conferences – Page 2 – Jonathan Eisen's Lab

ICG Europe starts w/ "Omics & the future of man" & sticks to men the rest of the time

Fun. Another day. Another YAMMGM (yet another mostly male genomics meeting). This one is the International Conference on Genomics Europe 2013. I have copied the program as it is now here and then highlighted the men and women as far as I can tell. And, well, it is not very balanced. It starts off, ironically, with “Omics and the future of man” and then stays on both omics and alas, men, for most of the meeting. The first woman does not talk until 5 pm on the first day. Nothing against BGI per se. But they seem to be repeat offenders in having meetings with mostly male speakers. A difference between countries? Perhaps. But unfortunate and unpleasant nevertheless.

Sessions with speakers:

Plenary Session 1: Omics and the future of man

09:00-09:10: Opening ICG-Europe 2013 & Welcome: Hans Galjaard, Chairman of the Department of Clinical Genetics at Erasmus University
09:10-09:55: Talk 1: Huanming Yang, BGI, China
9:55-10:25: Talk 2: Jeremy Nicholsen, Head of the Department of Surgery and Cancer, Imperial College London, UK
Topic: Molecular Phenotyping and Systems Medicine Approaches in Personalised and Public Healthcare

Chairman: Prof.Huanming Yang, BGI, China

Plenary Session 2 :

11:00-11:30: Talk 1 (30 min): Jun Wang, CEO, BGI, China
11:30-12:00: Talk 2 (30 min): Karsten Kristiansen, Head of the Department of Biology, University of Copenhagen, Denmark
12:00-12:30: Talk 3 (30 min): Nils Brunner, Director of the Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Denmark
Topic: Docetaxel resistance in vitro: Known mechanisms and novel pathways in breast cancer
Chairman: Prof. Jun Wang, BGI, China

Plenary Session 3: Plant and Animal Genomics

13:30-13.55: Talk 1: Rajeev K. Varshney, Director-Centre of Excellence in Genomics, ICRISA, Hyderabad, India
Topic: “Little” is “more” for chickpea and pigeonpea
13.55-14.20: Talk 2: Michael Bevan, Genomics and Functional Genomics of Bread Wheat for Crop Improvement, John Innes Centre, Norwich, UK
Topic: Genomics and Functional Genomics of Bread Wheat for Crop Improvement
14.20-14.45: Talk 3: Michel Georges, Unit of Animal Genomics, University of Liège, Belgium
14.45-15.15: Talk 4: Tomas Marques, ICREA Research Professor, Universitat Pompeu Fabra, Spain
Topic: Great Ape genetic diversity
15.15-15.35: Talk 5: TBC
Chairman: Prof. Marc Van Montagu , VIB, Belgium

Session 4: Cancer genomics and Transcriptional Regulation

16:00-16:20: Talk 1(20 min): Stein Aerts, Heading the Laboratory of Computational Biology, K.U.Leuven, Belgium
Topic: Probing into the genome, transcriptome, and regulatory network of T-cell acute lymphoblastic leukemia
16:20-16:40: Talk 2(20 min): Lars Bullinger, Assistant Professor, University of Ulm, Germany
Topic: Genomics in acute myeloid leukemia (AML) – clinical translation of findings
16:40-17:00: Talk 3(20 min): Diether Lambrechts, Assistant Professor, K.U.Leuven & VIB, Belgium
Topic: Mutation signatures of mismatch repair deficiency in cancer genomes
17:00-17:20: Talk 4(20 min): Lynnette Fernandez-Cuesta, University of Cologne, Germany
Topic: Characterization of lung neuroendocrine tumors
17:20-17:40: Talk 5(20 min): Henrik Ditzel, University of Southern Denmark, Denmark
Chairman: Dr. Jan Cools (K.U.Leuven, VIB)

Workshop：Innovation-Entrepreneurship and Venture creation-1

14:30-14:50: Talk 1 (20 min): Boo Edgar, Program Director, Innovation and entrepreneurship; The Sahlgrenska Academy, University of Gothenburg
14:50-15:10: Talk 2 (20 min): Martin Bonde, Chairman of Danish Biotech association
15:10-15:30: Talk 3 (20 min): Søren Møller, Managing Investment Director, Novo Seeds
Chairman: Johan Cardoen
16:00-16:20: Talk 1(20 min): Johan Cardoen, Managing Director VIB
16:20-16:40: Talk 2(20 min): Patrick Van Beneden, GIMV
16:40-17:00: Talk 3(20 min): Ann De Beuckelaer, Flanders Bio

Session 5: Human Disease- Structural Genomic Variation and Function

09:00-09:30: Talk 1 (30 min): Wigard Kloosterman, UMC Utrecht, The Netherlands
Topic: Cause and Consequence of Complex Genomic Rearrangements
09:30-10:00: Talk 2 (30 min): Michael Talkowski, Instructor, MGH, Harvard University, USA
Topic: Sequencing unique human genomes reveals novel loci in autism and predictive phenotypes in prenatal diagnostics
10:00-10:30: Talk 3 (30 min): Thierry Voet, K.U.Leuven
Chairman: Prof. Edwin Cuppen , Hubrecht Institute

Session 6: Metagenomics

09:00-09:30: Talk 1 (30 min): Hui Wang, The Centre for Ecology & Hydrology, UK
Topic: Virus discovery by using deep sequencing data
09.30-10:00: Talk 2 (30 min): TBC
10:00-10:30: Talk 3 (30 min): Bjoern Textor, New England Biolabs GmbH
Topic: Direct Selection of Microbiome DNA from Host DNA
11:00-11:30: Talk 1 (30 min): Jeroen Raes, Scientific Collaborator, VUB&VIB
11:30-12:00: Talk 2 (30 min): Rob Knight, Associate Professor, Colorado University
Topic: Characterizing microbial effects of family structure, including our furry family members?
12:00-12:30: Talk 3 (30 min): Ruth Ley, Cornell University
Topic: Host control of the microbiome
Chairman: Dr. Jeroen Raes (VUB, VIB)

Session 7(3 talks: include Q&A 5 mins): Human Disease – Clinical Genetics

11:00-11:35: Talk 1(35 min): Han Brunner, Department of Human Genetics, Radboud University Nijmegen Medical Centre, The Netherlands
Topic: Clinical Genetic Diagnostics by Genome Sequencing.
11:35-12:05: Talk 2(30 min): Wang Wei, BGI Health, Shenzhen, China
Topic: Non-invasive prenatal testing (NIPT): Current clinical application and future outlook
12:05-12:45: Talk 3(30 min): Gabor Vajta, BGI Europe, Copenhagen, Denmark and Central Queensland University, Rockhampton, Australia in concert with Du Yutao, BGI Health, Shenzhen, China
Topic: Pre-implantation Diagnostics by Blastocyst Biopsy, Vitrification and Genome Sequencing
Chairman: Prof. Lars Bolund, Aarhus University

Session 8: Health and Translational Medicine-1

13:30-13:55: Talk 1(25 min): Vince Gao, BGI
Topic: Development of Clinical Service at BGI Health
13.55-14:20: Talk 2(25 min): Attila Lorincz, UK
Topic: Clinical Validation of Genomic and Epigenomic Biomarker Panels
14:20-14:45: Talk 3(25 min): Maurizio Ferrari, Director of Clinical Molecular Biology and Cytogenetics Laboratory, and Head of Genomic Unit for the Diagnosis of Human Pathologies, Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele, Milan, Italian
Topic: From bench to bedside: new advanced molecular techniques for genetic diagnosis
14:45-15:10: Talk 4(25 min): Carlos Simón Vallés, Board Certified and Full Professor of Obstetrics and Gynecology at the University of Valencia,Spain
Topic: Clinical Application of the endometrial receptivity array
15:10-15:35: Talk 5(20 min): To be selected from submitted abstracts
Chairman: Dr. Vince Gao , BGI

Session 9: Human disease

13:30-13:55: Talk 1(25 min): Lars Bolund, Professor of Clinical Genetics at Aarhus University, Denmark, and Adjunct Professor of Human Genetics at Copenhagen University, Denmark
Topic: Chronic Disorders, Rare Genetic Variants and Pig Models of Degenerative Disease Processes
13:55-14:20: Talk 2(25 min): Tao Dong, Head of anti-viral T cell immunology group, MRC Human Immunology Unit, Oxford University, UK
14:20-14:45: Talk 3(25 min): Hartmut Wekerle, Honorary Professor, Max Planck Institute of Neurobiology, Martinsried, Germany
14:45-15:10: Talk 4(20 min): Ramneek Gupta, The Technical University of Denmark, Danmark
15:10-15:30: Talk 5(20 min): Anders Børglum, Professor, Aarhus University, Denmark
Chairman: TBC

Session 10: Health and Translational Medicine-2

16:00-16:20: Talk 1(20 min): Diana M Eccles, Academic Vice President of the Clinical Genetics Society, Southampton General Hospital, UK
16:20-16:40: Talk 2(20 min): E. Gomez Garcia, Maastricht University, the Netherlands
16:40-17:00: Talk 3(20 min): Pascal Pujol , Chu Montpellier, France
17:00-17:20: Talk 4(20 min): Atocha Romero, Hospital Clinico San Carlos, Spain
17:20-17:40: Talk 5(20 min): Ian Campbell, Peter MacCallum Cancer Centre, Australia
Topic: Identification and validation of familial cancer susceptibility genes using massively parallel sequencing
Chairman: Prof. Yves-Jean Bignon, Centre Jean Perrin

Workshop: Ethical, Legal and Social Implications (ELSI)

16:00-16:20: Talk 1(20 min): Lone Frank, Denmark
16:20-16:40: Talk 2(20 min): Pascal Borry, K.U.Leuven, Belgium
16:40-17:00: Talk 3(20 min): TBC
Chairman: Prof. Huanming Yang, BGI

Session 11: Biobanks

08:00-08:30: Talk 1 (30 min): Zhang Yong, BGI, China
08:30-09:00: Talk 2 (30 min): Kristian Hveem, Chief Scientific Officer, Nord-Trondelag County, Norway
09:00-09:30: Talk 3 (30 min): Shaoliang Peng, National University of Defense Technology, China
Topic: Bioinformatics and Computational Biology on TianHe Supercomputer
Chairman: Dr. Zhang Yong, BGI

Workshop: Use of Omics Technology for Personalized Medicine

08:00-08:30: Talk 1 (30 min): Jenny Wei, R&D Information China, AstraZeneca global R&D
Topic: Genomics for Personalized Medicine: From Discovery to Clinic
08:30-09:00:Talk 2 (30 min):André Rosenthal, CEO, Signature Diagnostics AG
Topic: Next-Gen Sequencing Tests for Prognosis and Prediction of Response to Therapy of Patients with Colorectal Cancer Using Somatic Mutation Signatures
09:00-09:30: Talk 3 (30 min):Radoje Drmanac, Complete Genomics, Inc. Mountain View, California, U.S.A.
Topic: Accurate whole genome sequencing as the ultimate genetic test enabling personalized disease prevention and treatment
Chairman: TBC

Session 12: Bioinformatics

10:00-10:30: Talk 1 (30 min): Nathaniel Street, Assistant professor, Umea University
Topic: Sequencing the Norway spruce genome reveals a unique history of repeat expansion
10:30-11:00: Talk 2 (30 min): Sofie Van Landeghem, Ghent University, VIB, Belgium
Topic: Mining the literature to enhance integrative network biology
11:00-11:30: Talk 3 (30 min): Mario Caccamo, Acting Director at The Genome Analysis Centre, Norwich, UK
Topic: Next Generation Genomics for Complex Crops
Chairman: Prof. Yves Van De Peer (U.Ghent, VIB)

For related posts see

YAMMGM: Yet another mostly male genomics meeting #2: Beyond the Genome 2013

Well, the “winner” of this months YAMMGM award is Beyond the Genome 2013 | Mission Bay | San Francisco

Alas, YAMMGM stands for “Yet another mostly male genomics meeting” so it is not an award to covet.

This meetings listed speakers are below with women highlighted in green.

Nicholas Navin -The University of Texas MD Anderson Cancer Center
Sunney Xie – Harvard
Xu Xun – BGI
James Hicks -CSHL
Fuchou Tang – Peking
Itai Yanai – Israel
Thierry Voet – Sanger
Jacob Kitzman – Plasma cell free DNA sequencing
Stephen Quake – Stanford and Fluidigm
Mario Caccamo – Genome Analysis Centre
Rob Martienssen – CSHL
Ryan Lister – University of Westerm Australia
Neelima Sinha – UC davis
Jorge Dubcovsky – UC Davis
Robert Schmitz (Salk) – 1001 Arabidopsis project and CHiP-Seq
Marja Timmermans (CSHL)
Magnus Nordborg
Chairs Alicia Oshlack, Yingrui Li and Michael Schatz to chair the bioinformatics challenge.
James Taylor – Emory and Galaxy
Chris Dagdigian – Bioteam
David Haussler -UC Santa Cruz
Janet Kelso – Max Planck Institute for Evolutionary Anthropology

That comes to 16.6% if you count all listed. If you exclude session chairs the numbers are a little different but still pretty low.

Certainly this does not prove any bias on the part of the meeting organizers. But it certainly suggests to me they might want to think about why the ratio is skewed.

YAMMGM: Yet another mostly male genomics meeting

Just got an email from Illumina – key parts are below:

2013 Illumina Scientific Summit

Dear Jonathan,

Illumina’s third annual Scientific Summit will be held June 3rd through 7th in charming New Orleans, Louisiana, at the Loews Hotel. Described by a past attendee as, “an upscale Gordon Conference”, the Scientific Summit is an invitation-only meeting of 120 leading scientists and thought leaders plus the Illumina executive and R&D leadership teams.

Plenary sessions will be focused on the Genetic Etiology of Cancer and Genetic Diseases, The Changing Landscape of Medical Genetics, Microbial Detection, and Epigenetics. The formal presentations will be complemented by attendee-driven discussion sessions on a variety of topics ranging from workflow bottlenecks to future applications of Next Generation Sequencing in single cells and diagnostics.

The following distinguished scientists are scheduled to speak:

Dr. Mark Adams, Scientific Director, J. Craig Venter Institute

Dr. Kenneth J. Bloom, Chief Medical Officer, Clarient

Dr. David Craig, Deputy Director of Bioinformatics, Associate Professor and Director, Neurogenomics Division, Head Neurobehavioral Research Unit, TGen

Dr. Richard Gibbs, Wofford Cain Chair in Molecular and Human Genetics, Professor, Department of Molecular and Human Genetics, Professor, Programs in Translational Biology & Molecular Medicine, Baylor College of Medicine

Dr. David Goldstein, Director, Duke Medical Center for Human Genome Variation, Duke University

Dr. Steven Jones, Head of Bioinformatics and Associate Director, Michael Smith Genome Sciences Centre, BC Cancer Agency

Dr. Michael Katze, Professor, Microbiology, University of Washington

Dr. Jim Knowles, Professor and Associate Chair for Research and Psychiatry and the Behavioral Sciences, USC

Dr. Peter Laird, Director, USC Epigenome Center, Professor of Surgery,Biochemistry and Molecular Biology, Keck School of Medicine, USC

Neil Miller, Director of Informatics and Software Development, Center for Pediatric Genomic Medicine, Children’s Mercy Hospital, Kansas City

Dr. Steven Musser, Director, Office of Regulatory Science, FDA Center for Food Safety and Applied Nutrition

Dr. Charles Perou, Distinguished Professor of Genetics, Professor, Pathology & Lab Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine

Dr. Jonathan Sebat, Chief, Beyster Center for Genomics of Neuropsychiatric Diseases, Associate Professor, Department of Psychiatry & Cellular and Molecular Medicine, University of California, San Diego

Dr. George Weinstock, Professor of Genetics and Molecular Microbiology, Washington University

Dr. Liz Worthey, Director of Genomic Informatics, Medical College of Wisconsin

I love Illumina sequencing toys. I really do. No so impressed with the gender ratio of this meeting however. Would not have gone anyway … but if I COULD have attended I would not have. I wonder -did they even think about whether there might be some bias here? There certainly are plenty of female candidates they could have invited. Maybe they did not invite women? Maybe all the women said no?

Genomics Education highlighted at 14th Annual International Meeting on Microbial Genomics

Just got back from the 14th Annual International Meeting on Microbial Genomics, where I gave talk on microbial symbiont genomics. This was one of the best meetings I have been to in a while. It had the right combination of everything including:

Many excellent talks and posters (OK, in the interest of not upsetting people for not saying their talk or poster was great, I will not make a big list of all the ones I thought were good, but I will give a few highlights below).
Excellent location (UCLAs Lake Arrowhead Conference Center, which is in the mountains east of Los Angeles). This is a place that is very conducive to getting to know colleagues and it almost forces interaction among people. There is one central building where there is a dining hall, a nice deck if you want to eat outside, the conference room, rooms for posters, and a large living room for hanging out. The rooms for sleeping are mostly great (e.g., mine was a split level condo like structure with a living room and a bedroom/bath on floor one and a bedroom/bath on floor 2). And being in the mountains is very pleasant. Plus there is a pool, jacuzzi, and sports facilities that are very nice. The only annoying thing is that the Lake itself, which is 100 yards away, but it really almost private, with most of the shoreline occupied by houses and private docks.
Good food. The food is not spectacular or anything but better than the food at 90% of the conferences I have been at.

In terms of talks, there were quite of few that were both interesting topics and very well presented. For example, Jessica Green from U. C. Merced gave a great talk about spatial distributions of microorganisms, Julian Parkhill from the Sanger Center put together a really nice story about mechanisms by which microbial pathogens generate phenotypic diversity, and Julie Huber from MBL impressed many with her talk about the “Deep Rare Biosphere.”

But to me, the best two talks were ones on science education reform by two people from UCLA. Erin Sanders-Lorenz presented a summary of her course she has been teaching at UCLA that has students doing “phylogenomic” analysis which takes them from isolating and culturing organisms from environmental samples to building evolutionary trees of genes isolated from these cultured species.. This seemed like a very creative, hand on, novel way to teach students the excitement of science and some things about evolution. It sounded so well thought out that I asked for (and got) a copy of her lab manual.

Much as I liked this class, the one described by Cheryl Kerfeld knocked my socks off. She described a program they have developed at UCLA called the Undergraduate Genomics Research Initiative. This is an interdepartmental multi-course collaboration with the central theme involving the sequencing and analysis of the genome of a bacterium called Ammonifex degensii. The various courses are organized around a central course on genome sequencing. The linked courses include ones in many different departments at UCLA as well as various courses at other universities. They have clearly given enormous thought to how to do a truly project based course which likely will catch students attention and interest much more than standard lectures or standard labs.

There have been other successful hands on genome sequencing courses before – perhaps the first being one by Brad Goodner at Hiram College who had students participate in the sequencing and analysis of the genome of Agrobacterium tumefaciens (e.g., see a press release here). The Kerfeld UCLA UGRI program sounds like it has gone to the next level by integrating many courses across departments and by having creative ways to encourage participation of students in multiple aspects of the project. It really is worth giving a look at the UCLA UGRI program’s web site.

Other tidbits about the meeting:

Jeffrey H. Miller from UCLA organized it
This is the same Jeffrey Miller who identified most of the mutator genes in E. coli with a really creative genetic screen
There was another Jeffrey Miller from UCLA at the meeting (will leave this up to google for people to figure out who this other Miller is).