Sol Katzman

Sol Katzman

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Sol Katzman

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Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome.

PLoS Genet 2019 Aug 22;15(8):e1008249. Epub 2019 Aug 22.

Center for Molecular Biology of RNA, Department of Molecular, Cell & Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1008249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6726248PMC
August 2019

Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes.

Stem Cell Reports 2019 Feb 10;12(2):245-257. Epub 2019 Jan 10.

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1016/j.stemcr.2018.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372947PMC
February 2019

Prp8 impacts cryptic but not alternative splicing frequency.

Proc Natl Acad Sci U S A 2019 02 23;116(6):2193-2199. Epub 2019 Jan 23.

Department of Molecular, Cellular, and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, CA 95064;

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http://dx.doi.org/10.1073/pnas.1819020116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369775PMC
February 2019

FOXG1 Orchestrates Neocortical Organization and Cortico-Cortical Connections.

Neuron 2018 12 1;100(5):1083-1096.e5. Epub 2018 Nov 1.

Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health & Science University, Portland, OR 97239, USA; Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S08966273183090
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http://dx.doi.org/10.1016/j.neuron.2018.10.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6428593PMC
December 2018

Neonatal Tbr1 Dosage Controls Cortical Layer 6 Connectivity.

Neuron 2018 11 11;100(4):831-845.e7. Epub 2018 Oct 11.

Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S08966273183082
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http://dx.doi.org/10.1016/j.neuron.2018.09.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6250594PMC
November 2018

SNRP-27, the homolog of the tri-snRNP 27K protein, has a role in 5' splice site positioning in the spliceosome.

RNA 2018 10 13;24(10):1314-1325. Epub 2018 Jul 13.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1261/rna.066878.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6140464PMC
October 2018

HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo.

Genome Res 2018 05 12;28(5):689-698. Epub 2018 Apr 12.

Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1101/gr.229062.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932609PMC
May 2018

Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay.

Proc Natl Acad Sci U S A 2018 01 16;115(5):968-973. Epub 2018 Jan 16.

Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642;

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http://dx.doi.org/10.1073/pnas.1715531115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798355PMC
January 2018

Autogenous cross-regulation of mRNA processing and translation balances functions in splicing and translation.

Genes Dev 2017 09 11;31(18):1894-1909. Epub 2017 Oct 11.

Sinsheimer Laboratories, Department of Molecular, Cell, and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz. Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1101/gad.302059.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5695090PMC
September 2017

Preferential expression of scores of functionally and evolutionarily diverse DNA and RNA-binding proteins during Oxytricha trifallax macronuclear development.

PLoS One 2017 16;12(2):e0170870. Epub 2017 Feb 16.

Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170870PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5312943PMC
August 2017

Modulation of nonsense mediated decay by rapamycin.

Nucleic Acids Res 2017 04;45(6):3448-3459

University of California Santa Cruz, Department of Molecular, Cellular and Developmental Biology, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkw1109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389481PMC
April 2017

TBR1 regulates autism risk genes in the developing neocortex.

Genome Res 2016 08 20;26(8):1013-22. Epub 2016 Jun 20.

Department of Computer Science, Stanford University, Stanford, California 94305, USA; Department of Developmental Biology, Stanford University, Stanford, California 94305, USA; Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1101/gr.203612.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971772PMC
August 2016

Mutual regulation between Satb2 and Fezf2 promotes subcerebral projection neuron identity in the developing cerebral cortex.

Proc Natl Acad Sci U S A 2015 Sep 31;112(37):11702-7. Epub 2015 Aug 31.

Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064;

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http://dx.doi.org/10.1073/pnas.1504144112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4577201PMC
September 2015

Coordinated tissue-specific regulation of adjacent alternative 3' splice sites in C. elegans.

Genome Res 2015 Jul 28;25(7):982-94. Epub 2015 Apr 28.

Department of Molecular, Cell, and Developmental Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA;

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http://dx.doi.org/10.1101/gr.186783.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484395PMC
July 2015

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.

Nature 2014 Dec 28;516(7530):242-5. Epub 2014 Sep 28.

1] Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA [2] Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1038/nature13760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4268317PMC
December 2014

Multiple conserved regulatory domains promote Fezf2 expression in the developing cerebral cortex.

Neural Dev 2014 Mar 12;9. Epub 2014 Mar 12.

Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.

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http://dx.doi.org/10.1186/1749-8104-9-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4008173PMC
March 2014

Nuclear factor one B regulates neural stem cell differentiation and axonal projection of corticofugal neurons.

J Comp Neurol 2014 Jan;522(1):6-35

Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064.

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http://doi.wiley.com/10.1002/cne.23373
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http://dx.doi.org/10.1002/cne.23373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058429PMC
January 2014

Frac-seq reveals isoform-specific recruitment to polyribosomes.

Genome Res 2013 Oct 19;23(10):1615-23. Epub 2013 Jun 19.

Biomolecular Engineering Department, Jack Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA;

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http://dx.doi.org/10.1101/gr.148585.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3787259PMC
October 2013

Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons.

Cancer Res 2013 Oct 12;73(19):6036-45. Epub 2013 Aug 12.

Authors' Affiliations: Five3 Genomics, LLC; Center for Biomolecular Science and Engineering, University of California; Howard Hughes Medical Institute, Santa Cruz, California; Human Oncology & Pathogenesis Program and Department of Neurosurgery; Cytogenetics Laboratory, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York; Departments of Neurology & Neurosurgery, Henry Ford Hospital, Detroit, Michigan; and Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.

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http://dx.doi.org/10.1158/0008-5472.CAN-13-0186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3800429PMC
October 2013

Competition between pre-mRNAs for the splicing machinery drives global regulation of splicing.

Mol Cell 2013 Aug 25;51(3):338-48. Epub 2013 Jul 25.

Center for Molecular Biology of RNA, Department of Molecular, Cell & Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1016/j.molcel.2013.06.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3771316PMC
August 2013

Gene isoform specificity through enhancer-associated antisense transcription.

PLoS One 2012 24;7(8):e43511. Epub 2012 Aug 24.

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043511PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427357PMC
April 2013

Mating of the stichotrichous ciliate Oxytricha trifallax induces production of a class of 27 nt small RNAs derived from the parental macronucleus.

PLoS One 2012 10;7(8):e42371. Epub 2012 Aug 10.

Department of Molecular, Cell and Developmental Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0042371PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416858PMC
March 2013

Human tRNA genes function as chromatin insulators.

EMBO J 2012 Jan 15;31(2):330-50. Epub 2011 Nov 15.

Department of MCD Biology, University of California, Santa Cruz, CA, USA.

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http://dx.doi.org/10.1038/emboj.2011.406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261562PMC
January 2012

Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots.

Genome Biol Evol 2011 21;3:614-26. Epub 2011 Jun 21.

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, USA.

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https://academic.oup.com/gbe/article/doi/10.1093/gbe/evr058/
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http://dx.doi.org/10.1093/gbe/evr058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157837PMC
December 2011

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.

Nat Methods 2010 Dec 7;7(12):995-1001. Epub 2010 Nov 7.

Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA.

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http://dx.doi.org/10.1038/nmeth.1529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3247016PMC
December 2010

GC-biased evolution near human accelerated regions.

PLoS Genet 2010 May 20;6(5):e1000960. Epub 2010 May 20.

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873926PMC
May 2010

PREDICT-2ND: a tool for generalized protein local structure prediction.

Bioinformatics 2008 Nov 30;24(21):2453-9. Epub 2008 Aug 30.

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

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http://dx.doi.org/10.1093/bioinformatics/btn438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732275PMC
November 2008

Human genome ultraconserved elements are ultraselected.

Science 2007 Aug;317(5840):915

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

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http://dx.doi.org/10.1126/science.1142430DOI Listing
August 2007

Forces shaping the fastest evolving regions in the human genome.

PLoS Genet 2006 Oct 23;2(10):e168. Epub 2006 Aug 23.

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0020168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1599772PMC
October 2006

An RNA gene expressed during cortical development evolved rapidly in humans.

Nature 2006 Sep 16;443(7108):167-72. Epub 2006 Aug 16.

Center for Biomolecular Science & Engineering, Department of Molecular, Cell & Developmental Biology, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1038/nature05113DOI Listing
September 2006

SAM-T04: what is new in protein-structure prediction for CASP6.

Proteins 2005 ;61 Suppl 7:135-42

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

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http://dx.doi.org/10.1002/prot.20730DOI Listing
May 2006

Differential expression of novel potential regulators in hematopoietic stem cells.

PLoS Genet 2005 Sep;1(3):e28

Department of Pathology, Institute of Cancer and Stem Cell Biology and Medicine, Stanford University Medical School, Stanford, California, USA.

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http://dx.plos.org/10.1371/journal.pgen.0010028
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http://dx.doi.org/10.1371/journal.pgen.0010028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1200425PMC
September 2005