Author details

Full Name

Alan D Frankel

Affiliation

University of California san francisco

ORCID

Career Start Year

1980

Papers

116

H Index

Expertise

CM4AI Collaborator

Trey Ideker (CM4AI)

PMID	Paper Title	Journal Title	Published Year
35511220	Functional and structural segregation of overlapping helices in HIV-1.	Elife	2022
32353859	A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.	Nature	2020
32084337	A Quantitative Genetic Interaction Map of HIV Infection.	Mol Cell	2020
33248025	Phosphoregulation of Phase Separation by the SARS-CoV-2Â N Protein Suggests a Biophysical Basis for its Dual Functions.	Mol Cell	2020
30914719	Highly Mutable Linker Regions Regulate HIV-1 Rev Function and Stability.	Sci Rep	2019
30289719	Discovery of a Branched Peptide That Recognizes the Rev Response Element (RRE) RNA and Blocks HIV-1 Replication.	J Med Chem	2018
29845934	The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation.	Elife	2018
28961413	Making Sense of Multifunctional Proteins: Human Immunodeficiency Virus Type 1 Accessory and Regulatory Proteins and Connections to Transcription.	Annu Rev Virol	2017
28345603	PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription.	Sci Rep	2017
28416550	Identification and Optimization of Thienopyridine Carboxamides as Inhibitors of HIV Regulatory Complexes.	Antimicrob Agents Chemother	2017
26929078	A structurally plastic ribonucleoprotein complex mediates post-transcriptional gene regulation in HIV-1.	Wiley Interdiscip Rev RNA	2016
27984726	Functional Segregation of Overlapping Genes in HIV.	Cell	2016
27685368	Oligomeric viral proteins: small in size, large in presence.	Crit Rev Biochem Mol Biol	2016
26422686	Thermodynamics of Rev-RNA interactions in HIV-1 Rev-RRE assembly.	Biochemistry	2015
26322864	Selective Targeting of Cells via Bispecific Molecules That Exploit Coexpression of Two Intracellular Proteins.	ACS Chem Biol	2015
25486594	RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex.	Elife	2014
25486595	The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA.	Elife	2014
22414755	Transcription control by long non-coding RNAs.	Transcription	2012
23007159	Transition step during assembly of HIV Tat:P-TEFb transcription complexes and transfer to TAR RNA.	Mol Cell Biol	2012
23133567	A cell-based method for screening RNA-protein interactions: identification of constitutive transport element-interacting proteins.	PLoS One	2012
22258145	The HIV-1 Rev response element: an RNA scaffold that directs the cooperative assembly of a homo-oligomeric ribonucleoprotein complex.	RNA Biol	2012
20708689	Purification and characterization of HIV-human protein complexes.	Methods	2011
22190034	Global landscape of HIV-human protein complexes.	Nature	2011
21777475	GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data.	BMC Bioinformatics	2011
21071404	An SF1 affinity model to identify branch point sequences in human introns.	Nucleic Acids Res	2011
20616058	HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes.	Proc Natl Acad Sci U S A	2010
21709748	HIV-1 Tat: Its Dependence on Host Factors is Crystal Clear.	Viruses	2010
21081095	Comparative analysis of RNA/protein dynamics for the arginine-rich-binding motif and zinc-finger-binding motif proteins encoded by HIV-1.	Biophys J	2010
20953181	Structural basis for cooperative RNA binding and export complex assembly by HIV Rev.	Nat Struct Mol Biol	2010
20562857	RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation.	Nat Struct Mol Biol	2010
19223581	Tat acetylation modulates assembly of a viral-host RNA-protein transcription complex.	Proc Natl Acad Sci U S A	2009
19478882	Host cell factors in HIV replication: meta-analysis of genome-wide studies.	PLoS Pathog	2009
18282001	ISFOLD: structure prediction of base pairs in non-helical RNA motifs from isostericity signatures in their sequence alignments.	J Biomol Struct Dyn	2008
18922466	A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA.	Mol Cell	2008
18667497	Targeting tat inhibitors in the assembly of human immunodeficiency virus type 1 transcription complexes.	J Virol	2008
16536504	An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction.	J Am Chem Soc	2006
16055152	A simple motif for protein recognition in DNA secondary structures.	J Mol Biol	2005
16407998	Viral RNA gymnastics.	Nat Chem Biol	2005
15857951	A single intermolecular contact mediates intramolecular stabilization of both RNA and protein.	Proc Natl Acad Sci U S A	2005
15850388	Localized influence of 2'-hydroxyl groups and helix geometry on protein recognition in the RNA major groove.	Biochemistry	2005
14719918	Ab initio interaction energies of hydrogen-bonded amino acid side chain[bond]nucleic acid base interactions.	J Am Chem Soc	2004
14972556	Evidence for conformational flexibility in the Tat-TAR recognition motif of cyclin T1.	Virology	2004
14722301	Selection of TAR RNA-binding chameleon peptides by using a retroviral replication system.	J Virol	2004
12525632	Replication of human immunodeficiency viruses engineered with heterologous Tat-transactivation response element interactions.	J Virol	2003
12925994	Sequence and structure space of RNA-binding peptides.	Biopolymers	2003
12654263	Recognition of nucleic acid bases and base-pairs by hydrogen bonding to amino acid side-chains.	J Mol Biol	2003
12654262	Structural diversity and isomorphism of hydrogen-bonded base interactions in nucleic acids.	J Mol Biol	2003
12554868	Selection of RRE RNA binding peptides using a kanamycin antitermination assay.	RNA	2003
11438677	Recognition of RNA branch point sequences by the KH domain of splicing factor 1 (mammalian branch point binding protein) in a splicing factor complex.	Mol Cell Biol	2001
11371457	Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex.	Biophys J	2001

1 - 50 of 116

Ivan A Belashov

University of Pittsburgh

Career Start Year 2012

Number of shared co-authors 1

Haran Sivakumaran

QIMR Berghofer Medical Research Institute

Career Start Year 2005

Number of shared co-authors 0

Nadine Czudnochowski

University of California san francisco

Career Start Year 2005

Number of shared co-authors 6

Rhiju Das

Stanford University School of Medicine

Career Start Year 2001

Number of shared co-authors 5

Cyril Dominguez

University of Leicester

Career Start Year 2000

Number of shared co-authors 4

May Khanna

College of Dentistry, New York University

Career Start Year 1999

Number of shared co-authors 1

Stephen M Fuchs

Tufts University

Career Start Year 1998

Number of shared co-authors 2

Andres Ramos

Institute of Structural and Molecular Biology (ISMB), University College London

Career Start Year 1997

Number of shared co-authors 4

Yun Bai

Carnegie Institution for Science

Career Start Year 1996

Number of shared co-authors 3

Takashi Nagata

Institute of Advanced Energy, Kyoto University

Career Start Year 1996

Number of shared co-authors 1

Maria R Conte

King's College London

Career Start Year 1993

Number of shared co-authors 4

Michael Sattler

Technical University of Munich, Institute of Structural Biology

Career Start Year 1991

Number of shared co-authors 4

Milton H Werner

Inhibikase Therapeutics Inc.

Career Start Year 1991

Number of shared co-authors 1

Tariq M Rana

Institute for Genomic Medicine, University of California San Diego

Career Start Year 1990

Number of shared co-authors 3

Anna Marie Pyle

Yale University, USA Howard Hughes Medical Institute

Career Start Year 1989

Number of shared co-authors 0

Ralph E Davis

Stanford University School of Medicine

Career Start Year 1988

Number of shared co-authors 2

Jennifer A Doudna

Innovative Genomics Institute, University of California berkeley

Career Start Year 1987

Number of shared co-authors 36

Arun Malhotra

University of Miami Miller School of Medicine

Career Start Year 1986

Number of shared co-authors 1

Ursula Schulze-Gahmen

Gladstone Institute of Virology, Gladstone Institutes San Francisco CA USA .

Career Start Year 1985

Number of shared co-authors 62

Opher Gileadi

Structural Genomics Consortium Karolinska Institute Stockholm Sweden.

Career Start Year 1984

Number of shared co-authors 1

Aled M Edwards

University of Toronto

Career Start Year 1984

Number of shared co-authors 6

Stephen K Burley

The State University of New Jersey

Career Start Year 1982

Number of shared co-authors 6

Peter Bayer

University of Duisburg-Essen

Career Start Year 1981

Number of shared co-authors 1

Michael Brenowitz

Albert Einstein College of Medicine

Career Start Year 1979

Number of shared co-authors 1

Shigeyuki Yokoyama

Shinshu University School of Medicine

Career Start Year 1979

Number of shared co-authors 10

Boris Matija Peterlin

University of California at San Francisco

Career Start Year 1978

Number of shared co-authors 16

Dino Moras

Laboratory IGBMC (Institute of Genetics and of Molecular and Cellular Biology)

Career Start Year 1973

Number of shared co-authors 0

Alain Laederach

University of North Carolina at Chapel Hill

Career Start Year 1972

Number of shared co-authors 0

Jack F Greenblatt

College Street, University of Toronto

Career Start Year 1969

Number of shared co-authors 10

Dinshaw J Patel

Memorial Sloan-Kettering Cancer Center

Career Start Year 1969

Number of shared co-authors 2

row(s) 1 - 30 of 30

Iv??n D'Orso

University of Texas Southwestern Medical Center

Co-authored papers 11

Bhargavi Jayaraman

University of California san francisco

Co-authored papers 9

Jason D Fernandes

University of California san francisco

Co-authored papers 9

Nevan J Krogan (CM4AI)

University of California San Francisco

Co-authored papers 8

Gwendolyn M Jang

Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes

Co-authored papers 7

Tyler B Faust

Dana-Farber Cancer Institute

Co-authored papers 6

Shumin Yang

Affiliated Cancer Hospital of Zhengzhou University

Co-authored papers 4

David C Crosby

University of California san francisco

Co-authored papers 4

Stefanie J??ger

Institute of Molecular Biosciences, Goethe University Frankfurt

Co-authored papers 3

Sumit K Chanda

The Scripps Research Institute

Co-authored papers 3

Gerard Cagney

Conway Institute of Biomedical and Biomolecular Sciences, University College Dublin

Co-authored papers 3

Charles S Craik

Department of Pharmaceutical Chemistry, University of California san francisco

Co-authored papers 3

John D Gross

Department of Pharmaceutical Chemistry, University of California san francisco

Co-authored papers 3

John A T Young

Roche Pharma

Co-authored papers 3

Amit Weiss

University of California san francisco

Co-authored papers 2

Joshua Kane

University of California, USA Quantitative Biosciences Institute (QBI) san francisco

Co-authored papers 2

Yifan Cheng

Quantitative Bioscience Institute, University of California san francisco

Co-authored papers 2

Ryan D Hernandez

University of California san francisco

Co-authored papers 2

Natali Gulbahce

Complete Genomics Inc.

Co-authored papers 2

Marie E Fahey

University of California San Francisco

Co-authored papers 2

Yang Li

University of California san francisco

Co-authored papers 2

Jeffrey R Johnson

Gladstone Institutes

Co-authored papers 2

Donald C Rio

University of California berkeley

Co-authored papers 2

David E Gordon

Emory University

Co-authored papers 2

Cathal Mahon

Denali Therapeutics Inc.

Co-authored papers 2

Jiewei Xu

Quantitative Biosciences Institute (QBI), University of California san francisco

Co-authored papers 2

Maliheh Safari

University of California san francisco

Co-authored papers 2

Andrej Sali (CM4AI)

University of California San Francisco

Co-authored papers 2

Alexander W Pastuszak

University of Utah School of Medicine

Co-authored papers 2

Melanie J Bennett

Quantitative Biosciences Institute (QBI), University of California San Francisco

Co-authored papers 2

1 - 30

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