Author details

Full Name

Ying Xu

Affiliation

Oak Ridge National Laboratory

ORCID

Career Start Year

1994

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
16267082	libSRES: a C library for stochastic ranking evolution strategy for parameter estimation.	Bioinformatics	2006
17085850	Efficient parameterized algorithms for biopolymer structure-sequence alignment.	IEEE/ACM Trans Comput Biol Bioinform	2006
16927360	Structure determination of a new protein from backbone-centered NMR data and NMR-assisted structure prediction.	Proteins	2006
15767773	More reliable protein NMR peak assignment via improved 2-interval scheduling.	J Comput Biol	2005
15852515	The probability distribution for a random match between an experimental-theoretical spectral pair in tandem mass spectrometry.	J Bioinform Comput Biol	2005
15048978	A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST.	Proteomics	2004
18265344	Protein databases on the internet.	Curr Protoc Mol Biol	2004
18429255	Protein databases on the internet.	Curr Protoc Protein Sci	2004
15088384	Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples.	Biotechniques	2004
12560490	Improving the performance of DomainParser for structural domain partition using neural network.	Nucleic Acids Res	2003
15260242	Characterization of protein structure and function at genome scale with a computational prediction pipeline.	Genet Eng (N Y)	2003
15290777	Computational assignment of protein backbone NMR peaks by efficient bounding and filtering.	J Bioinform Comput Biol	2003
14506847	A computational study of Shewanella oneidensis MR-1: structural prediction and functional inference of hypothetical proteins.	OMICS	2003
14500821	EXCAVATOR: a computer program for efficiently mining gene expression data.	Nucleic Acids Res	2003
14560049	PROSPECT II: protein structure prediction program for genome-scale applications.	Protein Eng	2003
14555633	A computational pipeline for protein structure prediction and analysis at genome scale.	Bioinformatics	2003
12603039	Identification of regulatory binding sites using minimum spanning trees.	Pac Symp Biocomput	2003
12016051	Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees.	Bioinformatics	2002
15838133	An efficient branch-and-bound algorithm for the assignment of protein backbone NMR peaks.	Proc IEEE Comput Soc Bioinform Conf	2002
12630408	Genomes to Life "Center for Molecular and Cellular Systems": a research program for identification and characterization of protein complexes.	OMICS	2002
12424113	PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.	Bioinformatics	2002
11455604	Model for the three-dimensional structure of vitronectin: predictions for the multi-domain protein from threading and docking.	Proteins	2001
18429154	Protein tertiary structure prediction.	Curr Protoc Protein Sci	2001
11835491	Application of PROSPECT in CASP4: characterizing protein structures with new folds.	Proteins	2001
11791221	Minimum spanning trees for gene expression data clustering.	Genome Inform	2001
11108473	A computational method for NMR-constrained protein threading.	J Comput Biol	2000
12369918	Computational tools for protein modeling.	Curr Protein Pept Sci	2000
10861926	Protein threading using PROSPECT: design and evaluation.	Proteins	2000
10869019	Sequence-structure specificity of a knowledge based energy function at the secondary structure level.	Bioinformatics	2000
10585495	Protein threading by PROSPECT: a prediction experiment in CASP3.	Protein Eng	1999
9773353	An efficient computational method for globally optimal threading.	J Comput Biol	1998
9697184	An editing environment for DNA sequence analysis and annotation (extended abstract).	Pac Symp Biocomput	1998
9322060	Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags.	Proc Int Conf Intell Syst Mol Biol	1997
9278063	Automated gene identification in large-scale genomic sequences.	J Comput Biol	1997
8891953	An iterative algorithm for correcting sequencing errors in DNA coding regions.	J Comput Biol	1996
9021270	A polynomial-time algorithm for a class of protein threading problems.	Comput Appl Biosci	1996
8877524	Gene prediction by pattern recognition and homology search.	Proc Int Conf Intell Syst Mol Biol	1996
8867844	Detection of RNA polymerase II promoters and polyadenylation sites in human DNA sequence.	Comput Chem	1996
8743689	Discovering and understanding genes in human DNA sequence using GRAIL.	Methods Enzymol	1996
7620982	Correcting sequencing errors in DNA coding regions using a dynamic programming approach.	Comput Appl Biosci	1995
7584416	An improved system for exon recognition and gene modeling in human DNA sequences.	Proc Int Conf Intell Syst Mol Biol	1994
7704660	Constructing gene models from accurately predicted exons: an application of dynamic programming.	Comput Appl Biosci	1994
7765200	Recognizing exons in genomic sequence using GRAIL II.	Genet Eng (N Y)	1994

1 - 43 of 43

Frank Dehne

Carleton University

Career Start Year 2006

Number of shared co-authors 0

George Karypis

University of Minnesota

Career Start Year 2003

Number of shared co-authors 0

Ying Xu

The China-Japan Union Hospital, Jilin University

Career Start Year 2002

Number of shared co-authors 10

Kevin Bryson

University of Glasgow

Career Start Year 1999

Number of shared co-authors 0

Daron M Standley

Osaka university

Career Start Year 1998

Number of shared co-authors 0

Pier Luigi Martelli

Department of Pharmacy and Biotechnology, University of Bologna

Career Start Year 1998

Number of shared co-authors 0

Iddo Friedberg

Iowa State University

Career Start Year 1997

Number of shared co-authors 0

Kentaro Tomii

National Institute of Advanced Industrial Science and Technology (AIST)

Career Start Year 1996

Number of shared co-authors 0

Asa Ben-Hur

Colorado State University

Career Start Year 1996

Number of shared co-authors 0

Lukasz Jaroszewski

University of California Riverside School of Medicine

Career Start Year 1995

Number of shared co-authors 2

Terry Gaasterland

Scripps Institution of Oceanography, University of California San Diego

Career Start Year 1994

Number of shared co-authors 0

Steven E Brenner

University of California berkeley

Career Start Year 1994

Number of shared co-authors 0

Simon Kasif

Boston University

Career Start Year 1993

Number of shared co-authors 0

Burkhard Rost

Technical University of Munich (TUM)

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 0

Jaap Heringa

VU University Amsterdam

Career Start Year 1991

Number of shared co-authors 0

Dietlind L Gerloff

Foundation for Applied Molecular Evolution (FfAME)

Career Start Year 1991

Number of shared co-authors 0

Baldo Oliva

Universitat Pompeu Fabra

Career Start Year 1991

Number of shared co-authors 0

Robert B Russell

Heidelberg University

Career Start Year 1991

Number of shared co-authors 0

Ramanathan Sowdhamini

Indian Institute of Science

Career Start Year 1989

Number of shared co-authors 0

Roland L Dunbrack

Fox Chase Cancer Center

Career Start Year 1989

Number of shared co-authors 0

Jadwiga Bienkowska

Pfizer Global Research and Development La Jolla

Career Start Year 1987

Number of shared co-authors 0

Christopher W V Hogue

National University of Singapore

Career Start Year 1987

Number of shared co-authors 0

Adam Godzik

University of California Riverside

Career Start Year 1987

Number of shared co-authors 3

Alfonso Valencia

Josep Carreras Leukaemia Research Institute (IJC)

Career Start Year 1986

Number of shared co-authors 1

Liisa Holm

Institute of Biotechnology, University of Helsinki

Career Start Year 1986

Number of shared co-authors 0

Chris Sander

Broad Institute of MIT and Harvard

Career Start Year 1979

Number of shared co-authors 1

Michael J E Sternberg

Imperial College London

Career Start Year 1976

Number of shared co-authors 0

Rita Casadio

Department of Pharmacy and Biotechnology, University of Bologna

Career Start Year 1974

Number of shared co-authors 0

Shoba Ranganathan

Macquarie University

Career Start Year 1972

Number of shared co-authors 0

row(s) 1 - 30 of 30

Dong Xu

University of Missouri

Co-authored papers 26

Victor Olman

University of Georgia

Co-authored papers 6

Dongsup Kim

Korea Advanced Institute of Science and Technology

Co-authored papers 4

Manesh Shah

University of Tennessee Knoxville

Co-authored papers 4

Tao Jiang

University of California riverside

Co-authored papers 3

Jizhong Zhou

Institute for Environmental Genomics, University of Oklahoma

Co-authored papers 3

Jun-Tao Guo

University of North Carolina at Charlotte

Co-authored papers 2

Sergei Passovets

Co-authored papers 2

Liyou Wu

Institute for Environmental Genomics, University of Oklahoma

Co-authored papers 2

Kyle Ellrott

Oregon Health & Science University

Co-authored papers 2

Philip F LoCascio

University of Oxford

Co-authored papers 2

Li Wang

Co-authored papers 2

H S Wiley

Co-authored papers 1

Karin D Rodland

Oregon Health and Science University

Co-authored papers 1

Richard D Smith

Pacific Northwest National Laboratory

Co-authored papers 1

Xiuzhen Huang

Cedars-Sinai Medical Center.

Co-authored papers 1

Michael W W Adams

University of Georgia

Co-authored papers 1

S A Matis

Co-authored papers 1

Inna Vokler

Co-authored papers 1

1 - 19

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