CRISPRitz: Rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing

Samuele Cancellieri, Matthew Canver, Nicola Bombieri, Rosalba Giugno and Luca Pinello

Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data

Wenjiang Deng, Tian Mou, Krishna R. Kalari, Nifang Niu, Liewei Wang, Yudi Pawitan and Trung Nghia Vu


Spherical thresholding improves sketching of single-cell transcriptomic heterogeneity

Van Hoan Do, Khaled Elbassioni and Stefan Canzar

HASLR: Fast hybrid assembly of long reads

Ehsan Haghshenas, Hossein Asghari, Jens Stoye, Cedric Chauve and Faraz Hach

BATMAN: Fast and accurate integration of single-cell RNA-Seq datasets via minimum-weight matching

Igor Mandric, Brian Hill, Malika Freund, Michael Thompson and Eran Halperin

Scalable pairwise whole-genome homology mapping of large genomes with BubbZ

Ilia Minkin and Paul Medvedev


Hierarchically labeled database indexing allows scalable characterization of microbiomes

Filippo Utro, Niina Haiminen, Enrico Siragusa, Laura-Jayne Gardiner, Edward Seabolt, Ritesh Krishna, James Kaufman and Laxmi Parida

Maximal perfect haplotype blocks with wildcards

Lucia Williams and Brendan Mumey

CONNET: Accurate diploid genome consensus in de novo assembly of nanopore sequencing data via deep learning

Yifan Zhang, Chi-Man Liu, Henry Cm Leung, Ruibang Luo and Tak-Wah Lam


TALC: Transcription-aware long read correction

Lucile Broseus, Aubin Thomas and William Ritchie


Metalign: Efficient alignment-based metagenomic profiling via containment min hash

Nathan Lapierre, Mohammed Alser, Eleazar Eskin, David Koslicki and Serghei Mangul

SCAPP: An algorithm for improved plasmid assembly in metagenomes
David Pellow, Maraike Probst, Ori Furman, Alvah Zorea, Arik Segal, Itzik Mizrahi and Ron Shamir