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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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	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 3′ terminal diversity of MRP RNA and other human noncoding RNAs revealed by deep sequencing Katherine C Goldfarb, Thomas R Cech BMC Molecular Biology 2013, 14:23 (21 September 2013) Abstract \| Full text \| PDF \| PubMed
	3.	Poster presentation Extreme genetic fragility of the HIV-1 capsid Suzannah Rihn, Sam Wilson, Nick Loman, Mudathir Alim, Saskia Bakker, David Bhella, Frazer Rixon, Paul Bieniasz Retrovirology 2013, 10(Suppl 1):P73 (19 September 2013) Full text \| PDF
	4.	Research *Assembly of a phased diploid Candida albicans* genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure** Dale Muzzey, Katja Schwartz, Jonathan S Weissman, Gavin Sherlock Genome Biology 2013, 14:R97 (11 September 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An assembly of a diploid Candida albicans phased genome helps detect allele-specific events and significantly expands the number of known polymorphisms
	5.	Research Glial scaffold required for cerebellar granule cell migration is dependent on dystroglycan function as a receptor for basement membrane proteins Huy Nguyen, Adam P Ostendorf, Jakob S Satz, Steve Westra, Susan E Ross-Barta, Kevin P Campbell, Steven A Moore Acta Neuropathologica Communications 2013, 1:58 (6 September 2013) Abstract \| Full text \| PDF
	6.	Research *Prevalence and patterns of antifolate and chloroquine drug resistance markers in Plasmodium vivax* across Pakistan** Aamer A Khattak, Meera Venkatesan, Lubna Khatoon, Amed Ouattara, Leo J Kenefic, Muhammad F Nadeem, Farida Nighat, Salman A Malik, Christopher V Plowe Malaria Journal 2013, 12:310 (5 September 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The work documents the prevalence of SNPs-haplotypes in genes that might be involved in anti-malarial drug resistance in P. vivax clinical isolates circulating in 14 different sites of Pakistan. The emergence of drug resistance in P. vivax isolates is a very important factor in its association with severe and fatal malaria.
	7.	Research article Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila Penelope Coggill, Ruth Y Eberhardt, Robert D Finn, Yuanyuan Chang, Lukasz Jaroszewski, Adam Godzik, Debanu Das, Qingping Xu, Herbert L Axelrod, L Aravind, Alexey G Murzin, Alex Bateman BMC Bioinformatics 2013, 14:265 (3 September 2013) Abstract \| Full text \| PDF \| PubMed
	8.	Research *A comprehensive survey of polymorphisms conferring anti-malarial resistance in Plasmodium falciparum* across Pakistan** Aamer A Khattak, Meera Venkatesan, Christopher G Jacob, Elena M Artimovich, Muhammad F Nadeem, Farida Nighat, Francis Hombhanje, Toshihiro Mita, Salman A Malik, Christopher V Plowe Malaria Journal 2013, 12:300 (29 August 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary This study investigates the prevalence of molecular markers of resistance to chloroquine (CQ) and sulphadoxine-pyrimethamine (SP) across several sites in Pakistan. The results suggest an emerging problem with multidrug resistant P. falciparum in Pakistan.
	9.	Research *Prevalence and distribution of human Plasmodium* infection in Pakistan** Aamer A Khattak, Meera Venkatesan, Muhammad F Nadeem, Humayoon S Satti, Adnan Yaqoob, Kathy Strauss, Lubna Khatoon, Salman A Malik, Christopher V Plowe Malaria Journal 2013, 12:297 (28 August 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A report aiming at improving the understanding of malaria epidemiology in Pakistan, which remains incompletely understood. A malariometric population survey was conducted in 2011 using blood samples collected from 801 febrile patients of all ages in four provinces and the capital city of Islamabad.
	10.	Research highlight Learning the language of post-transcriptional gene regulation Stefanie Gerstberger, Markus Hafner, Thomas Tuschl Genome Biology 2013, 14:130 (23 August 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary RNA-binding proteins: Stefanie Gerstberger, Markus Hafner and Thomas Tuschl on the language of post-transcriptional gene regulation
	11.	Research article Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA Walter N Moss, Joan A Steitz BMC Genomics 2013, 14:543 (9 August 2013) Abstract \| Full text \| PDF \| PubMed
	12.	Correction Correction: Global analysis of host response to induction of a latent bacteriophage Robin E Osterhout, Israel A Figueroa, Jay D Keasling, Adam P Arkin BMC Microbiology 2013, 13:183 (6 August 2013) Abstract \| Full text \| PDF \| PubMed
	13.	Research article Inflammasome activation mediates inflammation and outcome in humans and mice with pneumococcal meningitis Madelijn Geldhoff, Barry B Mook-Kanamori, Matthijs C Brouwer, Dirk Troost, Jaklien C Leemans, Richard A Flavell, Arie Van der Ende, Tom Van der Poll, Diederik Van de Beek BMC Infectious Diseases 2013, 13:358 (31 July 2013) Abstract \| Full text \| PDF \| PubMed
	14.	Original research A computational pipeline for quantification of pulmonary infections in small animal models using serial PET-CT imaging Ulas Bagci, Brent Foster, Kirsten Miller-Jaster, Brian Luna, Bappaditya Dey, William R Bishai, Colleen B Jonsson, Sanjay Jain, Daniel J Mollura EJNMMI Research 2013, 3:55 (23 July 2013) Abstract \| Full text \| PDF \| PubMed
	15.	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
	16.	Research Spatiotemporal mathematical modelling of mutations of the dhps gene in African Plasmodium falciparum Jennifer A Flegg, Anand P Patil, Meera Venkatesan, Cally Roper, Inbarani Naidoo, Simon I Hay, Carol Sibley, Philippe J Guerin Malaria Journal 2013, 12:249 (17 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary This paper uses extant data on the anti-malarial drug SP in spatio-temporal models to visualize both the changing spatial distribution over time and the areas of largest uncertainty and gaps in the dataset. With the current emergence of artemisinin resistance spreading in Asia, this work provides extremely important information about the historical pattern of the spread of antimalarial resistance.
	17.	Research A core microbiome associated with the peritoneal tumors of pseudomyxoma peritonei Jeremy J Gilbreath, Cristina Semino-Mora, Christopher J Friedline, Hui Liu, Kip L Bodi, Thomas J McAvoy, Jennifer Francis, Carol Nieroda, Armando Sardi, Andre Dubois, David W Lazinski, Andrew Camilli, Traci L Testerman, D Merrell Orphanet Journal of Rare Diseases 2013, 8:105 (12 July 2013) Abstract \| Full text \| PDF \| PubMed
	18.	Review Natural killer cells in human autoimmune disorders Leslie A Fogel, Wayne M Yokoyama, Anthony R French Arthritis Research & Therapy 2013, 15:216 (11 July 2013) Abstract \| Full text \| PDF \| PubMed
	19.	Keynote speaker presentation The brain activity map: imaging the activity of entire neural circuits Rafael Yuste BMC Neuroscience 2013, 14(Suppl 1):A4 (8 July 2013) Full text \| PDF
	20.	Featured talk presentation Consistency requirements determine optimal noise correlations in neural populations Joel Zylberberg, Maxwell Turner, Yu Hu, Jon Cafaro, Greg Schwartz, Fred Rieke, Eric Shea-Brown BMC Neuroscience 2013, 14(Suppl 1):F1 (8 July 2013) Full text \| PDF
	21.	Research Primary CD8⁺ T cells from elite suppressors effectively eliminate non-productively HIV-1 infected resting and activated CD4⁺ T cells Robert W Buckheit, Robert F Siliciano, Joel N Blankson Retrovirology 2013, 10:68 (1 July 2013) Abstract \| Full text \| PDF \| PubMed
	22.	Research Deficiency of complement component 5 ameliorates glaucoma in DBA/2J mice Gareth R Howell, Ileana Soto, Margaret Ryan, Leah C Graham, Richard S Smith, Simon WM John Journal of Neuroinflammation 2013, 10:76 (27 June 2013) Abstract \| Full text \| PDF \| PubMed
	23.	Review Macromolecular juggling by ubiquitylation enzymes Sonja Lorenz, Aaron J Cantor, Michael Rape, John Kuriyan BMC Biology 2013, 11:65 (25 June 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Post-translational modification with ubiquitin requires several distinct catalytic steps three of which must be performed serially by a single enzyme. Lorenz, Kuriyan and colleagues review the macromolecular juggling involved, with an animation set to music performed by the first author
	24.	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
	25.	Research Is metabotropic glutamate receptor 5 upregulated in prefrontal cortex in fragile X syndrome? Talakad G Lohith, Emily K Osterweil, Masahiro Fujita, Kimberly J Jenko, Mark F Bear, Robert B Innis Molecular Autism 2013, 4:15 (24 May 2013) Abstract \| Full text \| PDF \| PubMed