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Shared Support Member - Cold Spring Harbor Laboratory

CSHL is a research and educational institution. The laboratory has research programs focusing on cancer, neurobiology, plant genetics, genomics and bioinformatics, and a broad educational mission, including the recently established Watston School of Biological Sciences.

http://www.cshl.org

Research staff and students at Cold Spring Harbor Laboratory:

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Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at Cold Spring Harbor Laboratory

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	51.	Research High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans Arun K Ramani, Andrew C Nelson, Philipp Kapranov, Ian Bell, Thomas R Gingeras, Andrew G Fraser Genome Biology 2009, 10:R101 (24 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The high-resolution transcriptome of wild-type and nonsense-mediated decay (NMD) defective C. elegans during development reveals insights into the NMD pathway and it’s role in development.
	52.	Software SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services Damian DG Gessler, Gary S Schiltz, Greg D May, Shulamit Avraham, Christopher D Town, David Grant, Rex T Nelson BMC Bioinformatics 2009, 10:309 (23 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	53.	Research article *An archived activation tagged population of Arabidopsis thaliana* to facilitate forward genetics approaches** Stephen J Robinson, Lily H Tang, Brent AG Mooney, Sheldon J McKay, Wayne E Clarke, Matthew G Links, Steven Karcz, Sharon Regan, Yun-Yun Wu, Margaret Y Gruber, Dejun Cui, Min Yu, Isobel AP Parkin BMC Plant Biology 2009, 9:101 (31 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	54.	Research article *A Myc-regulated transcriptional network controls B-cell fate in response to BCR triggering* Jernej Murn, Irena Mlinaric-Rascan, Pierre Vaigot, Olivier Alibert, Vincent Frouin, Xavier Gidrol BMC Genomics 2009, 10:323 (17 July 2009) Abstract \| Full text \| PDF \| PubMed
	55.	Poster presentation Is the formation of ocular dominance patterns instructed by molecular labels? Dmitry Tsigankov, Alexei Koulakov BMC Neuroscience 2009, 10(Suppl 1):P65 (13 July 2009) Full text \| PDF
	56.	Research article GAGE: generally applicable gene set enrichment for pathway analysis Weijun Luo, Michael S Friedman, Kerby Shedden, Kurt D Hankenson, Peter J Woolf BMC Bioinformatics 2009, 10:161 (27 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	57.	Research article Determination of enriched histone modifications in non-genic portions of the human genome Jeffrey A Rosenfeld, Zhibin Wang, Dustin E Schones, Keji Zhao, Rob DeSalle, Michael Q Zhang BMC Genomics 2009, 10:143 (31 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	58.	Research article A mouse chromosome 4 balancer ENU-mutagenesis screen isolates eleven lethal lines Melissa K Boles, Bonney M Wilkinson, Andrea Maxwell, Lihua Lai, Alea A Mills, Ichiko Nishijima, Andrew P Salinger, Ivan Moskowitz, Karen K Hirschi, Bin Liu, Allan Bradley, Monica J Justice BMC Genetics 2009, 10:12 (6 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	59.	Research article Gene set-based module discovery in the breast cancer transcriptome Atsushi Niida, Andrew D Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q Zhang, Tetsu Akiyama BMC Bioinformatics 2009, 10:71 (26 February 2009) Abstract \| Full text \| PDF \| PubMed
	60.	Correction Correction: Reactome: a knowledge base of biologic pathways and processes Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Gopal Gopinath, David Croft, Bernard de Bono, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein Genome Biology 2009, 10:402 (4 February 2009) Abstract \| Full text \| PDF \| PubMed
	61.	Introduction The Seventh Asia Pacific Bioinformatics Conference (APBC2009) Michael Q Zhang, Michael S Waterman, Xuegong Zhang BMC Bioinformatics 2009, 10(Suppl 1):S1 (30 January 2009) Full text \| PDF \| PubMed
	62.	Research article nGASP – the nematode genome annotation assessment project Avril Coghlan, Tristan J Fiedler, Sheldon J McKay, Paul Flicek, Todd W Harris, Darin Blasiar, Lincoln D Stein BMC Bioinformatics 2008, 9:549 (19 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	63.	Opinion Bioinformatics: alive and kicking Lincoln D Stein Genome Biology 2008, 9:114 (17 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bioinformatics is alive and well in 2008 concludes Lincoln Stein, despite his earlier prediction of its imminent demise.
	64.	Research article Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information Weijun Luo, Kurt D Hankenson, Peter J Woolf BMC Bioinformatics 2008, 9:467 (3 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	65.	Research article Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats Thomas Wicker, Apurva Narechania, Francois Sabot, Joshua Stein, Giang TH Vu, Andreas Graner, Doreen Ware, Nils Stein BMC Genomics 2008, 9:518 (31 October 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	66.	Research article Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells Atsushi Niida, Andrew D Smith, Seiya Imoto, Shuichi Tsutsumi, Hiroyuki Aburatani, Michael Q Zhang, Tetsu Akiyama BMC Bioinformatics 2008, 9:404 (29 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	67.	Software Kismeth: Analyzer of plant methylation states through bisulfite sequencing Eyal Gruntman, Yijun Qi, R Keith Slotkin, Ted Roeder, Robert A Martienssen, Ravi Sachidanandam BMC Bioinformatics 2008, 9:371 (11 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	68.	Research article Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors LO Baumbusch, J Aarøe, FE Johansen, J Hicks, H Sun, L Bruhn, K Gunderson, B Naume, VN Kristensen, K Liestøl, A-L Børresen-Dale, OC Lingjærde BMC Genomics 2008, 9:379 (8 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	69.	Software GMODWeb: a web framework for the generic model organism database Brian D O'Connor, Allen Day, Scott Cain, Olivier Arnaiz, Linda Sperling, Lincoln D Stein Genome Biology 2008, 9:R102 (20 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GMODWeb is a software framework designed to speed the development of websites for model organism databases.
	70.	Research article Using quality scores and longer reads improves accuracy of Solexa read mapping Andrew D Smith, Zhenyu Xuan, Michael Q Zhang BMC Bioinformatics 2008, 9:128 (28 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	71.	Method Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza HyeRan Kim, Bonnie Hurwitz, Yeisoo Yu, Kristi Collura, Navdeep Gill, Phillip SanMiguel, James C Mullikin, Christopher Maher, William Nelson, Marina Wissotski, Michele Braidotti, David Kudrna, José Goicoechea, Lincoln Stein, Doreen Ware, Scott A Jackson, Carol Soderlund, Rod A Wing Genome Biology 2008, 9:R45 (28 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bacterial artificial chromosome (BAC) fingerprint and end-sequenced physical maps representing the ten genome types of Oryza are presented
	72.	Proceedings Mixture modeling of microarray gene expression data Yang Yang, Adam P Tashman, Jung Lee, Seungtai Yoon, Wenyang Mao, Kwangmi Ahn, Wonkuk Kim, Nancy R Mendell, Derek Gordon, Stephen J Finch BMC Proceedings 2007, 1(Suppl 1):S50 (18 December 2007) Abstract \| Full text \| PDF \| PubMed
	73.	Review Computational analyses of eukaryotic promoters Michael Q Zhang BMC Bioinformatics 2007, 8(Suppl 6):S3 (27 September 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	74.	Software Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context Jeremiah J Faith, Andrew J Olson, Timothy S Gardner, Ravi Sachidanandam BMC Bioinformatics 2007, 8:344 (18 September 2007) Abstract \| Full text \| PDF \| PubMed
	75.	Research article *A highly conserved regulatory element controls hematopoietic expression of GATA-2* in zebrafish** Zhongan Yang, Hong Jiang, Fang Zhao, Deepa B Shankar, Kathleen M Sakamoto, Michael Q Zhang, Shuo Lin BMC Developmental Biology 2007, 7:97 (20 August 2007) Abstract \| Full text \| PDF \| PubMed