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Emily Zhang, Lauren Coombe, Johnathan Wong, René L. Warren, Inanç Birol

Yasufumi Matsumura, Masaki Yamamoto, Ryota Gomi, Yasuhiro Tsuchido, Koh Shinohara, Taro Noguchi, Miki Nagao

Kinga Walczak, Marcin Piwczyński, Thomas Pape, Nikolas P. Johnston, James F. Wallman, Krzysztof Szpila, Andrzej Grzywacz

Ruchao Du, Jinxin Dong, Hua Jiang, Minyong Qi, Zuyao Zhao

Sedthapong Laojun, Pongmada Damapong, Peerada Damapong, Tanawat Chaiphongpachara

Kristen J. Wade, Rayo Suseno, Kerry Kizer, Jacqueline Williams, Juliano Boquett, Stacy Caillier, Nicholas R. Pollock, Adam Renschen, Adam Santaniello, Jorge R. Oksenberg, Paul J. Norman, Danillo G. Augusto, Jill A. Hollenbach

Meghashree H. R., S. Yuvaraj, Sunitha C. Mesta, J. Satish Kumar, E. Sumitha

Ayanda Manqele, Abiodun Adesiyun, Thendo Mafuna, Rian Pierneef, Rebone Moerane, Nomakorinte Gcebe

Usman Rashid, Chen Wu, Jason Shiller, Ken Smith, Ross Crowhurst, Marcus Davy, Ting-Hsuan Chen, Ignacio Carvajal, Sarah Bailey, Susan Thomson, Cecilia H Deng

Garrett J. Smith, Theo A. van Alen, Maartje A.H.J. van Kessel, Sebastian Lücker

Katie Vigil, Tiong Gim Aw

Mikhail I. Schelkunov

Benjamin N. Daniels, Cassidy L. Andrasz, Nicholas Zarate, Andy Lee, Cataixa López, Paul Anderson, Robert J. Toonen, Mark R. Christie, Crow White, Jean M. Davidson

Tu Luan, Harihara Subrahmaniam Muralidharan, Marwan Alshehri, Ipsa Mittra, Mihai Pop

Balan Ramesh, Clay M. Small, Hope Healey, Bernadette Johnson, Elyse Barker, Mark Currey, Susan Bassham, Megean Myers, William A. Cresko, Adam Gregory Jones

Paula Esteller-Cucala, Marc Palmada-Flores, Lukas F. K. Kuderna, Claudia Fontsere, Aitor Serres-Armero, Marc Dabad, María Torralvo, Armida Faella, Luis Ferrández-Peral, Laia Llovera, Oscar Fornas, Eva Julià, Erika Ramírez, Irene González, Jochen Hecht, Esther Lizano, David Juan, Tomàs Marquès-Bonet

Mekibib Million Mekso, Tileye Feyissa

Pedro Escudeiro, Christopher S. Henry, Ricardo P.M. Dias

Lotus A. Lofgren, Brandon S. Ross, Robert A. Cramer, Jason E. Stajich

Lucija Podrzaj, Johanna Burtscher, Konrad J. Domig

Ting Zhang, Qiang Zhou

Firaol Dida Midekso, Gangman Yi

2025	GoldPolish-target: targeted long-read genome assembly polishing BMC Bioinformatics Emily Zhang, Lauren Coombe, Johnathan Wong, René L. Warren, Inanç Birol
2025	Integrating whole-genome sequencing into antimicrobial resistance surveillance: methodologies, challenges, and perspectives Clinical Microbiology Reviews Yasufumi Matsumura, Masaki Yamamoto, Ryota Gomi, Yasuhiro Tsuchido, Koh Shinohara, Taro Noguchi, Miki Nagao
2025	Unravelling phylogenetic relationships within the genus Lispe (Diptera: Muscidae) through genome-assisted and de novo analyses of RAD-seq data Molecular Phylogenetics and Evolution Kinga Walczak, Marcin Piwczyński, Thomas Pape, Nikolas P. Johnston, James F. Wallman, Krzysztof Szpila, Andrzej Grzywacz
2025	Comparative study of tools for copy number variation detection using next-generation sequencing data Scientific Reports Ruchao Du, Jinxin Dong, Hua Jiang, Minyong Qi, Zuyao Zhao
2024	De Novo Genome Assembly of the Main Malaria Vector <i>Anopheles baimaii</i> Indian Journal of Entomology Sedthapong Laojun, Pongmada Damapong, Peerada Damapong, Tanawat Chaiphongpachara
2024	MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge Genome Biology Kristen J. Wade, Rayo Suseno, Kerry Kizer, Jacqueline Williams, Juliano Boquett, Stacy Caillier, Nicholas R. Pollock, Adam Renschen, Adam Santaniello, Jorge R. Oksenberg, Paul J. Norman, Danillo G. Augusto, Jill A. Hollenbach
2024	Systems Biology Approaches: Prevention, Diagnosis, and Understanding Mechanisms of Complex Diseases Meghashree H. R., S. Yuvaraj, Sunitha C. Mesta, J. Satish Kumar, E. Sumitha
2024	Virulence Potential and Antimicrobial Resistance of Listeria monocytogenes Isolates Obtained from Beef and Beef-Based Products Deciphered Using Whole-Genome Sequencing Microorganisms Ayanda Manqele, Abiodun Adesiyun, Thendo Mafuna, Rian Pierneef, Rebone Moerane, Nomakorinte Gcebe
2024	AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality Bioinformatics Usman Rashid, Chen Wu, Jason Shiller, Ken Smith, Ross Crowhurst, Marcus Davy, Ting-Hsuan Chen, Ignacio Carvajal, Sarah Bailey, Susan Thomson, Cecilia H Deng
2024	Simple, reference-independent assessment to empirically guide correction and polishing of hybrid microbial community metagenomic assembly PeerJ Garrett J. Smith, Theo A. van Alen, Maartje A.H.J. van Kessel, Sebastian Lücker
2023	Comparison of de novo assembly using long-read shotgun metagenomic sequencing of viruses in fecal and serum samples from marine mammals Frontiers in Microbiology Katie Vigil, Tiong Gim Aw
2023	Mabs, a suite of tools for gene-informed genome assembly BMC Bioinformatics Mikhail I. Schelkunov
2023	De novo genome and transcriptome assembly of Kelletia kelletii, a coastal gastropod and fisheries species exhibiting a northern range expansion Frontiers in Marine Science Benjamin N. Daniels, Cassidy L. Andrasz, Nicholas Zarate, Andy Lee, Cataixa López, Paul Anderson, Robert J. Toonen, Mark R. Christie, Crow White, Jean M. Davidson
2023	SCRAPT: an iterative algorithm for clustering large 16S rRNA gene data sets Nucleic Acids Research Tu Luan, Harihara Subrahmaniam Muralidharan, Marwan Alshehri, Ipsa Mittra, Mihai Pop
2023	Improvements to the Gulf pipefish Syngnathus scovelli genome Gigabyte Balan Ramesh, Clay M. Small, Hope Healey, Bernadette Johnson, Elyse Barker, Mark Currey, Susan Bassham, Megean Myers, William A. Cresko, Adam Gregory Jones
2023	Y chromosome sequence and epigenomic reconstruction across human populations Communications Biology Paula Esteller-Cucala, Marc Palmada-Flores, Lukas F. K. Kuderna, Claudia Fontsere, Aitor Serres-Armero, Marc Dabad, María Torralvo, Armida Faella, Luis Ferrández-Peral, Laia Llovera, Oscar Fornas, Eva Julià, Erika Ramírez, Irene González, Jochen Hecht, Esther Lizano, David Juan, Tomàs Marquès-Bonet
2022	RNA-Seq as an Effective Tool for Modern Transcriptomics, A Review-based Study Journal of Applied Research in Plant Sciences Mekibib Million Mekso, Tileye Feyissa
2022	Functional characterization of prokaryotic dark matter: the road so far and what lies ahead Current Research in Microbial Sciences Pedro Escudeiro, Christopher S. Henry, Ricardo P.M. Dias
2022	The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high levels of lineage-specific diversity driven by recombination PLOS Biology Lotus A. Lofgren, Brandon S. Ross, Robert A. Cramer, Jason E. Stajich
2022	Comparative Genomics Provides Insights Into Genetic Diversity of Clostridium tyrobutyricum and Potential Implications for Late Blowing Defects in Cheese Frontiers in Microbiology Lucija Podrzaj, Johanna Burtscher, Konrad J. Domig
2022	Using large-scale multi-module NRPS to heterologously prepare highly efficient lipopeptide biosurfactants in recombinant Escherichia coli Enzyme and Microbial Technology Ting Zhang, Qiang Zhou
2022	RFfiller: a robust and fast statistical algorithm for gap filling in draft genomes PeerJ Firaol Dida Midekso, Gangman Yi
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