Isidore Rigoutsos

Isidore Rigoutsos

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Isidore Rigoutsos

Publications by authors named "Isidore Rigoutsos"

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Exploration of CCA-added RNAs revealed the expression of mitochondrial non-coding RNAs regulated by CCA-adding enzyme.

RNA Biol 2019 Sep 12:1-9. Epub 2019 Sep 12.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia , PA , USA.

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http://dx.doi.org/10.1080/15476286.2019.1664885DOI Listing
September 2019

Short RNA regulators: the past, the present, the future, and implications for precision medicine and health disparities.

Curr Opin Biotechnol 2019 Aug 16;58:202-210. Epub 2019 Jul 16.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, United States. Electronic address:

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http://dx.doi.org/10.1016/j.copbio.2019.05.014DOI Listing
August 2019

TRNA-derived fragments as sex-dependent circulating candidate biomarkers for Parkinson's disease.

Parkinsonism Relat Disord 2019 Aug 25;65:203-209. Epub 2019 May 25.

Computational Medicine Center, Jefferson Alumni Hall #M81, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA. Electronic address:

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http://dx.doi.org/10.1016/j.parkreldis.2019.05.035DOI Listing
August 2019

IsomiRs and tRNA-derived fragments are associated with metastasis and patient survival in uveal melanoma.

Pigment Cell Melanoma Res 2019 Jul 8. Epub 2019 Jul 8.

Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1111/pcmr.12810DOI Listing
July 2019

tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities.

Cancer Res 2019 Jun 17;79(12):3034-3049. Epub 2019 Apr 17.

Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1158/0008-5472.CAN-19-0789DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6571059PMC
June 2019

Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap.

Methods Mol Biol 2018 ;1680:237-255

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.

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http://dx.doi.org/10.1007/978-1-4939-7339-2_16DOI Listing
May 2018

Race Disparities in the Contribution of miRNA Isoforms and tRNA-Derived Fragments to Triple-Negative Breast Cancer.

Cancer Res 2018 03 11;78(5):1140-1154. Epub 2017 Dec 11.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-1947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5935570PMC
March 2018

Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer.

Sci Rep 2018 03 28;8(1):5314. Epub 2018 Mar 28.

Computational Medicine Center, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.

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http://dx.doi.org/10.1038/s41598-018-22488-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5871839PMC
March 2018

MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects.

Nucleic Acids Res 2018 01;46(D1):D152-D159

Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.

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http://academic.oup.com/nar/article/46/D1/D152/4653530
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http://dx.doi.org/10.1093/nar/gkx1075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753276PMC
January 2018

The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells.

Nucleic Acids Res 2017 Sep;45(15):9108-9120

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1093/nar/gkx537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5587776PMC
September 2017

Threshold-seq: a tool for determining the threshold in short RNA-seq datasets.

Bioinformatics 2017 Jul;33(13):2034-2036

Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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https://academic.oup.com/bioinformatics/article/33/13/2034/2
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http://dx.doi.org/10.1093/bioinformatics/btx073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870860PMC
July 2017

Increasing cell density globally enhances the biogenesis of Piwi-interacting RNAs in Bombyx mori germ cells.

Sci Rep 2017 06 23;7(1):4110. Epub 2017 Jun 23.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1038/s41598-017-04429-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5482885PMC
June 2017

Assessment of isomiR Discrimination Using Commercial qPCR Methods.

Noncoding RNA 2017 Jun 24;3(2). Epub 2017 Mar 24.

Computational Medicine Center, http://cm.jefferson.edu/, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.3390/ncrna3020018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5514785PMC
June 2017

YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs.

Nucleic Acids Res 2017 May;45(9):e70

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1093/nar/gkx005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5605243PMC
May 2017

Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types.

Nucleic Acids Res 2017 04;45(6):2973-2985

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Thomas Jefferson University, PA 19107, USA.

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http://dx.doi.org/10.1093/nar/gkx082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389567PMC
April 2017

MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data.

Sci Rep 2017 02 21;7:41184. Epub 2017 Feb 21.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1038/srep41184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5318995PMC
February 2017

Aging-associated changes in microRNA expression profile of internal anal sphincter smooth muscle: Role of microRNA-133a.

Am J Physiol Gastrointest Liver Physiol 2016 11 15;311(5):G964-G973. Epub 2016 Sep 15.

Department of Medicine, Division of Gastroenterology & Hepatology, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1152/ajpgi.00290.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5130548PMC
November 2016

Post-transcriptional Regulation of BRCA2 through Interactions with miR-19a and miR-19b.

Front Genet 2016 31;7:143. Epub 2016 Aug 31.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA.

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http://dx.doi.org/10.3389/fgene.2016.00143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5005319PMC
September 2016

MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments.

Bioinformatics 2016 08 13;32(16):2481-9. Epub 2016 Apr 13.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978933PMC
August 2016

Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2.

Am J Hum Genet 2016 05 28;98(5):883-897. Epub 2016 Apr 28.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Statistics, Rice University, Houston, TX 77251, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.03.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863560PMC
May 2016

Consequential considerations when mapping tRNA fragments.

BMC Bioinformatics 2016 Mar 10;17:123. Epub 2016 Mar 10.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.

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http://dx.doi.org/10.1186/s12859-016-0921-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4785646PMC
March 2016

Mitochondrial tRNA-lookalikes in nuclear chromosomes: could they be functional?

RNA Biol 2015 ;12(4):375-80

a Computational Medicine Center; Sidney Kimmel Medical College at Thomas Jefferson University ; Philadelphia , PA USA.

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http://dx.doi.org/10.1080/15476286.2015.1017239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615777PMC
January 2016

Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity.

Nucleic Acids Res 2015 Oct 22;43(19):9158-75. Epub 2015 Sep 22.

Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkv922DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627084PMC
October 2015

Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies.

Oncotarget 2015 Sep;6(28):24797-822

Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.

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http://dx.doi.org/10.18632/oncotarget.4695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4694795PMC
September 2015

Post-transcriptional regulation of BRCA1 through its coding sequence by the miR-15/107 group of miRNAs.

Front Genet 2015 24;6:242. Epub 2015 Jul 24.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia PA, USA.

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http://journal.frontiersin.org/Article/10.3389/fgene.2015.00
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http://dx.doi.org/10.3389/fgene.2015.00242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4513244PMC
August 2015

Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers.

Proc Natl Acad Sci U S A 2015 Jul 29;112(29):E3816-25. Epub 2015 Jun 29.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107;

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http://dx.doi.org/10.1073/pnas.1510077112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517238PMC
July 2015

Reply to Backes and Keller: Identification of novel tissue-specific and primate-specific human microRNAs.

Proc Natl Acad Sci U S A 2015 Jun 15;112(22):E2851. Epub 2015 May 15.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107

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http://dx.doi.org/10.1073/pnas.1505397112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460515PMC
June 2015

The emerging roles of GPRC5A in diseases.

Oncoscience 2014 25;1(12):765-76. Epub 2014 Nov 25.

Computational Medicine Center, Jefferson Alumni Hall, Thomas Jefferson University, Philadelphia, PA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4303886PMC
http://dx.doi.org/10.18632/oncoscience.104DOI Listing
January 2015

Nuclear and mitochondrial tRNA-lookalikes in the human genome.

Front Genet 2014 8;5:344. Epub 2014 Oct 8.

Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University Philadelphia, PA, USA.

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http://dx.doi.org/10.3389/fgene.2014.00344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189335PMC
October 2014

MiR-103a-3p targets the 5' UTR of GPRC5A in pancreatic cells.

RNA 2014 Sep 1;20(9):1431-9. Epub 2014 Jul 1.

Computational Medicine Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA

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http://dx.doi.org/10.1261/rna.045757.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138326PMC
September 2014

IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies.

Oncotarget 2014 Sep;5(18):8790-802

Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226722PMC
http://dx.doi.org/10.18632/oncotarget.2405DOI Listing
September 2014

Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types.

Sci Rep 2014 Aug 8;4:5947. Epub 2014 Aug 8.

Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.

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http://dx.doi.org/10.1038/srep05947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4894423PMC
August 2014

HuR posttranscriptionally regulates WEE1: implications for the DNA damage response in pancreatic cancer cells.

Cancer Res 2014 Feb;74(4):1128-40

Authors' Affiliations: Department of Surgery, Division of Surgical Research, Jefferson Pancreas, Biliary and Related Cancer Center, Jefferson Medical College; Computational Medicine Center; Kimmel Cancer Center, Thomas Jefferson University; Fox Chase Cancer Center, Philadelphia; and Lankenau Institute for Medical Research, Wynnewood, Pennsylvania.

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http://dx.doi.org/10.1158/0008-5472.CAN-13-1915DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4353573PMC
February 2014

Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets.

Sci Rep 2012 10;2:569. Epub 2012 Aug 10.

Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA.

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http://dx.doi.org/10.1038/srep00569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415692PMC
March 2013

The complex transcriptional landscape of the anucleate human platelet.

BMC Genomics 2013 Jan 16;14. Epub 2013 Jan 16.

Cardeza Foundation for Hematologic Research, Division of Hematology, Department of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.

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http://dx.doi.org/10.1186/1471-2164-14-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3722126PMC
January 2013

Interactive exploration of RNA22 microRNA target predictions.

Bioinformatics 2012 Dec 16;28(24):3322-3. Epub 2012 Oct 16.

Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts615DOI Listing
December 2012

microRNAs in colon cancer: a roadmap for discovery.

FEBS Lett 2012 Sep;586(19):3000-7

Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://dx.doi.org/10.1016/j.febslet.2012.07.048DOI Listing
September 2012

Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs.

Cell 2011 Oct;147(2):344-57

Cancer Genetics Program, Division of Genetics, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.cell.2011.09.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235920PMC
October 2011

OMiR: Identification of associations between OMIM diseases and microRNAs.

Genomics 2011 Feb 23;97(2):71-6. Epub 2010 Oct 23.

Dept. of Experimental Therapeutics, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.ygeno.2010.10.004DOI Listing
February 2011

The Evi1, microRNA-143, K-Ras axis in colon cancer.

FEBS Lett 2011 Feb 26;585(4):693-9. Epub 2011 Jan 26.

Division of Infectious Diseases, Department of Medicine, Miriam and Rhode Island Hospitals, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA.

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http://doi.wiley.com/10.1016/j.febslet.2011.01.033
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http://dx.doi.org/10.1016/j.febslet.2011.01.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440864PMC
February 2011

Gene-expression forum: Decoy for microRNAs.

Nature 2010 Jun;465(7301):1016-7

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http://dx.doi.org/10.1038/4651016aDOI Listing
June 2010

Atypical transcription of microRNA gene fragments.

Nucleic Acids Res 2010 May 21;38(9):2775-87. Epub 2010 Jan 21.

Laboratory of Retrovirology, Division of Infectious Diseases, Rhode Island and Miriam Hospitals, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA.

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http://dx.doi.org/10.1093/nar/gkp1242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875006PMC
May 2010

Dynamic changes in the human methylome during differentiation.

Genome Res 2010 Mar 4;20(3):320-31. Epub 2010 Feb 4.

UCSD Medical Center, Department of Reproductive Medicine, San Diego, California 92103, USA.

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http://dx.doi.org/10.1101/gr.101907.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840979PMC
March 2010

Short RNAs: how big is this iceberg?

Curr Biol 2010 Feb;20(3):R110-3

Bioinformatics and pattern Discovery Group, Computation Biology Center, IBM Thomas J. Watson Research Center, PO BOX 218, Yonktown Heights, NY 10598, USA.

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http://dx.doi.org/10.1016/j.cub.2009.12.036DOI Listing
February 2010

Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes.

PLoS Comput Biol 2009 Dec 18;5(12):e1000610. Epub 2009 Dec 18.

Bioinformatics and Pattern Discovery Group, IBM Thomas J. Watson Research Center, Yorktown Heights, New York, USA.

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http://dx.plos.org/10.1371/journal.pcbi.1000610
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http://dx.doi.org/10.1371/journal.pcbi.1000610DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784220PMC
December 2009

Insights into the regulation of a common variant of HMGA2 associated with human height during embryonic development.

Stem Cell Rev Rep 2009 Dec;5(4):328-33

Neural Stem Cells, Institute of Medical Biology, Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, Singapore 138648, Singapore.

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http://dx.doi.org/10.1007/s12015-009-9095-8DOI Listing
December 2009

MicroRNA 125a and its regulation of the p53 tumor suppressor gene.

FEBS Lett 2009 Nov 8;583(22):3725-30. Epub 2009 Oct 8.

Division of Infectious Diseases, Department of Medicine, Laboratory of Retrovirology, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA.

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http://dx.doi.org/10.1016/j.febslet.2009.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3594778PMC
November 2009

miR-34a contributes to megakaryocytic differentiation of K562 cells independently of p53.

Blood 2009 Sep 7;114(10):2181-92. Epub 2009 Jul 7.

Immune Disease Institute and Department of Pediatrics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1182/blood-2009-02-205062DOI Listing
September 2009

Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability.

Nat Cell Biol 2009 May 19;11(5):652-8. Epub 2009 Apr 19.

Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1038/ncb1872DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746449PMC
May 2009

New tricks for animal microRNAS: targeting of amino acid coding regions at conserved and nonconserved sites.

Cancer Res 2009 Apr 7;69(8):3245-8. Epub 2009 Apr 7.

Bioinformatics and Pattern Discovery Group, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-09-0352DOI Listing
April 2009

MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation.

Nature 2008 Oct 17;455(7216):1124-8. Epub 2008 Sep 17.

Stem Cell and Developmental Biology, Genome Institute of Singapore, Agency for Science Technology and Research, #08-01, Genome, 60 Biopolis Street, Singapore 138672, Singapore.

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http://dx.doi.org/10.1038/nature07299DOI Listing
October 2008

Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs.

Nucleic Acids Res 2008 Jun 1;36(10):3484-93. Epub 2008 May 1.

Bioinformatics and Pattern Discovery Group, IBM Thomas J. Watson Research Center, PO Box 218, Yorktown Heights, NY 10598, USA.

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http://dx.doi.org/10.1093/nar/gkn155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2425492PMC
June 2008

What's in the mix: phylogenetic classification of metagenome sequence samples.

Curr Opin Microbiol 2007 Oct 22;10(5):499-503. Epub 2007 Oct 22.

Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA.

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http://dx.doi.org/10.1016/j.mib.2007.08.004DOI Listing
October 2007

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods.

Nat Methods 2007 Jun 29;4(6):495-500. Epub 2007 Apr 29.

Department of Energy Joint Genome Institute (DOE-JGI), 2800 Mitchell Drive, Walnut Creek, California 94598, USA.

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http://dx.doi.org/10.1038/nmeth1043DOI Listing
June 2007

Pattern-based phylogenetic distance estimation and tree reconstruction.

Evol Bioinform Online 2007 Feb 25;2:359-75. Epub 2007 Feb 25.

Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674673PMC
February 2007

Accurate phylogenetic classification of variable-length DNA fragments.

Nat Methods 2007 Jan 10;4(1):63-72. Epub 2006 Dec 10.

Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, USA.

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http://www.nature.com/articles/nmeth976
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http://dx.doi.org/10.1038/nmeth976DOI Listing
January 2007

Data mining and clinical data repositories: Insights from a 667,000 patient data set.

Comput Biol Med 2006 Dec 22;36(12):1351-77. Epub 2005 Dec 22.

Department of Public Health Sciences, University of Virginia Health System, Charlottesville, VA, USA.

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http://dx.doi.org/10.1016/j.compbiomed.2005.08.003DOI Listing
December 2006

A linguistic model for the rational design of antimicrobial peptides.

Nature 2006 Oct;443(7113):867-9

Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1038/nature05233DOI Listing
October 2006

A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes.

Cell 2006 Sep;126(6):1203-17

Bioinformatics and Pattern Discovery Group, IBM Thomas J. Watson Research Center, Yorktown Heights, P.O. Box 218, NY 10598, USA.

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http://dx.doi.org/10.1016/j.cell.2006.07.031DOI Listing
September 2006

An extension and novel solution to the (l,d)-motif challenge problem.

Genome Inform 2004 ;15(2):63-71

Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

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https://www.jsbi.org/pdfs/journal1/GIW04/GIW04F007.pdf
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January 2006

A generic motif discovery algorithm for sequential data.

Bioinformatics 2006 Jan 27;22(1):21-8. Epub 2005 Oct 27.

Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti745DOI Listing
January 2006

Sensitive detection of sequence similarity using combinatorial pattern discovery: a challenging study of two distantly related protein families.

Proteins 2005 Dec;61(4):926-37

Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge, UK.

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http://dx.doi.org/10.1002/prot.20608DOI Listing
December 2005

A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes.

Nucleic Acids Res 2005 8;33(12):3699-707. Epub 2005 Jul 8.

New York University, Computer Science, New York, NY 10021, USA.

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http://dx.doi.org/10.1093/nar/gki660DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1174904PMC
July 2005

Evolution of distinct EGF domains with specific functions.

Protein Sci 2005 Apr;14(4):1091-103

Computational Biology and Bioinformatics Program, Victor Chang Cardiac Research Institute, 384 Victoria St., Darlinghurst, Sydney, NSW 2010, Australia.

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http://dx.doi.org/10.1110/ps.041207005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253431PMC
April 2005

A new computational method for the detection of horizontal gene transfer events.

Nucleic Acids Res 2005 16;33(3):922-33. Epub 2005 Feb 16.

New York University, Computer Science New York, NY 10021, USA.

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http://dx.doi.org/10.1093/nar/gki187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC549390PMC
March 2005

Transcriptional organization of the Clostridium acetobutylicum genome.

Nucleic Acids Res 2004 1;32(6):1973-81. Epub 2004 Apr 1.

Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.

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http://dx.doi.org/10.1093/nar/gkh509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC390361PMC
July 2004

The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W10-5

Bioinformatics and Pattern Discovery group, IBM T.J. Watson Research Center, PO Box 218, Yorktown Heights, NY 10598, USA.

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http://dx.doi.org/10.1093/nar/gkh367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441505PMC
July 2004

Metabolic and transcriptional patterns accompanying glutamine depletion and repletion in mouse hepatoma cells: a model for physiological regulatory networks.

Physiol Genomics 2004 Jan 15;16(2):247-55. Epub 2004 Jan 15.

Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1152/physiolgenomics.00088.2003DOI Listing
January 2004

Global secondary structure packing angle bias in proteins.

Proteins 2003 Nov;53(2):252-61

Bioinformatics and Pattern Discovery, IBM T. J. Watson Research Center, Yorktown Heights, New York, USA.

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http://dx.doi.org/10.1002/prot.10448DOI Listing
November 2003

Reevaluation of human cytomegalovirus coding potential.

Proc Natl Acad Sci U S A 2003 Nov 30;100(23):13585-90. Epub 2003 Oct 30.

Department of Molecular Biology, Princeton University, Princeton, NJ 80544, USA.

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http://dx.doi.org/10.1073/pnas.1735466100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC263857PMC
November 2003

Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors.

Nucleic Acids Res 2003 Aug;31(15):4625-31

Bioinformatics and Pattern Discovery Research Group, IBM Thomas J. Watson Research Center, PO Box 218, Yorktown Heights, NY 10598, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC169910PMC
http://dx.doi.org/10.1093/nar/gkg639DOI Listing
August 2003

The web server of IBM's Bioinformatics and Pattern Discovery group.

Nucleic Acids Res 2003 Jul;31(13):3645-50

Bioinformatics and Pattern Discovery Group, IBM TJ Watson Research Center, PO BOX 218, Yorktown Heights, NY 10598, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC169027PMC
http://dx.doi.org/10.1093/nar/gkg621DOI Listing
July 2003

In silico pattern-based analysis of the human cytomegalovirus genome.

J Virol 2003 Apr;77(7):4326-44

Bioinformatics and Pattern Discovery Group, IBM TJ Watson Research Center, Yorktown Heights, New York 10598, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC150618PMC
http://dx.doi.org/10.1128/jvi.77.7.4326-4344.2003DOI Listing
April 2003

The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.

Science 2002 Dec;298(5601):2157-67

U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1126/science.1080049DOI Listing
December 2002

Dictionary-driven protein annotation.

Nucleic Acids Res 2002 Sep;30(17):3901-16

Bioinformatics and Pattern Discovery Group, IBM TJ Watson Research Center, Yorktown Heights, NY 10598, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137405PMC
http://dx.doi.org/10.1093/nar/gkf464DOI Listing
September 2002

Dictionary-driven prokaryotic gene finding.

Nucleic Acids Res 2002 Jun;30(12):2710-25

Exploratory Technology, IBM Tokyo Research Laboratory, 1623-14 Shimotsuruma, Yamato-shi, Kanagawa 242-8502, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC117281PMC
http://dx.doi.org/10.1093/nar/gkf338DOI Listing
June 2002