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BioC 2019: Where Software and Biology Connect

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

Main Conference (June 25-26)

Day 1: Tuesday June 25

8:00 - 8:45 – Registration and breakfast
8:45 - 9:00 – Welcoming remarks – (Martin Morgan)
9:00 - 9:30 – Jeffrey Leek
9:30 - 10:00 – Elli Papaemmanuil
10:00 - 10:30 – Simina Boca
10:30 - 11:00 – Break
11:00 - 12:00 – Contributed talks Session 1a - Single-cell theme
  • Robert A. Amezquita – Orchestrating Single-Cell Analysis with Bioconductor
  • Helena L. Crowell – Analysis of multi-sample multi-group scRNA-seq data
  • Shian Su – CellBench: A Framework for Evaluating Single Cell Analysis Pipelines
  • Stephanie Hicks – mbkmeans: fast clustering for single cell data using mini-batch k-means
  • Deepayan Sarkar – Gene Set Enrichment Analysis with Multi-omics Data
11:00 - 12:00 – Contributed talks Session 1b - Statistical methods
  • Nima Hejazi – Generalized Variance Moderation for Locally Efficient Estimation in High-Dimensional Biology
  • John Lawson – Coordinate Covariation Analysis (COCOA): Understanding Interindividual Variation in Data with Genomic Coordinates
  • Ingo Ruczinski – Detection of rare disease variants in extended pedigrees using RVS
  • Svetlana Vinogradova – ASER: eliminating transcriptome-wide batch effects results in higher precision in allele-specific expression measurements
  • Katharina Imkeller – Improving accuracy of phenotype detection in whole-genome CRISPR screens
12:00 - 1:00 – Lunch / Birds-of-a-feather, sponsored by F1000 Research
1:00 - 1:50 – Workshop Session 2a
  • The Basics: Bioconductor for Everyone – Martin Morgan and Lori Shepherd
  • SingleCell: Effectively using the DelayedArray framework to support the analysis of large data sets – Pete Hickey
  • RNAseq & Omics: Workflow for Multi-omics Analysis with MultiAssayExperiment and curatedTCGAData – Marcel Ramos, Ludwig Geistlinger, and Levi Waldron
  • Genomics & Enrichment Analysis: Tools for region-based genomic analysis – Nathan Sheffield
2:00 - 2:50 – Workshops Session 2b
  • The Basics: Bioconductor for Everyone – Martin Morgan and Lori Shepherd
  • SingleCell: Effectively using the DelayedArray framework to support the analysis of large data sets – Pete Hickey
  • RNAseq & Omics: Workflow for Multi-omics Analysis with MultiAssayExperiment and curatedTCGAData – Marcel Ramos, Ludwig Geistlinger, and Levi Waldron
  • Genomics & Enrichment Analysis: Tools for region-based genomic analysis – Nathan Sheffield
2:50 - 3:10 – Break
3:10 - 4:00 – Workshops Session 3a
  • The Basics: Fluent genomic workflows with plyranges –
  • SingleCell: Orchestrating Single-Cell Analysis with Bioconductor: Overview and Workflows – Robert A. Amezquita, Vince J. Carey, Lindsay N. Carpp, Ludwig Geistlinger, Aaron T. L.Lun, et al.
  • Genomics & Enrichment Analysis: Copy number variation analysis with Bioconductor – Ludwig Geistlinger, Marcel Ramos, Seyhun Oh, and Levi Waldron
4:10 - 5:00 – Workshops Session 3b
  • The Basics: A plyranges and tximeta case study: differential expression and accessibility
  • SingleCell: Analysis of large single-cell RNA-seq datasets in R/Bioconductor – Davide Risso and Stephanie Hicks
  • RNAseq & Omics: Working with open-source Human Microbiome Project Data: Efficient Data Access and Analysis Workflow – Levi Walrdon, Ni Zhao, Mikhail Dozmorov, Ekaterina Smirnova
  • Genomics & Enrichment Analysis: ATAC-seq data quality control using the ATACseqQC package – Haibo Liu, Jianghong Ou, and Julie Lihua Zhu
5:30 - 7:30 – Contributed posters
  • Poster dimensions up to 58 inches wide x 40 inches tall; posters displayed both days.

Day 2: Wednesday June 26

8:00 - 8:30 – Breakfast
8:30 - 9:00 – Lieven Clement
9:00 - 9:30 – Lihua Julie Zhu
9:30 - 10:00 – Anshul Kundaje
10:00 - 10:30 – Break
10:30 - 12:00 – Contributed talks Session 4a – Software focus
  • 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
  • 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
1:00 - 1:50 – Workshops Session 5a
  • The Basics: Introduction to Bioconductor Annotation Resources – Lori Shepherd and Jim MacDonald
  • SingleCell: Analysis of multi-sample multi-group scRNA-seq data – Helena L. Crowell, Charlotte Soneson, Pierre-Luc Germain, and Mark Robinson
  • RNAseq & Omics: Using the recount2 resource and related tools – Collado-Torres L, Nellore A, Jaffe AE
  • Genomics & Enrichment Analysis: Easy and efficient ensemble gene set testing with EGSEA – Alhamdoosh M, Law CW, Tian L, Sheridan JM, Ng M, Ritchie ME
2:00 - 2:50 – Workshops Session 5b
  • The Basics: Introduction to Bioconductor Annotation Resources – Lori Shepherd and Jim MacDonald
  • SingleCell: Analysis of multi-sample multi-group scRNA-seq data – Helena L. Crowell, Charlotte Soneson, Pierre-Luc Germain, and Mark D. Robinson
  • RNAseq & Omics: Using the recount2 resource and related tools – Collado-Torres L, Nellore A, Jaffe AE
  • Genomics & Enrichment Analysis: Functional enrichment analysis of high-throughput omics data – Ludwig Geistlinger and Levi Waldron
2:50 - 3:10 – Break
3:10 - 4:00 – Workshops Session 6a
  • The Basics: Public data resources and Bioconductor
  • SingleCell: iSEE: Interactive visualization of SummarizedExperiment objects – Kevin Rue-Albrecht and Charlotte Soneson
  • 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
  • Genomics & Enrichment Analysis: Integrative pathway analysis with pathwayPCA – Odom G, Ban Y, Liu L, Wang L, Chen X
4:10 - 5:00 – Workshops Session 6b
  • The Basics: Public data resources and Bioconductor
  • SingleCell: iSEE: Interactive visualization of SummarizedExperiment objects – Kevin Rue-Albrecht and Charlotte Soneson
  • RNAseq & Omics: Epidemiology for Bioinformaticians – Mirzayi C and Levi Waldron
5:30 - 7:30 – Contributed posters
  • Poster dimensions up to 58 inches wide x 40 inches tall; posters displayed both days.