Author details

Full Name

Stefano Lonardi

Affiliation

University of California Riverside

ORCID

Career Start Year

1996

Papers

H Index

Expertise

CM4AI Collaborator

Jake Y. Chen (CM4AI)

PMID	Paper Title	Journal Title	Published Year
36778461	A Drug Repurposing Approach Reveals Targetable Epigenetic Pathways in <i>Plasmodium vivax</i> Hypnozoites.	bioRxiv	2024
36778461	A Drug Repurposing Approach Reveals Targetable Epigenetic Pathways in <i>Plasmodium vivax</i> Hypnozoites.	bioRxiv	2024
36946261	A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.).	Plant Genome	2024
36946261	A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.).	Plant Genome	2024
37055610	Babesia duncani multi-omics identifies virulence factors and drug targets.	Nat Microbiol	2023
37797695	Babesia BdFE1 esterase is required for the anti-parasitic activity of the ACE inhibitor fosinopril.	J Biol Chem	2023
37055610	Babesia duncani multi-omics identifies virulence factors and drug targets.	Nat Microbiol	2023
37797695	Babesia BdFE1 esterase is required for the anti-parasitic activity of the ACE inhibitor fosinopril.	J Biol Chem	2023
35177617	Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica.	Nat Commun	2022
36215336	Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly.	PLoS Pathog	2022
35177617	Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica.	Nat Commun	2022
36215336	Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly.	PLoS Pathog	2022
33367499	Prediction of histone post-translational modifications using deep learning.	Bioinformatics	2021
33367499	Prediction of histone post-translational modifications using deep learning.	Bioinformatics	2021
34656081	Reference-agnostic representation and visualization of pan-genomes.	BMC Bioinformatics	2021
34656081	Reference-agnostic representation and visualization of pan-genomes.	BMC Bioinformatics	2021
32998698	DeeplyEssential: a deep neural network for predicting essential genes in microbes.	BMC Bioinformatics	2020
31794680	OMGS: Optical Map-Based Genome Scaffolding.	J Comput Biol	2020
32998764	Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation.	Genome Biol	2020
32998698	DeeplyEssential: a deep neural network for predicting essential genes in microbes.	BMC Bioinformatics	2020
31794680	OMGS: Optical Map-Based Genome Scaffolding.	J Comput Biol	2020
32998764	Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation.	Genome Biol	2020
30295726	Accurate detection of chimeric contigs via Bionano optical maps.	Bioinformatics	2019
31708953	Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.).	Front Plant Sci	2019
30295726	Accurate detection of chimeric contigs via Bionano optical maps.	Bioinformatics	2019
31510653	Selfish: discovery of differential chromatin interactions via a self-similarity measure.	Bioinformatics	2019
31017340	The genome of cowpea (Vigna unguiculata [L.] Walp.).	Plant J	2019
31216436	Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica.	Metab Eng	2019
30953547	Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.	Genome Biol	2019
31708953	Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.).	Front Plant Sci	2019
31216436	Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica.	Metab Eng	2019
31510653	Selfish: discovery of differential chromatin interactions via a self-similarity measure.	Bioinformatics	2019
31017340	The genome of cowpea (Vigna unguiculata [L.] Walp.).	Plant J	2019
30953547	Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.	Genome Biol	2019
29356213	A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.).	Plant J	2018
29949964	Novo&Stitch: accurate reconciliation of genome assemblies via optical maps.	Bioinformatics	2018
29356213	A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.).	Plant J	2018
29949964	Novo&Stitch: accurate reconciliation of genome assemblies via optical maps.	Bioinformatics	2018
27775877	Genome resources for climate-resilient cowpea, an essential crop for food security.	Plant J	2017
28448065	Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.	Sci Data	2017
28447635	A chromosome conformation capture ordered sequence of the barley genome.	Nature	2017
28934964	Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.	Genome Biol	2017
28521789	A comparative evaluation of genome assembly reconciliation tools.	Genome Biol	2017
27775877	Genome resources for climate-resilient cowpea, an essential crop for food security.	Plant J	2017
28448065	Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.	Sci Data	2017
28447635	A chromosome conformation capture ordered sequence of the barley genome.	Nature	2017
28934964	Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.	Genome Biol	2017
28521789	A comparative evaluation of genome assembly reconciliation tools.	Genome Biol	2017
27540266	Higher classification sensitivity of short metagenomic reads with CLARK-S.	Bioinformatics	2016
27153660	BRAT-nova: fast and accurate mapping of bisulfite-treated reads.	Bioinformatics	2016

1 - 50 of 156

David Tse

Stanford University

Career Start Year 2013

Number of shared co-authors 0

Jared T Simpson

Ontario Institute for Cancer Research

Career Start Year 2009

Number of shared co-authors 1

Jaebum Kim

Konkuk University

Career Start Year 2007

Number of shared co-authors 0

Geir Kjetil Sandve

University of Oslo

Career Start Year 2006

Number of shared co-authors 0

Gang Fang

Icahn School of Medicine at Mount Sinai

Career Start Year 2005

Number of shared co-authors 1

Carl Kingsford

Carnegie Mellon University

Career Start Year 2005

Number of shared co-authors 1

Benedict Paten

UC Santa Cruz Genomics Institute, University of California

Career Start Year 2005

Number of shared co-authors 3

Daniel R Zerbino

European Bioinformatics Institute

Career Start Year 2005

Number of shared co-authors 2

Michael C Schatz

Johns Hopkins University

Career Start Year 2004

Number of shared co-authors 12

Brad A Chapman

Harvard T.H. Chan School of Public Health

Career Start Year 2003

Number of shared co-authors 2

Scott J Emrich

The Pennsylvania State University College of Medicine

Career Start Year 2002

Number of shared co-authors 3

Adam M Phillippy

National Human Genome Research Institute, National Institutes of Health

Career Start Year 2002

Number of shared co-authors 11

Suleyman Cenk Sahinalp

National Cancer Institute, National Institutes of Health

Career Start Year 2001

Number of shared co-authors 1

Martin C Frith

Artificial Intelligence Research Center, University of Tokyo

Career Start Year 2001

Number of shared co-authors 0

Michael Brudno

University of Toronto

Career Start Year 2000

Number of shared co-authors 4

Jeong-Hyeon Choi

National Marine Biodiversity Institute of Korea

Career Start Year 2000

Number of shared co-authors 1

Haixu Tang

Indiana University

Career Start Year 2000

Number of shared co-authors 3

C Titus Brown

University of California davis

Career Start Year 1999

Number of shared co-authors 0

Ian Korf

University of California davis

Career Start Year 1998

Number of shared co-authors 2

Vineet Bafna

University of California San Diego

Career Start Year 1998

Number of shared co-authors 19

Louxin Zhang

National University of Singapore

Career Start Year 1996

Number of shared co-authors 0

Ron Shamir

Tel Aviv University

Career Start Year 1995

Number of shared co-authors 0

Terry Gaasterland

Scripps Institution of Oceanography, University of California San Diego

Career Start Year 1994

Number of shared co-authors 0

Bonnie Berger

Massachusetts Institute of Technology

Career Start Year 1994

Number of shared co-authors 1

Ewan Birney

European Bioinformatics Institute

Career Start Year 1992

Number of shared co-authors 16

Steven L Salzberg

Center for Computational Biology, Johns Hopkins University

Career Start Year 1992

Number of shared co-authors 21

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 2

Pavel A Pevzner

University of California

Career Start Year 1987

Number of shared co-authors 3

Lincoln Stein

Ontario Institute for Cancer Research, University Avenue

Career Start Year 1986

Number of shared co-authors 5

Richard Durbin

University of Cambridge

Career Start Year 1964

Number of shared co-authors 7

row(s) 1 - 30 of 30

Karine G Le Roch

Co-authored papers 13

Tao Jiang

University of California riverside

Co-authored papers 7

Vladimir Vacic

Stanley Institute for Cognitive Genomics

Co-authored papers 5

Andrew D Farmer

National Center for Genome Resources

Co-authored papers 3

Denisa Duma

Baylor College of Medicine

Co-authored papers 3

Xueqing Maggie Lu

Co-authored papers 2

Christopher E Mason

Feil Family Brain and Mind Research Institute.

Co-authored papers 2

Paul Kersey

European Bioinformatics Institute

Co-authored papers 2

Alex R Hastie

Co-authored papers 2

Jonathan Foox

Co-authored papers 2

Noah Alexander

David Geffen School of Medicine, university of california los angeles

Co-authored papers 2

Shawn Levy

HudsonAlpha Institute for Biotechnology

Co-authored papers 2

Choukri Ben Mamoun

Co-authored papers 2

Shengqiang Shu

US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory

Co-authored papers 2

Jake Y. Chen (CM4AI)

University of Alabama at Birmingham

Co-authored papers 2

Jake Y Chen

Co-authored papers 2

Gail L Rosen

Drexel University

Co-authored papers 2

Zhongwu Lai

Oncology R&D

Co-authored papers 1

Karin A Remington

The J. Craig Venter Institute.

Co-authored papers 1

Clark Mobarry

Co-authored papers 1

Malina A Bakowski

a division of The Scripps Research Institute La Jolla

Co-authored papers 1

Burkhard Morgenstern

Institute of Microbiology and Genetics

Co-authored papers 1

Knut Reinert

Institut fur Informatik, Freie Universitat Berlin

Co-authored papers 1

Rod A Wing

Arizona Genomics Institute, University of Arizona

Co-authored papers 1

Yinsheng Wang

Co-authored papers 1

Heather Witt

Co-authored papers 1

Anna C Pavlick

Co-authored papers 1

Alan Keith Dunker

Center for Computational Biology, Indiana University School of Medicine

Co-authored papers 1

Predrag Radivojac

Indiana University

Co-authored papers 1

J C Venter

The J. Craig Venter Institute

Co-authored papers 1

1 - 30

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