Publications
(If you need preprints, please send an email to
)
Select a year (or in press) to go to the desired section:
- QI. Liu, V. Olman, H. Liu, X. Ye, S. Qiu, Y. Xu.
RNACluster: An Integrated Tool for RNA Secondary Structure Comparison
and Clustering.
Journal of Computational Chemistry, 2008 Jul 15;29(9):1517-26.
RNACluster documentation and download.
- Dongsheng Che, Guojun Li, Shane T. Jensen, Jun S. Liu and Ying Xu
PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic
Genomes.
Lecture Notes in Computer Science, 4983:110-121, 2008.
- M. Jang, Y. Xu, B. Zhu.
Protein Structure-Structure Alignment with Discrete Fréchet Distance.
Journal of Bioinformatics and Computational Biology, 6:51-64, 2008.
- J-T. Guo, K. Ellrott, Y. Xu.
A Historical Perspective of Template-based Protein Structure Prediction.
in Book Protein Structure Prediction, Book Series Methods in
Molecular Biology, 413:3-42, 2008.
- F. Zhou, T. Tran, Y. Xu.
Nezha, a novel active miniature inverted-repeat transposable element in
cyanobacteria.
Biochemical and Biophysical Research Communications, 365:790-794,
2008.
- J-T. Guo, Y. Xu.
Towards Modeling of Amyloid Fibril Structures.
Frontiers in Bioscience, 13:4039-4050, 2008.
- K. Ellrott, J-T. Guo, V. Olman, Y. Xu.
Improvement in Protein Sequence Structure Alignment using Insertion/Deletion
Frequency Array.
Proceedings of CSB2007, 6:335-342, 2007.
Selected to be published as:
IMPROVING THE PERFORMANCE OF PROTEIN THREADING USING INSERTION/DELETION
FREQUENCY ARRAYS.
Journal
of Bioinformatics and Computational Biology 6(3):585-602, 2008.
- HQ. Liu, S. Dalton, Y. Xu.
Transcriptional Profiling of Definitive Endoderm Derived from Human Embryonic
Stem Cells.
Proceedings of CSB2007, 6:79-82, 2007.
- G. Li, J. Lu, V. Olman, Y. Xu.
Prediction of cis-Regulatory Elements: From High-Information Content Analysis
to Motif Identification.
Journal of Bioinformatics and Computational Biology, 5(4):817-838,
2007.
- H. Liu, L. Wong, Y. Xu.
Patient Survival Prediction from Gene Expression Data.
in Knowledge Discovery in Bioinformatics: Techniques, Methods and Applications,
(Chapter 6), Yi Pan and Xiaohua. Hu (eds), John Wiley and Sons, 89-112,
June 2007.
- G. Li, Z. Liu, J-T. Guo, Y. Xu.
An Algorithm for Simultaneous Backbone Threading and Side-Chain Packing.
Algorithmica, 48(4):329-342, 2007.
- Z. Su, V. Olman, Y. Xu.
Computational prediction of Pho regulons in Cyanobacteria.
BMC Genomics, 8:156-157, 2007.
- H. Wu, F. Mao, V. Olman, and Y. Xu.
An Algorithm for Hierarchical Classification of Prokaryotic Genes.
Lecture Notes in Bioinformatics, (4463) 551-563, 2007.
- D. Che, J. Zhao, L. Cai and Y. Xu.
Operon prediction in microbial genomes using decision tree approach.
Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics
and Computational Biology, 135-142, 2007.
- M. Jiang, Y. Xu, B. Zhu.
The Discrete Frechet Distance and Its Application to Protein Structure-Structure
Alignment.
Proceedings of Asia-Pacific Bioinformatics Conference (APBC), 131-141,
2007.
- J-T. Guo, J.W. Jaromczyk, Y. Xu.
Analysis of chameleon sequences and their implications in biological
processes.
Proteins, 67(3):548-58, 2007.
- H. Wu, F. Mao, V. Olman, Y. Xu.
Hierarchical classification of functionally equivalent genes
in prokaryotes.
Nucleic Acids Res., 35(7):2125-40, 2007.
- AB. McLean, KA. D'Amour, KL. Jones, M. Krishnamoorthy, MJ. Kulik, DM.
Reynolds, AM. Sheppard, H. Liu, Y. Xu, EE. Baetge, S. Dalton.
Activin a efficiently specifies definitive endoderm from human
embryonic stem cells only when phosphatidylinositol 3-kinase signaling
is suppressed.
Stem Cells, 25(1):29-38, 2007.
- TT. Tran, P. Dam, Z. Su, FL. Poole 2nd, MW. Adams, GT. Zhou, Y. Xu.
Operon prediction in Pyrococcus furiosus.
Nucleic Acids Res., 35(1):11-20,2007.
- P. Dam, V. Olman, K. Harris, Z. Su, Y. Xu.
Operon prediction using both genome-specific and general genomic
information.
Nucleic Acids Res., 35(1):288-98, 2007.
-
Ellrott, K. Guo, J-T. Olman, V. and Xu, Y.
A Generalized
Threading Model using Integer Programming with Secondary Structure
Element Deletion.
Genome Informatics, 17(2):248-258, 2006.
-
Olman V, Hicks C, Wang P, Xu Y.
Gene expression data analysis in subtypes of
ovarian cancer using covariance analysis.
J Bioinform Comput Biol, 4(5):999-1014, 2006.
-
C. Liu, Y. Song, B Yan, Ying Xu, L. Cai.
Fast De Novo sequencing
and spectral alignment via tree decomposition.
Proceedings of PSB'06, 2655-266, 2006.
-
C. Liu, B. Yan, Y. Song, Ying Xu and L. Cai.
Blind
Post-Translational Modification Identification by Combining Peptide
Sequence Tag Generation and Database Search.
Bioinformatics Special Issue for ISMB'06,, vol 22(14), pp 307 - 313, 2006.
-
X. Qi, S. Li, G. Li and Ying Xu.
Sorting genomes by
translocations and deletions.
Proceedings of CSB2006,, 157-166, 2006.
-
Y Xue, F Zhou, C Fu, Ying Xu and X. Yao,.
SUMOsp: a web server for sumoylation site
prediction.
Nucleic Acids Research,, Vol 34: W254 - W257, 2006.
-
JT. Guo, C. Hall, Ying Xu and R. Wetzel.
Modeling Protein
Aggregate Assembly and Structure.
Computational Methods for Protein Structure Prediction and
Modeling, (a chapter, vols I and II), Y. Xu, D. Xu and J. Liang
(eds), Springer, 279-318, 2006.
-
Z. Chen and Ying Xu.
Structure prediction on helical transmembrane
proteins at two length scales.
Jounral of Bioinformatics and Computational Biology, (by
invitation), 4(2):317-333, 2006.
-
X. Ji and Ying Xu.
A C library for stochastic ranking evolution
strategy for parameter estimation.
Bioinformatics,, 22:124-126, 2006.
-
F. Zhou, Y. Xue, X. Yao and Ying Xu,.
CSS-Palm: Palmitoylation site prediction with a
clustering and scoring strategy.
Bioinformatics,, 22(7):894-896,2006.
-
Z. Chen and Y. Xu.
Energetics and Stability of Transmembrane Helix
Packing: A Replica-exchange Simulation with a Knowledge-based
Helix-lipid Potential.
Proteins: structure, function and bioinformatics,,
62(2):539-552, 2006.
-
J. Guo and Ying Xu.
Computational approaches to amyloid beta fibril
core structures.
Methods in Enzymology,, 412:300-314, 2006.
-
Z. Su, P. Dam, F. Mao, V. Olman, I. Paulsen, B. Palenik and Ying
Xu.
Computational inference and experimental validation
of nitrogen assimilation regulatory networks in cyanobacterium
Synechococcus sp. WH8102.
Nucleic Acids Research, 34(3):1050-1065, 2006.
-
D. Che, G Li, F. Mao, H Wu, and Ying Xu,.
Detecting uber-operons in prokaryotic
genomes.
Nucleic Acids Research,, 34(8):2418-2427,2006.
-
F. Mao, Z. Su, V. Olman, P. Dam, Z. Liu, Ying Xu.
Mapping of orthologous genes in the context of
biological pathways: an application of integer programming.
PNAS,, 103(1):129-134, 2006.
-
B. Yan, T. Zhou, P. Wang, Z. Liu, V. Emanuele II, V. Olman,
Y. Xu.
A point process model for rapid identification of
post-translational modifications in proteins.
Proceedings of the PSB'06,, 327-338, 2006.
-
H. Wu, F. Mao, Z. Su, V Olman, Ying Xu.
Prediction of functional
modules based on gene distributions in microbial genomes.
Proceedings of the 16th International Conference on Genome Informatics, 16:247-259, 2005.
-
P. Wang, B. Yan, J. Guo, C. Hicks, Ying Xu.
Structural genomics analysis of alternative
splicing and its application in modeling structures of alternatively
spliced variants.
PNAS, 102(52):18920-18925, 2005 .
-
Y Song, C Liu, X Huang, R Malmberg, Ying Xu, and L. Cai.
Efficient Parameterized Algorithm for Biopolymer Structural-Sequence
Alignment.
Proceedings of WABI, LNBI 3692:376-388,2005.
-
C. Chen, G Li, Z. Li, Ying Xu.
On connected [g, f+1]-factors in
graphs.
Combinatorica,, 25(4):393-405, 2005.
-
Z. Chen and Ying Xu.
Multi-Scale Hierarchical Structure
Prediction of Helical Transmembrane Proteins.
Proceedings of the IEEE Computational Systems Bioinformatics
Conference, pp203-208, 2005.
-
H. Wu, F. Mao, V. Olman, Ying Xu.
Accurate Prediction of
Orthologous Gene Groups in Microbes.
Proceedings of the IEEE Computational Systems Bioinformatics
Conference, pp73-79, 2005.
-
J. Huang, Ying Xu, J.P. Gogarten.
The Presence of a Haloarchaeal Type Tyrosyl-tRNA
Synthetase Marks the Opisthokonts as Monophyletic.
Molecular Biology and Evolution, 22(11):2142-2146, 2005.
-
Z. Su, V. Olman, F. Mao and Ying Xu.
Comparative genomics analysis of NtcA regulons in
cyanobacteria: regulation of nitrogen assimilation and its coupling
to photosynthesis.
Nucleic Acids Research, 33(16):5156-5171, 2005.
-
B. Yan, Y. Qu, F. Mao, V Olman, Ying Xu.
PRIME: A Mass Spectrum
Data Mining Tool for De Novo Sequencing and PTMs Identification.
Journal of Computer Science and Technology, (by invitation) 20(4):483-490, 2005.
-
T. Fridman, J. Razumovskaya, N. Verberkmoes, Ying Xu.
The probability distribution for a random match
between an experimental - theoretical spectral pair in tandem mass
spectrometry.
Journal of Bioinformatics and Computational Biology, vol 3(2), 455-476, 2005.
-
H. Wu, Z. Su, F. Mao, V Olamn, Ying Xu.
Prediction of functional modules through comparative
genome analysis and application of gene ontology.
Nucleic Acids Research, 33:2822-2837, 2005.
-
J. Wen, Z. Chen, R. Rizzi, D. Xu, G. Lin, Ying Xu, T. Jiang.
An
improved approximation algorithm for 2-interval scheduling and NMR
spectral peak assignment.
Journal of Computational Biology, 12 (2): 129-146, 2005.
-
B. Yan, C. Pan, V. Olman, R. Hettich, Ying Xu.
A graph-theoretic approach to separation of b- and
y- ions in tandem mass spectra.
Bioinformatics, Vol 21: 563-574, 2005.
-
JS Sharp, J. Guo, T. Ychiki, Ying Xu, C. Dealwis, R. Hettich.
Photochemical surface mapping of C14S-Sml1p for
constrained computational modeling of protein structure.
Anal Biochem, 2005 May 15;340(2):201-12.
-
Z. Liu, F. Mao, JT Guo, B Yan, Ying Xu.
Quantitative Validation of Protein-DNA Interaction
using an Optimized Knowlege-based Potential.
Nucleic Acids Research, Vol 33:2, pp546-558, 2005.
-
J. Xu, M Li, and Ying Xu.
Protein threading by linear
programming: theoretical analysis and computational results.
Journal of Combinatorial Optimization, 8:403-418, 2004.
-
X. Chen, Z. Su, Ying Xu and T Jiang.
Computational Prediction of Operons in Synechococcus
sp WH8102.
Proceedings of 15th International Conference on Genome
Informatics, pp 211 - 222, 2004 (Best paper award of
GIW04).2004.
-
P. Dam, Z. Su, V Olman, Ying Xu.
In silico construction of the
carbon fixation pathway in Synechococcus sp. WH8102.
Journal of Biological Systems, vol. 12, pp.97-125,2004.
-
J. Xu, M Li, and Ying Xu.
Protein threading by linear
programming: theoretical analysis and computational results.
Journal of Combinatorial Optimization, 8:403-418, 2004.
-
X. Chen, Z. Su, P. Dam, B. Palenik, Ying Xu, and T. Jiang.
Operon prediction by comparative genomics: an
application to the Synechococcus WH8102 genome.
Nucleic Acids Research, Vol32 (7), 2147 - 2157,2004.
-
V. Olman, H. Peng, Z. Su, Ying Xu.
Mapping of microbial pathways
through constrained mapping of orthologous genes.
Proceedings of The IEEE Computational Systems Bionformatics Conference (CSB'04), pp 363 - 370, 2004.
-
B. Yan, C. Pan, R. Heittich, V Olman, Ying Xu.
Separation of ion
types in tandem mass spectrometry data interpretation -a
graph-theoretic approach.
Proceedings of The IEEE Computational Systems Bionformatics Conference (CSB'04), pp. 236 - 244, 2004.
-
Guo, J-T.; R. Wetzel and Ying Xu.
Molecular modeling of the core of Abeta amyloid
fibrils.
PROTEINS, 7(2):357-364, 2004.
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Y. Zou, Z. Yang, IG Minko, H. Ma, SM Shell, Y, QU, Ying Xu,
NE. Geacintov and RS Lloyd.
DNA damage recognition of nucleotide
excission repair protein UvrB.
Biochemistry, 43 : 4196 - 4205, 2004.
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Gupta, V. Peterson, C.B. Dice, L. Uchiki, T. Guo, J-T. Xu,
Y. Hettich, R. Dealwis, C..
Sml1p Protein is a Dimer in Solution:
Characterization of Denaturation and Renaturation of Recombinant
Sml1p.
Biochemistry, 2004, 43(26):8568-8578.
-
Guo, J-T. Ellrott, K. Chung, WJ. Xu, D. Passovets, S. Xu, Y..
PROSPECT-PSPP: An Automatic Computational Pipeline
for Protein Structure Prediction.
Nucleic Acids Res., 2004, 32:W522-5.
-
Tiquia SM, Wu L, Chong SC, Passovets S, Xu D, Xu Y, Zhou J.
Evaluation of 50-mer oligonucleotide arrays for
detecting microbial populations in environmental samples.
Biotechniques, 36(4):664-70,2004.
-
Jane Razumovskaya, Victor Olman, Dong Xu, Ed Uberbacher, Ying
Xu.
A Computational Method for Assessing
Peptide-Identification Reliability in Tandem Mass Spectrometry
Analysis with SEQUEST.
Proteomics, 4(4):961-9, 2004.
-
Qu,Y. Guo,J-T. Olman,V. and Xu,Y..
Protein Structure Prediction Using Sparse Dipolar
Coupling Data.
Nucleic Acids Res., 32(2):551-561, 2004.
-
Williams, A. Portelius, E. Kheterpal, I. Guo, J-T. Cook, K. Xu,
Y. Wetzel, R..
Mapping Abeta Amyloid Fibril Secondary Structure
Using Scanning proline Mutagenesis.
J. Mol. Biol., 335:833-842, 2004.
-
Y. Qu, J-T. Guo, V. Olman, and Y. Xu.
Protein Fold Recognition Through Application of
Residual Dipolar Coupling Data.
Proceedings of the 9th Pacific Symposium on Biocomputing
(PSB), 9:459-470, 2004.
-
Z. Su, A. Dam, X. Chen, V Olman, T. Jiang, B. Palenik, and Ying
Xu.
Computational Inference of Regulatory Pathways in Microbes:
an application to the construction of phosphorus assimilation
pathways in Synechococcus WH8102.
Proceedings of 14th International Conference on Genome
Informatics, pp:3-13,Universal Academy Publishing, 2003.
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ZZ. Chen, T Jiang, G. Lin, R. Rizzi, Z. Wen, D. Xu, Ying Xu.
More reliable protein NMR peak assignment via improved algorithm for
2-interval scheduling.
Proceedings of the 11th European Symposium on Algorithms,
580-592, 2003.
-
D. Xu, V. Olman, L. Wang, and Ying Xu.
EXCAVATOR: a computer program for gene expression
data analysis.
Nucleic Acid Research, 31(19), 5582-5589, 2003.
-
D. Kim, D. Xu, J-T. Guo, K. Ellrott, Ying Xu.
PROSPECT II:
protein structure prediction program for genome-scale
application.
Protein Engineering, 16(9), 641-650, 2003.
-
V. Olman, D. Xu, and Ying Xu.
CUBIC: Identification of Regulatory Binding Sites
through Data Clustering.
Journal of Bioinformatics and Computational Biology, 1(1), 21-40, 2003.
-
C. Secrest, L. Hauser, F. Larimer, D Thompson, A Beliaev, J. Zhou,
Ying Xu, and D. Xu.
A computational study of Shewanella
oneidensis MR-1: Discovering the role of hypothetical proteins.
OMICS, 7: 177-192, 2003.
-
Y. Chen, Y Liu, K.M. Goldstein, J. M. Becker, Ying Xu, D. Xu.
A
computational study on yeast signal transduction pathway for amino
acid transport.
Applied Genomics and Proteomics, 2(1), 43-50, 2003.
-
J. Xu, M Li, D. Kim and Ying Xu.
RAPTOR: rapid protein threading
by operations research techniques.
Journal of Bioinformatics and Computational Biology, 1(1),
pp95-118, 2003.
-
D. Xu, P. Dam, D. Kim, M. Shah, E. Uberbacher, and Ying Xu.
Characterization of protein structure and function
at genome scale with a computational prediction pipeline.
Genetic Engineering: Principles and Methods, Vol 32, Jane
Setlow (Ed.), Plenum Press, 2003.
-
V Olman, D Xu, and Ying Xu.
Solving data clustering problem as a
string search problem.
Proceedings of Conference on Statistical Data Mining and
Knowledge Discovery, (ed by Hamparsum Bozdogan), Chapman &
Hall/CRC, 417-434, 2003.
-
M. Shah, S. Passovets, D. Kim, K. Ellrott, L. Wang, I. Vokler,
P. Locascio, D. Xu, Ying Xu.
A Computational Pipeline for Protein Structure
Prediction and Analysis at Genome Scale.
Proceedings of IEEE Conference on Bioinformatics and
Biotechnology, 3-10, IEEE/CS Press, 2003 (An expanded journal
version is published in Bioinformatics ,19(15):1985-1996, 2003).
-
Y Chen, T Joshi, Ying Xu, and D Xu.
Towards Automated Derivation of Biological Pathways
Using High-Throughput Biological Data.
Proceedings of the IEEE Conference on Bioinformatics and
Biotechnology, 18-25, IEEE/CS Press, 2003.
-
G. Lin, D. Xu, Z. Chen, G. Lin, and T. Jiang, and Ying Xu.
Computational assignments of protein backbone NMR
peaks by efficient bounding and filtering.
Journal of Bioinformatics and Computational Biology, 1(2),
387-410, 2003.
-
V. Olman, D. Xu and Ying Xu.
Identification of Regulatory Binding-sites using
Minimum Spanning Trees.
Proceedings of the 7th Pacific Symposium on Biocomputing
(PSB), pp 327 - 338, 2003.
-
Y Li, J Yu, D Liu, W Yan, R Xu and Ying Xu.
Design of Zeolite
Frameworks with Defined Pore Geometry through Constrained Assembly
of Atoms.
Chem Mater, 15, 2780-2785, 2003.
-
J. Xu, M Li, G. Lin, D. Kim, and Ying Xu.
Protein threading by linear programming.
Proceedings of The 7th Pacific Symposium on Biocomputing
(PSB), pp 264- 275 2003.
-
J-T. Guo, D. Kim,. D Xu, and Ying Xu.
Improving the Performance of DomainParser for
Structural Domain Partition using Neural Network.
Nucleic Acids Research, 31(3), 944-952, 2003.
-
H. Sun, M LI and Ying Xu.
Molvie: an interactive visualization
enviroment for molecular structures.
Computer Methods and Programs in Biomedicine, vol 71, 85-90,
2003.
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Z. Chen, T. Jiang, G. Lin, J. Wen, D. Xu, J. Xu, Ying Xu.
Approximation Algorithms for NMR Spectral Peak
Assignment.
Theoretical Computer Science, 299:211-229, 2003.
-
Z. Liu and Ying Xu.
Adaptive support vector classification.
Proceedings of the Second Conference on Hybrid Intelligent
Systems, (edited by A. Abraham), IOS Press, pp 702-711, 2002.
-
G. Heffelfinger, A. Martino, A. Gorin, Ying Xu, et al..
Carbon Sequestration in Synechococcus Sp.: From
Molecular Machines to Hierarchical Modeling.
OMICS, 6(4), 305-330, 2002.
-
Z. Chen, T. Jiang, G. Lin, J. Wen, D. Xu, Ying Xu.
Approximation
algorithms for NMR Spectral Peak Assignments.
Proceedings of The Second Workshop on Algorithms in
Bioinformatics (WABI), Lecture Notes in Computer Science
2452:82-96, 2002.
-
MV. Buchanan, FW Larimer, HS Wiley, S. Kennel, TJ Squier, JM Ramsey,
KD Rodland, GB Hurst, RD. Smith, Ying Xu, D. Dixon, MJ Doktycs,
S. Colson, and R. Gesteland.
"Genomes to Life Center for Molecular and Cellular
Systems": a research program for identification and characterization
of protein complexes.
OMICS, (by invitation), 6(4), 287-303, 2002.
-
G. Lin, D. Xu, Z. Chen, G. Lin, and T. Jiang, and Ying Xu.
A
Branch and Bound Algorithm for assignment of protein backbone NMR
peaks.
Proceedings of First IEEE Bioinformatics Conference, pp. 165
- 174, August 2002.
-
Dong Xu, Guangshan Li, Liyou Wu, Jizhong Zhou, and Ying Xu.
PRIMEGENS: robust and efficient design of
gene-specific probes for microarray analysis.
Bioinformatics, 18(11):1432-1437, 2002.
-
Ying Xu, V. Olman, and D. Xu.
Clustering Gene Expression Data Using a
Graph-Theoretic Approach: An Application of Minimum Spanning
Tree.
Bioinformatics, Vol 18 (4), 526 - 535, 2002.
-
Ying Xu, D. Xu, D. Kim, V. Olman, J. Razumovskaya, and T. Jiang.
Automated Assignment of Backbone NMR Peaks using
Constrained Bipartite Matching.
IEEE Computing in Science and Engineering, vol 4 (1), pp
50-62, Jan. 2002.
-
Ying Xu, D. Xu and V. Olman.
A practical method for
interpretation of threading scores: an application of neural
networks.
Statistica Sinica Special issue on Bioinformatics, 12, 159 -
177, 2002.
-
D. Xu, O. Crawford, P. LoCascio, and Ying Xu.
Application of PROSPECT in CASP4: characterizing
protein structures with new folds.
Proteins: Structure, Function, Genetics, special issue on
CASP4, Suppl 5, 140 - 148, 2001.
-
Ying Xu, V Olman and D. Xu.
Minimum Spanning Trees for Gene-Expression Data
Clustering.
The Twelfth International Conference on Genomics Informatics,
pp. 24 ¨C 33, 2001, Tokyo, Japan.
-
Dong Xu, Kunnumal Baburaj, Cynthia B. Peterson, and Ying Xu.
Model for the Three-Dimensional Structure of
Vitronectin: Predictions for the Multi-Domain Protein from Threading
and Docking.
Proteins: Structure, Function, and Genetics,
44:312-320. 2001.
-
Ying Xu, Dong Xu, and Harold N. Gabow.
Protein Domain Decomposition using a Graph-Theoretic
Approach.
Bioinformatics, 16:1091-1104. 2000.
-
Ying Xu, Dong Xu. Oakley H. Crawford, and J. Ralph Einstein.
A computational method for NMR-constrained protein
threading.
Journal of Computational Biology, 7:449-467. 2000.
-
Ying Xu and Dong Xu.
Protein threading using PROSPECT: Design and
evaluation.
Proteins: Structure, Function, and Genetics,
40:343-354. 2000.
-
Dong Xu, Ying Xu, Gary Li, and Jizhong Zhou.
A Computer Program for Generating Gene-Specific
Fragments for Microarrays.
Currents in Computational Molecular Biology, edited by
S. Miyano, R. Shamir and T. Takagi. Universal Academy Press,
Inc. Tokyo, Japan. Pages 3-4. 2000.
-
Dong Xu, Ying Xu, and Edward C. Uberbacher.
Computational tools for protein modeling.
Current Protein and Peptide Science, 1:1-21. 2000.
-
Dong Xu and Ying Xu.
Protein tertiary structure prediction.
Current Protocols in Protein Science, edited by J. E. Coligan,
B. M. Dunn, H. L. Ploegh, D. W. Speicher, and P. T. Wingfield. John
Wiley & Sons, New York. Volume 1, pages 2.7.1-2.7.17. 2000.
-
Dong Xu and Ying Xu.
Protein Databases on the Internet.
Current Protocols in Protein Science, edited by J. E. Coligan,
B. M. Dunn, H. L. Ploegh, D. W. Speicher, and P. T. Wingfield. John
Wiley & Sons, New York. Volume 1, pages 2.6.1-2.6.15. 2000.
-
Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, and Engin
Serpersu.
Protein structure determination using protein
threading and sparse NMR data.
The Fourth Annual
International Conference on Computational Molecular Biology,
edited by R. Shamir, S. Miyano, S. Istrail, P. Pevzner, and
M. Waterman. Pages 299-307, ACM, Tokyo, Japan. 2000.
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