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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.

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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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	1.	Research article *The Caenorhabditis elegans* voltage-gated calcium channel subunits UNC-2 and UNC-36 and the calcium-dependent kinase UNC-43/CaMKII regulate neuromuscular junction morphology** Raymond C Caylor, Yishi Jin, Brian D Ackley Neural Development 2013, 8:10 (10 May 2013) Abstract \| Full text \| PDF \| PubMed
	2.	Review Now on display: a gallery of group II intron structures at different stages of catalysis Marco Marcia, Srinivas Somarowthu, Anna Marie Pyle Mobile DNA 2013, 4:14 (1 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary This review by Anna Pyle and colleagues provides a framework for classifying and understanding new crystal structures of these mobile genetic elements.
	3.	Research article Ancient origin of somatic and visceral neurons Marc Nomaksteinsky, Stefan Kassabov, Zoubida Chettouh, Henri-Corto Stoeklé, Laure Bonnaud, Gilles Fortin, Eric R Kandel, Jean-François Brunet BMC Biology 2013, 11:53 (30 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The great American palaeontologist and anatomist Alfred Romer speculated that early in animal life, an emerging somatic nervous system, focused on the outside world, struggled to dominate the visceral nervous system that takes care of the internal systems that keep us alive. Jean-François Brunet and colleagues identify the molecular signatures that tell the evolutionary tale of this duality.
	4.	Opinion Sixty years of genome biology W 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
	5.	Research highlight The complex binding of PRDM9 Laure Ségurel Genome Biology 2013, 14:112 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Laure Segurel offers a perspective on this issue's Research Article delineating the DNA-binding properties of PRDM9
	6.	Research ZASC1 knockout mice exhibit an early bone marrow-specific defect in murine leukemia virus replication Shannon Seidel, James Bruce, Mathias Leblanc, Kuo-Fen Lee, Hung Fan, Paul Ahlquist, John AT Young Virology Journal 2013, 10:130 (24 April 2013) Abstract \| Full text \| PDF \| PubMed
	7.	Research article *Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis* f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors** Dario Cantu, Vanesa Segovia, Daniel MacLean, Rosemary Bayles, Xianming Chen, Sophien Kamoun, Jorge Dubcovsky, Diane GO Saunders, Cristobal Uauy BMC Genomics 2013, 14:270 (22 April 2013) Abstract \| Full text \| PDF \| PubMed
	8.	Opinion Of flies and men: insights on organismal metabolism from fruit flies Akhila Rajan, Norbert Perrimon BMC Biology 2013, 11:38 (15 April 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary For many reasons metabolism is now a high-profile topic, and in an update to mark the tenth anniversary of BMC Biology, Norbert Perrimon and Akhila Rajan review the remarkable similarities that make Drosophila a model for mammalian metabolism, and some recent advances made possible by the advantages of this model organism.
	9.	Interview Two structure papers, a call from Frankfurt airport, and how to escape from reviewer delays: An interview with Peter Walter Peter Walter, Miranda Robertson BMC Biology 2013, 11:34 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
	10.	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.
	11.	Poster presentation High-resolution mapping of transcription factor binding sites on native chromatin Sivakanthan Kasinathan, Steven Henikoff Epigenetics & Chromatin 2013, 6(Suppl 1):P114 (8 April 2013) Full text \| PDF
	12.	Methods Generation of a luciferase-based reporter for CHH and CG DNA methylation in Arabidopsis thaliana Thanh Theresa Dinh, Michael O’Leary, So Youn Won, Shengben Li, Lorena Arroyo, Xigang Liu, Andrew Defries, Binglian Zheng, Sean R Cutler, Xuemei Chen Silence 2013, 4:1 (5 April 2013) Abstract \| Full text \| PDF \| PubMed
	13.	Correction Correction: Mechanisms of stomatal development: an evolutionary view Anne Vatén, Dominique C Bergmann EvoDevo 2013, 4:11 (4 April 2013) Abstract \| Full text \| PDF \| PubMed
	14.	Research The pea aphid uses a version of the terminal system during oviparous, but not viviparous, development Ryan D Bickel, Hillary C Cleveland, Joanna Barkas, Caitlin C Jeschke, Amelie A Raz, David L Stern, Gregory K Davis EvoDevo 2013, 4:10 (3 April 2013) Abstract \| Full text \| PDF \| PubMed
	15.	Research highlight Pushing the (nuclear) envelope into meiosis Abby F Dernburg Genome Biology 2013, 14:110 (27 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Abby Dernburg discusses recent research linking nuclear lamins to chromosome pairing in meiosis
	16.	Poster presentation Centromere-specific histone Cse4 by the chaperone Scm3 Uhn-Soo Cho, Stephen C Harrison Epigenetics & Chromatin 2013, 6(Suppl 1):P95 (18 March 2013) Full text \| PDF
	17.	Poster presentation Genome-wide analysis reveals TET-and TDG-mediated 5-methylcytosine oxidation dynamics Li Shen, Hao Wu, Dinh Diep, Ana C D’Alessio, Alan Fung, Kun Zhang, Yi Zhang Epigenetics & Chromatin 2013, 6(Suppl 1):P88 (18 March 2013) Full text \| PDF
	18.	Poster presentation MeCP2 binds to 5hmc enriched within active genes and accessible chromatin in the nervous system Marian Mellen, Pinar Ayata, Scott Dewell, Skirmantas Kriaucionis, Nathaniel Heintz Epigenetics & Chromatin 2013, 6(Suppl 1):P52 (18 March 2013) Full text \| PDF
	19.	Oral presentation The roles of long noncoding RNA in epigenetic regulation Jeannie T Lee Epigenetics & Chromatin 2013, 6(Suppl 1):O31 (18 March 2013) Full text \| PDF
	20.	Oral presentation ISWI and CHD chromatin remodelers bind to promoters but act in gene bodies Gabriel E Zentner, Toshio Tsukiyama, Steven Henikoff Epigenetics & Chromatin 2013, 6(Suppl 1):O29 (18 March 2013) Full text \| PDF
	21.	Oral presentation Germline epigenetics, and reprogramming in zebrafish early embryos Magdalena E Potok, David A Nix, Timothy J Parnell, Bradley R Cairns Epigenetics & Chromatin 2013, 6(Suppl 1):O23 (18 March 2013) Full text \| PDF
	22.	Oral presentation Chromatin and higher-order chromosome organization shape the recombination landscape in C. elegans Chitra V Kotwaliwale, Sasha A Langley, Andrea C Dose, Clara W Wang, Abby F Dernburg Epigenetics & Chromatin 2013, 6(Suppl 1):O17 (18 March 2013) Full text \| PDF
	23.	Oral presentation Methylation of histone H3 at lysine 23 in meiotic heterochromatin Romeo Papazvan, Ekaterina Voronina, Jessica R Chapman, Tonya M Gilbert, Elizabeth Meier, Jeffrey Shabanowitz, Donald F Hunt, Yifan Liu, Sean D Taverna Epigenetics & Chromatin 2013, 6(Suppl 1):O13 (18 March 2013) Full text \| PDF
	24.	Research Retrotransposition of gene transcripts leads to structural variation in mammalian genomes Adam D Ewing, Tracy J Ballinger, Dent Earl, Christopher C Harris, Li Ding, Richard K Wilson, David Haussler Genome Biology 2013, 14:R22 (13 March 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of gene retrocopy insertion polymorphisms in the germlines of individual humans, chimpanzees and mice, and in cancerous somatic tissues
	25.	Research article Comparative analysis of protein-protein interactions in the defense response of rice and wheat Dario Cantu, Baoju Yang, Randy Ruan, Kun Li, Virginia Menzo, Daolin Fu, Mawsheng Chern, Pamela C Ronald, Jorge Dubcovsky BMC Genomics 2013, 14:166 (12 March 2013) Abstract \| Full text \| PDF \| PubMed
	26.	Research article A distance-field based automatic neuron tracing method Jinzhu Yang, Paloma T Gonzalez-Bellido, Hanchuan Peng BMC Bioinformatics 2013, 14:93 (12 March 2013) Abstract \| Full text \| PDF \| PubMed
	27.	Methodology article **In situ hybridization protocol for enhanced detection of gene expression in the planarian Schmidtea mediterranea** Ryan S King, Phillip A Newmark BMC Developmental Biology 2013, 13:8 (12 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Modification of multiple steps in in situ hybridization methods for the freshwater planarian Schmidtea mediterranea greatly increase signal detection and may prove useful for whole-mount fluorescent in situ hybridization (FISH) in other model organisms
	28.	Review Molecular signaling and targets from itch: lessons for cough Pamela Colleen LaVinka, Xingzhong Dong Cough 2013, 9:8 (6 March 2013) Abstract \| Full text \| PDF \| PubMed
	29.	Research Spatio-temporal analysis of malaria within a transmission season in Bandiagara, Mali Drissa Coulibaly, Stanislas Rebaudet, Mark Travassos, Youssouf Tolo, Matthew Laurens, Abdoulaye K Kone, Karim Traore, Ando Guindo, Issa Diarra, Amadou Niangaly, Modibo Daou, Ahmadou Dembele, Mody Sissoko, Bourema Kouriba, Nadine Dessay, Jean Gaudart, Renaud Piarroux, Mahamadou A Thera, Christopher V Plowe, Ogobara K Doumbo Malaria Journal 2013, 12:82 (1 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Describes the spatial and temporal variation of Plasmodium falciparum infections in children from a rural population from Mali, based on a longitudinal study on malaria incidence in Bandiagara. The spatial and temporal variation of malaria incidence is mapped and interpolated. Clusters of low incidence are identified.
	30.	Editorial Epigenetics & Chromatin: interactions and processes Steven Henikoff, Frank Grosveld Epigenetics & Chromatin 2013, 6:2 (27 February 2013) Abstract \| Full text \| PDF \| PubMed
	31.	Review Nucleoplasmic calcium signaling and cell proliferation: calcium signaling in the nucleus Rodrigo R Resende, Lidia M Andrade, Andre G Oliveira, Erika S Guimarães, Silvia Guatimosim, M Fatima Leite Cell Communication and Signaling 2013, 11:14 (21 February 2013) Abstract \| Full text \| PDF \| PubMed
	32.	Research article MicroRNAs miR-26a, miR-26b, and miR-29b accelerate osteogenic differentiation of unrestricted somatic stem cells from human cord blood Hans-Ingo Trompeter, Janine Dreesen, Eugenie Hermann, Katharina M Iwaniuk, Markus Hafner, Neil Renwick, Thomas Tuschl, Peter Wernet BMC Genomics 2013, 14:111 (19 February 2013) Abstract \| Full text \| PDF \| PubMed
	33.	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 \| F1000 Biology \| 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.
	34.	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
	35.	Research Altered responsiveness to extracellular ATP enhances acetaminophen hepatotoxicity Sylvia S Amaral, André G Oliveira, Pedro E Marques, Jayane L D Quintão, Daniele A Pires, Rodrigo R Resende, Bruna R Sousa, Juliana G Melgaço, Marcelo A Pinto, Remo C Russo, Ariane K C Gomes, Lidia M Andrade, Rafael F Zanin, Rafaela V S Pereira, Cristina Bonorino, Frederico M Soriani, Cristiano X Lima, Denise C Cara, Mauro M Teixeira, Maria F Leite, Gustavo B Menezes Cell Communication and Signaling 2013, 11:10 (5 February 2013) Abstract \| Full text \| PDF \| PubMed
	36.	Research Role of SUMO-1 and SUMO interacting motifs in rhesus TRIM5α-mediated restriction Zana Lukic, Stephen P Goff, Edward M Campbell, Gloria Arriagada Retrovirology 2013, 10:10 (1 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary This study finds that the rhTRIM5alpha B30.2/SPRY domain is not only important for the recognition of the HIV-1 CA, but it is also important for its association with SUMO-1 or SUMO-1 modified proteins. These interactions help to maintain TRIM5alpha protein levels and its nuclear localization into specific nuclear bodies.
	37.	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 \| Full text \| 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.
	38.	Research Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution Daniël P Melters, Keith R Bradnam, Hugh A Young, Natalie Telis, Michael R May, J Ruby, Robert Sebra, Paul Peluso, John Eid, David Rank, José Garcia, Joseph L DeRisi, Timothy Smith, Christian Tobias, Jeffrey Ross-Ibarra, Ian Korf, Simon WL Chan Genome Biology 2013, 14:R10 (30 January 2013) Abstract \| Provisional PDF \| PubMed \| F1000 Biology \| Editor’s summary An analysis of centromere tandem repeats in 282 species reveals similar modes of evolution despite the lack of sequence conservation
	39.	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
	40.	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
	41.	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
	42.	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
	43.	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
	44.	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
	45.	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
	46.	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
	47.	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
	48.	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
	49.	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
	50.	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