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Shared Support Member - Cold Spring Harbor Laboratory

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

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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.

Research article   Open Access

Modelling 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 | Provisional PDF

2.

Research   Open Access

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

3.

Software   Open Access Highly Accessed

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 | Provisional PDF | PubMed

4.

Software   Open Access Highly Accessed

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

5.

Comment   Subscription Highly Accessed

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

6.

Musings   Subscription

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.

7.

Research article   Open Access

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

8.

Methodology   Open Access

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.

9.

Oral presentation   Open Access

Illuminating the genetics of complex human diseases

Michael C Schatz BMC Proceedings 2012, 6(Suppl 6):O4 (1 October 2012)

Full text | PDF

10.

Research article   Open Access Highly Accessed

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

11.

Research   Open Access Highly Accessed

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 |  Editor’s summary

Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method

12.

Open letter   Free Highly Accessed

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 |  Editor’s summary

The Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome

13.

Review   Subscription Highly Accessed

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.

14.

Commentary   Open Access

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"

15.

Research article   Open Access Highly Accessed

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

16.

Review   Open Access Highly Accessed

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

17.

Review   Subscription Highly Accessed

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

18.

Research   Open Access Highly Accessed

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 |  Editor’s summary

An investigation of when the gamma polyploidization event occurred in relation to speciation events in angiosperm history

19.

Research   Open Access Highly Accessed

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

20.

Method   Open Access

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

21.

Meeting report   Free Highly Accessed

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.

22.

Review   Open Access Highly Accessed

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.

23.

Research article   Open Access Highly Accessed

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

24.

Research article   Open Access

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

25.

Research   Open Access Highly Accessed

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

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