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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 University, New York City, USA
Twitter: #bioc2019


Poster sessions will be held in Weiss lobby in the 5:30 to 7:30pm sessions in two groups on the 25th (Group A) and the 26th (Group B) of June.

Please affix your poster to your allocated poster board during the lunch break session (12-1pm) on the day of presentation and remove posters by 12pm the following day. Poster boards will be allocated with presenters names affixed to the board.

Session 1 - Group A - 5:30 to 7:30 (25th June) in Weiss lobby

Jianhong Ou*, Julie Zhu. TrackViewer: Lollipop/dandelion plots for methylation status and mutation data. Keywords: Software, Visualization, VariantAnnotation.

Lluís Revilla Sancho*, Pau Sancho-Bru, Juan José Salvatella Lozano. BioCor: a package to measure functional similarities. Keywords: Pathways, StatisticalMethod, SystemsBiology, Similarity, Clustering.

Carey VJ*, Stubbs BJ, Gopaulakrishnan S, Pollack S, Davis S. Bioconductor at cloud scale. Keywords: Software, GenomicVariation, CloudComputing, ImmunoOncology.

Tang M*, Kaymaz Y, Eichhorn S, Liang Z, Dulac C, Sackton T. Scclusteval: An R package for evaluating single cell RNAseq clustering. Keywords: GeneExpression Transcriptomics Clustering SingleCell.

Vaestermark AJ, Walters JR*. Title TBD. Keywords: DataRepresentation, Sequencing, GeneExpression, SystemsBiology, DifferentialExpression.

Hejazi, NS*, van der Laan MJ, Hubbard AE. Generalized Variance Moderation for Locally Efficient Estimation in High-Dimensional Biology. Keywords: GeneExpression, DifferentialExpression, Microarray, RNASeq, MultipleComparison.

Srivastava A*, Malik L, Smith T, Sudbery I, Patro R. Alevin efficiently estimates accurate gene abundances from dscRNA-seq data. Keywords: dscRNA-seq, Quantification, UMI-Deduplication, salmon, alevin.

Barrows D*, Allis CD, Carroll T. Visualization and annotation of read signal over genomic ranges with profileplyr. Keywords: ChIPSeq, ChipOnChip, Coverage, DataImport, Sequencing.

Eliatan Niktab*, Dinindu S Senanayake, Andrew B Munkacsi, Paul H Atkinson, Kelly V. Ruggles, Mark Walterfang. Title TBD. Keywords: GraphAndNetwork, GenomeWideAssociation, AnnotationData, SNPData.

Odom G*, Ban Y*, Liu L, Wang L, Chen X. Integrative pathway analysis with modern PCA methodology and gene selection. Keywords: Pathways, GeneSetEnrichment, DimensionReduction, FeatureExtraction, PrincipalComponent.

Eric Bouillet, Christine Choirat*, Rok Roskar, Chandrasekhar Ramakrishnan, Olivier Verscheure, and the RENKU development team. Reproducible workflows and Bionconductor package development with the RENKU platform. Keywords: Reproducibility, Common Workflow Language, Continuous Integration, Docker.

Ward C, To TH, Pederson S*. ngsReports and strandCheckR: Two QC packages for bolting directly into NGS pipelines. Keywords: QualityControl, ReportWriting.

Burton D*, McCall MN. Likelihood Based Mixture Modeling in Gene Regulatory Network Inference. Keywords: NetworkInference, SystemsBiology, GeneRegulation, GeneExpression, CancerData.

Zhu A*, Srivastava A, Ibrahim J, Patro R, and Love M. Nonparametric method for Differential Analysis of RNA-Seq with Quantification Uncertainty. Keywords: GeneExpression, RNAseq, Sequencing, GeneExpression, DifferentialExpression.

Session 2 - Group B - 5:30 to 7:30 (26th June) in Weiss lobby

Robert A. Amezquita*, Vince J. Carey, Lindsay N. Carpp, Ludwig Geistlinger, Aaron T. L.Lun, Federico Marini, Kevin Rue-Albrecht, Davide Risso, Charlotte Soneson, Levi Waldron, Mike Smith, Wolfgang Huber, Hervé Pagès, Martin Morgan, Raphael Gottardo, and Stephanie C. Hicks. Orchestrating Single-Cell Analysis with Bioconductor. Keywords: scRNAseq, singlecell, genomics, review.

Farias Amorim C*, Berry A, Beiting DP. Title TBD. Keywords: Parasite, Host, RNAseq, Transcriptomics, Infectious Diseases.

Sonali Arora*, Siobhan Pattwell, Eric Holland, Hamid Bolouri. Gene specific variability between commonly used RNA-seq pipelines. Keywords: TCGA, GTEx, rna-seq, big-data, genomics.

Avshalumov A*, Rahman M*, Wultsch C, and Krampis K. MicrobiomeExplorer: An interactive and web-based R Shiny analysis platform for microbiome research. Keywords: Microbiome, Metagenomics, Clustering, Visualization, Software.

Belleau P*, Deschenes A*, Adelaja A, Medina S, Ranade N, and Dillman A. HLAClusteRView: HLA typing clustering and visualization based on specific similarity metrics. Keywords: Visualization, Software, ImmunoOncology, Clustering, BiologicalQuestion.

Brehm Z*, Halushka M and McCall M. Deconvolutional mixture modeling to account for cell-type composition in tissue samples. Keywords: RNASeq, GeneExpression.

Antonio Colaprico*, Catharina Olsen, Claudia Cava, Thilde Terkelsen, Matthew H. Bailey, Tiago C. Silva, André Vidas Olsen, Laura Cantini, Andrei Zinovyev, Emmanuel Barillot, Gloria Bertoli, Isabella Castiglioni, Houtan Noushmehr, Gabriel J. Odom, Xi Chen, Gianluca Bontempi, Elena Papaleo. Title TBD. Keywords: DNAMethylation, GeneExpression, Pathways, Sequencing, Software.

Dragich J*. A BioC workflow to go from high-throughput genetic data back to detailed, personalized genetic insights. Keywords: Genetic, variant, human, haploinsufficient, protein.

Jessica R. Holmes, Jenny Drnevich*, Lois L. Hoyer, Christopher J. Fields. Broadening the impact of bioinformatics in research and education. Keywords: RNASeq.

Huang D*, Coban EB, Wultsch C, Liu J, Casaccia P, Krampis K. Noise filtering, exploratory data analysis and trajectory inference from single-cell (scSeq) genomic sequencing using the R / Bioconductor software libraries. Keywords: SingleCellWorkflow, SingleCell, Transcriptomics, Visualization, BiomedicalInformatics.

Nahed Jalloul*, Greg Reidlinger, Shridar Ganesan, Hossein Khiabanian. Title TBD. Keywords: targeted sequencing panels, bioinformatics analysis, clinical implementation.

Lawson J*, Smith J, Garrett-Bakelman F, Bekiranov S, and Sheffield N. Coordinate Covariation Analysis (COCOA): Understanding Interindividual Variation in Data with Genomic Coordinates. Keywords: Epigenetics, GenomeAnnotation, GenomicVariation, PrincipalComponent.

Loh JW*, Guccione C, Di Clemente F, Riedlinger G, Ganesan S, and Khiabanian H. All-FIT: Allele-Frequency-based Imputation of Tumor Purity from High-Depth Sequencing Data. Keywords: clinical sequencing, specimen purity estimation, tumor-only sequencing.

Martin, T.C.*, Bell, J.T. coMET: visualization of regional epigenome-wide association scan results and DNA co-methylation patterns. Keywords: Visualization, ChIPSeq, DNAMethylation, GenomeWideAssociation, MethylSeq.

Gu Y, McDavid A*. CellaRepertorium Facilitates scRNAseq Immune Repertoire Analysis. Keywords: SingleCell, ImmunoOncology, Sequencing, QualityControl, MultipleComparison.

Hatice U. Osmanbeyoglu*, Fumiko Shimizu, Angela Rynne-Vidal, Direna Alonso-Curbelo, Hsuan-An Chen, Hannah Y. Wen, Tsz-Lun Yeung, Petar Jelinic, Pedram Razavi, Scott W. Lowe, Samuel C. Mok, Gabriela Chiosis, Douglas A. Levine, Christina S. Leslie. Title TBD. Keywords: software.

Ploenzke MS*, Irizarry RI. Shallow convolutional methods for learning genomic sequence motifs. Keywords: convolution neural network motif interpretable.

Anna Quaglieri*, Christoffer Flensburg. Varikondo: spark joy in your variants!. Keywords: DataImport, Sequencing, GeneticVariants, Tidy, Standardise.

Sanjeev Sariya* and Giuseppe Tosto. Epistasis analysis for Late-Onset of Alzheimer’s disease (LOAD) using Exome-Chip data. Keywords: Epistasis, interaction, exome.

Hirak Sarkar*, Avi Srivastava and Rob Patro. Minnow: A principled framework for rapid simulation of dscRNA-seq data at the read level. Keywords: scRNA-seq, simulation, multi mapping.

Singh A*, Bhanot G, Khiabanian H. TuBA: Tunable Biclustering Algorithm for uncovering altered transcriptional profiles in large gene expression datasets of tumors. Keywords: Transcriptomics, biclustering, gene co-expression, tumor heterogeneity.

Singh R*, Ramzan T*, Avshalumov A, Rahman M, Wultsch C, Krampis K. Human microbiome and minority health: unravelling variations associated with disease and ethnicity. Keywords: Microbiome, MultipleComparison, Metagenomics, BiomedicalInformatics.

Elitsa Stoyanova*, Eric Schmidt, Thomas Carroll, Nathaniel Heintz. trapr And trapr.db: A software package for the curation, assessment and visualization of trap-seq data. Keywords: RNASeq, GeneExpression.

A. B. Villaseñor-Altamirano*, Y. I. Balderas-Martínez, M. Moretto, A. Zayas-Del Moral, M. Maldonado, A. Munguía-Reyes, J. S. García-Sotelo, L. A. Aguilar Bautista, K. Engelen, M. Selman, A. Medina-Rivera, J. Collado-Vides. Title TBD. Keywords: None Given.