November 12, 2011

8:30-10:00

Session 1

8:30-9:10

Yury Khudyakov, CDC (Keynote, Talk)

"Uniting Trends in Molecular Epidemiology"

9:10-9:35

Pavel Skums, David S. Campo, Zoya Dimitrova,

"Modeling differential interferon resistance of HCV

Gilberto Vaughan, Daryl T. Lau, Yury Khudyakov

 quasispecies"

9:35-10:00

James Lara, John E. Tavis, Maureen J. Donlin,

"Host-specific HCV evolution and response

William Lee, He-Jun Yuan, Brian Pearlman, Gilberto

to the combined interferon and ribavirin therapy"

Vaughan, Joseph Forbi, Guo-liang Xia, Yury Khudyakov

10:00-10:20

Cofee break

10:20-12:25

Session 2

10:20-11:10

Fiona Hyland, Life Technologies (Keynote, Talk))

Semiconductor sequencing; speed, simplicity and scalability

with Ion Torrent sequencing

11:10-11:35

Nicholas Mancuso, Bassam Tork, Ion Mandoiu,

"Viral Quasispecies Reconstruction from

Alex Zelikovsky, Pavel Skums

Amplicon 454 Pyrosequencing Reads"

11:35-12:00

Austin Huang, Rami Kantor, Allison DeLong,

"QColors: An Algorithm for Conservative Viral Quasispecies

Leeann Schrier, Sorin Istrail

 Reconstruction from Short and Non-Contiguous Next

 Generation Sequencing Reads"

12:00-12:25

Zoya Dimitrova, David S. Campo, Sumathi

"Assessments of Intra- and Inter-Host Diversity

Ramachandran, Gilberto Vaughan, Lilia Ganova-Raeva,

of Hepatitis C Virus using Next Generation

Yulin Lin, Joseph Forbi, Guo-liang Xia, Pavel Skums,

Sequencing and Mass Spectrometry"

Brian Pearlman, Christiane Honisch, Yury Khudyakov

12:25-1:30

Lunch

1:30-3:00

Session 3

1:30-2:10

Sergei Kosakovsky Pond, UCSD (Keynote Talk)

"Computational analysis of HIV-1 evolution and epidemiology"

2:10-2:35

Yufeng Shen, Yee Him Cheung, Shuang Wang,

"A parametric Bayesian method to test the association of rare

Itsik Pe'er

 variants"

2:35-3:00

David S. Campo, Zoya Dimitrova, James Lara,

"Network of coordinated substitutions in the Hepatitis B

 Mike Purdy, Hong Thai, Sumathi Ramachandran,

Virus Polymerase"

 Lilia Ganova-Raeva, Joseph Forbi, Chong-Gee Teo,

Yury Khudyakov

3:00-3:20

Cofee break

3:20-5:00

Session 4A

3:20-3:45

Serghei Mangul, Adrian Caciula, Ion Mandoiu, 

"RNA-Seq based discovery and reconstruction of un-annotated

Alex Zelikovsky

 transcripts in partially annotated genomes"

3:45-4:10

Irina V Astrakhantseva, David S. Campo, Aufra Araujo,

"Variation in Physicochemical Properties of the Hypervariable Region

Chong-Gee Teo, Yury Khudyakov,  Saleem Kamili

1 During Acute and Chronic Stages of Hepatitis C Virus Infection"

4:10-4:35

James Lara, Yury Khudyakov

"Modeling antigenic properties of the hepatitis C virus NS3 protein"

4:35-5:00

Kristin Bennett, Cagri Ozcaglar, Janani Ranganathan,

"Visualization of tuberculosis patient and Mycobacterium

 Srivatsan Raghavan, Jacob Katz, Dan Croft,

tuberculosis complex genotype data via host-pathogen maps"

Bulent Yener, Amina Shabbeer

5:00-5:15

Break

5:15-6:30

Session 4B

5:15-5:40

Arthi Ramachandran, Mariann Micsinai, Itsik Pe'er

"CONDEX: COpy Number Detection in EXome Sequences"

5:40-6:05

Xiu-Feng Wan, Zhipeng Cai, Li-Ping Long,

"Integration of genetic distance measurement and mixture model

analysis in understanding evolutionary dynamics"

6:05-6:30

Ion Mandoiu, UConn (Invited Talk)

"Reconstruction of infectious bronchitis virus quasispecies from

shotgun 454 pyrosequencing reads"