Author details

Full Name

Nirav Malani

Affiliation

University of Pennsylvania Perelman School of Medicine

ORCID

Career Start Year

2008

Papers

H Index

Expertise

CM4AI Collaborator

Trey Ideker (CM4AI)

PMID	Paper Title	Journal Title	Published Year
36944408	Detection of Biallelic Loss of DNA Repair Genes in Formalin-Fixed, Paraffin-Embedded Tumor Samples Using a Novel Tumor-Only Sequencing Panel.	J Mol Diagn	2023
37632661	Personalized Cancer Monitoring Assay for the Detection of ctDNA in Patients with Solid Tumors.	Mol Diagn Ther	2023
32427098	Apolipoprotein L-1 renal risk variants form active channels at the plasma membrane driving cytotoxicity.	Elife	2020
32345712	Feasibility of blood testing combined with PET-CT to screen for cancer and guide intervention.	Science	2020
29305523	Role of the PWWP domain of lens epithelium-derived growth factor (LEDGF)/p75 cofactor in lentiviral integration targeting.	J Biol Chem	2018
28344988	INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions.	Mol Ther Methods Clin Dev	2016
28344990	INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes.	Mol Ther Methods Clin Dev	2016
26029726	Coherence analysis discriminates between retroviral integration patterns in CD34(+) cells transduced under differing clinical trial conditions.	Mol Ther Methods Clin Dev	2015
25898053	Outcomes following gene therapy in patients with severe Wiskott-Aldrich syndrome.	JAMA	2015
25969444	Structural and sequencing analysis of local target DNA recognition by MLV integrase.	Nucleic Acids Res	2015
24489369	Comparing DNA integration site clusters with scan statistics.	Bioinformatics	2014
25295500	A modified Î³-retrovirus vector for X-linked severe combined immunodeficiency.	N Engl J Med	2014
24904063	Allosteric inhibition of human immunodeficiency virus integrase: late block during viral replication and abnormal multimerization involving specific protein domains.	J Biol Chem	2014
24874515	A new class of multimerization selective inhibitors of HIV-1 integrase.	PLoS Pathog	2014
24520112	Bimodal high-affinity association of Brd4 with murine leukemia virus integrase and mononucleosomes.	Nucleic Acids Res	2014
24516383	The major cellular sterol regulatory pathway is required for Andes virus infection.	PLoS Pathog	2014
24623816	Altering murine leukemia virus integration through disruption of the integrase and BET protein family interaction.	Nucleic Acids Res	2014
23091042	A resurrected mammalian hAT transposable element and a closely related insect element are highly active in human cell culture.	Proc Natl Acad Sci U S A	2013
24183673	The BET family of proteins targets moloney murine leukemia virus integration near transcription start sites.	Cell Rep	2013
23818621	BET proteins promote efficient murine leukemia virus integration at transcription start sites.	Proc Natl Acad Sci U S A	2013
23953889	HIV latency and integration site placement in five cell-based models.	Retrovirology	2013
23661057	Viral DNA tethering domains complement replication-defective mutations in the p12 protein of MuLV Gag.	Proc Natl Acad Sci U S A	2013
23621841	Recombinant adeno-associated virus integration sites in murine liver after ornithine transcarbamylase gene correction.	Hum Gene Ther	2013
23723351	piggyBac transposase tools for genome engineering.	Proc Natl Acad Sci U S A	2013
23719353	Bringing it all together: big data and HIV research.	AIDS	2013
23348058	Quantitation of HIV DNA integration: effects of differential integration site distributions on Alu-PCR assays.	J Virol Methods	2013
23046603	HRP-2 determines HIV-1 integration site selection in LEDGF/p75 depleted cells.	Retrovirology	2012
23166581	Comparative analysis of the recently discovered hAT transposon TcBuster in human cells.	PLoS One	2012
21228324	The host genomic environment of the provirus determines the abundance of HTLV-1-infected T-cell clones.	Blood	2011
21987578	Role of the PWWP domain of lens epithelium-derived growth factor (LEDGF)/p75 cofactor in lentiviral integration targeting.	J Biol Chem	2011
21791101	A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing.	BMC Genomics	2011
21561906	Gammaretroviral integration into nucleosomal target DNA in vivo.	J Virol	2011
21706032	In vivo genome editing restores haemostasis in a mouse model of haemophilia.	Nature	2011
21386821	Distribution of lentiviral vector integration sites in mice following therapeutic gene transfer to treat Î²-thalassemia.	Mol Ther	2011
21415009	A method to sequence and quantify DNA integration for monitoring outcome in gene therapy.	Nucleic Acids Res	2011
21423673	HIV integration targeting: a pathway involving Transportin-3 and the nuclear pore protein RanBP2.	PLoS Pathog	2011
21106988	Assessing the potential for AAV vector genotoxicity in a murine model.	Blood	2011
21151124	Genomic safe harbors permit high Î²-globin transgene expression in thalassemia induced pluripotent stem cells.	Nat Biotechnol	2011
20228274	Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial.	Blood	2010
21203516	High-definition mapping of retroviral integration sites defines the fate of allogeneic T cells after donor lymphocyte infusion.	PLoS One	2010
20195265	LEDGF hybrids efficiently retarget lentiviral integration into heterochromatin.	Mol Ther	2010
19038346	Methods for integration site distribution analyses in animal cell genomes.	Methods	2009
19550285	HIV integration site distributions in resting and activated CD4+ T cells infected in culture.	AIDS	2009
19478882	Host cell factors in HIV replication: meta-analysis of genome-wide studies.	PLoS Pathog	2009
19270161	Integration target site selection by a resurrected human endogenous retrovirus.	Genes Dev	2009
19259065	Analysis of lentiviral vector integration in HIV+ study subjects receiving autologous infusions of gene modified CD4+ T cells.	Mol Ther	2009
18614863	Massively parallel pyrosequencing in HIV research.	AIDS	2008
18953026	Bacteriophage Mu integration in yeast and mammalian genomes.	Nucleic Acids Res	2008

1 - 48 of 48

Thiago Y Oliveira

The Rockefeller University

Career Start Year 2010

Number of shared co-authors 2

Joseph B Hiatt

Fred Hutchinson Cancer Center

Career Start Year 2009

Number of shared co-authors 4

Will Dampier

Drexel University College of Medicine

Career Start Year 2007

Number of shared co-authors 0

Kristen K Dang

Benaroya Research Institute at Virginia Mason

Career Start Year 2006

Number of shared co-authors 0

Lara Manganaro

National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi"

Career Start Year 2005

Number of shared co-authors 7

Guillaume J Filion

University of Toronto Scarborough

Career Start Year 2004

Number of shared co-authors 1

Xiaolin Wu

Leidos Biomedical Research Inc.

Career Start Year 2003

Number of shared co-authors 0

Geoffrey J Faulkner

Mater Research Institute - University of Queensland

Career Start Year 2003

Number of shared co-authors 1

Rituparna Mukhopadhyay

Albert Einstein College of Medicine

Career Start Year 2002

Number of shared co-authors 1

Tarjei S Mikkelsen

Harvard University, USA Broad Institute, USA Harvard Stem Cell Institute

Career Start Year 2001

Number of shared co-authors 1

Edward P Browne

University of North Carolina at Chapel Hill

Career Start Year 2000

Number of shared co-authors 0

Jason F Kreisberg

University of California San Diego

Career Start Year 2000

Number of shared co-authors 3

Tokameh Mahmoudi

Erasmus University Medical Center

Career Start Year 1999

Number of shared co-authors 1

Martin Hirst

University of British Columbia

Career Start Year 1998

Number of shared co-authors 0

Adam Pavlicek

Monoceros Biosystems LLC

Career Start Year 1998

Number of shared co-authors 0

Keiko Akagi

The University of Texas MD Anderson Cancer Center

Career Start Year 1997

Number of shared co-authors 1

Jay Shendure

University of Washington

Career Start Year 1996

Number of shared co-authors 0

Robert A Holt

BC Cancer Research Institute

Career Start Year 1996

Number of shared co-authors 2

Gregory J Cost

Metagenomi Inc., Pre-clinical

Career Start Year 1995

Number of shared co-authors 0

Wei Shao

Inc., Frederick National Laboratory for Cancer Research

Career Start Year 1993

Number of shared co-authors 1

Melanie Ott

Gladstone Institute of Virology

Career Start Year 1993

Number of shared co-authors 5

Lubbertus C F Mulder

Icahn School of Medicine at Mount Sinai

Career Start Year 1993

Number of shared co-authors 4

Ren Sun

University of California los angeles

Career Start Year 1992

Number of shared co-authors 3

Matthew D Weitzman

The Children's Hospital of Philadelphia

Career Start Year 1992

Number of shared co-authors 10

Pavel Sova

Altius Institute for Biomedical Sciences

Career Start Year 1990

Number of shared co-authors 0

Frank Buchholz

University Hospital Carl Gustav Carus, Technische Universitat (TU) Dresden

Career Start Year 1989

Number of shared co-authors 2

Andreas Gnirke

The Center for Genome Architecture, Baylor College of Medicine

Career Start Year 1986

Number of shared co-authors 3

Ivan Sadowski

University of British Columbia

Career Start Year 1984

Number of shared co-authors 1

David E Symer

The University of Texas MD Anderson Cancer Center

Career Start Year 1984

Number of shared co-authors 1

Luigi Naldini

Vita-Salute San Raffaele University

Career Start Year 1980

Number of shared co-authors 4

row(s) 1 - 30 of 30

Frederic D Bushman

Perelman School of Medicine, University of Pennsylvania

Co-authored papers 44

Shoshannah L Roth

Cornell University

Co-authored papers 6

Aubrey Bailey

Perelman School of Medicine, University of Pennsylvania

Co-authored papers 4

John A T Young

Roche Pharma

Co-authored papers 3

Sumit K Chanda

The Scripps Research Institute

Co-authored papers 3

Renate K??nig

Paul-Ehrlich-Institut

Co-authored papers 2

Pablo Tebas

Perelman School of Medicine, University of Pennsylvania

Co-authored papers 2

Kyle Bittinger

Children's Hospital of Philadelphia

Co-authored papers 2

Peter W Atkinson

University of California riverside

Co-authored papers 2

Nevan J Krogan (CM4AI)

University of California San Francisco

Co-authored papers 2

Gaetano T Montelione

Rensselaer Polytechnic Institute

Co-authored papers 2

Sourav Bandyopadhyay

University of California San Francisco

Co-authored papers 2

Alan D Frankel

University of California san francisco

Co-authored papers 1

Michael Zinda

Repare Therapeutics Inc.

Co-authored papers 1

Atif Shahab

Co-authored papers 1

Jorge S Reis-Filho

Memorial Sloan-Kettering Cancer Center

Co-authored papers 1

Christian Hoffmann

Food Research Center (FoRC)

Co-authored papers 1

Kimberly Gilmour

NIHR Great Ormond Street Hospital BRC

Co-authored papers 1

Sara Cherry

University of Pennsylvania

Co-authored papers 1

Carl H June

University of Pennsylvania Department of Pathology & Laboratory Medicine

Co-authored papers 1

Kenneth W Kinzler

Co-authored papers 1

Pier Selenica

Memorial Sloan Kettering Cancer Center

Co-authored papers 1

Jonas Demeulemeester

VIB-KU Leuven Center for Cancer Biology

Co-authored papers 1

Timo Otonkoski

Co-authored papers 1

Christina S Leslie

Co-authored papers 1

Nickolas Papadopoulos

Co-authored papers 1

Christopher D Still

Co-authored papers 1

Li Zhong

Co-authored papers 1

Iv??n D'Orso

University of Texas Southwestern Medical Center

Co-authored papers 1

Stephen P Goff

Columbia University

Co-authored papers 1

1 - 30

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