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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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	26.	Review Following the genes: a framework for animal modeling of psychiatric disorders Kevin J Mitchell, Z Josh Huang, Bita Moghaddam, Akira Sawa BMC Biology 2011, 9:76 (11 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Following a brief overview of the revolution in psychiatric genetics, Kevin Mitchell and colleagues explain how the effects of causal mutations can be studied in animals to elucidate pathogenic mechanisms and neurobiological phenotypes of direct relevance to human disease.
	27.	Research article *Functional annotation of the transcriptome of Sorghum bicolor* in response to osmotic stress and abscisic acid** Diana V Dugas, Marcela K Monaco, Andrew Olson, Robert R Klein, Sunita Kumari, Doreen Ware, Patricia E Klein BMC Genomics 2011, 12:514 (18 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	28.	Research article Establishing the baseline level of repetitive element expression in the human cortex Svitlana Tyekucheva, Robert H Yolken, W McCombie, Jennifer Parla, Melissa Kramer, Sarah J Wheelan, Sarven Sabunciyan BMC Genomics 2011, 12:495 (10 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	29.	Research A comparative analysis of exome capture Jennifer S Parla, Ivan Iossifov, Ian Grabill, Mona S Spector, Melissa Kramer, W Richard McCombie Genome Biology 2011, 12:R97 (29 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The coverage of two solution exome capture kits is compared
	30.	Method Mutation discovery in mice by whole exome sequencing Heather Fairfield, Griffith J Gilbert, Mary Barter, Rebecca R Corrigan, Michelle Curtain, Yueming Ding, Mark D'Ascenzo, Daniel J Gerhardt, Chao He, Wenhui Huang, Todd Richmond, Lucy Rowe, Frank J Probst, David E Bergstrom, Stephen A Murray, Carol Bult, Joel Richardson, Benjamin T Kile, Ivo Gut, Jorg Hager, Snaevar Sigurdsson, Evan Mauceli, Federica Di Palma, Kerstin Lindblad-Toh, Michael L Cunningham, Timothy C Cox, Monica J Justice, Mona S Spector, Scott W Lowe, Thomas Albert, Leah Donahue, Jeffrey Jeddeloh, Jay Shendure, Laura G Reinholdt et al. Genome Biology 2011, 12:R86 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary In solution capture reagents are developed for the mouse exome and demonstrated in multiple inbred strains and novel mutant strains
	31.	Research article Integrative network analysis identifies key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma Siyuan Zheng, William P Tansey, Scott W Hiebert, Zhongming Zhao BMC Medical Genomics 2011, 4:62 (8 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	32.	Review Future medical applications of single-cell sequencing in cancer Nicholas Navin, James Hicks Genome Medicine 2011, 3:31 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Navin and Hicks provide an overview of recent methods for sequencing in single cells and discuss how this approach will be useful for detection of copy number variation for improving cancer outcomes.
	33.	Research article Time series gene expression profiling and temporal regulatory pathway analysis of BMP6 induced osteoblast differentiation and mineralization Weijun Luo, Michael S Friedman, Kurt D Hankenson, Peter J Woolf BMC Systems Biology 2011, 5:82 (23 May 2011) Abstract \| Full text \| PDF \| PubMed
	34.	Software PeakRanger: A cloud-enabled peak caller for ChIP-seq data Xin Feng, Robert Grossman, Lincoln Stein BMC Bioinformatics 2011, 12:139 (9 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	35.	Research article Spliceosomal intron size expansion in domesticated grapevine (Vitis vinifera) Ke Jiang, Leslie R Goertzen BMC Research Notes 2011, 4:52 (8 March 2011) Abstract \| Full text \| PDF \| PubMed
	36.	Editorial 3D culture reveals a signaling network Senthil K Muthuswamy Breast Cancer Research 2011, 13:103 (27 January 2011) Abstract \| Full text \| PDF \| PubMed
	37.	Research article Sperry versus Hebb: Topographic mapping in Isl2/EphA3 mutant mice Dmitry Tsigankov, Alexei A Koulakov BMC Neuroscience 2010, 11:155 (29 December 2010) Abstract \| Full text \| PDF \| PubMed
	38.	Software Quake: quality-aware detection and correction of sequencing errors David R Kelley, Michael C Schatz, Steven L Salzberg Genome Biology 2010, 11:R116 (29 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Quake employs a sophisticated approach to error identification and correction in next generation sequencing data.
	39.	Research article Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs Vamsi K Kundeti, Sanguthevar Rajasekaran, Hieu Dinh, Matthew Vaughn, Vishal Thapar BMC Bioinformatics 2010, 11:560 (15 November 2010) Abstract \| Full text \| PDF \| PubMed
	40.	Research article Localizing triplet periodicity in DNA and cDNA sequences Liya Wang, Lincoln D Stein BMC Bioinformatics 2010, 11:550 (8 November 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	41.	Selected oral presentation From identification to validation to gene count Clara Amid, Adam Frankish, Bronwen Aken, Iakes Ezkurdia, Felix Kokocinsk, James Gilbert, Simon White, Piero Carninci, Thomas Gingeras, Roderic Guigo, Steve Searle, Michael L Tress, Jennifer Harrow, Tim Hubbard Genome Biology 2010, 11(Suppl 1):O1 (11 October 2010) Full text \| PDF
	42.	Research highlight The missing graphical user interface for genomics Michael C Schatz Genome Biology 2010, 11:128 (25 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Galaxy package for genomic analysis empowers regular users through a much-needed and user-friendly graphical web interface.
	43.	Research Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration Rex T Nelson, Shulamit Avraham, Randy C Shoemaker, Gregory D May, Doreen Ware, Damian DG Gessler BioData Mining 2010, 3:3 (4 June 2010) Abstract \| Full text \| PDF \| PubMed
	44.	Research A human functional protein interaction network and its application to cancer data analysis Guanming Wu, Xin Feng, Lincoln Stein Genome Biology 2010, 11:R53 (19 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A high-quality human functional protein interaction network is constructed. Its utility is demonstrated in the identification of cancer candidate genes.
	45.	Methodology article Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome Hideaki Mizuno, Gurinder Atwal, Haijian Wang, Arnold J Levine, Alexei Vazquez BMC Genetics 2010, 11:27 (23 April 2010) Abstract \| Full text \| PDF \| PubMed
	46.	Review Insulin receptor signaling in the development of neuronal structure and function Shu-Ling Chiu, Hollis T Cline Neural Development 2010, 5:7 (15 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	47.	Research Development of the human cancer microRNA network Sanghamitra Bandyopadhyay, Ramkrishna Mitra, Ujjwal Maulik, Michael Q Zhang Silence 2010, 1:6 (2 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Cancer-microRNA network elucidates the association between miRNAs and cancer types. The network indicates neighboring miRNAs are differentially co-expressed, and could be used to detect miRNAs with strong onco/ tumor suppressor characteristics.
	48.	Research article Transcriptional changes in response to X chromosome dosage in the mouse: implications for X inactivation and the molecular basis of Turner Syndrome Alexandra M Lopes, Paul S Burgoyne, Andrew Ojarikre, Julien Bauer, Carole A Sargent, António Amorim, Nabeel A Affara BMC Genomics 2010, 11:82 (1 February 2010) Abstract \| Full text \| PDF \| PubMed
	49.	Research SFSSClass: an integrated approach for miRNA based tumor classification Ramkrishna Mitra, Sanghamitra Bandyopadhyay, Ujjwal Maulik, Michael Q Zhang BMC Bioinformatics 2010, 11(Suppl 1):S22 (18 January 2010) Abstract \| Full text \| PDF \| PubMed
	50.	Oral presentation Chronux: a platform for analyzing neural signals Hemant S Bokil, Peter Andrews, Hiren Maniar, Bijan Pesaran, Jayant Kulkarni, Catherine Loader, Partha P Mitra BMC Neuroscience 2009, 10(Suppl 1):S3 (29 September 2009) Full text \| PDF