Author details

Full Name

Dennis Shasha

Affiliation

Courant Institute of Mathematical Sciences, New York University

ORCID

Career Start Year

1994

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36964499	EnsInfer: a simple ensemble approach to network inference outperforms any single method.	BMC Bioinformatics	2023
31380747	SafePredict: A Meta-Algorithm for Machine Learning That Uses Refusals to Guarantee Correctness.	IEEE Trans Pattern Anal Mach Intell	2021
34941412	Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization.	Science	2021
34215187	Pheniqs 2.0: accurate, high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing.	BMC Bioinformatics	2021
32321967	OutPredict: multiple datasets can improve prediction of expression and inference of causality.	Sci Rep	2020
32716914	Inexpensive, non-invasive biomarkers predict Alzheimer transition using machine learning analysis of the Alzheimer's Disease Neuroimaging (ADNI) database.	PLoS One	2020
32811842	Author Correction: OutPredict: multiple datasets can improve prediction of expression and inference of causality.	Sci Rep	2020
30790228	Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics.	Interdiscip Sci	2019
31757212	TACITuS: transcriptomic data collector, integrator, and selector on big data platform.	BMC Bioinformatics	2019
30952851	Network Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions.	Nat Commun	2019
29769331	Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants.	Proc Natl Acad Sci U S A	2018
30200901	SuperNoder: a tool to discover over-represented modular structures in networks.	BMC Bioinformatics	2018
30407584	An adaptive geometric search algorithm for macromolecular scaffold selection.	Protein Eng Des Sel	2018
27604469	An expanded evaluation of protein function prediction methods shows an improvement in accuracy.	Genome Biol	2016
24627222	miR-Synth: a computational resource for the design of multi-site multi-target synthetic miRNAs.	Nucleic Acids Res	2014
25566532	Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools.	Front Bioeng Biotechnol	2014
24922051	Negative example selection for protein function prediction: the NoGO database.	PLoS Comput Biol	2014
23511543	Parametric Bayesian priors and better choice of negative examples improve protein function prediction.	Bioinformatics	2013
24167551	GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures.	PLoS One	2013
23815292	A subgraph isomorphism algorithm and its application to biochemical data.	BMC Bioinformatics	2013
23805876	Gene regulatory networks in plants: learning causality from time and perturbation.	Genome Biol	2013
23044546	miR-EdiTar: a database of predicted A-to-I edited miRNA target sites.	Bioinformatics	2012
21912654	Rational design of temperature-sensitive alleles using computational structure prediction.	PLoS One	2011
22025711	Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand.	Proc Natl Acad Sci U S A	2011
21824995	The Proteome Folding Project: proteome-scale prediction of structure and function.	Genome Res	2011
20007449	VirtualPlant: a software platform to support systems biology research.	Plant Physiol	2010
21087504	Predicting genome-wide redundancy using machine learning.	BMC Evol Biol	2010
21182762	Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate.	Genome Biol	2010
20170516	SING: subgraph search in non-homogeneous graphs.	BMC Bioinformatics	2010
19300494	A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis.	PLoS Comput Biol	2009
20157481	miRÃ²: a miRNA knowledge base.	Database (Oxford)	2009
18387196	An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis.	BMC Syst Biol	2008
18460171	GraphFind: enhancing graph searching by low support data mining techniques.	BMC Bioinformatics	2008
17217541	Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis.	Genome Biol	2007
19325851	Fast structural search in phylogenetic databases.	Evol Bioinform Online	2007
17646351	Homology search for genes.	Bioinformatics	2007
17277332	NetMatch: a Cytoscape plugin for searching biological networks.	Bioinformatics	2007
17470441	Insights into the genomic nitrate response using genetics and the Sungear Software System.	J Exp Bot	2007
17018536	Sungear: interactive visualization and functional analysis of genomic datasets.	Bioinformatics	2007
15699630	In vitro and in silico cloning of Xenopus laevis SOD2 cDNA and its phylogenetic analysis.	DNA Cell Biol	2005
16240772	MetricMap: an embedding technique for processing distance-based queries in metric spaces.	IEEE Trans Syst Man Cybern B Cybern	2005
15955912	Systems biology for the virtual plant.	Plant Physiol	2005
17051692	Adaptive combinatorial design to explore large experimental spaces: approach and validation.	Syst Biol (Stevenage)	2004
12546786	Trait-to-gene: a computational method for predicting the function of uncharacterized genes.	Curr Biol	2003
16452808	AntiClustal: Multiple Sequence Alignment by antipole clustering and linear approximate 1-median computation.	Proc IEEE Comput Soc Bioinform Conf	2003
14671301	A gene expression map of the Arabidopsis root.	Science	2003
12805577	Light- and carbon-signaling pathways. Modeling circuits of interactions.	Plant Physiol	2003
12805571	Plant systems biology: lessons from a fruitful collaboration.	Plant Physiol	2003
11544201	cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships.	Genome Res	2001
11743103	Using combinatorial design to study regulation by multiple input signals. A tool for parsimony in the post-genomics era.	Plant Physiol	2001

1 - 50 of 53

Anna Ritz

Reed College

Career Start Year 2007

Number of shared co-authors 0

Anthony Gitter

University of Wisconsin

Career Start Year 2007

Number of shared co-authors 1

Gergely Csaba

Ludwig-Maximilians-Universitat Munchen

Career Start Year 2007

Number of shared co-authors 0

Jan Baumbach

University of Hamburg

Career Start Year 2006

Number of shared co-authors 2

Chad L Myers

University of Minnesota - Twin Cities

Career Start Year 2004

Number of shared co-authors 2

Tanusya M Murali

Yong Loo Lin School of Medicine, National University of Singapore

Career Start Year 2003

Number of shared co-authors 2

Quaid Morris

Sloan Kettering Institute

Career Start Year 2003

Number of shared co-authors 3

Olga G Troyanskaya

Lewis-Sigler Institute for Integrative Genomics, Princeton University

Career Start Year 2001

Number of shared co-authors 4

Marcio Luis Acencio

Norwegian University of Science and Technology

Career Start Year 2000

Number of shared co-authors 3

Vladimir B Bajic

King Abdullah University of Science and Technology (KAUST)

Career Start Year 2000

Number of shared co-authors 5

Roded Sharan

Tel Aviv University

Career Start Year 2000

Number of shared co-authors 1

Thomas Girke

Institute for Integrative Genome Biology, University of California Riverside

Career Start Year 1998

Number of shared co-authors 0

Lars Juhl Jensen

Novo Nordisk Foundation Center for Protein Research, University of Copenhagen

Career Start Year 1998

Number of shared co-authors 12

Benno Schwikowski

Center for Bioinformatics, Institut Pasteur CNRS

Career Start Year 1997

Number of shared co-authors 3

Panayiotis V Benos

University of Florida

Career Start Year 1996

Number of shared co-authors 2

Trey Ideker (CM4AI)

University of California San Diego

Career Start Year 1996

Number of shared co-authors 4

Dirk Walther

Max Planck Institute of Molecular Plant Physiology

Career Start Year 1995

Number of shared co-authors 0

Ralf Zimmer

Ludwig-Maximilians-Universitat Munchen

Career Start Year 1995

Number of shared co-authors 0

Ron Shamir

Tel Aviv University

Career Start Year 1995

Number of shared co-authors 1

Christopher T Workman

Technical University of Denmark

Career Start Year 1995

Number of shared co-authors 3

Bonnie Berger

Massachusetts Institute of Technology

Career Start Year 1994

Number of shared co-authors 5

Ioannis Xenarios

University of Lausanne

Career Start Year 1994

Number of shared co-authors 23

Joel S Bader

Johns Hopkins University

Career Start Year 1993

Number of shared co-authors 1

Edward M Marcotte

University of Texas

Career Start Year 1993

Number of shared co-authors 5

Simon Kasif

Boston University

Career Start Year 1993

Number of shared co-authors 4

Tommi S Jaakkola

Massachusetts Institute of Technology

Career Start Year 1992

Number of shared co-authors 0

Erik L L Sonnhammer

Stockholm University

Career Start Year 1992

Number of shared co-authors 9

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 11

Lincoln Stein

Ontario Institute for Cancer Research, University Avenue

Career Start Year 1986

Number of shared co-authors 8

Martin Kuiper

Norwegian University of Science and Technology

Career Start Year 1983

Number of shared co-authors 5

row(s) 1 - 30 of 30

Richard Bonneau

Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation

Co-authored papers 8

Noah Youngs

Center for Genomics and Systems Biology, New York University Abu Dhabi

Co-authored papers 4

Christopher S Poultney

Co-authored papers 3

Duncan Penfold-Brown

New York University

Co-authored papers 3

Kristin C Gunsalus

Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD)

Co-authored papers 2

Gung-Wei Chirn

Co-authored papers 2

Christopher Funk

University of Colorado School of Medicine

Co-authored papers 1

Michael Riffle

University of Washington

Co-authored papers 1

Prajwal Bhat

Royal Holloway University of London

Co-authored papers 1

Marco Mesiti

Universita degli Studi di Milano

Co-authored papers 1

Sanja Glisic

Vinca Institute of Nuclear Sciences, The University of Belgrade

Co-authored papers 1

Angela Del Pozo

Instituto de Genetica Medica y Molecular (INGEMM), Hospital Universitario La Paz

Co-authored papers 1

Maria J Martin

European Bioinformatics Institute (EMBL-EBI)

Co-authored papers 1

Christophe Dessimoz

University of Lausanne

Co-authored papers 1

Kai Hakala

University of Turku

Co-authored papers 1

Domenico Cozzetto

Imperial College London

Co-authored papers 1

Amos Stern

Life Science Institute

Co-authored papers 1

Shanshan Zhang

Temple University

Co-authored papers 1

Marina Marcet-Houben

Institute for Research in Biomedicine (IRB)

Co-authored papers 1

Hans J Vogel

University of Calgary

Co-authored papers 1

Pooya Zakeri

Aarhus University

Co-authored papers 1

Alfredo Benso

Italy Consorzio Interuniversitario Nazionale per l'Informatica

Co-authored papers 1

Federico Minneci

University College London

Co-authored papers 1

Elena Cibri??n-Uhalte

European Bioinformatics Institute

Co-authored papers 1

Malvika Sharan

The Alan Turing Institute

Co-authored papers 1

Burkhard Rost

Technical University of Munich (TUM)

Co-authored papers 1

Dan Ofer

Tel Aviv University

Co-authored papers 1

Veljko Veljkovic

Institute of Nuclear Sciences VINCA

Co-authored papers 1

Yves Moreau

KU Leuven - University of Leuven

Co-authored papers 1

Paul Pavlidis

University of British Columbia

Co-authored papers 1

1 - 30

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