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Member - Howard Hughes Medical Institute

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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   Open Access

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access

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   Open Access Highly Accessed

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   Open Access

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   Open Access Highly Accessed

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   Open Access

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   Open Access

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   Open Access

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   Open Access Highly Accessed

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   Open Access

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   Open Access

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   Open Access

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access

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   Subscription Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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   Open Access Highly Accessed

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

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