table of contentsreg.conferences.dce.ufl.edu/docs/veme/vemeprogram.pdfjournal of virology, trends in...

18th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME) 1

VEME Organizers.............................................................................................................................. page 2

Module Organizers............................................................................................................................ page 3

General Information.......................................................................................................................... page 4

Map..................................................................................................................................................... page 5

Sponsors.............................................................................................................................................. page 6

Module Schedules:

Phylogenetic Inference................................................................................................................ pages 7-8

Hypothesis Testing...................................................................................................................... pages 9-10

Large Dataset Analysis................................................................................................................ pages 11-12

Notes................................................................................................................................................... pages 13-16

Table of Contents

25-30 August, 2013 Gainesville, Florida, USA2

VEME Organizers

Prof Dr Anne-Mieke Vandamme was trained as biochemist, and holds a PhD in sciences since 1986. She joined the Rega Institute at the Katholieke Universiteit Leuven in 1990, where she started a unit on virus genetic testing for clinical practice. Together with Professor Van Ranst, she founded a new division, Clinical and Epidemiological Virology.

Anne-Mieke Vandamme and her team perform research on the molecular epidemiology of HIV, HTLV and HCV, on HIV and HCV drug resistance (genotyping, phenotyping) in clinical context, and on bioinformatics (data mining, phylogenetic analysis) technology. In the fields of HIV molecular epidemiology and drug resistance, she has an extensive and widely recognized expertise. She has been participating in several European projects (ENVA, SPREAD, EHR, Virolab, CHAIN). She supported the development of a few widely used (bioinformatics) tools, the Rega HIV Drug Resistance algorithm, the Rega HIV typing and subtyping tool, and recently also RegaDB, a free and open source software for collecting and sharing HIV epidemiological, clinical and virological data. She authored more than 300 publications in international journals such as Lancet, Nature Medicine, Lancet Infectious Diseases, PNAS, Journal of Virology, Trends in Microbiology, half of them with first and/or last author from the lab. More than 500 abstracts were presented at International Meetings.

In addition to her research activities, Anne-Mieke Vandamme is founder and (co-)organizer of the yearly International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (18th in 2013), is co-initiator and co-organizer of the European HIV Drug Resistance Workshop (10th in 2012), is coordinating the European HIV Drug Resistance Guidelines initiatives, is Head of a Bioinformatics unit at the ‘Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal. She also teaches Evolutionary Genetics and Bioinformatics at the Katholieke Universiteit Leuven.

Dr. Anne-Mieke Vandamme

Dr. Marco Salemi

Dr. Marco Salemi is an internationally recognized expert in the field of molecular evolution of viruses and phylogenetic analysis, producing seminal and elegant work on the molecular evolution of the human immunodeficiency virus (HIV) at both the global population level and within individual patients. He is perhaps best known for his groundbreaking research on how HIV spreads through different tissues in the human body. More recently, his research has expanded to integrate geographic information system and phylogenetic data to study the emergence and spread of viral and microbial epidemics. He is also co-editor of one of the major textbooks in molecular phylogeny, “The phylogenetic Handbook: a practical approach to phylogenetic analysis and hypothesis testing” (Cambridge University Press, 1st ed. 2003, 2nd ed. 2009). He has published 95 papers in peer-reviewed journals, including Nature, Nature Medicine and P.N.A.S., and is an associate editor of Journal of Virology, Retrovirology and PLoS ONE.

Dr. Salemi is an Associate Professor at the Department of Pathology, Immunology and Laboratory Medicine of the University of Florida (UF) College of Medicine, Gainesville, USA. He is a member of the UF Emerging Pathogens Institute (EPI) where he leads a research group working on molecular evolution of pathogens.

In 1996 he was awarded the prestigious Marie-Curie Fellowship to join the Rega Institute of the Catholic University of Leuven, Belgium. There he earned his PhD in 1999 under the supervision of Profs. Anne-Mieke Vandamme and Jan Desmyter with a dissertation on the origin and evolution of human and primate T-cell lymphotropic viruses. After a two-year postdoctoral fellowship at the Rega Institute, where he continued to study the phylogeny of human retroviruses, he worked from 2002 to 2004 in the laboratory of Prof. Walter M. Fitch, one of the founding fathers of molecular evolution, at the University of California, Irvine, USA.


Module Organizers

Li Yin, M.D., Ph.D., Assistant Professor in the Department of Pathology, Immunology and Laboratory Medicine at University of Florida, College of Medicine. Main research focus is to study immunoglobulin repertoires in health and diseases, and viral population diversity and structure by Next-Gen deep sequencing.

Dr. Mattia Prosperi is Lecturer in Biomedical Modelling at the University of Manchester, UK. He holds a MEng in Computer Science and a PhD in Computer Science and Automation.

In the past years Dr. Prosperi has been active in the development/application of statistical and computational models in large interdisciplinary areas of research across computational biology, medicine and public health. Among his works, he developed methods and software for personalised therapy optimisation (human immunodeficiency virus, HIV), analysis of mechanisms of evolution of drug resistance (HIV, hepatitis), phylodynamic tracing of epidemics and relation with demographic factors (HIV, Influenza, Staphylococcus aureus), new methods for phylogenetics, original algorithms to analyse large high-throughput sequencing data (viral quasispecies assembly), and computational solutions for big data mining.

He is currently team leader of the SEA-3 package of HeRC (http://www.herc.ac.uk/), a large research project of the UK MRC. Dr. Prosperi published -as first author- 20+ papers in peer-reviewed international journals. His total publication record includes 60+ works.”

Dr. Rebecca Rose’s research interests involve understanding the complexity of interactions between pathogens and a heterogeneous environment. In particular, her work focuses on developing models to find ecological associations and predictors of infectious disease epidemics. This framework can be applied to multiple scales of analysis, from the global scale of pandemics to a single host organism. Specific biological questions that intrigue me include the evolutionary behaviour of the hepatitis C virus within individuals over time, and the impact of modern farming practices on the emergence and spread of viral diseases.

Professor Tulio de Oliveira is a bioinformatician that has been working with HIV research since 1997. He has received his PhD at the Nelson R Mandela School of Medicine, University of KwaZulu-Natal, South Africa. He was a Marie Curie research fellow at the University of Oxford, U.K. from 2004 to 2006, where he received in depth training on virus genetic analysis and molecular evolution. He is recognized as an expert on HIV genetic data and bioinformatics and has published many high-impact articles including the one that presents the Rega Subtyping tools (de Oliveira et al. Bioinformatics 2005), one that proof the innocence of the six foreign medical personnel condemned to death for infecting with HIV 438 children in a hospital in Libya (de Oliveira et al. Nature 2006), open access and public HIV drug resistance databases in Africa (de Oliveira et al. Nature 2010) and the first case of proven HIV surrogate transmission in South Africa (Goedhals et al. Lancet 2012). He is currently a professor on genomics and bioinformatics at University of KwaZulu-Natal and a senior researcher at the Wellcome Trust-Africa Centre for Health and Population Studies, UKZN and the director of the Southern African Treatment Research Network (SATuRN).

Phylogenetic Inference Module: Dr. Tulio de Oliveira

Hypothesis Testing Module : Dr. Rebecca Rose

Large Dataset Analysis Module: Dr. Mattia Prosperi and Dr. Li Yin


General InformationDates: Sunday, August 25 - Friday, August 30, 2013

Meeting Site: Hilton University of Florida Conference Center Gainesville, Florida, USA

Registration: Conference registration includes admission to all sessions , conference materials, AM & PM coffee breaks each day and lunch on 8/26-30. It also includes the Welcome Reception.

Registration/Information Hours: Monday, August 26, 07:30-17:30 Tuesday, August 27, 08:00-17:30 Wednesday, August 28, 08:00-17:30 Thursday, August 29, 08:00-17:30 Friday, August 30, 08:00-17:30

Welcome Reception: The welcome reception will take place the evening of August 25th at the Florida Museum of Natural History. The reception is scheduled to start at 18:30. Complimentary transportation will run between the museum and host hotels continuously beginning at 18:15. Attire is casual and you may bring a guest free of charge.

Florida Museum of Natural HistoryUniversity of Florida Cultural Plaza3215 Hull Road, Gainesville, Florida1-352-846-2000

Poster Set-up and Breakdown: Set-up: Please hang your poster no later than 15:00 on Monday (8/26) prior to the first Poster Viewing Session which will be held from 15:30-16:00.

Breakdown: Please remove your poster on Thursday (8/29) following the afternoon Poster Viewing Session which will be held from 15:30-16:00.

Phylogenetic Handbook: The handbook will not be available for purchase at the workshop but it can be purchased on Amazon.com.

Area information:For more information about the Gainesville area, please visit www.VisitGainesville.com.

Laptops: Laptops will be provided for each student during the week of the workshop. Laptops will have Windows 7 and Microsoft Office 2007. Free Wi-Fi access will also be available. Host Hotels: Hilton University of Florida Conference Center 1714 SW 34th Street, Gainesville, Florida 32607 1-352-371-3600

Residence Inn Gainesville I-753275 SW 40th Boulevard, Gainesville, Florida 326081-352-264-0000

Transportation: To and from the Workshop (UF Hilton) - If you’re staying at the Residence Inn I-75, Bus transportation will be provided to and from the workshop every day. The bus will pick up outside Residence Inn every day at 07:30.

To and from the Gainesville Airport - The Hilton provides a shuttle between 07:00 and 20:00. Please email Diana Benintend at [email protected] with your name, date, arrival time, flight number and contact phone number so they can schedule the shuttle for you. If you’re not staying at the Hilton you will need to take a taxi or rent a car.

Contacts: For questions about Registration & Logistics: Jenn Jasinski; [email protected]

For questions about Meeting Content: Marco Salemi; [email protected]

VEME Organizers:Dr. Marco Salemi, University of Florida Associate ProfDr. Anne-Mieke Vandamme, Prof, Catholic University of Leuven, Belgium

Phylogenetic Inference Module:Dr. Tulio de Oliveira - [email protected]

Hypothesis Testing Module:Dr. Rebecca Rose - [email protected]

Large Dataset Analysis Module:Dr. Mattia Prosperi - [email protected]. Li Yin - [email protected]


Map

PoolFitness Center

Main Entrance

Albert’s Restaurants

Dining Pavilion

2-Bits Lounge

elevators

Restrooms

FrontDesk

Gift Shop

Business Center

BreakPavilion

Regi

stra

tion

BoardRoomPrivateDining

Room

Program RoomEvolutionary Hypothesis

Testing Module Hawthorne

Phylogenetic Inference Module Azalea

Large Dataset Module Hickory

Welcome, Keynote Lecture, Q & A Session Century Ballroom A

Hilton University of Florida Conference Center

BusPick-up

&Drop-off

Post

er V

iew

ing

Area

Hick

ory

Azal

ea

Haw

thor

ne

CenturyBallroom A


Sponsors

Dr. David Norton, UF Vice President, Office of Research

Dr. Michael Claire-Salzler, Chairman, Dept. of Pathology, Immunology and Laboratory Medicine

Dr. Glenn Morris, Director of Emerging Pathogens Institute

Dr. Patrick Concannon, Director of Genetics Institute

Dr. Henry V. Baker, Senior Vice President, Health Science Center

Special thanks to ...

Office of ResearchDepartment of Pathology, ImmunologyCollege of Medicineand Laboratory Medicine

Genetics InstituteUNIVERSITY of FLORIDA

Emerging Pathogens InstituteUNIVERSITY of FLORIDA


Day Title Instructor

Sunday

18:30 Welcome Reception at the Florida Museum of Natural History

Monday

08:30 - 09:00 Welcome and Practical Instructions

09:00 - 10:30 Fundamentals of Molecular Evolution: Theory Anne-Mieke Vandamme

10:30 - 11:00 Coffee Break

11:00 - 12:30 Stanford Databases/Viral Sequence Databases Soo-Yon Rhee & Brian Foley

12:30 - 13:30 Lunch

13:30 - 15:30 Alignment Algorithms: Theoretical Lecture Anne-Mieke Vandamme

15:30 - 16:00 Coffee Break and Poster Viewing

16:00 - 17:30 Sequence Alignment and Editing: Practical Computer Session Brian Foley

Tuesday

08:30 - 10:30 Methods for Phylogenetic Tree Reconstruction: Theory Anne-Mieke Vandamme


11:00 - 12:30 Constructing Phylogenetic Trees: PAUP/Mega: Computer SessionTulio de Oliveira & Luiz Alcantara

12:30 - 13:30 Lunch

13:30 - 15:30 Detecting Recombination: Theory Tulio de Oliveira


16:00 - 17:30 Free Computer Time

Wednesday

08:30 - 10:30 Detecting Recombination: Practical Computer Session Tulio de Oliveira & Luiz Alcantara10:30 - 11:00 Coffee Break and Poster Viewing11:00 - 12:30 Markov models in molecular evolution: Theory Marco Salemi12:30 - 13:30 Lunch13:30 - 16:00 Free Computer time16:00 - 16:30 Coffee Break and Poster Viewing16:30 - 17:30 Keynote Lecture Maureen M. Goodenow18:30 - 21:00 Instructor Session: Poster Judging and Dinner

Schedule: Phylogenetic Inference

Genetics InstituteUNIVERSITY of FLORIDA


Schedule: Phylogenetic Inference


Thursday

08:30 - 10:30 Testing Evolutionary Models: Practical Computer Session Rebecca Rose


11:00 - 12:30 ML Methods in Molecular Phylogenetics Marco Salemi

12:30 - 13:30 Lunch

13:30 - 15:30 ML Methods in Molecular Phylogenetics: Computer Session Marco Salemi &Tulio de Oliveira15:30 - 16:00 Coffee Break and Poster Viewing16:00 - 17:30 Free Computer Time/Remove Posters from boards

Friday

08:30 - 09:30 Using Pipelines for Viral Analysis: Practical Session Tulio de Oliveira

09:30 - 10:30 Rega DB: Practical Session Anne-Mieke Vandamme10:30 - 11:00 Coffee Break

11:00 - 12:30 Molecular Clocks Marco Salemi

12:30 - 13:30 Lunch



16:00 - 17:30 Q&A Session: Power and Pitfalls of Phylogeny Inference Anne-Mieke VandammeTulio de OliveiraMarco SalemiRebecca RoseMattia Prosperi


Schedule: Hypothesis Testing


Sunday


Monday


09:00 - 10:30 Experimental Design and Phylodynamic Inference Melissa Norstrom


11:00 - 12:30 Advanced Evolutionary Models Marco Salemi

12:30 - 13:30 Lunch

13:30 - 15:30 ML Trees and Likelihood-based Tree Topology Testing: Theory Heiko Schimidt


16:00 - 17:30 ML Practical Session I Heiko Schmidt & Marco Salemi

Tuesday

08:30 - 09:30 Molecular Clocks - Advanced Marco Salemi

09:30 - 10:30 ML Practical Session II Rebecca Rose &Heiko Schmidt10:30 - 11:00 Coffee Break and Poster Viewing

11:00 - 12:30 Bayesian Phylogenetic Inference: Theory Guy Baele

12:30 - 13:30 Lunch

13:30 - 15:30 Bayesian Phylogenetic Inference (Mr. Bayes): Practice Nuno Faria



Wednesday

08:30 - 10:30 Coalescent Inference and Phylodynamics Marco Salemi


11:00 - 12:30 BEAST: Practical 1 (Estimating Rates and Dates), using Pathogen Nuno Faria

12:30 - 13:30 Lunch

13:30 - 16:00 Bayesian Model Testing Guy Baele


16:30 - 17:30 Keynote Lecture Maureen M Goodenow

18:30-21:00 Instructor Session: Poster Judging and Dinner



Thursday

08:30 - 10:30 BEAST: Practical 2 (Model Testing) Guy Baele &Nuno Faria


11:00 - 12:30 Phylogeography: Theory Rebecca Rose

12:30 - 13:30 Lunch

13:30 - 15:30 Phylogeography: Practice (BEAST) Rebecca Rose & Nuno Faria


16:00 - 17:30 Free Computer Time/Remove Posters from boards

Friday

08:30 - 10:30 Molecular Adaptation: Theory Sergei Kosakovsky-Pond10:30 - 11:00 Coffee Break

11:00 - 12:30 Molecular Adaptation: Practice (HYPHY)Sergei Kosakovsky-Pond & Melissa Norstrom

12:30 - 13:30 Lunch



16:00 - 17:30 Q&A Session: Power and Pitfalls of Phylogeny Inference Anne-Mieke Vandamme Tulio de Oliveira Marco Salemi Rebecca Rose Mattia Prosperi

Schedule: Hypothesis Testing



Sunday


Monday


09:00 - 10:30 Introduction to Next Generation Sequencing (NGS): Technologies and Challenges Li Yin


11:00 - 12:30 Introduction to Statistical Learning (SL) Mattia Prosperi

12:30 - 13:30 Lunch

13:30 - 14:30 Introduction to Large Scale Computing and NGS Software Oleksander Moskalenko

14:30 - 15:30Overview on NGS software (Multi-platform, Platform-dependent, Programming Paradigms) and Integrated Solutions (e.g. UGene, Geneious, Galaxy, CLC bio)

Oleksander Moskalenko with Matt Gitzendanner


16:00 - 17:30 Biostat Primer: Distributions and Univariable Tests with Basic hypothesis testing and SL software intro Mattia Propseri

Tuesday

08:30 - 10:30 SL Theory: Model, Search & Optimization Algorithms Andre Altmann


11:00 - 12:30 NGS Theory: Reference Mapping and Error Correction Algorithms Mattia Prosperi

12:30 - 13:30 Lunch

13:30 - 15:30 SL Practical Session: R and Weka Mattia Prosperi and Andre Altmann


16:00 - 17:30 NGS Practical Session: Bowtie, KEG, Segminator II, QuRE, ShoRAH Mattia Prosperi

Wednesday

08:30 - 10:30 SL theory II: Tree-based Learning, Goodness-of-fit Function, Performance assessment and Methods for Feature Selection

Andre Altmann

10:30 - 11:00 Coffee Break and Poster Viewing11:00 - 12:30 NGS Theory II: De Novo Assembly (De Bruijn, Overlap Graph) Andre Altmann12:30 - 13:30 Lunch13:30 - 16:00 Free Computer time16:00 - 16:30 Coffee Break and Poster Viewing16:30 - 17:30 Keynote Lecture Maureen M. Goodenow18:30-21:00 Instructor Session: Poster Judging and Dinner

Schedule: Large Dataset Analysis


Schedule: Large Dataset Analysis


Thursday

08:30 - 10:30 NGS Theory III: Overview on Pipelines for Large-Genome Analysis and SNPs Analysis

Andre Altmann


11:00 - 12:30 NGS practical session: quasispecies assemblers QuRe, ShoRAH Mattia Prosperi

12:30 - 13:30 Lunch

13:30 - 15:30 NGS practical session: SHARCGS and other de novo assemblers Oleksander Moskalenko & Matt Gitzendanner


16:00 - 17:30 Free Computer Time/Remove Posters from boards

Friday

08:30 - 09:30 Interdisciplinary Lecture: Application of NGS in HIV-1 and Immuno-globulin Studies Li Yin

09:30 - 10:30 Interdisciplinary Lecture: Partition of Large Phylogenetic Trees Mattia Prosperi


11:00 - 12:30 Interdisciplinary Lecture: Inference of Large Phylogenies via Parallel Programming Heiko Schmidt

12:30 - 13:30 Lunch



16:00 - 17:30 Q&A Session: Power and Pitfalls of Phylogeny Inference Anne-Mieke VandammeTulio de OliveiraMarco SalemiRebecca RoseMattia Prosperi


Notes

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