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Member - Howard Hughes Medical Institute

Howard Hughes Medical Institute, a biomedical research organization, serves society by investigating human health and disease and by providing support to improve science education at all levels.

www.hhmi.org

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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	1.	Editorial Epigenetics & chromatin: interactions and processes Steven Henikoff, Frank Grosveld Epigenetics & Chromatin 2013, 6:2 (27 February 2013) Abstract \| Full text \| PDF \| PubMed
	2.	Research article *Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris* genome sequence** Chris M Rands, Aaron Darling, Matthew Fujita, Lesheng Kong, Matthew T Webster, Céline Clabaut, Richard D Emes, Andreas Heger, Stephen Meader, Michael Brent Hawkins, Michael B Eisen, Clotilde Teiling, Jason Affourtit, Benjamin Boese, Peter R Grant, Barbara Rosemary Grant, Jonathan A Eisen, Arhat Abzhanov, Chris P Ponting BMC Genomics 2013, 14:95 (12 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 204 years after Charles Darwin’s birth, sequencing of the genome of the Darwin’s Finch Geospiza magnirostris reveals over 13,000 predicted genes, of which two under positive selection may have contributed to beak morphology evolution, which so interested Darwin.
	3.	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
	4.	Methodology article Multi-channel acoustic recording and automated analysis of Drosophila courtship songs Benjamin J Arthur, Tomoko Sunayama-Morita, Philip Coen, Mala Murthy, David L. Stern BMC Biology 2013, 11:11 (31 January 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Drosophila fruit flies' "singing" during courtship is a model system for both genetic and neural control of behaviour. A newly-designed recording system allows for analysis of the songs' various rhythms and cycles in unprecedented detail.
	5.	Research article Seq2Ref: a web server to facilitate functional interpretation Wenlin Li, Qian Cong, Lisa N Kinch, Nick V Grishin BMC Bioinformatics 2013, 14:30 (28 January 2013) Abstract \| Full text \| PDF \| PubMed
	6.	Study protocol 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
	7.	Research article Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe Ian Carter-O’Connell, Michael T Peel, Dennis D Wykoff, Erin K O’Shea BMC Genomics 2012, 13:697 (12 December 2012) Abstract \| Full text \| PDF \| PubMed
	8.	Research Identification of new cell size control genes in S. cerevisiae Huzefa Dungrawala, Hui Hua, Jill Wright, Lesley Abraham, Thivakorn Kasemsri, Anthony McDowell, Jessica Stilwell, Brandt L Schneider Cell Division 2012, 7:24 (12 December 2012) Abstract \| Full text \| PDF \| PubMed
	9.	Research Identification of a 3-aminoimidazo[1,2-a]pyridine inhibitor of HIV-1 reverse transcriptase Daniel Elleder, Thomas J Baiga, Rebecca L Russell, John A Naughton, Stephen H Hughes, Joseph P Noel, John AT Young Virology Journal 2012, 9:305 (11 December 2012) Abstract \| Full text \| PDF \| PubMed
	10.	Meeting Report Genomic impact of eukaryotic transposable elements Irina R Arkhipova, Mark A Batzer, Juergen Brosius, Cédric Feschotte, John V Moran, Jürgen Schmitz, Jerzy Jurka Mobile DNA 2012, 3:19 (21 November 2012) Abstract \| Full text \| PDF \| PubMed
	11.	Methodology article Identification of proteins binding coding and non-coding human RNAs using protein microarrays Zurab Siprashvili, Dan E Webster, Markus Kretz, Danielle Johnston, John L Rinn, Howard Y Chang, Paul A Khavari BMC Genomics 2012, 13:633 (16 November 2012) Abstract \| Full text \| PDF \| PubMed
	12.	Poster presentation The ciliary proteins Meckelin and Jouberin are required for retinoic acid-dependent neural differentiation of mouse embryonic stem cells S Romani, B Illi, R De Mori, JG Gleeson, EM Valente Cilia 2012, 1(Suppl 1):P77 (16 November 2012) Full text \| PDF
	13.	Oral presentation Exome resequencing identifies novel NPHP genes, implicating DNA damage response signaling in the pathogenesis of ciliopathies F Hildebrandt Cilia 2012, 1(Suppl 1):O2 (16 November 2012) Full text \| PDF
	14.	Keynote lecture presentation Translational benefits to patients in the post-genomic era JG Gleeson Cilia 2012, 1(Suppl 1):K1 (16 November 2012) Full text \| PDF
	15.	Software Oculus: faster sequence alignment by streaming read compression Brendan A Veeneman, Matthew K Iyer, Arul M Chinnaiyan BMC Bioinformatics 2012, 13:297 (13 November 2012) Abstract \| Full text \| PDF \| PubMed
	16.	Question and Answer Q&A: What is regeneration, and why look to planarians for answers? Alejandro Sánchez Alvarado BMC Biology 2012, 10:88 (8 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary What controls regeneration? Alejandro Sanchez Alvarado explores this old question in biology in a Q&A explaining what we understand from planarians - non-parasitic flatworms all of whose tissues can regenerate.
	17.	Research article Identification of essential genes of the periodontal pathogen Porphyromonas gingivalis Brian A Klein, Elizabeth L Tenorio, David W Lazinski, Andrew Camilli, Margaret J Duncan, Linden T Hu BMC Genomics 2012, 13:578 (31 October 2012) Abstract \| Full text \| PDF \| PubMed
	18.	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.
	19.	Commentary Chromatin roadblocks to reprogramming 50 years on Peter J Skene, Steven Henikoff BMC Biology 2012, 10:83 (29 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary This year, John Gurdon, with Shinya Yamanaka, won the Nobel Prize in Physiology or Medicine for the discovery that nuclei from adult cells can be reprogrammed to an undifferentiated state. In a commentary on a paper in Epigenetics & Chromatin from John Gurdon and colleagues, Skene and Henikoff explain how the variant histone H3.3 links the findings of the two prizewinners.
	20.	Research article Euchromatin islands in large heterochromatin domains are enriched for CTCF binding and differentially DNA-methylated regions Bo Wen, Hao Wu, Yuin-Han Loh, Eirikur Briem, George Q Daley, Andrew P Feinberg BMC Genomics 2012, 13:566 (26 October 2012) Abstract \| Full text \| PDF \| PubMed
	21.	Research Quantitative myocardial perfusion in mice based on the signal intensity of flow sensitized CMR Sumeda Abeykoon, Michelle Sargent, Janaka P Wansapura Journal of Cardiovascular Magnetic Resonance 2012, 14:73 (24 October 2012) Abstract \| Full text \| PDF \| PubMed
	22.	Review Surveying the epigenomic landscape, one base at a time Gabriel E Zentner, Steven Henikoff Genome Biology 2012, 13:250 (22 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary New methods for mapping histones at higher resolution open many new doors in epigenomics research
	23.	Methodology article Gene Fusion Markup Language: a prototype for exchanging gene fusion data Shanker Kalyana-Sundaram, Achiraman Shanmugam, Arul M Chinnaiyan BMC Bioinformatics 2012, 13:269 (16 October 2012) Abstract \| Provisional PDF \| PubMed
	24.	Research Common genetic variants, acting additively, are a major source of risk for autism Lambertus Klei, Stephan J Sanders, Michael T Murtha, Vanessa Hus, Jennifer K Lowe, A Willsey, Daniel Moreno-De-Luca, Timothy W Yu, Eric Fombonne, Daniel Geschwind, Dorothy E Grice, David H Ledbetter, Catherine Lord, Shrikant M Mane, Christa Martin, Donna M Martin, Eric M Morrow, Christopher A Walsh, Nadine M Melhem, Pauline Chaste, James S Sutcliffe, Matthew W State, Edwin H Cook, Kathryn Roeder, Bernie Devlin Molecular Autism 2012, 3:9 (15 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Common genetic variants have a substantial additive genetic effect on autism spectrum disorder liability and this effect differs between simplex and multiplex families.
	25.	Research article An olfactory demography of a diverse metropolitan population Andreas Keller, Margaret Hempstead, Iran A Gomez, Avery N Gilbert, Leslie B Vosshall BMC Neuroscience 2012, 13:122 (10 October 2012) Abstract \| Full text \| PDF \| PubMed