Fengzhu Sun

Fengzhu Sun

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Fengzhu Sun

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MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations.

Genome Biol 2019 08 6;20(1):154. Epub 2019 Aug 6.

Quantitative and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1186/s13059-019-1773-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6683435PMC
August 2019

NetGO: improving large-scale protein function prediction with massive network information.

Nucleic Acids Res 2019 Jul;47(W1):W379-W387

School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai 200433, China.

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http://dx.doi.org/10.1093/nar/gkz388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602452PMC
July 2019

SolidBin: Improving Metagenome Binning with Semi-supervised Normalized Cut.

Bioinformatics 2019 Apr 12. Epub 2019 Apr 12.

School of Computer Science and Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/btz253DOI Listing
April 2019

A new statistic for efficient detection of repetitive sequences.

Bioinformatics 2019 Apr 16. Epub 2019 Apr 16.

Department of Automation, MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist, Tsinghua University, Beijing, China.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/btz262DOI Listing
April 2019

Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.

Brief Bioinform 2019 Mar 11. Epub 2019 Mar 11.

Shanghai Key Lab of Intelligent Information Processing, the School of Computer Science and the Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China.

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https://academic.oup.com/bib/advance-article/doi/10.1093/bib
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http://dx.doi.org/10.1093/bib/bbz025DOI Listing
March 2019

Statistical significance approximation for local similarity analysis of dependent time series data.

BMC Bioinformatics 2019 Jan 28;20(1):53. Epub 2019 Jan 28.

School of Mathematics, Shandong University, Jinan, Shandong, 250100, China.

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http://dx.doi.org/10.1186/s12859-019-2595-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6348690PMC
January 2019

Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA.

BMC Genomics 2018 Dec 10;19(1):896. Epub 2018 Dec 10.

Quantitative and Computational Biology Program, University of Southern California, Los Angeles, CA, 90089, USA.

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http://dx.doi.org/10.1186/s12864-018-5253-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288960PMC
December 2018

Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients.

FEMS Microbiol Ecol 2018 09;94(9)

Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA 3315 McGaugh Hall, Irvine, CA, USA 92697.

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http://dx.doi.org/10.1093/femsec/fiy133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454419PMC
September 2018

Classifying Alzheimer's disease with brain imaging and genetic data using a neural network framework.

Neurobiol Aging 2018 08 24;68:151-158. Epub 2018 Apr 24.

USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neurobiolaging.2018.04.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993633PMC
August 2018

GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank.

Bioinformatics 2018 07;34(14):2465-2473

School of Computer Science and Shanghai Key Lab of Intelligent Information Processing.

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http://dx.doi.org/10.1093/bioinformatics/bty130DOI Listing
July 2018

Comparative studies of alignment, alignment-free and SVM based approaches for predicting the hosts of viruses based on viral sequences.

Authors:
Han Li Fengzhu Sun

Sci Rep 2018 Jul 3;8(1):10032. Epub 2018 Jul 3.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.

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http://dx.doi.org/10.1038/s41598-018-28308-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030160PMC
July 2018

Identifying Sequences for Microbial Communities Using Long -mer Sequence Signatures.

Front Microbiol 2018 3;9:872. Epub 2018 May 3.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA, United States.

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http://dx.doi.org/10.3389/fmicb.2018.00872DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5943621PMC
May 2018

Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer.

Front Microbiol 2018 16;9:711. Epub 2018 Apr 16.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States.

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http://dx.doi.org/10.3389/fmicb.2018.00711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5911508PMC
April 2018

Deep sequencing of HBV pre-S region reveals high heterogeneity of HBV genotypes and associations of word pattern frequencies with HCC.

PLoS Genet 2018 02 23;14(2):e1007206. Epub 2018 Feb 23.

Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China.

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http://dx.doi.org/10.1371/journal.pgen.1007206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5841821PMC
February 2018

Sparse generalized linear model with approximation for feature selection and prediction with big omics data.

BioData Min 2017 19;10:39. Epub 2017 Dec 19.

Foundation Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, 90048 CA USA.

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http://dx.doi.org/10.1186/s13040-017-0159-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5735537PMC
December 2017

Towards enhanced and interpretable clustering/classification in integrative genomics.

Nucleic Acids Res 2017 Nov;45(20):e169

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, CA, USA.

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http://dx.doi.org/10.1093/nar/gkx767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714251PMC
November 2017

Next-generation sequencing revealed divergence in deletions of the preS region in the HBV genome between different HBV-related liver diseases.

J Gen Virol 2017 11 12;98(11):2748-2758. Epub 2017 Oct 12.

1​Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, PR China.

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http://dx.doi.org/10.1099/jgv.0.000942DOI Listing
November 2017

Optimal choice of word length when comparing two Markov sequences using a χ -statistic.

BMC Genomics 2017 Oct 3;18(Suppl 6):732. Epub 2017 Oct 3.

Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, China.

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http://dx.doi.org/10.1186/s12864-017-4020-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629589PMC
October 2017

Improving contig binning of metagenomic data using [Formula: see text] oligonucleotide frequency dissimilarity.

BMC Bioinformatics 2017 Sep 20;18(1):425. Epub 2017 Sep 20.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, CA, 90089, USA.

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http://dx.doi.org/10.1186/s12859-017-1835-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5607646PMC
September 2017

CAFE: aCcelerated Alignment-FrEe sequence analysis.

Nucleic Acids Res 2017 07;45(W1):W554-W559

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, CA 90089, USA.

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https://academic.oup.com/nar/article/45/W1/W554/3791208
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http://dx.doi.org/10.1093/nar/gkx351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793812PMC
July 2017

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data.

Microbiome 2017 07 6;5(1):69. Epub 2017 Jul 6.

Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.

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http://microbiomejournal.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/s40168-017-0283-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501583PMC
July 2017

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge.

Bioinformatics 2017 03;33(6):791-798

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw290DOI Listing
March 2017

Prediction of virus-host infectious association by supervised learning methods.

BMC Bioinformatics 2017 Mar 14;18(Suppl 3):60. Epub 2017 Mar 14.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA.

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http://dx.doi.org/10.1186/s12859-017-1473-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374558PMC
March 2017

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences.

Nucleic Acids Res 2017 01 28;45(1):39-53. Epub 2016 Nov 28.

Department of Biological Sciences, University of Southern California, 3616 Trousdale Pkwy Los, Angeles, CA 90089, USA.

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http://dx.doi.org/10.1093/nar/gkw1002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224470PMC
January 2017

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains.

Sci Rep 2016 11 23;6:37243. Epub 2016 Nov 23.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, CA 90089 USA.

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http://www.nature.com/articles/srep37243
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http://dx.doi.org/10.1038/srep37243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120338PMC
November 2016

Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.

Bioinformatics 2016 04 30;32(7):993-1000. Epub 2015 Jun 30.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA, USA, Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, China.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/
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http://dx.doi.org/10.1093/bioinformatics/btv395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169497PMC
April 2016

Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships.

BMC Syst Biol 2016 Jan 11;10 Suppl 1. Epub 2016 Jan 11.

Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, USA.

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http://dx.doi.org/10.1186/s12918-015-0247-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895779PMC
January 2016

Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes.

ISME J 2015 Dec 19;9(12):2573-86. Epub 2015 May 19.

Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1038/ismej.2015.76DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817623PMC
December 2015

Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains.

BMC Bioinformatics 2015 Sep 21;16:301. Epub 2015 Sep 21.

Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, 90089-2910, CA, USA.

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http://dx.doi.org/10.1186/s12859-015-0732-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578688PMC
September 2015

Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data.

Bioinformatics 2015 Apr 20;31(7):1067-74. Epub 2014 Nov 20.

Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA, Molecular and Computational Biology Program, Department of Biological Sciences, USC, Los Angeles, CA 90089, USA, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA and F. Widjaja Foundation - Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4382903PMC
April 2015

Finding genetic overlaps among diseases based on ranked gene lists.

J Comput Biol 2015 Feb;22(2):111-23

Molecular and Computational Biology Program, University of Southern California , Los Angeles, California.

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http://www.liebertpub.com/doi/10.1089/cmb.2014.0149
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http://dx.doi.org/10.1089/cmb.2014.0149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4326265PMC
February 2015

Comparison of metatranscriptomic samples based on k-tuple frequencies.

PLoS One 2014 2;9(1):e84348. Epub 2014 Jan 2.

Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084348PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879298PMC
November 2014

Alignment-free protein interaction network comparison.

Bioinformatics 2014 Sep;30(17):i430-7

Department of Statistics, University of Oxford, Oxford OX1 3TG, UK and Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, CA 90089-2910, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147900PMC
September 2014

New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.

Brief Bioinform 2014 May 23;15(3):343-53. Epub 2013 Sep 23.

Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA. or

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http://dx.doi.org/10.1093/bib/bbt067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4017329PMC
May 2014

Multiple alignment-free sequence comparison.

Bioinformatics 2013 Nov 29;29(21):2690-8. Epub 2013 Aug 29.

School of Mathematics, Peking University, Beijing 100871, PR China, Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA, MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, PR China and Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK.

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http://dx.doi.org/10.1093/bioinformatics/btt462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799466PMC
November 2013

Research in Computational Molecular Biology (RECOMB 2013).

Authors:
Fengzhu Sun

J Comput Biol 2013 Oct;20(10):713

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http://dx.doi.org/10.1089/cmb.2013.020pDOI Listing
October 2013

A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms.

BMC Genomics 2013 21;14 Suppl 1:S1. Epub 2013 Jan 21.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1186/1471-2164-14-S1-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549804PMC
August 2013

Alignment-free sequence comparison based on next-generation sequencing reads.

J Comput Biol 2013 Feb;20(2):64-79

School of Mathematics, Peking University, Beijing, PR China.

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http://dx.doi.org/10.1089/cmb.2012.0228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581251PMC
February 2013

CEDER: accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq.

Authors:
Lin Wan Fengzhu Sun

IEEE/ACM Trans Comput Biol Bioinform 2012 Sep-Oct;9(5):1281-92

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA.

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http://ieeexplore.ieee.org/document/6205734/
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http://dx.doi.org/10.1109/TCBB.2012.83DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488134PMC
January 2013

Efficient statistical significance approximation for local similarity analysis of high-throughput time series data.

Bioinformatics 2013 Jan 23;29(2):230-7. Epub 2012 Nov 23.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990825PMC
January 2013

Comparison of metagenomic samples using sequence signatures.

BMC Genomics 2012 Dec 27;13:730. Epub 2012 Dec 27.

MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST / Department of Automation, Tsinghua University, Beijing 100084, China.

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http://dx.doi.org/10.1186/1471-2164-13-730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549735PMC
December 2012

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates.

BMC Syst Biol 2011 14;5 Suppl 2:S15. Epub 2011 Dec 14.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1186/1752-0509-5-S2-S15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287481PMC
November 2012

Association of genetic variation in the mitochondrial genome with blood pressure and metabolic traits.

Hypertension 2012 Oct 4;60(4):949-56. Epub 2012 Sep 4.

National Heart, Lung, and Blood Institute’s Framingham Heart Study, 73 Mt Wayte Ave, Suite 2, Framingham, MA 01702, USA.

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http://dx.doi.org/10.1161/HYPERTENSIONAHA.112.196519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753106PMC
October 2012

Modeling RNA degradation for RNA-Seq with applications.

Biostatistics 2012 Sep 21;13(4):734-47. Epub 2012 Feb 21.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1093/biostatistics/kxs001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616752PMC
September 2012

Accurate genome relative abundance estimation based on shotgun metagenomic reads.

PLoS One 2011 6;6(12):e27992. Epub 2011 Dec 6.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027992PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232206PMC
July 2012

Computational methods for the analysis of tag sequences in metagenomics studies.

Front Biosci (Schol Ed) 2012 Jun 1;4:1333-43. Epub 2012 Jun 1.

School of Mathematics, Shandong University, Jinan, Shandong 250100, PR China.

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June 2012

Normal and compound poisson approximations for pattern occurrences in NGS reads.

J Comput Biol 2012 Jun;19(6):839-54

School of Mathematics, Shandong University, Jinan, Shandong, China.

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http://dx.doi.org/10.1089/cmb.2012.0029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375642PMC
June 2012

Marine bacterial, archaeal and protistan association networks reveal ecological linkages.

ISME J 2011 Sep 24;5(9):1414-25. Epub 2011 Mar 24.

Department of Biological Sciences and Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1038/ismej.2011.24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160682PMC
September 2011

New powerful statistics for alignment-free sequence comparison under a pattern transfer model.

J Theor Biol 2011 Sep 25;284(1):106-16. Epub 2011 Jun 25.

School of Physics, South China University of Technology, Guangzhou, PR China.

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http://dx.doi.org/10.1016/j.jtbi.2011.06.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146591PMC
September 2011

Detection of parent-of-origin effects for quantitative traits in complete and incomplete nuclear families with multiple children.

Am J Epidemiol 2011 Jul 1;174(2):226-33. Epub 2011 Jun 1.

Department of Statistics and Actuarial Science, Faculty of Science, University of Hong Kong, China.

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https://academic.oup.com/aje/article-lookup/doi/10.1093/aje/
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http://dx.doi.org/10.1093/aje/kwr056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167678PMC
July 2011

Sequence alignment as hypothesis testing.

J Comput Biol 2011 May;18(5):677-91

MOE Key Lab of Bioinformatics and Bioinformatics Division of TNLIST/Department of Automation, Tsinghua University, Beijing, P.R. China.

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http://dx.doi.org/10.1089/cmb.2010.0328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3122928PMC
May 2011

DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases.

BMC Syst Biol 2011 Apr 19;5:55. Epub 2011 Apr 19.

MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing, China.

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http://dx.doi.org/10.1186/1752-0509-5-55DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108930PMC
April 2011

Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny.

BMC Bioinformatics 2011 Apr 25;12:118. Epub 2011 Apr 25.

School of Mathematics, Shandong University, Jinan, Shandong, PR China.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-12-118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108311PMC
April 2011

Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach.

BMC Bioinformatics 2011 Feb 15;12 Suppl 1:S11. Epub 2011 Feb 15.

MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 10084, China.

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http://dx.doi.org/10.1186/1471-2105-12-S1-S11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044265PMC
February 2011

Alignment-free sequence comparison (II): theoretical power of comparison statistics.

J Comput Biol 2010 Nov 25;17(11):1467-90. Epub 2010 Oct 25.

Molecular and Computational Biology, University of Southern California , Los Angeles, California 90089-2910, USA.

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http://dx.doi.org/10.1089/cmb.2010.0056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123933PMC
November 2010

The power of detecting enriched patterns: an HMM approach.

J Comput Biol 2010 Apr;17(4):581-92

School of Mathematics, Shandong University, Jinan, Shandong, PR China.

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http://dx.doi.org/10.1089/cmb.2009.0218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203519PMC
April 2010

Alignment-free sequence comparison (I): statistics and power.

J Comput Biol 2009 Dec;16(12):1615-34

Department of Statistics, University of Oxford, Oxford OX1 3TG, UK.

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http://dx.doi.org/10.1089/cmb.2009.0198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818754PMC
December 2009

Chromatin regulation and gene centrality are essential for controlling fitness pleiotropy in yeast.

PLoS One 2009 Nov 30;4(11):e8086. Epub 2009 Nov 30.

Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2778950PMC
November 2009

Ecdysone receptor acts in fruitless- expressing neurons to mediate drosophila courtship behaviors.

Curr Biol 2009 Sep 30;19(17):1447-52. Epub 2009 Jul 30.

Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1016/j.cub.2009.06.063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763606PMC
September 2009

A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila.

BMC Genomics 2009 May 12;10:220. Epub 2009 May 12.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1186/1471-2164-10-220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697172PMC
May 2009

Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy.

Genome Biol 2008 16;9(12):R174. Epub 2008 Dec 16.

Molecular and Computational Biology, Department of Biology Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1186/gb-2008-9-12-r174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2646278PMC
March 2009

Somatic, germline and sex hierarchy regulated gene expression during Drosophila metamorphosis.

BMC Genomics 2009 Feb 13;10:80. Epub 2009 Feb 13.

Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA.

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http://dx.doi.org/10.1186/1471-2164-10-80DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656526PMC
February 2009

Compound poisson approximation of the number of occurrences of a position frequency matrix (PFM) on both strands.

J Comput Biol 2008 Jul-Aug;15(6):547-64

Computational Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.

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http://dx.doi.org/10.1089/cmb.2007.0084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2607244PMC
October 2008

Testing gene set enrichment for subset of genes: Sub-GSE.

BMC Bioinformatics 2008 Sep 2;9:362. Epub 2008 Sep 2.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1186/1471-2105-9-362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2543030PMC
September 2008

The effects of protein interactions, gene essentiality and regulatory regions on expression variation.

BMC Syst Biol 2008 Jun 26;2:54. Epub 2008 Jun 26.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2913, USA.

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http://dx.doi.org/10.1186/1752-0509-2-54DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2474594PMC
June 2008

Inferring activity changes of transcription factors by binding association with sorted expression profiles.

BMC Bioinformatics 2007 Nov 16;8:452. Epub 2007 Nov 16.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2194743PMC
November 2007

Sequence-based prioritization of nonsynonymous single-nucleotide polymorphisms for the study of disease mutations.

Am J Hum Genet 2007 Aug 22;81(2):346-60. Epub 2007 Jun 22.

Molecular and Computational Biology Program, Signal and Image Processing Institute, Department of Electrical Engineering, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1086/519747DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950793PMC
August 2007

The transmission disequilibrium test and imprinting effects test based on case-parent pairs.

Genet Epidemiol 2007 May;31(4):273-87

Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.

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http://dx.doi.org/10.1002/gepi.20208DOI Listing
May 2007

CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data.

Bioinformatics 2007 Jan 10;23(2):215-21. Epub 2006 Nov 10.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl569DOI Listing
January 2007

MARD: a new method to detect differential gene expression in treatment-control time courses.

Bioinformatics 2006 Nov 23;22(21):2650-7. Epub 2006 Aug 23.

Molecular and Computational Biology Program, Department of Biological Sciences, Computational Biology, University of Southern California Los Angeles, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl451DOI Listing
November 2006

Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors.

Bioinformatics 2006 Oct 31;22(20):2532-8. Epub 2006 Jul 31.

Department of Mathematics, University of Southern California 3620 Vermont Avenue, KAP 108, Los Angeles, CA 90089-2532, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl417DOI Listing
October 2006

Diffusion kernel-based logistic regression models for protein function prediction.

OMICS 2006 ;10(1):40-55

Department of Computer Science, University of Southern California, Los Angeles, 90089, USA.

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http://dx.doi.org/10.1089/omi.2006.10.40DOI Listing
September 2006

Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy.

BMC Bioinformatics 2006 Sep 19;7:417. Epub 2006 Sep 19.

Molecular and Computational Biology, University of Southern California, MCB201, 1050 Childs way, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1186/1471-2105-7-417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618409PMC
September 2006

An integrative approach for causal gene identification and gene regulatory pathway inference.

Bioinformatics 2006 Jul;22(14):e489-96

Molecular and Computational Biology Program, University of Southern California, Los Angeles, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl234DOI Listing
July 2006

A dynamic programming algorithm for binning microbial community profiles.

Bioinformatics 2006 Jun 27;22(12):1508-14. Epub 2006 Mar 27.

Department of Mathematics, University of Southern California 3620 South Vermont Avenue, KAP 108, Los Angeles, California 90089-253, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl114DOI Listing
June 2006

Network motif identification in stochastic networks.

Proc Natl Acad Sci U S A 2006 Jun 12;103(25):9404-9. Epub 2006 Jun 12.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1073/pnas.0507841103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480420PMC
June 2006

A model-based approach to selection of tag SNPs.

BMC Bioinformatics 2006 Jun 15;7:303. Epub 2006 Jun 15.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, USA.

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http://dx.doi.org/10.1186/1471-2105-7-303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1525207PMC
June 2006

An integrated approach to the prediction of domain-domain interactions.

BMC Bioinformatics 2006 May 25;7:269. Epub 2006 May 25.

Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1186/1471-2105-7-269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1481624PMC
May 2006

Further understanding human disease genes by comparing with housekeeping genes and other genes.

BMC Genomics 2006 Feb 21;7:31. Epub 2006 Feb 21.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089, USA.

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http://dx.doi.org/10.1186/1471-2164-7-31DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1397819PMC
February 2006

Assessing the power of tag SNPs in the mapping of quantitative trait loci (QTL) with extremal and random samples.

BMC Genet 2005 Oct 19;6:51. Epub 2005 Oct 19.

Department of Biostatistics, School of Public Health, University of Alabama, Birmingham, AL 35294, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1274312PMC
October 2005

Prediction of protein function using protein-protein interaction data.

Proc IEEE Comput Soc Bioinform Conf 2002 ;1:197-206

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-1113, USA.

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May 2005

HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination.

Bioinformatics 2005 Jan 1;21(1):90-103. Epub 2004 Jul 1.

Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, AL 35294, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth388DOI Listing
January 2005

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms.

Bioinformatics 2005 Jan 27;21(1):131-4. Epub 2004 Aug 27.

Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bth482DOI Listing
January 2005

Extreme value distribution based gene selection criteria for discriminant microarray data analysis using logistic regression.

J Comput Biol 2004 ;11(2-3):215-26

The Robert S. Boas Center for Genomics and Human Genetics, North Shore LIJ Research Institute, 350 Community Drive, Manhasset, NY 11030, USA.

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http://www.liebertpub.com/doi/10.1089/1066527041410445
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August 2004

An integrated probabilistic model for functional prediction of proteins.

J Comput Biol 2004 ;11(2-3):463-75

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, 1042 West 36th Place, Los Angeles, CA 90089-1113, USA.

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http://dx.doi.org/10.1089/1066527041410346DOI Listing
August 2004

Mitochondrial genome mutations in hypertensive individuals.

Am J Hypertens 2004 Jul;17(7):629-35

Department of Medicine, Genetics Program, Boston University School of Medicine, Boston, Massachusetts 02118, USA.

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http://dx.doi.org/10.1016/j.amjhyper.2004.02.020DOI Listing
July 2004

Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies.

Genome Res 2004 May 12;14(5):908-16. Epub 2004 Apr 12.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-1113, USA.

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http://dx.doi.org/10.1101/gr.1837404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC479119PMC
May 2004

Sampling distribution for microsatellites amplified by PCR: mean field approximation and its applications to genotyping.

J Theor Biol 2004 May;228(2):185-94

Department of Mathematics, University of Southern California, 1042 West 36th Place, DRB 288 Los Angeles, CA 90089-1113, USA.

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May 2004