Aggressive assembly of pyrosequencing reads with mates. - Jason R. Miller; Arthur L. Delcher; Sergey Koren; Eli Venter; Brian Walenz; Anushka Brownley; Justin Johnson 002; Kelvin Li; Clark M. Mobarry; Granger G. Sutton (Bioinform., 2008)

A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. - Tobias Rausch; Sergey Koren; Gennady Denisov; David Weese; Anne-Katrin Emde; Andreas Döring 001; Knut Reinert (Bioinform., 2009)

An algorithm for automated closure during assembly. - Sergey Koren; Jason R. Miller; Brian Walenz; Granger G. Sutton (BMC Bioinform., 2010)

Bambus 2: scaffolding metagenomes. - Sergey Koren; Todd J. Treangen; Mihai Pop (Bioinform., 2011)

Genome Assembly: Novel Applications by Harnessing Emerging Sequencing Technologies and Graph Algorithms. - Sergey Koren (2012)

De novo likelihood-based measures for comparing metagenomic assemblies. - Christopher Michael Hill; Irina Astrovskaya; Howard Huang; Sergey Koren; Atif Memon; Todd J. Treangen; Mihai Pop (BIBM, 2013)

Automated ensemble assembly and validation of microbial genomes. - Sergey Koren; Todd J. Treangen; Christopher Michael Hill; Mihai Pop; Adam M. Phillippy (BMC Bioinform., 2014)

A fast adaptive algorithm for computing whole-genome homology maps. - Chirag Jain; Sergey Koren; Alexander T. Dilthey; Adam M. Phillippy; Srinivas Aluru (Bioinform., 2018)

A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases. - Chirag Jain; Alexander T. Dilthey; Sergey Koren; Srinivas Aluru; Adam M. Phillippy (J. Comput. Biol., 2018)

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. - Nathan D. Olson; Todd J. Treangen; Christopher Michael Hill; Victoria Cepeda-Espinoza; Jay Ghurye; Sergey Koren; Mihai Pop (Briefings Bioinform., 2019)

HLA*LA - HLA typing from linearly projected graph alignments. - Alexander T. Dilthey; Alexander J. Mentzer; Raphael Carapito; Clare Cutland; Nezih Cereb; Shabir A Madhi; Arang Rhie; Sergey Koren; Seiamak Bahram; Gil McVean; Adam M. Phillippy (Bioinform., 2019)

Integrating Hi-C links with assembly graphs for chromosome-scale assembly. - Jay Ghurye; Arang Rhie; Brian Walenz; Anthony D. Schmitt; Siddarth Selvaraj; Mihai Pop; Adam M. Phillippy; Sergey Koren (PLoS Comput. Biol., 2019)

Weighted minimizer sampling improves long read mapping. - Chirag Jain; Arang Rhie; Haowen Zhang; Claudia Chu; Brian Walenz; Sergey Koren; Adam M. Phillippy (Bioinform., 2020)