BioC 2019: Where Software and Biology Connect

When: June 24 - 27, 2019
What: Developer Day, Main Conference, Symposium
Where: NYU and Rockefeller University, New York City, USA
Slack: Bioconductor Team (#bioc2019 channel)
Twitter: #bioc2019

Day 2: Wednesday June 26

8:00 - 8:30 – Breakfast – Abby Lounge

8:30 - 9:00 – Lieven Clement – Caspary Auditorium

9:00 - 9:30 – Lihua Julie Zhu – Caspary Auditorium

9:30 - 10:00 – Anshul Kundaje – Caspary Auditorium

10:00 - 10:30 – Break – CRC Lower Level

10:30 - 12:00 – Contributed talks Session 4a – Software focus – Caspary Auditorium

• Nitesh Turaga – 3 reasons to “Bioconductor” on containers
• Vincent Carey – Bioconductor at “cloud scale”
• Stuart Lee – Tidy coverage analysis with superintronic and plyranges
• Nathan Sheffield – BiocProject, a new Bioconductor-oriented project management class
• Karun Rajesh – Storage and Analysis of Microbiome Quality Control Project Data through phyloseq Package
• Ana Beatriz Villaseñor-Altamirano – PulmonDB with an accessible web interface of integrated and curated public transcriptomic data for the understanding of lung diseases
• Christopher Wilks – Snapcount: rapid and flexible querying of over 70,000 gene, exon, and splice junction expression summaries

10:30 - 12:00 – Contributed talks Session 4b – Biological focus – Carson Auditorium

• Benjamin Haibe-Kains – mCI: Robust biomarker discovery from cancer pharmacogenomic data
• Aedin Culhane – Discovery of cancer immune molecular subtypes
• Joselyn Cristina Chavez Fuentes – A collaborative approach to improve access to bacterial regulatory networks using R/Bioconductor.
• Robert Castelo – RNA sequencing and mass spectometry proteomics of neonatal dried blood spots
• Cesar Miguel Valdez Cordova – histoneSig: working with continuous signal representations from the genome
• Antonio Colaprico – DeepBlueR and MoonlightR
• Charlotte Soneson – On the characterisation of complex transcriptomes with Nanopore native RNA sequencing

12:00 - 1:00 – Lunch / Birds-of-a-feather – Weiss South Room

1:00 - 1:50 – Workshop Session 5a

• The Basics: Introduction to Bioconductor Annotation Resources – Lori Shepherd and Jim MacDonald – RRB 110
• SingleCell: Analysis of multi-sample multi-group scRNA-seq data – Helena L. Crowell, Charlotte Soneson, Pierre-Luc Germain, and Mark Robinson – Carson Auditorium
• RNAseq & Omics: Using the recount2 resource and related tools – Collado-Torres L, Nellore A, Jaffe AE – Weiss 305
• Genomics & Enrichment Analysis: Easy and efficient ensemble gene set testing with EGSEA – Alhamdoosh M, Law CW, Tian L, Sheridan JM, Ng M, Ritchie ME – Weiss 301

2:00 - 2:50 – Workshop Session 5b

• The Basics: Introduction to Bioconductor Annotation Resources – Lori Shepherd and Jim MacDonald – RRB 110
• SingleCell: Analysis of multi-sample multi-group scRNA-seq data – Helena L. Crowell, Charlotte Soneson, Pierre-Luc Germain, and Mark D. Robinson – Carson Auditorium
• RNAseq & Omics: Using the recount2 resource and related tools – Collado-Torres L, Nellore A, Jaffe AE – Weiss 305
• Genomics & Enrichment Analysis: Functional enrichment analysis of high-throughput omics data – Ludwig Geistlinger and Levi Waldron – Weiss 301

2:50 - 3:10 – Break – Weiss South Room

3:10 - 4:00 – Workshop Session 6a

• The Basics: Public data resources and Bioconductor – Levi Waldron, Benjamin Haibe-Kains, and Sean Davis – RBB 110
• SingleCell: iSEE: Interactive visualization of SummarizedExperiment objects – Kevin Rue-Albrecht and Charlotte Soneson – Carson Auditorium
• RNAseq & Omics: RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR – Law CW, Alhamdoosh M, Su S, Dong X, Tian L et al – Weiss 305
• Genomics & Enrichment Analysis: Integrative pathway analysis with pathwayPCA – Odom G, Ban Y, Liu L, Wang L, Chen X – Weiss 301

4:10 - 5:00 – Workshop Session 6b

• The Basics: Public data resources and Bioconductor – Levi Waldron, Benjamin Haibe-Kains, and Sean Davis – RRB 110
• SingleCell: iSEE: Interactive visualization of SummarizedExperiment objects – Kevin Rue-Albrecht and Charlotte Soneson – Carson Auditorium
• RNAseq & Omics: Epidemiology for Bioinformaticians – Mirzayi C and Levi Waldron – Weiss 305

5:30 - 7:30 – Contributed posters

• Group-B posters – Weiss Lobby
• Poster dimensions up to 58 inches wide x 40 inches tall. Individual poster allocations will be affixed to poster boards.