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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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	1.	Opinion Sixty years of genome biology W Doolittle, Peter Fraser, Mark B Gerstein, Brenton R Graveley, Steven Henikoff, Curtis Huttenhower, Alicia Oshlack, Chris P Ponting, John L Rinn, Michael C Schatz, Jernej Ule, Detlef Weigel, George M Weinstock Genome Biology 2013, 14:113 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Members of Genome Biology's Editorial Board select their highlights from the 60 years of genome biology that followed the double helix
	2.	Proceedings Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA) Jesse Gillis, Paul Pavlidis BMC Bioinformatics 2013, 14(Suppl 3):S15 (22 April 2013) Abstract \| Full text \| PDF \| PubMed
	3.	Research Whole-genome sequencing in an autism multiplex family Lingling Shi, Xu Zhang, Ryan Golhar, Frederick G Otieno, Mingze He, Cuiping Hou, Cecilia Kim, Brendan Keating, Gholson J Lyon, Kai Wang, Hakon Hakonarson Molecular Autism 2013, 4:8 (18 April 2013) Abstract \| Full text \| PDF \| PubMed
	4.	Research Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing Jason O'Rawe, Tao Jiang, Guangqing Sun, Yiyang Wu, Wei Wang, Jingchu Hu, Paul Bodily, Lifeng Tian, Hakon Hakonarson, W Evan Johnson, Zhi Wei, Kai Wang, Gholson J Lyon Genome Medicine 2013, 5:28 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Head-to-head comparison of widely used variant calling pipelines including SOAP, GATK and Complete Genomics using default parameters reveals discrepancies between the pipelines.
	5.	Research article Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process Liya Wang, Lincoln D Stein BMC Evolutionary Biology 2013, 13:57 (28 February 2013) Abstract \| Full text \| PDF \| PubMed
	6.	Research *Improvement of the Oryza sativa* Nipponbare reference genome using next generation sequence and optical map data** Yoshihiro Kawahara, Melissa de la Bastide, John P Hamilton, Hiroyuki Kanamori, W Richard McCombie, Shu Ouyang, David C Schwartz, Tsuyoshi Tanaka, Jianzhong Wu, Shiguo Zhou, Kevin L Childs, Rebecca M Davidson, Haining Lin, Lina Quesada-Ocampo, Brieanne Vaillancourt, Hiroaki Sakai, Sung Shin Lee, Jungsok Kim, Hisataka Numa, Takeshi Itoh, C Robin Buell, Takashi Matsumoto Rice 2013, 6:4 (6 February 2013) Abstract \| Full text \| PDF
	7.	Software Kerfuffle: a web tool for multi-species gene colocalization analysis Robert Aboukhalil, Bernard Fendler, Gurinder S Atwal BMC Bioinformatics 2013, 14:22 (17 January 2013) Abstract \| Full text \| PDF \| PubMed
	8.	Software The taxonomic name resolution service: an online tool for automated standardization of plant names Brad Boyle, Nicole Hopkins, Zhenyuan Lu, Juan Antonio Raygoza Garay, Dmitry Mozzherin, Tony Rees, Naim Matasci, Martha L Narro, William H Piel, Sheldon J Mckay, Sonya Lowry, Chris Freeland, Robert K Peet, Brian J Enquist BMC Bioinformatics 2013, 14:16 (16 January 2013) Abstract \| Full text \| PDF \| PubMed
	9.	Comment Computational thinking in the era of big data biology Michael C Schatz Genome Biology 2012, 13:177 (29 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary by Mike Schatz
	10.	Musings Broad applications of single-cell nucleic acid analysis in biomedical research Michael Wigler Genome Medicine 2012, 4:79 (30 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Following the advent of single-cell analyses, Michael Wigler muses on how these will be valuable in the study and diagnosis of diseases other than cancer, as well as in basic cell biology.
	11.	Research article Unique small RNA signatures uncovered in the tammar wallaby genome James Lindsay, Dawn M Carone, Judy Brown, Laura Hall, Sohaib Qureshi, Sarah E Mitchell, Nicholas Jannetty, Greg Hannon, Marilyn Renfree, Andrew Pask, Michael O’Neill, Rachel O’Neill BMC Genomics 2012, 13:559 (17 October 2012) Abstract \| Full text \| PDF \| PubMed
	12.	Methodology *FACS-based purification of Arabidopsis* microspores, sperm cells and vegetative nuclei** Filipe Borges, Rui Gardner, Telma Lopes, Joseph P Calarco, Leonor C Boavida, R Slotkin, Robert A Martienssen, Jörg D Becker Plant Methods 2012, 8:44 (17 October 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary The paper provides simple and efficient FACS-based purification protocols for Arabidopsis microspores, vegetative nuclei and sperm cells.
	13.	Oral presentation Illuminating the genetics of complex human diseases Michael C Schatz BMC Proceedings 2012, 6(Suppl 6):O4 (1 October 2012) Full text \| PDF
	14.	Research article Cul4B regulates neural progenitor cell growth Helio C Liu, Grigori Enikolopov, Yuzhi Chen BMC Neuroscience 2012, 13:112 (19 September 2012) Abstract \| Full text \| PDF \| PubMed
	15.	Research Modeling gene expression using chromatin features in various cellular contexts Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng Genome Biology 2012, 13:R53 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method
	16.	Open letter An encyclopedia of mouse DNA elements (Mouse ENCODE) John A Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Thomas Gingeras, David M Gilbert, Mark Groudine, Michael Bender, Rajinder Kaul, Theresa Canfield, Erica Giste, Audra Johnson, Mia Zhang, Gayathri Balasundaram, Rachel Byron, Vaughan Roach, Peter J Sabo, Richard Sandstrom, A Sandra Stehling, Robert E Thurman, Sherman M Weissman, Philip Cayting, Manoj Hariharan, Jin Lian, Yong Cheng, Stephen G Landt, Zhihai Ma, Barbara J Wold, Job Dekker et al. Genome Biology 2012, 13:418 (13 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome
	17.	Review Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress Gholson J Lyon, Kai Wang Genome Medicine 2012, 4:58 (26 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gholson Lyon and Kai Wang review the challenges in applying genome sequencing to identify and catalog disease mutations, and they consider how to facilitate better collaboration to accelerate progress.
	18.	Commentary The rise of a digital immune system Michael C Schatz, Adam M Phillippy GigaScience 2012, 1:4 (12 July 2012) Abstract \| Full text \| PDF \| Editor’s summary Mike Schatz and Adam Phillippy feel the time is right for developing a sequencing-based pathogen surveillance system, and discuss the idea of a "digital immune system"
	19.	Research article Computational identification and analysis of novel sugarcane microRNAs Flávia Thiebaut, Clícia Grativol, Mariana Carnavale-Bottino, Cristian Rojas, Milos Tanurdzic, Laurent Farinelli, Robert A Martienssen, Adriana Hemerly, Paulo Cavalcanti Ferreira BMC Genomics 2012, 13:290 (2 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	20.	Review A generalizable pre-clinical research approach for orphan disease therapy Chandree L Beaulieu, Mark E Samuels, Sean Ekins, Christopher R McMaster, Aled M Edwards, Adrian R Krainer, Geoffrey G Hicks, Brendan J Frey, Kym M Boycott, Alex E MacKenzie Orphanet Journal of Rare Diseases 2012, 7:39 (15 June 2012) Abstract \| Full text \| PDF \| PubMed
	21.	Review *Current challenges in de novo* plant genome sequencing and assembly** Michael C Schatz, Jan Witkowski, W Richard McCombie Genome Biology 2012, 13:243 (27 April 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Michael Schatz and colleagues assess challenges in de novo plant genome assembly and review the best practices for the plant community
	22.	Research A genome triplication associated with early diversification of the core eudicots Yuannian Jiao, Jim Leebens-Mack, Saravanaraj Ayyampalayam, John E Bowers, Michael R McKain, Joel McNeal, Megan Rolf, Daniel R Ruzicka, Eric Wafula, Norman J Wickett, Xiaolei Wu, Yong Zhang, Jun Wang, Yeting Zhang, Eric J Carpenter, Michael K Deyholos, Toni M Kutchan, Andre S Chanderbali, Pamela S Soltis, Dennis W Stevenson, Richard McCombie, J Pires, Gane Wong, Douglas E Soltis, Claude W dePamphilis Genome Biology 2012, 13:R3 (26 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An investigation of when the gamma polyploidization event occurred in relation to speciation events in angiosperm history
	23.	Research Genetic adaptation to high altitude in the Ethiopian highlands Laura B Scheinfeldt, Sameer Soi, Simon Thompson, Alessia Ranciaro, Dawit Woldemeskel, William Beggs, Charla Lambert, Joseph P Jarvis, Dawit Abate, Gurja Belay, Sarah A Tishkoff Genome Biology 2012, 13:R1 (20 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genetics of hypoxia selection in an Ethiopian high-altitude population are distinct from Andean and Tibetan genotypes, suggestive of convergent evolution
	24.	Method Accurate proteome-wide protein quantification from high-resolution ¹⁵N mass spectra Zia Khan, Sasan Amini, Joshua S Bloom, Cristian Ruse, Amy A Caudy, Leonid Kruglyak, Mona Singh, David H Perlman, Saeed Tavazoie Genome Biology 2011, 12:R122 (19 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A fast, user-friendly bioinformatic tool for accurate quantification of proteins in 15N mass spectrometry data
	25.	Meeting report Epigenomic insights into common disease Kate Revill, Benjamin Tycko Genome Medicine 2011, 3:71 (15 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Revill and Tycko report on the Wellcome Trust Scientific Conference on 'Epigenomics of Common Diseases', highlighting this fast-moving field with particular emphasis on genome-wide studies.