Whole issues of Genome Biology/Genome Medicine on "Genomics of Infectious Disease"

Wow this has really got some nice papers: BioMed Central | Article collections | Genomics of infectious diseases special issue.  I note - this goes well as a follow up to the series I co-coordinated in PLOS a few years back: Genomics of Emerging Infectious Disease - PLOS Collections

From their site:

Infectious diseases are major contributors to global morbidity and mortality, and have a devastating impact on public health. The World Health Organization estimates that 1 in 3 deaths worldwide are due to an infectious disease, with a disproportionate number occurring in developing regions. 

While the completion of the first genome sequence of a pathogen, Haemophilus influenzae, in 1995 took decades of work, in recent years, high-throughput technologies have revolutionized the study of pathogens. Whole-genome sequences are now achievable within days and available for multiple pathogens, including those that cause neglected tropical diseases, which has advanced our understanding of the biology and evolution of pathogens. Crucially, such research has enabled important advances in the clinical management of infectious diseases, and continues to guide public health interventions worldwide. 

In this cross-journal special issue, guest edited by George Weinstock (The Jackson Laboratory for Genomic Medicine, USA) and Sharon Peacock (University of Cambridge, UK), Genome Biology and Genome Medicine take stock of where we are now, with a collection of primary research and commissioned articles that discuss different aspects of the genomics of infectious diseases in human populations, including the progress made towards their eradication, and the remaining challenges in terms of both fundamental science and clinical management.

I have copied the list from their site (I am pretty sure this is OK since these are #OpenAccess journals but not 100% sure):

	Editorial    Human infectious diseases in the genomics era: where do we go from here? Ripudaman K Bains Genome Biology 2014, 15:529 (22 November 2014) Abstract | Full text | PDF| Editor’s summary
	Review    Genomic analysis of emerging pathogens: methods, application and future  trends Lucy M Li, Nicholas C Grassly, Christophe Fraser Genome Biology 2014, 15:541 (22 November 2014) Abstract | Full text | PDF| Editor’s summary
	Research    The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated  from  the biopsy of a migrating brain lesion Hayley M Bennett, Hoi Ping Mok, Effrossyni Gkrania-Klotsas, Eleanor J Stanley, Isheng J Tsai, Nagui M Antoun, Avril Coghlan, Bhavana Harsha, Alessandra Traini,  Diogo M Ribeiro, Sascha Steinbass, Sebastian B Lucas, Kieren S.J Allinson,  Stephen J Price, Thomas S Santarius, Andrew J Carmichael, Peter L Chiodini,  Nancy Holroyd, Andrew F Dean, Matthew Berriman  Genome Biology 2014, 15:510 (21 November 2014) Abstract | Provisional PDF| Editor’s summary
	Research highlight    Stopping outbreaks with real-time genomic epidemiology Patrick Tang, Jennifer L Gardy Genome Medicine 2014, 6:104 (20 November 2014) Abstract | Full text | PDF| Editor’s summary
	Software    YMAP: a pipeline for visualization of copy number variation and loss of  heterozygosity  in  eukaryotic  pathogens Darren Abbey, Jason Funt, Mor N Lurie-Weinberger, Dawn A Thompson, Aviv Regev, Chad L Myers, Judith Berman Genome Medicine 2014, 6:100 (20 November 2014) Abstract | Provisional PDF| Editor’s summary
	Comment    Single cell genomics of bacterial pathogens: outlook for infectious disease  research Jeffrey S McLean, Roger S Lasken Genome Medicine 2014, 6:108 (20 November 2014) Abstract | Full text | PDF| Editor’s summary
	Software    SRST2: Rapid genomic surveillance for public health and hospital microbiology  labs Michael Inouye, Harriet Dashnow, Lesley-Ann Raven, Mark B Schultz, Bernard J Pope, Takehiro Tomita, Justin Zobel, Kathryn E Holt  Genome Medicine 2014, 6:90 (20 November 2014) Abstract | Full text | PDF| Editor’s summary
	Research    Genomic epidemiology of a protracted hospital outbreak caused by  multidrug-resistant  Acinetobacter baumannii in Birmingham, England Mihail R Halachev, Jacqueline Chan, Chrystala I Constantinidou, Nicola Cumley, Craig Bradley, Matthew Smith-Banks, Beryl Oppenheim, Mark J Pallen  Genome Medicine 2014, 6:70 (20 November 2014) Abstract | Full text | PDF| Editor’s summary
	Editorial    Next-generation pathogen genomics George M Weinstock, Sharon J Peacock Genome Biology 2014, 15:528 (19 November 2014) Abstract | Full text | PDF| Editor’s summary
	Software    Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific  Microbial Genomes Todd J Treangen, Brian D Ondov, Sergey Koren, Adam M Phillippy Genome Biology 2014, 15:524 (19 November 2014) Abstract | Provisional PDF| Editor’s summary
	Method    BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads Lewis Z Hong, Shuzhen Hong, Han Teng Wong, Pauline PK Aw, Cheng Yan, Andreas Wilm, Paola F de Sessions, Seng Gee Lim, Niranjan Nagarajan, Martin L Hibberd, Stephen R Quake, William F Burkholder Genome Biology 2014, 15:517 (19 November 2014) Abstract | Provisional PDF| Editor’s summary
	Editorial    Microbial sequencing to improve individual and population health Sharon J Peacock, George M Weinstock Genome Medicine 2014, 6:103 (19 November 2014) Abstract | Full text | PDF| Editor’s summary
	Opinion    Genomics and infectious disease: a call to identify the ethical, legal and social  implications  for public health and clinical practice Gail Geller, Rachel Dvoskin, Chloe L Thio, Priya Duggal, Michelle H Lewis, Theodore C Bailey, Andrea Sutherland, Daniel A Salmon, Jeffrey P Kahn Genome Medicine 2014, 6:106 (18 November 2014) Abstract | Full text | PDF| Editor’s summary
	Review    Epidemiologic data and pathogen genome sequences: a powerful synergy for public  health Yonatan H Grad, Marc Lipsitch Genome Biology 2014, 15:538 (18 November 2014) Abstract | Full text | PDF| Editor’s summary
	Method    Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA  viruses in clinical and biological samples Christian B Matranga, Kristian G Andersen, Sarah Winnicki, Michele Busby, Adrianne D Gladden, Ryan Tewhey, Matthew Stremlau, Aaron Berlin, Stephen K Gire,  Eleina England, Lina M Moses, Tarjei S Mikkelsen, Ikponmwosa Odia, Philomena E Ehiane,  Onikepe Folarin, Augustine Goba, S.Humarr Khan, Donald S Grant, Anna Honko,  Lisa Hensley, Christian Happi, Robert F Garry, Christine M Malboeuf, Bruce W Birren,  Andreas Gnirke, Joshua Z Levin, Pardis C Sabeti Genome Biology 2014, 15:519 (18 November 2014) Abstract | Provisional PDF | PubMed| Editor’s summary
	Research    The conjunctival microbiome in health and trachomatous disease: a  case control study Yanjiao Zhou, Martin J Holland, Pateh Makalo, Hassan Joof, Chrissy h Roberts, David Maybe, Robin L Bailey, Matthew J Burton, George M Weinstock, Sarah E Burr  Genome Medicine 2014, 6:99 (15 November 2014) Abstract | Provisional PDF| Editor’s summary
	Research    Proteomics informed by transcriptomics reveals Hendra virus sensitizes  bat cells to  TRAIL mediated apoptosis James W Wynne, Brian J Shiell, Glenn A Marsh, Victoria Boyd, Jennifer A Harper, Kate Heesom, Paul Monaghan, Peng Zhou, Jean Payne, Reuben Klein, Shawn Todd,  Lawrence Mok, Diane Green, John Bingham, Mary Tachedjian, Michelle L Baker,  David Matthews, Lin-Fa Wang  Genome Biology 2014, 15:532 (15 November 2014) Abstract | Provisional PDF | PubMed| Editor’s summary
	Method    A phylogeny-based sampling strategy and power calculator informs  genome-wide associations study design for microbial pathogens Maha R Farhat, B Shapiro, Samuel K Sheppard, Caroline Colijn, Megan Murray Genome Medicine 2014, 6:101 (15 November 2014) Abstract | Provisional PDF| Editor’s summary
	Review    Engineering the control of mosquito-borne infectious diseases Paolo Gabrieli, Andrea Smidler, Flaminia Catteruccia Genome Biology 2014, 15:535 (15 November 2014) Abstract | Full text | PDF| Editor’s summary
	Research    A Genomic and Evolutionary Approach Reveals Non-Genetic Drug Resistance  in Malaria Jonathan D Herman, Daniel P Rice, Ulf Ribacke, Jacob Silterra, Amy A Deik, Eli Moss, Kate M Broadbent, Daniel E Neafsey, Michael M Desai, Clary B Clish, Ralph Mazitschek, Dyann F Wirth Genome Biology 2014, 15:511 (14 November 2014) Abstract | Provisional PDF| Editor’s summary
	Research highlight    The road to drug resistance in Mycobacterium tuberculosis Anastasia Koch, Robert Wilkinson Genome Biology 2014, 15:520 (13 November 2014) Abstract | Full text | PDF| Editor’s summary
	Research highlight    A CRISPR design for next-generation antimicrobials Chase L Beisel, Ahmed A Gomaa, Rodolphe Barrangou Genome Biology 2014, 15:516 (8 November 2014) Abstract | Full text | PDF| Editor’s summary
	Research     Evolution of extensively drug-resistant Mycobacterium tuberculosis from a  susceptible  ancestor in a single patient Vegard Eldholm, Gunnstein Norheim, Bent von der Lippe, Wibeke Kinander, Ulf R Dahle, Dominique A Caugant, Turid Mannsåker, Anne Mengshoel,  Anne Dyrhol-Riise, Francois Balloux  Genome Biology 2014, 15:490 (7 November 2014) Abstract | Full text | PDF| Editor’s summary
	Opinion    Translating genomics research into control of tuberculosis: lessons learned  and future prospects Digby F Warner, Valerie Mizrahi Genome Biology 2014, 15:514 (7 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Comment     Empowering African genomics for infectious disease control Onikepe A Folarin, Anise N Happi, Christian T Happi Genome Biology 2014, 15:515 (7 November 2014) Abstract | Full text | PDF| Editor’s summary
	Research highlight    Bringing non-human primate research into the post-genomic era: how  monkeys are teaching us about elite controllers of HIV/AIDS Eric J Vallender Genome Biology 2014, 15:507 (7 November 2014) Abstract | Full text | PDF| Editor’s summary
	Research    Whole genome sequencing of SIV-infected macaques identifies candidate loci that  may contribute to host control of virus replication Adam J Ericsen, Gabriel J Starrett, Justin M Greene, Michael Lauck, Muthuswamy Raveendran,  David Deiros, Mariel S Mohns, Nicolas Vince, Brian T Cain, Ngoc H Pham, Jason T Weinfurter, Adam L Bailey, Melisa L Budde, Roger W Wiseman, Richard Gibbs, Donna Muzny, T homas C Friedrich, Jeffrey Rogers, David H O’Connor Genome Biology 2014, 15:478 (7 November 2014) Abstract | Full text | PDF| Editor’s summary
	Research    Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' Disease  Laura Gomez Valero, Christophe Rusniok, Monica Rolando, Mario Neou, Delphine Dervins-Ravault, Jasmin Demirtas, Zoe Rouy, Robert J Moore, Honglei Chen,  Nicola K Petty, Sophie Jarraud, Jerome Etienne, Michael Steinert, Klaus Heuner,  Simonetta Gribaldo, Claudine Médigue, Gernot Glöckner, Elizabeth L Hartland,  Carmen Buchrieser  Genome Biology 2014, 15:505 (3 November 2014) Abstract | Provisional PDF| Editor’s summary
	Research    Staphylococcus aureus gene expression in a rat model of infective endocarditis Frank Hanses, Christelle Roux, Paul M Dunman, Bernd Salzberger, Jean C Lee Genome Medicine 2014, 6:93 (3 November 2014) Abstract | Full text | PDF | PubMed| Editor’s summary
	Research     Gene flow in environmental Legionella pneumophila leads to genetic and  pathogenic heterogeneity within a Legionnaires' disease outbreak Paul McAdam, Charles vander broek, Diane Lindsay, Melissa Ward, Mary Hanson, Michael Gillies, Mike Watson, Joanne Stevens, Giles Edwards, Ross Fitzgerald  Genome Biology 2014, 15:504 (3 November 2014) Abstract | Provisional PDF | PubMed| Editor’s summary
	Research     Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a  transcription factor overexpression-derived regulatory network Tige R Rustad, Kyle J Minch, Shuyi Ma, Jessica K Winkler, Samuel Hobbes, Mark J Hickey, William Brabant, Serdar Turkarslan, Nathan D Price, Nitin S Baliga, David R Sherman Genome Biology 2014, 15:502 (3 November 2014) Abstract | Provisional PDF | PubMed| Editor’s summary

Strangest microbial headline of month: Bacteria on Russian ‘sex satellite’ survive reentry

There is really not much to say other than to point everyone to this article: Bacteria on Russian ‘sex satellite’ survive reentry | Science | The Guardian



It defininely wins the strangest microbial headline of the month.  The article restates some of the silly claims about how what they are finding supports panspermia .. but ignore the article and just enjoy the headline.

Moore Foundation: Request for Expressions of Interest: Increasing the Potential of Marine Microeukaryotes as Experimental Model Systems through the Development of Genetic Tools

Got this from the Gordon and Betty Moore Foundation and they said I could post it here.

Request for Expressions of Interest: Increasing the Potential of Marine Microeukaryotes as Experimental Model Systems through the Development of Genetic Tools

Marine Microbiology Initiative Gordon and Betty Moore Foundation November 21, 2014

The Marine Microbiology Initiative (MMI) at the Gordon and Betty Moore Foundation aims to enable scientists to uncover the principles that govern the interactions among microbes and that influence nutrient flow in the marine environment. MMI is targeting closing gaps in and supporting the advancement of experimental model systems in microbial oceanography to enable new ways to uncover fundamental biological mechanisms.

We are soliciting expressions of interest (EOIs) for early-stage research projects to develop methods to genetically manipulate marine microeukaryotes as a first step in breaking current bottlenecks in the advancement of experimental model systems. MMI has two primary foci for this expression of interest:

1. Development of genetic tools for diatoms. Diatoms are key players in the world’s oceans, generating ~20% of the world’s organic carbon, and a strong community of researchers is in place suggesting broad use of successfully developed methods. We are specifically interested in projects to develop reverse and/or forward genetics.
   
2. Screening laboratory-scale culture collections for transformable marine microeukaryotes.
   

MMI will also consider projects to develop genetic tools and methods with other microeukaryotes that show promise for expanding the way the field can test hypotheses. If your idea does not fit category 1 or 2 above, please contact us prior to submitting your EOI.

MMI encourages EOIs from “inter-organismal” teams of researchers – i.e., complementary groups that have experience in a well-established model system and with a microeukaryote that is not currently genetically tractable – whose collaborative effort will bring innovative approaches to the field.

MMI invites you to send an expression of interest via email that briefly outlines a research project (one paragraph or less), using the following template:

1. The lead researcher’s name, institution, and expertise.
2. Indication of focus on genetic tools for diatoms (category 1 above) or laboratory culture screening for transformability (category 2 above).
3. For category 1, the name of the organism(s); or, for category 2, the taxonomic group(s) to be screened. 
4. A methodological or technical challenge that is hindering the development of a genetically manipulable marine microeukaryotic system that is ripe for solving and how you would address this challenge (3-5 sentences).
5. The research team that would tackle this challenge, and why each team member’s expertise is relevant (one sentence per team member; please include institutional affiliations).

The opportunities that best align with MMI’s strategies and goals will be invited to submit proposals. MMI has allocated $7–10M to support this effort and anticipates making multiple, 2–3 year awards beginning in mid- 2015.

Please submit your EOI by Tuesday January 6, 2015 to Samantha Forde at samantha.forde@moore.org.