric poorly differentiated carcinoma.	Genome Med	2016
27322546	Functional characterization of somatic mutations in cancer using network-based inference of protein activity.	Nat Genet	2016
27518566	Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks.	Cell	2016
25336442	Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency.	Stem Cells	2015
26248315	SPARC Controls Melanoma Cell Plasticity through Rac1.	PLoS One	2015
26338767	DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes.	Bioinformatics	2015
26227964	Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers.	Genes Dev	2015
26146077	The Regulatory Machinery of Neurodegeneration in In Vitro Models of Amyotrophic Lateral Sclerosis.	Cell Rep	2015
26214373	Identification of neurodegenerative factors using translatome-regulatory network analysis.	Nat Neurosci	2015
25886852	Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks.	Genome Biol	2015
25608936	A systems approach to drug discovery in Alzheimer's disease.	Neurotherapeutics	2015
24823640	Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy.	Cancer Cell	2014
25419740	A community computational challenge to predict the activity of pairs of compounds.	Nat Biotechnol	2014
25303533	Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks.	Cell	2014
23178486	STK38 is a critical upstream regulator of MYC's oncogenic activity in human B-cell lymphoma.	Oncogene	2013
23671412	Improving breast cancer survival analysis through competition-based multidimensional modeling.	PLoS Comput Biol	2013
21985558	PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis.	Plant J	2012
22308355	Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis.	Proc Natl Acad Sci U S A	2012
21862554	Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling.	Development	2011
20032975	The transcriptional network for mesenchymal transformation of brain tumours.	Nature	2010
20531406	A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.	Mol Syst Biol	2010
19965633	Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells.	Blood	2010
19209707	Dissecting the interface between signaling and transcriptional regulation in human B cells.	Pac Symp Biocomput	2009
20042104	Correlating measurements across samples improves accuracy of large-scale expression profile experiments.	Genome Biol	2009
19741643	Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.	Nat Biotechnol	2009
19187043	A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature.	Plant J	2009
17349040	Model based analysis of real-time PCR data from DNA binding dye protocols.	BMC Bioinformatics	2007

1 - 50 of 55

Matias M Falco

University of Helsinki

Career Start Year 2016

Number of shared co-authors 0

Mehdi Bouhaddou

J. David Gladstone Institutes

Career Start Year 2014

Number of shared co-authors 5

Tuo Zhang

Weill Cornell Medical College.

Career Start Year 2013

Number of shared co-authors 2

Murat Iskar

Friedrich Miescher Institute for Biomedical Research

Career Start Year 2010

Number of shared co-authors 1

Frederick S Vizeacoumar

College of Medicine, University of Saskatchewan

Career Start Year 2010

Number of shared co-authors 0

Elana J Fertig

Johns Hopkins University School of Medicine

Career Start Year 2010

Number of shared co-authors 7

Ganiraju C Manyam

the University of Texas MD Anderson Cancer Center

Career Start Year 2009

Number of shared co-authors 11

Matti Nykter

Prostate Cancer Research Center, Tampere University and Tays Cancer Center

Career Start Year 2006

Number of shared co-authors 2

Chao Cheng

Baylor College of Medicine

Career Start Year 2005

Number of shared co-authors 4

Armand Bankhead

Rogel Cancer Center, University of Michigan ann arbor

Career Start Year 2005

Number of shared co-authors 2

Gabriela Alexe

Dana-Farber Cancer Institute

Career Start Year 2004

Number of shared co-authors 10

Silvano Piazza

International Centre for Genetic Engineering and Biotechnology

Career Start Year 2004

Number of shared co-authors 3

Benjamin Haibe-Kains

Princess Margaret Cancer Centre, University Health Network

Career Start Year 2004

Number of shared co-authors 0

Amy G Robertson

Present address: Dxige Research Inc.

Career Start Year 2003

Number of shared co-authors 19

F??tima Al-Shahrour

Spanish National Cancer Research Centre (CNIO)

Career Start Year 2003

Number of shared co-authors 4

Andrew V Kossenkov

The Wistar Institute

Career Start Year 2003

Number of shared co-authors 1

Aik Choon Tan

Huntsman Cancer Institute, The University of Utah

Career Start Year 2003

Number of shared co-authors 2

Laura Riva

Sanford Burnham Prebys Medical Discovery Institute

Career Start Year 2003

Number of shared co-authors 4

Habib Hamidi

Genentech Inc.

Career Start Year 2002

Number of shared co-authors 0

Olivier Elemento

Meyer Cancer Center

Career Start Year 2002

Number of shared co-authors 13

Yidong Chen

The University of Texas Health Science Center at San Antonio

Career Start Year 2001

Number of shared co-authors 5

Dana Pe'er

Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center

Career Start Year 2000

Number of shared co-authors 10

Joshua M Stuart

University of California at Santa Cruz

Career Start Year 2000

Number of shared co-authors 27

Lodewyk F A Wessels

University Medical Centre Mannheim, University of Heidelberg

Career Start Year 2000

Number of shared co-authors 12

Tero Aittokallio

Institute for Molecular Medicine Finland (FIMM), University of Helsinki

Career Start Year 1999

Number of shared co-authors 16

Igor Jurisica

Schroeder Arthritis Institute

Career Start Year 1998

Number of shared co-authors 3

Benedikt Brors

German Cancer Research Center (DKFZ)

Career Start Year 1997

Number of shared co-authors 10

Luigi Marchionni

Weill-Cornell School of Medicine

Career Start Year 1989

Number of shared co-authors 3

Todd R Golub

Broad Institute of MIT and Harvard

Career Start Year 1989

Number of shared co-authors 20

Pablo Tamayo

University of California San Diego

Career Start Year 1988

Number of shared co-authors 15

row(s) 1 - 30 of 30

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

1 - 30

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