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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.	Research article Male-specific fruitless isoforms have different regulatory roles conferred by distinct zinc finger DNA binding domains Justin E Dalton, Justin M Fear, Simon Knott, Bruce S Baker, Lauren M McIntyre, Michelle N Arbeitman BMC Genomics 2013, 14:659 (27 September 2013) Abstract \| Provisional PDF \| PubMed
	2.	Research article Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls Meeta Mistry, Jesse Gillis, Paul Pavlidis BMC Neuroscience 2013, 14:105 (26 September 2013) Abstract \| Full text \| PDF \| PubMed
	3.	Research *Organization of Plasmodium falciparum* spliceosomal core complex and role of arginine methylation in its assembly** Manzar Hossain, Shweta Sharma, Reshma Korde, Shivani Kanodia, Monika Chugh, Khushboo Rawat, Pawan Malhotra Malaria Journal 2013, 12:333 (18 September 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary This paper compiles a substantial amount of experimental data that shed light on the organization of the spliceosome in Plasmodium.
	4.	Database Gentrepid V2.0: a web server for candidate disease gene prediction Sara Ballouz, Jason Y Liu, Richard A George, Naresh Bains, Arthur Liu, Martin Oti, Bruno Gaeta, Diane Fatkin, Merridee A Wouters BMC Bioinformatics 2013, 14:249 (16 August 2013) Abstract \| Full text \| PDF \| PubMed
	5.	Research *Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1* in a novel Mendelian disease with neuromuscular and cardiac involvement** Kai Wang, Cecilia Kim, Jonathan Bradfield, Yunfei Guo, Elina Toskala, Frederick G Otieno, Cuiping Hou, Kelly Thomas, Christopher Cardinale, Gholson J Lyon, Ryan Golhar, Hakon Hakonarson Genome Medicine 2013, 5:67 (26 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary DNA and RNA sequencing identifies mutations within RBCK1 in children with a previously undiagnosed disease characterised by progressive muscular weakness and cardiomyopathy.
	6.	Research *Assemblathon 2: evaluating de novo* methods of genome assembly in three vertebrate species** Keith R Bradnam, Joseph N Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, Inanç Birol, Sébastien Boisvert, Jarrod A Chapman, Guillaume Chapuis, Rayan Chikhi, Hamidreza Chitsaz, Wen-Chi Chou, Jacques Corbeil, Cristian Del Fabbro, T Docking, Richard Durbin, Dent Earl, Scott Emrich, Pavel Fedotov, Nuno A Fonseca, Ganeshkumar Ganapathy, Richard A Gibbs, Sante Gnerre, Élénie Godzaridis, Steve Goldstein, Matthias Haimel, Giles Hall, David Haussler, Joseph B Hiatt, Isaac Y Ho et al. GigaScience 2013, 2:10 (22 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Assemblathon 2 is the largest systematic assessment of how the process of genome assembly is carried out, with 21 participating teams submitting 43 entries based on data from 3 different genomes
	7.	Poster presentation The structure of human olfactory space Alexei Koulakov, Dmitry Rinberg BMC Neuroscience 2013, 14(Suppl 1):P323 (8 July 2013) Full text \| PDF
	8.	Poster presentation Long-term memory stabilized by noise-induced rehearsal Yi Wei, Alexei Koulakov BMC Neuroscience 2013, 14(Suppl 1):P220 (8 July 2013) Full text \| PDF
	9.	Correspondence The advantages of SMRT sequencing Richard J Roberts, Mauricio O Carneiro, Michael C Schatz Genome Biology 2013, 14:405 (3 July 2013) Abstract \| Full text \| PDF \| PubMed \| 2 comments \| Editor’s summary Rich Roberts, Mauricio Carneiro and Michael Schatz argue for a greater uptake of the impressive PacBio SMRT sequencing platform
	10.	Comment The DNA60IFX contest Michael C Schatz, James Taylor, Sven-Eric Schelhorn Genome Biology 2013, 14:124 (28 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The curators and winner of Genome Biology's DNA60IFX challenge offer their thoughts on code cracking and crowd bioinformatics - includes full solutions
	11.	Methodology Article Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets Xiao Xu, Yuanhao Zhang, Jennie Williams, Eric Antoniou, W McCombie, Song Wu, Wei Zhu, Nicholas O Davidson, Paula Denoya, Ellen Li BMC Bioinformatics 2013, 14(Suppl 9):S1 (28 June 2013) Abstract \| Full text \| PDF \| PubMed
	12.	Methodology A fluorometric assay for trehalose in the picomole range Petronia Carillo, Regina Feil, Yves Gibon, Namiko Satoh-Nagasawa, David Jackson, Oliver E Bläsing, Mark Stitt, John Lunn Plant Methods 2013, 9:21 (20 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Trehalose is a disaccharide that is found in a wide variety of species but whose functions are not always clear. The authors describe a novel assay, based on the use of recombinant bacterial trehalase, which is both sensitive and highly specific for trehalose. The method has been validated by studying diurnal patterns of trehalose content of Arabidopsis leaves and the effect of the maize ramosa3 mutant on trehalose levels in inflorescence primordia.
	13.	Research CK2-dependent phosphorylation of occludin regulates the interaction with ZO-proteins and tight junction integrity Max J Dörfel, Julie K Westphal, Christian Bellmann, Susanne M Krug, Jimmi Cording, Sonnhild Mittag, Rudolf Tauber, Michael Fromm, Ingolf E Blasig, Otmar Huber Cell Communication and Signaling 2013, 11:40 (10 June 2013) Abstract \| Full text \| PDF \| PubMed
	14.	Research A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress Palitha Dharmawardhana, Liya Ren, Vindhya Amarasinghe, Marcela Monaco, Jim Thomason, Dean Ravenscroft, Susan McCouch, Doreen Ware, Pankaj Jaiswal Rice 2013, 6:15 (29 May 2013) Abstract \| Full text \| PDF
	15.	Research DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus Lucas TJ Kaaij, Marc van de Wetering, Fang Fang, Benjamin Decato, Antoine Molaro, Harmen JG van de Werken, Johan H van Es, Jurian Schuijers, Elzo de Wit, Wouter de Laat, Gregory J Hannon, Hans C Clevers, Andrew D Smith, René F Ketting Genome Biology 2013, 14:R50 (28 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Intriguingly, DNA methylation in mouse intestinal cells does not change much during differentiation
	16.	Research *Genome of the long-living sacred lotus (Nelumbo nucifera* Gaertn.)** Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell, Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, Giuseppe Narzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, Yuannian Jiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Min, Karen A Hudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer R Watling, Kikukatsu Ito et al. Genome Biology 2013, 14:R41 (10 May 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| f1000 \| Editor’s summary The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability
	17.	Opinion Sixty years of genome biology W Ford 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
	18.	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
	19.	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
	20.	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 \| Cited on BioMed Central \| 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.
	21.	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
	22.	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
	23.	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
	24.	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 \| Cited on BioMed Central
	25.	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 \| Cited on BioMed Central \| Editor’s summary by Mike Schatz