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Member - Howard Hughes Medical Institute

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Research staff at Howard Hughes Medical Institute HHMI:

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Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at Howard Hughes Medical Institute

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	26.	Methods Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection Zhao Zhang, William E Theurkauf, Zhiping Weng, Phillip D Zamore Silence 2012, 3:9 (28 December 2012) Abstract \| Full text \| PDF \| PubMed
	27.	Review Clamp loader ATPases and the evolution of DNA replication machinery Brian A Kelch, Debora L Makino, Mike O'Donnell, John Kuriyan BMC Biology 2012, 10:34 (20 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The speed of DNA replication depends on the sliding clamp which encircles the DNA and holds the polymerase in place. Mike O'Donnell, John Kuriyan and colleagues review the growing understanding of the conformational rearrangements whereby the clamp loader opens the clamp and screws it on to the DNA throughout DNA synthesis.
	28.	Original article A high-density 3D localization algorithm for stochastic optical reconstruction microscopy Hazen Babcock, Yaron M Sigal, Xiaowei Zhuang Optical Nanoscopy 2012, 1:6 (16 July 2012) Abstract \| Full text \| PDF
	29.	Software MESSA: MEta-Server for protein Sequence Analysis Qian Cong, Nick V Grishin BMC Biology 2012, 10:82 (2 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Using amalgamated sequence alignments to generate information about local sequence properties, 3D structure and protein function, the new meta-server MESSA provides an integrated, holistic view of proteins via a user-friendly interface.
	30.	Research article Multiparameter behavioral profiling reveals distinct thermal response regimes in Caenorhabditis elegans Rajarshi Ghosh, Aylia Mohammadi, Leonid Kruglyak, William S Ryu BMC Biology 2012, 10:85 (31 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By developing a novel assay to quantitate C elegans thermal avoidance behavior, William Ryu and colleagues discovered that different genes are utilized to provide the same phenotypic response, depending on the severity of the applied stimulus.
	31.	Methods Development of a luciferase-based reporter of transcriptional gene silencing that enables bidirectional mutant screening in Arabidopsis thaliana So Youn Won, Shengben Li, Binglian Zheng, Yuanyuan Zhao, Dongming Li, Xin Zhao, Huilan Yi, Lei Gao, Thanh Theresa Dinh, Xuemei Chen Silence 2012, 3:6 (7 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A luciferase-based reporter system, LUCH, is used to screen for bidirectional mutants that enhance or suppress transcriptional gene silencing, elucidating the mechanisms of DNA methylation and demethylation.
	32.	Research Accelerated exon evolution within primate segmental duplications Belen Lorente-Galdos, Jonathan Bleyhl, Gabriel Santpere, Laura Vives, Oscar Ramírez, Jessica Hernandez, Roger Anglada, Gregory M Cooper, Arcadi Navarro, Evan E Eichler, Tomas Marques-Bonet Genome Biology 2013, 14:R9 (29 January 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study looks at segmental duplication genes in humans and macaques to elucidate exon evolution in primates
	33.	Research Dissecting the regulatory architecture of gene expression QTLs Daniel J Gaffney, Jean-Baptiste Veyrieras, Jacob F Degner, Roger Pique-Regi, Athma A Pai, Gregory E Crawford, Matthew Stephens, Yoav Gilad, Jonathan K Pritchard Genome Biology 2012, 13:R7 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary An analysis of eQTLs located in regulatory elements in the human genome
	34.	Research article The structure of the leukemia drug imatinib bound to human quinone reductase 2 (NQO2) Jonathan A Winger, Oliver Hantschel, Giulio Superti-Furga, John Kuriyan BMC Structural Biology 2009, 9:7 (24 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The tyrosine-kinase inhibitor imatinib is revealed by X-ray crystallography to occupy the active site of the oxidoreductase NQO2, a secondary target whose inhibition may be responsible for side effects in leukaemia patients receiving treatment with the drug.
	35.	Methodology article Efficient counting of k -mers in DNA sequences using a bloom filter Páll Melsted, Jonathan K Pritchard BMC Bioinformatics 2011, 12:333 (10 August 2011) Abstract \| Full text \| PDF \| PubMed
	36.	Methodology A clinical genetic method to identify mechanisms by which pain causes depression and anxiety Mitchell B Max, Tianxia Wu, Steven J Atlas, Robert R Edwards, Jennifer A Haythornthwaite, Antonella F Bollettino, Heather S Hipp, Colin D McKnight, Inge A Osman, Erin N Crawford, Maryland Pao, Jemiel Nejim, Albert Kingman, Daniel C Aisen, Michele A Scully, Robert B Keller, David Goldman, Inna Belfer Molecular Pain 2006, 2:14 (19 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	37.	Methodology article Genotyping 1000 yeast strains by next-generation sequencing Stefan Wilkening, Manu M Tekkedil, Gen Lin, Emilie S Fritsch, Wu Wei, Julien Gagneur, David W Lazinski, Andrew Camilli, Lars M Steinmetz BMC Genomics 2013, 14:90 (9 February 2013) Abstract \| Full text \| PDF \| PubMed
	38.	Research ScanImage: Flexible software for operating laser scanning microscopes Thomas A Pologruto, Bernardo L Sabatini, Karel Svoboda BioMedical Engineering OnLine 2003, 2:13 (17 May 2003) Abstract \| Full text \| PDF \| PubMed
	39.	Research Microarray analysis of microRNA expression in the developing mammalian brain Eric A Miska, Ezequiel Alvarez-Saavedra, Matthew Townsend, Akira Yoshii, Nenad Šestan, Pasko Rakic, Martha Constantine-Paton, H Robert Horvitz Genome Biology 2004, 5:R68 (31 August 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A microarray technology suitable for analyzing the expression of microRNAs and of other small RNAs was used to determine the microRNA expression profile during mouse-brain development and observed a temporal wave of gene expression of sequential classes of microRNAs.
	40.	Research Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark Genome Biology 2011, 12:R100 (17 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The genome of the pathogenic ciliate Ichthyophthirius multifiliis, which causes white spot disease in fish, is presented
	41.	Review Mechanisms of stomatal development: an evolutionary view Anne Vatén, Dominique C Bergmann EvoDevo 2012, 3:11 (12 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	42.	Preliminary communication Exploding vesicles Ting F Zhu, Jack W Szostak Journal of Systems Chemistry 2011, 2:4 (1 December 2011) Abstract \| Full text \| PDF \| Editor’s summary A dramatic phenomenon in which light triggers the sudden rupture of fatty acid vesicles has been observed in a primitive cell membrane model, and could lead to applications such as targeted drug delivery
	43.	Research A comparative analysis of DNA methylation across human embryonic stem cell lines Pao-Yang Chen, Suhua Feng, Jong Joo, Steve E Jacobsen, Matteo Pellegrini Genome Biology 2011, 12:R62 (6 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparison of DNA methylation in three human embryonic stem cell lines
	44.	Technical Note The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, J Caporaso GigaScience 2012, 1:7 (12 July 2012) Abstract \| Full text \| PDF
	45.	Research *A 5′-uridine amplifies miRNA/miRNA asymmetry in Drosophila by promoting RNA-induced silencing complex formation** Hervé Seitz, Jogender S Tushir, Phillip D Zamore Silence 2011, 2:4 (7 June 2011) Abstract \| Full text \| PDF \| PubMed
	46.	Research *Developmental roles of 21 Drosophila* transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions** Stewart MacArthur, Xiao-Yong Li, Jingyi Li, James B Brown, Hou Cheng Chu, Lucy Zeng, Brandi P Grondona, Aaron Hechmer, Lisa Simirenko, Soile VE Keränen, David W Knowles, Mark Stapleton, Peter Bickel, Mark D Biggin, Michael B Eisen Genome Biology 2009, 10:R80 (23 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Distinct developmental fates in Drosophila melanogaster are specified by quantitative differences in transcription factor occupancy on a common set of bound regions.
	47.	Review Embryonic stem cell-specific signatures in cancer: insights into genomic regulatory networks and implications for medicine Jonghwan Kim, Stuart H Orkin Genome Medicine 2011, 3:75 (29 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Jonghwan Kim and Stuart Orkin review recent genome-scale and systems approaches to understand the regulatory networks that are common to embryonic stem (ES) cells and cancer.
	48.	Research *Annotation of the Drosophila melanogaster* euchromatic genome: a systematic review** Sima Misra, Madeline A Crosby, Christopher J Mungall, Beverley B Matthews, Kathryn S Campbell, Pavel Hradecky, Yanmei Huang, Joshua S Kaminker, Gillian H Millburn, Simon E Prochnik, Christopher D Smith, Jonathan L Tupy, Eleanor J Whitfield, Leyla Bayraktaroglu, Benjamin P Berman, Brian R Bettencourt, Susan E Celniker, Aubrey DNJ de Grey, Rachel A Drysdale, Nomi L Harris, John Richter, Susan Russo, Andrew J Schroeder, ShengQiang Shu, Mark Stapleton, Chihiro Yamada, Michael Ashburner, William M Gelbart, Gerald M Rubin, Suzanna E Lewis Genome Biology 2002, 3:research0083-0083.22 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to significantly improve genomic annotations.
	49.	Research A DNA microarray survey of gene expression in normal human tissues Radha Shyamsundar, Young H Kim, John P Higgins, Kelli Montgomery, Michelle Jorden, Anand Sethuraman, Matt van de Rijn, David Botstein, Patrick O Brown, Jonathan R Pollack Genome Biology 2005, 6:R22 (14 February 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A systematic survey of gene expression in 115 human tissue samples using cDNA microarrays provides a dataset that can be used as a baseline for comparison with expression in diseased tissue.
	50.	Interview An interview with Patrick O Brown on the origins and future of open access Patrick O Brown BMC Biology 2013, 11:33 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In an interview for the BMC Biology tenth anniversary collection, Patrick O Brown excavates his memory for the origins of open access publishing, and finds a vision of the future still to be fulfilled.