Monday, November 24, 2014

A night with Matt Groening and the importance of faeces, feces and faces

So - I participated in a fundraiser for Emily Levine's "The Edge of Chaos" film a week ago. And one of the key guests was Matt Groening. Not only did I get to hang out with him and discuss fecal transplants with him (really) but I had a front row seat to Matt discussing the history of how he came up with the general outline of the Simpson's characters.



And in addition to this being just awesome to witness, one part of it struck me. See the video below and in particular the part that struck me was the beginning:

  Groening
basically said that only a few simple changes in faces can be recognized by people very easily. This reminds me of Jenna Lang's talk at the Lake Arrowhead meeting this year where she discussed using facial drawings as a form of visualizing microbiome data.

 

So - since I discussed fecal transplants with Matt and since he gave a good description of facial characteristics being easy to identify, I think we should definitely (1) try and get him to include microbiomes on the Simpsons and (2) for our work we should use Simpsons characters as model faces for different microbiomes ...

Oh and I also showed Groening some of the pics of my kids reading his "Hell" books:





So - basically it was a night of feces, faeces and faces.  Seems ideal.

Sunday, November 23, 2014

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   Open Access
Ripudaman K Bains Genome Biology 2014, 15:529 (22 November 2014)
Review   Subscription
Lucy M Li, Nicholas C Grassly, Christophe Fraser Genome Biology 2014, 15:541 (22 November 2014)
Research   Open Access
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)
Research highlight   Subscription
Patrick Tang, Jennifer L Gardy Genome Medicine 2014, 6:104 (20 November 2014)
Software   Open Access
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)
Comment   Subscription
Jeffrey S McLean, Roger S Lasken Genome Medicine 2014, 6:108 (20 November 2014)
Software   Open Access
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)
Research   Open Access
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)
Editorial   Open Access
George M Weinstock, Sharon J Peacock Genome Biology 2014, 15:528 (19 November 2014)
Software   Open Access
Todd J Treangen, Brian D Ondov, Sergey Koren, Adam M Phillippy Genome Biology 2014, 15:524 (19 November 2014)
Method   Open Access
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)
Editorial   Open Access
Sharon J Peacock, George M Weinstock Genome Medicine 2014, 6:103 (19 November 2014)
Opinion   Free
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)
Review   Subscription
Yonatan H Grad, Marc Lipsitch Genome Biology 2014, 15:538 (18 November 2014)
Method   Open Access
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, T
arjei 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)
Research   Open Access
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)
Research   Open Access
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)
Method   Open Access
Maha R Farhat, B Shapiro, Samuel K Sheppard, Caroline Colijn, Megan Murray Genome Medicine 2014, 6:101 (15 November 2014)
Review   Subscription
Paolo Gabrieli, Andrea Smidler, Flaminia Catteruccia Genome Biology 2014, 15:535 (15 November 2014)
Research   Open Access
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)
Research highlight   Subscription
Anastasia Koch, Robert Wilkinson Genome Biology 2014, 15:520 (13 November 2014)
Research highlight   Subscription
Chase L Beisel, Ahmed A Gomaa, Rodolphe Barrangou Genome Biology 2014, 15:516 (8 November 2014)
Research   Open Access Highly Accessed
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)
Opinion   Open Access
Digby F Warner, Valerie Mizrahi Genome Biology 2014, 15:514 (7 November 2014)
Comment   Open Access Highly Accessed
Onikepe A Folarin, Anise N Happi, Christian T Happi Genome Biology 2014, 15:515 (7 November 2014)
Research highlight   Subscription
Eric J Vallender Genome Biology 2014, 15:507 (7 November 2014)
Research   Open Access
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)
Research   Open Access
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)
Research   Open Access
Frank Hanses, Christelle Roux, Paul M Dunman, Bernd Salzberger, Jean C Lee Genome Medicine 2014, 6:93 (3 November 2014)
Research   Open Access Highly Accessed
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)
Research   Open Access Highly Accessed
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)