Richard E Green

Richard E Green

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Richard E Green

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A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos.

BMC Genomics 2019 Dec 27;20(1):1023. Epub 2019 Dec 27.

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.

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http://dx.doi.org/10.1186/s12864-019-6355-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6935139PMC
December 2019

Structural Variation Detection by Proximity Ligation from Formalin-Fixed, Paraffin-Embedded Tumor Tissue.

J Mol Diagn 2019 May 31;21(3):375-383. Epub 2018 Dec 31.

Department of Pathology, Stanford University School of Medicine, Stanford, California; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15251578183017
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http://dx.doi.org/10.1016/j.jmoldx.2018.11.003DOI Listing
May 2019

New Approaches for Genome Assembly and Scaffolding.

Annu Rev Anim Biosci 2019 02 28;7:17-40. Epub 2018 Nov 28.

Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA; email: ,

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http://dx.doi.org/10.1146/annurev-animal-020518-115344DOI Listing
February 2019

Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA.

Proc Natl Acad Sci U S A 2018 09 10;115(39):9726-9731. Epub 2018 Sep 10.

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064;

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http://dx.doi.org/10.1073/pnas.1806447115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6166824PMC
September 2018

Epigenetic maintenance of topological domains in the highly rearranged gibbon genome.

Genome Res 2018 07 18;28(7):983-997. Epub 2018 Jun 18.

Bioinformatics and Computational Biology Division, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA.

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http://dx.doi.org/10.1101/gr.233874.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028127PMC
July 2018

Minimizing polymerase biases in metabarcoding.

Mol Ecol Resour 2018 May 24. Epub 2018 May 24.

Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California.

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http://dx.doi.org/10.1111/1755-0998.12895DOI Listing
May 2018

Ancient DNA Resolves the History of Tetragnatha (Araneae, Tetragnathidae) Spiders on Rapa Nui.

Genes (Basel) 2017 Dec 20;8(12). Epub 2017 Dec 20.

Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.3390/genes8120403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5748721PMC
December 2017

A phylogenetic approach for haplotype analysis of sequence data from complex mitochondrial mixtures.

Forensic Sci Int Genet 2017 09 29;30:93-105. Epub 2017 May 29.

Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1016/j.fsigen.2017.05.007DOI Listing
September 2017

AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data.

BMC Bioinformatics 2017 Apr 4;18(1):203. Epub 2017 Apr 4.

Department of Biomolecular Engineering, University of California, Santa Cruz, USA.

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http://dx.doi.org/10.1186/s12859-017-1613-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381037PMC
April 2017

Erratum to "Impact of uncertainty in soil, climatic, and chemical information in a pesticide leaching assessment".

J Contam Hydrol 2016 11 8;194:59-72. Epub 2016 Aug 8.

Department of Agronomy and Soil Science, University of Hawaii, Honolulu, HI 96822, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S01697722163005
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http://dx.doi.org/10.1016/j.jconhyd.2016.04.003DOI Listing
November 2016

The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae).

Mar Genomics 2016 Aug 16;28:107-112. Epub 2016 Mar 16.

Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95060, USA.

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http://dx.doi.org/10.1016/j.margen.2016.03.006DOI Listing
August 2016

Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data.

Philos Trans R Soc Lond B Biol Sci 2016 07;371(1699)

Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95060, USA

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http://dx.doi.org/10.1098/rstb.2015.0138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920339PMC
July 2016

Detecting hybridization using ancient DNA.

Mol Ecol 2016 Jun 23;25(11):2398-412. Epub 2016 Mar 23.

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5063030PMC
http://dx.doi.org/10.1111/mec.13556DOI Listing
June 2016

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.

Genome Res 2016 Mar 4;26(3):342-50. Epub 2016 Feb 4.

Dovetail Genomics LLC, Santa Cruz, California 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, California 95066, USA;

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http://dx.doi.org/10.1101/gr.193474.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772016PMC
March 2016

Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves.

Mol Ecol 2016 01 24;25(1):357-79. Epub 2015 Dec 24.

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E Young Dr East, Los Angeles, CA, 90095, USA.

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http://dx.doi.org/10.1111/mec.13467DOI Listing
January 2016

A method for positive forensic identification of samples from extremely low-coverage sequence data.

BMC Genomics 2015 Dec 7;16:1034. Epub 2015 Dec 7.

Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High St, Santa Cruz, CA, 95064, USA.

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http://dx.doi.org/10.1186/s12864-015-2241-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4672566PMC
December 2015

Genome-Directed Lead Discovery: Biosynthesis, Structure Elucidation, and Biological Evaluation of Two Families of Polyene Macrolactams against Trypanosoma brucei.

ACS Chem Biol 2015 Oct 13;10(10):2373-81. Epub 2015 Aug 13.

Department of Chemistry and Biochemistry, University of California Santa Cruz , Santa Cruz, California 95064, United States.

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http://dx.doi.org/10.1021/acschembio.5b00308DOI Listing
October 2015

Development. Aneuploidy and mother's genes.

Science 2015 Apr;348(6231):180-1

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95060, USA.

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http://dx.doi.org/10.1126/science.aab0877DOI Listing
April 2015

Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears.

Mol Ecol 2015 Mar 5;24(6):1205-17. Epub 2015 Feb 5.

Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA.

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http://dx.doi.org/10.1111/mec.13038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409089PMC
March 2015

Early mesozoic coexistence of amniotes and hepadnaviridae.

PLoS Genet 2014 Dec 11;10(12):e1004559. Epub 2014 Dec 11.

Department of Evolutionary Biology (EBC), Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1371/journal.pgen.1004559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263362PMC
December 2014

Comparative genomics reveals insights into avian genome evolution and adaptation.

Science 2014 Dec 11;346(6215):1311-20. Epub 2014 Dec 11.

China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Department of Medicine, University of Hong Kong, Hong Kong.

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http://jarvislab.net/wp-content/uploads/2014/12/Science-2014
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http://www.sciencemag.org/cgi/doi/10.1126/science.1251385
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http://dx.doi.org/10.1126/science.1251385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390078PMC
December 2014

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Authors:
Erich D Jarvis Siavash Mirarab Andre J Aberer Bo Li Peter Houde Cai Li Simon Y W Ho Brant C Faircloth Benoit Nabholz Jason T Howard Alexander Suh Claudia C Weber Rute R da Fonseca Jianwen Li Fang Zhang Hui Li Long Zhou Nitish Narula Liang Liu Ganesh Ganapathy Bastien Boussau Md Shamsuzzoha Bayzid Volodymyr Zavidovych Sankar Subramanian Toni Gabaldón Salvador Capella-Gutiérrez Jaime Huerta-Cepas Bhanu Rekepalli Kasper Munch Mikkel Schierup Bent Lindow Wesley C Warren David Ray Richard E Green Michael W Bruford Xiangjiang Zhan Andrew Dixon Shengbin Li Ning Li Yinhua Huang Elizabeth P Derryberry Mads Frost Bertelsen Frederick H Sheldon Robb T Brumfield Claudio V Mello Peter V Lovell Morgan Wirthlin Maria Paula Cruz Schneider Francisco Prosdocimi José Alfredo Samaniego Amhed Missael Vargas Velazquez Alonzo Alfaro-Núñez Paula F Campos Bent Petersen Thomas Sicheritz-Ponten An Pas Tom Bailey Paul Scofield Michael Bunce David M Lambert Qi Zhou Polina Perelman Amy C Driskell Beth Shapiro Zijun Xiong Yongli Zeng Shiping Liu Zhenyu Li Binghang Liu Kui Wu Jin Xiao Xiong Yinqi Qiuemei Zheng Yong Zhang Huanming Yang Jian Wang Linnea Smeds Frank E Rheindt Michael Braun Jon Fjeldsa Ludovic Orlando F Keith Barker Knud Andreas Jønsson Warren Johnson Klaus-Peter Koepfli Stephen O'Brien David Haussler Oliver A Ryder Carsten Rahbek Eske Willerslev Gary R Graves Travis C Glenn John McCormack Dave Burt Hans Ellegren Per Alström Scott V Edwards Alexandros Stamatakis David P Mindell Joel Cracraft Edward L Braun Tandy Warnow Wang Jun M Thomas P Gilbert Guojie Zhang

Science 2014 Dec;346(6215):1320-31

China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1126/science.1253451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904PMC
December 2014

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Science 2014 Dec 11;346(6215):1254449. Epub 2014 Dec 11.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

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http://jarvislab.net/wp-content/uploads/2012/02/Green-et-al-
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http://www.sciencemag.org/cgi/doi/10.1126/science.1254449
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http://dx.doi.org/10.1126/science.1254449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873PMC
December 2014

Transoceanic drift and the domestication of African bottle gourds in the Americas.

Proc Natl Acad Sci U S A 2014 Feb 10;111(8):2937-41. Epub 2014 Feb 10.

Department of Anthropology and Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA 16802.

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http://dx.doi.org/10.1073/pnas.1318678111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3939861PMC
February 2014

Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution.

PLoS Genet 2013 14;9(3):e1003345. Epub 2013 Mar 14.

Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America.

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https://dx.plos.org/10.1371/journal.pgen.1003345
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http://dx.doi.org/10.1371/journal.pgen.1003345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597504PMC
June 2013

Human evolution: turning back the clock.

Curr Biol 2013 Apr;23(7):R286-8

Department of Biomolecular Engineering, University of California, Santa Cruz, USA.

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http://dx.doi.org/10.1016/j.cub.2013.02.050DOI Listing
April 2013

A mouse following in the footsteps of human prehistory.

Cell 2013 Feb;152(4):667-8

Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1016/j.cell.2013.01.039DOI Listing
February 2013

Evolution of a tissue-specific splicing network.

Genes Dev 2011 Mar;25(6):608-20

Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA.

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http://genesdev.cshlp.org/content/25/6/608.full.pdf
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http://genesdev.cshlp.org/lookup/doi/10.1101/gad.2009011
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http://dx.doi.org/10.1101/gad.2009011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059834PMC
March 2011

Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants.

PLoS Biol 2010 Dec 21;8(12):e1000564. Epub 2010 Dec 21.

Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1000564DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3006346PMC
December 2010

Computational challenges in the analysis of ancient DNA.

Genome Biol 2010 6;11(5):R47. Epub 2010 May 6.

Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.

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http://dx.doi.org/10.1186/gb-2010-11-5-r47DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898072PMC
September 2010

The Neandertal genome and ancient DNA authenticity.

EMBO J 2009 Sep 6;28(17):2494-502. Epub 2009 Aug 6.

Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

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http://dx.doi.org/10.1038/emboj.2009.222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2725275PMC
September 2009

PatMaN: rapid alignment of short sequences to large databases.

Bioinformatics 2008 Jul 8;24(13):1530-1. Epub 2008 May 8.

Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btn223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718670PMC
July 2008

The joint allele-frequency spectrum in closely related species.

Genetics 2007 Sep 1;177(1):387-98. Epub 2007 Jul 1.

Department of Integrative Biology, University of California, Berkeley, California 94720, USA.

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http://www.genetics.org/lookup/doi/10.1534/genetics.107.0707
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http://dx.doi.org/10.1534/genetics.107.070730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2013700PMC
September 2007

Patterns of damage in genomic DNA sequences from a Neandertal.

Proc Natl Acad Sci U S A 2007 Sep 21;104(37):14616-21. Epub 2007 Aug 21.

Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany.

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http://dx.doi.org/10.1073/pnas.0704665104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976210PMC
September 2007

Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements.

Nature 2007 Apr 14;446(7138):926-9. Epub 2007 Mar 14.

Department of Molecular and Cell Biology and, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1038/nature05676DOI Listing
April 2007

Analysis of one million base pairs of Neanderthal DNA.

Nature 2006 Nov;444(7117):330-6

Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany.

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http://dx.doi.org/10.1038/nature05336DOI Listing
November 2006

Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap.

Bioinformatics 2005 Oct 16;21(20):3824-31. Epub 2005 Aug 16.

Department of Bioengineering, University of California, Berkeley, 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti627DOI Listing
October 2005

Pairwise alignment incorporating dipeptide covariation.

Bioinformatics 2005 Oct 25;21(19):3704-10. Epub 2005 Aug 25.

Department of Plant and Microbial Biology 111 Koshland Hall #3102 University of California, Berkeley, CA 94720-3102, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti616DOI Listing
October 2005

Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila.

Genes Dev 2005 Jun;19(11):1306-14

Department of Molecular and Cell Biology, Center for Integrative Genomics, Plant and Microbial Biology, University of California, Berkeley, 94720-3204 USA.

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http://dx.doi.org/10.1101/gad.1314205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1142554PMC
June 2005

An unappreciated role for RNA surveillance.

Genome Biol 2004 2;5(2):R8. Epub 2004 Feb 2.

Department of Bioengineering, University of California, Berkeley, CA 94720-3102, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2004-5-2-r8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC395752PMC
March 2005

Widespread predicted nonsense-mediated mRNA decay of alternatively-spliced transcripts of human normal and disease genes.

Bioinformatics 2003 ;19 Suppl 1:i118-21

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg1015DOI Listing
October 2004

The evolving roles of alternative splicing.

Curr Opin Struct Biol 2004 Jun;14(3):273-82

Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S0959440X0400076
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http://dx.doi.org/10.1016/j.sbi.2004.05.002DOI Listing
June 2004

Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs.

Mol Cell 2004 Jun;14(6):775-86

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.molcel.2004.06.012DOI Listing
June 2004

Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans.

Proc Natl Acad Sci U S A 2003 Jan 26;100(1):189-92. Epub 2002 Dec 26.

Department of Plant and Microbial Biology, Graduate Group, University of California, Berkeley, 94720, USA.

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http://dx.doi.org/10.1073/pnas.0136770100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC140922PMC
January 2003

Sulfotransferases and sulfatases in mycobacteria.

Chem Biol 2002 Jul;9(7):767-76

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/s1074-5521(02)00175-8DOI Listing
July 2002