Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Expert translation of details on "Clinical trial for autologous stool transplant" that is seeking volunteers

Well, if you are between 18 and 70 and are healthy and want to participate in a  clinical trial this may be for you.  Titled Autologous Fecal Therapy the description uses some science jargon to describe the plan.  They say

“Ten healthy volunteers will be recruited to receive either an autologous stool transplant or a saline enema to determine if autologous fecal microbiota therapy will be able to rapidly, and safely, restore a patient’s fecal microbiome after antimicrobial exposure.”

Or, in other words – they want you to (1) save your shit (2) take some antibiotics and (3) deliver either salt water or your own shit back into your rear.

Actually quite interesting.  And I encourage people to consider volunteering.  But I just thought it would be good to make sure you knew what this was about …

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Sarah Kendzior @sarahkendzior on “What’s the Point of Academic Publishing?”

In the run up to our meeting on “Publish or perish? The future of academic publishing and careers February 13 – 14, 2014 at UC Davis” I am going to be writing some blog posts about the topics of the meeting.  Just as I started to do a few web searches for one such post – I discovered a very timely article published a few days ago in Vitae: What’s the Point of Academic Publishing?.  The article is by Sarah Kendzior who is a writer who I have interacted with a few times here and there (she writes for Al Jazeera English and writes a lot about Academia).  It is an interesting read.

Winner of the biggest & best overselling of the microbiome -@theallium on Salmonella Diet

OK.  Now this is some serious overselling of the microbiome: New Salmonella diet achieves “amazing” weight-loss for microbiologist | The Allium.  A must read for anyone interested in microbes and microbiomes.  My favorite part:

“For some time now, we have known that the microbes of the gut – what we term the “microbiome” – play a very important role in our daily lives. What we eat, how healthy we feel, etc. is all controlled by our microbiome. In fact, nothing else is important to our health, except the microbiome – it can defeat cancer, cure hunger, poverty, restore amputated limbs, everything”, said Dr. Nofit.

Although it might seem to be an exaggeration, I think this Dr. Nofit must be correct.  I will now never claim that anyone has oversold the microbiome, because, well, it does everything.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Some readings on Gender Disparities in Scientific Publishing

Just a little post here with a collection of links to what I have been reading recently on Gender disparities in scientific publishing

Bibliometrics: Global gender disparities in science : Nature News & Comment

which I found out about from

How to calculate #MyGenderGap for publishing scientists

which I found out about from

My Gender Gap: Is there value in calculating the gender ratio of coauthors?

which I found out about from

Gina Baucom on Facebook

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Some other reading of interest:

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Another good collection of recommended papers from Pubchase

Got my weekly “Recommended papers” from Pubchase today.  I wrote about this here: Pubchase recommended papers to read system pretty good …
Below is the email I got: many of direct relevance to my work.  Thanks Pubchase. 

Jan 23, 2014 Journal Of Clinical Microbiology
Lim YW, Evangelista JS, Schmieder R, Bailey B, Haynes M, Furlan M, Maughan H, Edwards R, Rohwer F, Conrad D, Forbes BA
Jan 17, 2014 GigaScience
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF
Jan 23, 2014 Nature
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ
Jan 17, 2014 Nature Reviews. Genetics
Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP
Jan 21, 2014 The ISME Journal
Blasiak LC, Zinder SH, Buckley DH, Hill RT
Jan 15, 2014 BioEssays : News And Reviews In Molecular, Cellular And Developmental Biology
List JM, Nelson-Sathi S, Geisler H, Martin W
Jan 21, 2014 The ISME Journal
Wasmund K, Schreiber L, Lloyd KG, Petersen DG, Schramm A, Stepanauskas R, Jørgensen BB, Adrian L
Jan 22, 2014 MBio
Wright MS, Haft DH, Harkins DM, Perez F, Hujer KM, Bajaksouzian S, Benard MF, Jacobs MR, Bonomo RA, Adams MD
Jan 15, 2014 World Journal Of Microbiology & Biotechnology
Tindall BJ
Jan 16, 2014 Nature
Roy MG, Livraghi-Butrico A, Fletcher AA, McElwee MM, Evans SE, Boerner RM, Alexander SN, Bellinghausen LK, Song AS, Petrova YM, Tuvim MJ, Adachi R, Romo I, Bordt AS, Bowden MG, Sisson JH, Woodruff PG, Thornton DJ, Rousseau K, De la Garza MM, Moghaddam SJ, Karmouty-Quintana H, Blackburn MR, Drouin SM, Davis CW, Terrell KA, Grubb BR, O’Neal WK, Flores SC, Cota-Gomez A, Lozupone CA, Donnelly JM, Watson AM, Hennessy CE, Keith RC, Yang IV, Barthel L, Henson PM, Janssen WJ, Schwartz DA, Boucher RC, Dickey BF, Evans CM
Jan 17, 2014 Applied And Environmental Microbiology
Porras-Alfaro A, Liu KL, Kuske CR, Xie G
Jan 17, 2014 Astrobiology
La Duc MT, Venkateswaran K, Conley CA
Jan 17, 2014 Molecular Ecology
Primmer CR, Papakostas S, Leder EH, Davis MJ, Ragan MA
Jan 20, 2014 Water Research
Holinger EP, Ross KA, Robertson CE, Stevens MJ, Harris JK, Pace NR
Jan 17, 2014 Applied And Environmental Microbiology
Toenshoff ER, Szabó G, Gruber D, Horn M
Jan 15, 2014 Clinical Microbiology And Infection : The Official Publication Of The European Society Of Clinical Microbiology And Infectious Diseases
Bichaud L, Izri A, de Lamballerie X, Moureau G, Charrel RN
Jan 17, 2014 Astrobiology
Venkateswaran K, Vaishampayan P, Benardini JN, Rooney AP, Spry JA
Jan 16, 2014 Bioinformatics (Oxford, England)
Matias Rodrigues JF, von Mering C
Jan 16, 2014 American Journal Of Respiratory And Critical Care Medicine
Depner M, Fuchs O, Genuneit J, Karvonen AM, Hyvärinen A, Kaulek V, Roduit C, Weber J, Schaub B, Lauener R, Kabesch M, Pfefferle PI, Frey U, Pekkanen J, Dalphin JC, Riedler J, Braun-Fahrländer C, von Mutius E, Ege MJ, PASTURE Study Group
Jan 17, 2014 Genome Biology And Evolution
Oakeson KF, Gil R, Clayton AL, Dunn DM, von Niederhausern AC, Hamil C, Aoyagi A, Duval B, Baca A, Silva FJ, Vallier A, Jackson DG, Latorre A, Weiss RB, Heddi A, Moya A, Dale C
Jan 20, 2014 American Journal Of Epidemiology
Carlton EJ, Eisenberg JN, Goldstick J, Cevallos W, Trostle J, Levy K
Jan 17, 2014 Astrobiology
Benardini JN, La Duc MT, Beaudet RA, Koukol R
Jan 17, 2014 Astrobiology
Benardini JN, La Duc MT, Ballou D, Koukol R
Jan 15, 2014 Proceedings Of The National Academy Of Sciences Of The United States Of America
Wales DJ, Salamon P
Jan 23, 2014 Journal Of Clinical Microbiology
Toval F, Köhler CD, Vogel U, Wagenlehner F, Mellmann A, Fruth A, Schmidt MA, Karch H, Bielaszewska M, Dobrindt U, Forbes BA
Jan 24, 2014 Omics : A Journal Of Integrative Biology
Kolker E, Ozdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, Macnealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G
Jan 17, 2014 Molecular Phylogenetics And Evolution
Smith DR, Arrigo KR, Alderkamp AC, Allen AE
Jan 24, 2014 Current Biology : CB
Peacock L, Bailey M, Carrington M, Gibson W
Jan 23, 2014 PloS One
Xie G, Lo CC, Scholz M, Chain PS
Jan 24, 2014 Omics : A Journal Of Integrative Biology
Snyder M, Mias G, Stanberry L, Kolker E
Jan 24, 2014 Omics : A Journal Of Integrative Biology
Ozdemir V, Kolker E, Hotez PJ, Mohin S, Prainsack B, Wynne B, Vayena E, Coşkun Y, Dereli T, Huzair F, Borda-Rodriguez A, Bragazzi NL, Faris J, Ramesar R, Wonkam A, Dandara C, Nair B, Llerena A, Kılıç K, Jain R, Reddy PJ, Gollapalli K, Srivastava S, Kickbusch I
Jan 14, 2014 World Journal Of Microbiology & Biotechnology
Yuan P, Ogawa A, Ramamurthy T, Nair GB, Shimada T, Shinoda S, Takeda T
Jan 17, 2014 Planta
Brandt P
Jan 15, 2014 Planta
Brandt P
Jan 21, 2014 Water Research
Ofiţeru ID, Bellucci M, Picioreanu C, Lavric V, Curtis TP
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Kudos to the DOE-JGI for organizing a genomics meeting w/ a good gender ratio – no kudos to BGI – yet again.

Very happy to see the preliminary speaker list for The Annual DOE JGI User Meeting.  As many are aware, I have blogged and posted extensively about gender ratio at conferences and in particular at conferences related to genomics.  And alas, many people running genomics related meetings seem incapable of organizing a meeting with a reasonable gender ratio.  Some of my past posts on this and related topics include

But of course, there are some meetings out there that do a good job in having speakers represent at least some aspects of the diversity of scientists.  I am for example proud of the 2012 Lake Arrowhead Small Genomes meeting I co-organized: Lake Arrowhead Microbial Genomes Meeting 2012 Speaker Gender Ratio #LAMG12.  But I do not frequently write about meetings that are doing a good job with gender ratio and I am trying to also give props to such cases here.  And thus I was very pleased when I received an email telling me about the The Annual DOE JGI User Meeting.  From their web site here are the current confirmed speakers:

Keynotes:

  • Annalee Newitz, io9 “How humans will survive a mass extinction”
  • Steve Quake, Stanford University “Single cell genomics”

Other confirmed speakers:

  • Martin Ackermann, ETH Zurich – “A single cell perspective on bacterial interactions”
  • Luke Alphey, Oxitec – “Genetic control of mosquitoes”
  • Mary Berbee, University of British Columbia – “Genomes of early-diverging fungi reveal evidence of enzymes for breakdown of plant cell walls”
  • David Berry, University of Vienna (Austria) – “Single cell isotope probing of microbes via Raman microspectroscopy: A new way of in situ functional analyses and cell sorting”
  • Nicole Dubilier, Max Planck Institute for Marine Microbiology “Metagenomic and metaproteomic analyses of symbioses between bacteria and gutless marine worms”
  • Katrina Edwards, University of Southern California – “Genomics and proteomics of zeta proteobacteria”
  • Michael Fischbach, University of California, San Francisco -“A gene-to-molecule approach to the discovery and characterization of natural products”
  • Phil McClean, North Dakota State University -“Uncovering signatures of domestication using genomic resequencing and association mapping”
  • June Medford, Colorado State University -“Making better plants: synthetic approaches in plant engineering”
  • Maria Mercedes Roca, Zamorano University (Honduras) -“Synthetic biology & bioenergy: helping the good guys and stopping the bad”
  • Anne Osbourn, John Innes Centre -“Plant specialized Metabolites – Synthesis, function and mechanisms of metabolic diversification”
  • Pamela Ronald, UC Davis – “Whole genome sequencing of rice mutants to identify genes controlling response to strss and cell wall saccharification”
  • Steve Rounsley, Dow Agrosciences – “Cassava genomics – applying genomic technologies to benefit smallholder farmers in Africa.”
  • Kankshita Swaminathan, University of Illinois, Urbana-Champaign – “Genome biology of Miscanthus”
  • Rytas Vilgalys, Duke University -“Understanding the forest microbiome: a fungal perspective”
  • Dan Voytas, University of Minnesota – “Precise engineering of genomes with sequence-specific nucleases”
So that is a ratio of 9:9 male to female and a ratio of 1:1 for keynote speakers.  Good to see.  Now if only everyone else would do this.  In contrast to DOE-JGI consider the recent BGI organized meeting  “The 8th International Conference on Genomics” that was at the end of October in 2013.  By browsing through the interactive list of Speakers and their Agenda I come up with the following:
Keynote talks: Male 2: Female 0
Session Chairs Male 15: Female 4
Any role:  96 male: 17 female

Pretty painful.  It is even more painful to me to look at the whole list.  The full list with people I have classified as men highlighted in yellow and women in green.  Just look at the overrepresentation of yellow. 

Opening Remarks

  • Jun Wang, BGI
  • Huanming Yang, BGI

Keynote Speech

  • Technologies for Reading, Writing & Interpreting Omes –George Church, Harvard Medical School

Plenary Session 1: Emerging Technology Innovation

  • Chairman: Radoje Drmanac, Complete Genomics
  • Advanced Diploid Genome Sequencing Using Long Fragment Read Technology Radoje Drmanac, Complete Genomics
  • The Application of SmartChip on Target Region Capture Sequencing Hui Jiang, BGI
  • What Happens When Sequencing Becomes Really Cheap, Really Easy, and Really Fast Stefan Roever, Genia Technologies
  • Ion Torrent Semiconductor Technology – Targeted & Exome Sequencing Made Simple Andy Felton, Life Technologies

Plenary Session 2: Human Genome Projects and Big Data Management

  • Chairman: Stephan Beck, UCL Cancer Institute
  • TBC George Church, Harvard Medical School
  • Genomic Medicine in China and HVP-China Database Ming Qi, BGI
  • Population Genomics: Pan Asia Population Genomics Initiative and Korean Personal Genome Project Jong Bhak, Genome Research Foundation/Personal Genomics Institute
  • Gene Discovery and Data Sharing in Genome Wide Association Analyses: Lessons Form AIDS Genetic Restriction Genes Steve O’Brien, St. Petersburg State University
  • Systems Thinking in Clinical Genomics: a Requirements Perspective Sanjay Joshi, EMC

Plenary Session 3: Crowdsourcing and Crowdfunding Open-source Genomics, a New Model of Scientific Research

  • Chairman: Scott Edmunds, GigaScience
  • uBiome-Sequencing the Human Microbiome Using Citizen Science Zachary Apte, uBiome
  • Crowdsourcing Analyses of the Emergent Pathogen Ash Dieback Dan MacLean, The Sainsbury Laboratory
  • Parrots of the Caribbean: from One Genome to an Evolutionary Model of Island Evolution Taras Oleksyk, University of Puerto Rico
  • TBC Jacob Shiach, Brightwork CoResearch

Keynote Speech

  • The Omics World: To Explore the Unexplorable – Personalized Health will Depend on Your Gut Flora Jun Wang, BGI

Session 4: Clinical Transomics

  • Chairman: Vince Gao, BGI
  • Clinical Transomics Approaches for 4 P Medicine Vince Gao, BGI
  • Insights Into The Lethal Phenotype of Prostate Cancer Colin Collins, Vancouver Prostate Centre
  • Metabonomics in Clinical Research Jia Li, Imperial College London
  • The Ultimate Genetic Test: Accurate and Affordable WGS for Advanced Reproductive Health and Genomic Healthcare Radoje Drmanac, Complete Genomics

Session 5: Newborn and Reproductive Health

  • Chairman: Yutao Du, BGI
  • Pre- and Postimplantation Aneuploidy Testing in Germany Tina Buchholz, Centre for Reproductive Genetics
  • Metabolomics in Newborn Health: Newborn Screening for the Identification of Metabolic Disorders of Inborn Errors of Metablism (IEM) Enzo Ranieri, SA Neonatal Screening Centre
  • The Application of Molecular Biological Technologies in Prenatal Diagnosis Tze Kin LAU, The Chinese Fetal Medicine Foundation
  • NGS Technology in Clinical Genetic Practice in India – Successes and Pitfalls Ishwar Verma, Sir Ganga Ram Hospital

Session 6: Animal Genomics

  • Chairman: Robin Gasser, University of Melbourne
  • The Genomics of Socioeconomically Important Parasites – Recent Breakthroughs and Prospects Robin Gasser, University of Melbourne
  • Strategies for de novo Assembling Complex Genomes Xiaodong Fang, BGI
  • Poultry Genomics: Current Status and Future Trends from Next Generation Sequencing David W. Burt, The Roslin Institute, University of Edinburgh
  • Genomics and Genetic Design of Pigs Lars Bolund, Aarhus University
  • Mining Important Agronomic Trait Genes by Evolutionary Genomics Wen Wang, Kunming Institute of Zoology, CAS

Session 7: Crop Genomics

  • Chairman: Yong Pyo Lim, Chungnam National University
  • Genetics to Genomics : Dissecting Brassica Genome for Applied Breeding Yong Pyo Lim, Chungnam National University
  • The Draft Aegilops tauschii Genome Sequencing and Its Application in Wheat Gene discovery and Breeding Jizeng Jia, Crop Science Research Institute, CAAS
  • Dynamic Changes of Rice Transcriptome Revealed by Large-scale RNA-seq Analysis Takeshi Itoh, National Institute of Agrobiological Sciences
  • New Trends in RNA Sequencing and the Emerging Impact on Crop Genomics David L. Delano, Illumina
  • Whole Genome Molecular Marker Assisted Selection—from Concepts to Application Gengyun Zhang, BGI
  • Next Generation Genomics for Hexaploid Wheat Mario Caccamo, The Genome Analysis Centre
  • Using Genetics to Protecting the World’s Cereal Crops from the Rust Diseases Robert Park, The University of Sydney Plant Breeding Institute
  • Enabling Complete Transcriptome Sequencing with SENSE and SQUARE RNA-Seq. Alexander Seitz, Lexogen GmbH

Session 8: Disease Genomics-1

  • Chairman: Lennart Hammarstrom, Karolinska Institute
  • Genetic Analysis of Major Depression in 10,000 Chinese Women Using Low Pass Sequencing Data Jonathan Flint, Wellcome Trust Centre For Human Genetics
  • Integrated Systems Analysis of Schizophrenia Murray Cairns, University of Newcastle
  • Using Gene Expression Data to Help Identify Causal Genes in Inherited Disorders and Its Application to Brain Disorders Melanie Bahlo, Walter and Eliza Hall Institute of Medical Research
  • New Functional Genomics Strategies to Find Conserved Regulators of Disease Greg Neely, Garvan Institute

Session 9: Disease Genomics-2

  • Chairman: Jonathan Flint, Wellcome Trust Centre For Human Genetics
  • Genetics of Early Onset Myasthenia Gravis Lennart Hammarstrom, Karolinska Institute
  • Frequent Observation of Human Betaretrovirus proviral Integrations in Autoimmune Liver Disease Gane Ka-Shu Wong, University of Alberta
  • Experience with Cardiogenetics Jumana Yousif Adeeb Al-Aama, King Abdulaziz University
  • Application of Second Generation Sequencing to Transplantation Rejection Arena Brendan Keating, University of Pennsylvania / Children’s Hospital of Philadelphia
  • The Future of Genome Medicine in Patient Care Hakon Hakonarson, University of Pennsylvania / Children’s Hospital of Philadelphia

WS1: Science and Society – An Open Discussion on Burning Issues

  • Chairman: Frederick Dubee, United Nations Global Compact; Atsun Guo, BGI
  • TBC Frederick Dubee, United Nations Global Compact
  • TBC Laurie Goodman, GigaScience
  • Ethical Issues Raised by Synthetic Biology Ruipeng Lei, Huazhong University of Science and Technology
  • Genomics and Human Dignity Xinyu Cheng, Huazhong University of Science and Technology

Questions and Answers

  • Atsun Guo, BGI

Session 10: Marine Genomics

  • Chairman: B. Venkatesh, Institute of Molecular and Cell Biology, A-STAR
  • Evolutionary History of the Early Branching Lineage of Vertebrates B. Venkatesh, Institute of Molecular and Cell Biology, A-STAR
  • Whole Genome Sequencing, Assembly, and Annotation of Odontesthes Bonariensis (Pejerrey), a Fish with Temperature-dependent Sex Determination Guillermo Orti, George Washington University
  • How Did Ultrarapid Evolution Remodel the Chordate Genome in the Tunicate Branch Daniel Chourrout, Sars International Centre
  • Turtle also Follows the General Formulation of Embryonic Evolution Naoki Irie, University of Tokyo

Session 11: Personal Genome

  • Chairman: Cliff Reid, Complete Genomics
  • IntroductionCliff Reid, Complete Genomics
  • Personal Genomes, from Beginning to Today Dietrich Stephan, SVBio and Navigenics
  • Interpreting Genomes at Scale for Clinical Relevance Martin Reese, Omicia, Inc.
  • TBC Hai Mi, SB China Venture Capital Limited
  • TBC Brian Gu, JP Morgan

Session 12: Cancer Research-1

  • Chairman: Colin Collins, Vancouver Prostate Centre
  • The Challenges and Promises of Cancer Research: Lessons from the Laboratory Yuzhuo Wang, Vancouver Prostate Centre, BC Cancer Agency
  • Cancer Transcriptome Sequencing Tatsuhiro Shibata, Division of Cancer Genomics, National Cancer Center
  • Whole Genome Sequencing Analysis of Liver Cancer, Forwarding to Personalized Cancer Medicine Hidewaki Nakagawa, RIKEN Center for Genomic Medicine
  • Identification of PCDHB3 as a Potential Tumor Suppressor Gene in Colorectal Cancer by Exome Sequencing: A Highthroughput Sequencing Study Wenlin Huang, Sun Yat-Sen University Cancer Center
  • Biomarkers and Personalised Cancer Treatment — Clinical Validation and Application of ALK Fusion Testing in NSCLC Shuwen Huang, Central Manchester University Hospitals NHS Foundation Trust

Session 13: Genomic Evolution and Biodiversity

  • Chairman: Guojie Zhang, BGI
  • Comparative Genomics of Climate Change Adaptation Among Drosophila Species John Oakeshott, CSIRO Ecosystem Sciences
  • Artiodactyl Genome Evolution Harris A. Lewin, University of California, Davis
  • The Making of Differences Between Fins and Limbs: Developmental Aspects of Fin-to-limb Transition Koji Tamura,Tohoku University
  • Building the Link Between Micro-evolution and Macro-evolution -Lesson from Avian Phylogenomic Study Guojie Zhang, BGI
  • Genomic Hotspots of Adaptation- Reshuffling of Modular Enhancers Underlies Phenotypic Change in Heliconius Butterflies Owen McMillan, Smithsonian Tropical Research Institute
  • Sequencing Virus Population, Divergence and Evolution Hui Wang, Centre For Ecology & Hydrology
  • Genomic Revolution in Inset Phylogeny and Biodiversity Studies Xin Zhou, BGI

Session 14: Open Platforms for Biological Data

  • Chairman: Peter Li, GigaScience
  • Using Galaxy for Metabolomics Robert Davidson, Natural Environmental Research Council (NERC), Birmingham University
  • The IRRI Genotyping Service Laboratory Galaxy: Bioinformatics for Rice Scientists Ramil Mauleon, International Rice Research Institute
  • DNA Barcoding Illuminates Dark Taxa and Advances Turbo Taxonomy Robert Hanner, University of Guelph/Centre for Biodiversity Genomics
  • A new standard for eukaryotic species description, combining transcriptomic, DNA barcoding, and micro-CT imaging data Pavel Stoev, Pensoft Publishers Ltd.

Session 15: Informatics for Genomic Medicine

  • Genomic Medicine Pauline Ng, Genome Institute of Singapore
  • Research Data Management and Analysis as a Service : Experiences in building Globus Genomics Ravi K Madduri, Argonne National Laboratory Computation Institute, University of Chicago
  • Making a Definitive Diagnosis: On the Path to Realizing the Promise of Genomic Medicine Elizabeth Worthey, Medical College of Wisconsin
  • Genomic Medicine and beyond in IBM Takahiko Koyama, IBM

Session 16: Cancer Research-2

  • Chairman: Qiang Pan Hammarstrom, Karolinska Institute
  • Genetic Identification of Key Pathways in Lung Adenocarcinoma Metastasis Qiang Pan Hammarstrom, Karolinska Institute
  • Probing the Cancer Methylome Stephan Beck, UCL Cancer Institute
  • Making Sense of Cancer Genomes Steve Rozen, Duke-NUS Graduate Medical School Singapore
  • An Integrative Genomics Study on Angioimmunoblastic T-cell Lymphoma Sanghyuk Lee, Ewha Womans University
  • Multidiscilinary Role in Molecular/Genomic Diagnostics and Personalized Cancer Medicine Dongfeng Tan, MD Anderson Cancer Center

Session 17: Metagenomics and Health

  • Chairman: Karsten Kristiansen, University of Copenhagen
  • Establishment of the Human Gut Microbiota after Birth Karsten Kristiansen, University of Copenhagen
  • Gut Microbiota—Our ‘Other’ Genome Huijue Jia, BGI
  • Elucidating the Role of Human Gut Microbiota in Diseases: Metagenomics to the Rescue Manimozhiyan Arumugam, University of Copenhagen
  • Deep Metagenomic Sequencing of Multiple Ruminant Guts Reveals Species-specific Microbiomes Mick Watson, ARK-Genomics, Centre for Comparative & Functional Genomics
  • Our Second Genome, Environment and Allergy are Related Petri Auvinen, University of Helsinki

WS2: Human Genomic Data and Society

  • Chairman: Laurie Goodman, GigaScience
  • Translating Scientific Information to the Public Laurie Goodman, GigaScience
  • Genetic Counseling and Genetic Testing in the Genomics Era Thong Meow Keong, University of Malaya
  • Conflicting Open Access data Sharing and Patient Privacy in Genome Association- Can We Fix This Steve O’Brien, St. Petersburg State University
  • Family Genome Analysis When Privacy Issues Are Not A Concern Manuel Corpas, Norwich Research Park
  • Strategies for Engaging the Public on Personal Genetics Ting Wu, Harvard Medical School
I note – I was invited to the BGI meeting that was co-hosted by my own institution – UC Davis last year  – but I turned down the invitation due to the gender ratio of speakers on their preliminary list.  This was certainly awkward for me and who knows if it did some damage to how I am viewed by some people on campus.  But we as a community need to take stands on such issues.  Sure – there are many explanations for why a meeting might have a skewed ratio of genders in the speakers. But given that this is a persistent / consistent pattern at meetings organized by BGI – I think this is at the point where I would definitely recommend people stop paying to attend their meetings.  And I would not recommend speaking at their meetings either.  That is, until they make a serious commitment to doing something about their apparent bias against women.  I would even go so far as to say it is time to consider not working with BGI in any way until they address this issue.

UPDATE – 12:00 PM 1/26 – Here are some of my previous posts about BGI organized meetings

UPDATE 2: 12:30 PM 1/26
Somewhat hard to find information on their past meetings on the web because they use a static web site for the meetings some years but I was able to find some information on their sites:
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

The start of a slow poop movement?

Well I am not 100% sure I believe all the claims in this but it is fascinating: What Drives a Sloth’s Ritualistic Trek to Poop? | Articles | Smithsonian.  I knew nothing about sloths and their poop until reading this.  The key part of the article to me:

The scientists’ results point to linked mutualisms between the sloths, the algae, and the moths: the sloth climbs down the tree to poop and, because the ground around the tree is littered with poop from previous descents, moth larvae growing in the poop can hitch a ride on the sloth’s back. The moths find shelter and thrive in the fur ecosystem. They also bring nutrients to their new home from the poop they were born in and when they die and decompose. Those nutrients fuel algae growth in the fur, and the algae supplement sloths’ foliage diets with lipids that the scientists speculate could serve as a high-energy snack. Then, when the sloths go down to do their business again, moths hop on their back and the cycle starts over again. 

I think this could be the start of a slow poop movement …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Wanted from #UCDavis peeps: visual media that integrates “Art and Biology”

Just got this email from Daniel Friedman here and thought I would share (with his permission)

Dear Dr. Eisen

This quarter, within MCB121 a group of students are starting a journal that integrates molecular biology with writing and creative work by campus community members. I am the art editor for the journal, and would be honored if I could solicit a commissioned piece from you to be published in an upcoming issue. Should you so decide to participate in this fun challenge, your prompt would be:

With visual media (digital, pen/paper, paint etc) and no written words, represent, explore, or explain a biological phenomenon that excites you – perhaps from your own research, perhaps just something you have always thought was cool.

It would be awesome to see the intersection of personality and quirkiness of each individual professor’s worldview against the common backdrop of a subject matter that we all know and love. Also, please feel free to send this email to any of your colleagues who might be interested – I have certainly only encountered a small fraction of the interesting campus peoples.

Thank you very much for your time, let me know if you have any questions. Peace,

Daniel Friedman

danielarifriedman@gmail.com

Quick ego-post – link to interview of me by National Geographic Weekend show

Quick post here.  Was interviewed for National Geographic Weekend by Boyd Matson a few days ago and the show was just posted online: January 19, 2013: Waging War Against Whalers, Paragliding Above Pakistan and More – News Watch.  Scroll down to find the link to my part ..

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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At #UCDavis 1/23 – Mercedes Pascual “Climate forcing and the population dynamics of infectious diseases in changing human landscapes”

STORER LIFE SCIENCES ENDOWMENT

PRESENTS

MAJOR ISSUES IN MODERN BIOLOGY

Mercedes Pascual

Rosemary Grant Collegiate Professor of Ecology and Evolutionary Biology Research Professor, Center for Computational Medicine and Bioinformatics, University of Michigan

SEMINAR TITLE:

Climate forcing and the population dynamics of infectious diseases in changing human landscapes

Dr. Pascual is an internationally recognized theoretical ecologist interested in the population dynamics of infectious diseases, their response to changing environments, and their interplay with pathogen diversity. Her cutting edge research on responses to climate forcing considers in particular water-borne and vector-borne infections. She is also interested in the structure and dynamics of large ecological networks of consumer- resource interactions known as food webs.

Dr. Pascual received her Ph.D. degree from the joint program of the Woods Hole Oceanographic Institution and the Massachusetts Institute of Technology. She was awarded a U.S. Department of Energy Alexander Hollaender Distinguished Postdoctoral Fellowship for studies at Princeton University, and a Centennial Fellowship in the area of Global and Complex Systems awarded by the James S. McDonnell Foundation for her research at UM. She is a fellow of the American Association for the Advancement of Science, an external faculty member of the Santa Fe Institute, and is a Howard Hughes Medical Institute Investigator.

Sponsored by Department of Evolution and Ecology College of Biological Sciences Storer Life Sciences Endowment University of California, Davis

Thursday January 23, 2014 4:10 P.M.

100 Hunt Hall

Storer_Mercedes Pascula flyer.doc.pdf