Publications

R2C2: Improving nanopore read accuracy enables the sequencing of highly-multiplexed full-length single-cell cDNA

By: Roger Volden, Theron Palmer, Ashley Byrne, Charles Cole, Robert J. Schmitz, Richard Edward Green, Christopher Vollmers Abstract High-throughput short-read sequencing has revolutionized how transcriptomes are quantified and annotated. However, while Illumina short-read sequencers can be used to analyze entire transcriptomes down to the level of individual splicing events with great accuracy, they fall short of analyzing how these …

A graph-based approach to diploid genome assembly

By: Shilpa Garg, Mikko Rautiainen, Adam M Novak, Erik Garrison, Richard Durbin, Tobias Marschall Abstract Motivation Constructing high-quality haplotype-resolved de novo assemblies of diploid genomes is important for revealing the full extent of structural variation and its role in health and disease. Current assembly approaches often collapse …

A Distinct DNA Methylation Shift in a Subset of Glioma CpG Island Methylator Phenotypes during Tumor Recurrence

By: Camila Ferreirade Souza, Thais S. Sabedot, Tathiane M. Malta, Lindsay Stetson, Olena Morozova, Artem Sokolov, Peter W. Laird, Maciej Wiznerowicz, Antonio Iavarone, James Snyder, Anade Carvalho, Zachary Sanborn, Kerrie L. McDonald, William A. Friedman, Daniela Tirapelli, Laila Poisson, Tom Mikkelsen, Carlos G. Carlotti Jr., Steven Kalkanis, Jean Zenklusen, Sofie R. Salama, Jill S. Barnholtz-Sloan, Houtan Noushmehr Abstract Glioma diagnosis is based on histomorphology and grading; however, such classification does not have predictive clinical outcome after glioblastomas have developed. To date, no bona fide biomarkers that significantly translate into a …

Recommendations for the packaging and containerizing of bioinformatics software [version 1; referees: 2 approved with reservations]

By: Bjorn Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O’Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jimenez, BioContainers Community, Yasset Perez-Riverol Abstract Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of …

Superbubbles, Ultrabubbles, and Cacti

By: Benedict Paten, Jordan M. Eizenga, Yohei M. Rosen, Adam M. Novak, Erik Garrison, and Glenn Hickey Abstract A superbubble is a type of directed acyclic subgraph with single distinct source and sink vertices. In genome assembly and genetics, the possible paths through a superbubble can …

Figure 1 of Publication.

The NIH BD2K center for big data in translational genomics

By: Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, Kent WJ, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, Smuga-Otto M, Stuart JM, Van’t Veer L, Wold B, Haussler D. Abstract The world’s genomics …

A Flow Procedure for Linearization of Genome Sequence Graphs

By: David Haussler, Maciej Smuga-Otto, Jordan M. Eizenga, Benedict Paten, Adam M. Novak, Sergei Nikitin, Maria Zueva, and Dmitrii Miagkov Abstract Efforts to incorporate human genetic variation into the reference human genome have converged on the idea of a graph representation of genetic variation within …

Mapping DNA methylation with high-throughput nanopore sequencing

DNA chemical modifications regulate genomic function. We present a framework for mapping cytosine and adenosine methylation with the Oxford Nanopore Technologies MinION using this nanopore sequencer’s ionic current signal. We map three cytosine variants and two adenine variants. The results show that our model is …

Computational pan-genomics: status, promises and challenges.

Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply …