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Marios I. Valmas, Konstantinos Kormas, Dimitrios G. Karpouzas, Konstantinos T. Konstantinidis, Svjetlana Dekić Rozman, Nikolina Udiković-Kolić, Mitja N.P. Remus-Emsermann, Sotirios Vasileiadis

Angus M. O'Ferrall, Alexandra Juhász, Sam Jones, Peter Makaula, Gladys Namacha, Shaali Ame, David Oguttu, Aidan Foo, Sekeleghe A. Kayuni, E. James LaCourse, Janelisa Musaya, J. Russell Stothard, Adam P. Roberts

Shaopeng Liu, Judith S. Rodriguez, Viorel Munteanu, Cynthia Ronkowski, Nitesh Kumar Sharma, Mohammed Alser, Francesco Andreace, Ran Blekhman, Dagmara Błaszczyk, Rayan Chikhi, Keith A. Crandall, Katja Della Libera, Dallace Francis, Alina Frolova, Abigail Shahar Gancz, Naomi E. Huntley, Pooja Jaiswal, Tomasz Kosciolek, Pawel P. Łabaj, Wojciech Łabaj, Tu Luan, Christopher Mason, Ahmed M. Moustafa, Harihara Subrahmaniam Muralidharan, Onur Mutlu, Nika Mansouri Ghiasi, Ali Rahnavard, Fengzhu Sun, Shuchang Tian, Braden T. Tierney, Emily Van Syoc, Riccardo Vicedomini, Joseph P. Zackular, Alex Zelikovsky, Kinga Zielińska, Erika Ganda, Emily R. Davenport, Mihai Pop, David Koslicki, Serghei Mangul

Emilie Egholm Bruun Jensen, Saria Otani, Ivan Liachko, Benjamin Auch, Frank M. Aarestrup

Roshan Regmi, Jonathan Anderson, Lauren Burgess, Hayley Mangelson, Ivan Liachko, Gupta Vadakattu

Xiangpeng Li, Linfeng Xu, Benjamin Demaree, Cecilia Noecker, Jordan E. Bisanz, Daniel W. Weisgerber, Cyrus Modavi, Peter J. Turnbaugh, Adam R. Abate

Yuxuan Du, Wenxuan Zuo, Fengzhu Sun

Jacques Serizay, Cyril Matthey-Doret, Amaury Bignaud, Lyam Baudry, Romain Koszul

Mir Henglin, Maryam Ghareghani, William T. Harvey, David Porubsky, Sergey Koren, Evan E. Eichler, Peter Ebert, Tobias Marschall

Lucy Androsiuk, Sivan Maane, Shay Tal

Petr A. Zaytsev, Vladimir A. Rodin, Anna A. Zaytseva, Maria I. Zvereva, Alexei E. Solovchenko

Bram Danneels, Aurélien Carlier

Stephen R Stockdale, Colin Hill

Harrison Ho, Mansi Chovatia, Rob Egan, Guifen He, Yuko Yoshinaga, Ivan Liachko, Ronan O’Malley, Zhong Wang

Quentin Lamy-Besnier, Amaury Bignaud, Julian R. Garneau, Marie Titecat, Devon E. Conti, Alexandra Von Strempel, Marc Monot, Bärbel Stecher, Romain Koszul, Laurent Debarbieux, Martial Marbouty

Yuxuan Du, Fengzhu Sun

Yuxuan Du, Jed A. Fuhrman, Fengzhu Sun

Gregory E. McCallum, Amanda E. Rossiter, Mohammed Nabil Quraishi, Tariq H. Iqbal, Sarah A. Kuehne, Willem van Schaik

Martial Marbouty, Romain Koszul

Lajos Kalmar, Srishti Gupta, Iain R. L. Kean, Xiaoliang Ba, Nazreen Hadjirin, Elizabeth M. Lay, Stefan P. W. de Vries, Michael Bateman, Harriet Bartlet, Juan Hernandez-Garcia, Alexander W. Tucker, Olivier Restif, Mark P. Stevens, James L. N. Wood, Duncan J. Maskell, Andrew J. Grant, Mark A. Holmes

Elizabeth G Wilbanks, Hugo Doré, Meredith H Ashby, Cheryl Heiner, Richard J Roberts, Jonathan A Eisen

Yuxuan Du, Sarah M. Laperriere, Jed Fuhrman, Fengzhu Sun

David Kneis, Thomas U. Berendonk, Sofia K. Forslund, Stefanie Hess

Nitan Shalon, David A. Relman, Eitan Yaffe

Sophie E Smith, Wanqi Huang, Kawtar Tiamani, Magdalena Unterer, Mohammadali Khan Mirzaei, Li Deng

Yuxuan Du, Fengzhu Sun

Gleb Goussarov, Mohamed Mysara, Peter Vandamme, Rob Van Houdt

Jean-Sebastien Gounot, Minghao Chia, Denis Bertrand, Woei-Yuh Saw, Aarthi Ravikrishnan, Adrian Low, Yichen Ding, Amanda Hui Qi Ng, Linda Wei Lin Tan, Yik-Ying Teo, Henning Seedorf, Niranjan Nagarajan

Anna Cuscó, Daniel Pérez, Joaquim Viñes, Norma Fàbregas, Olga Francino

Yuxuan Du, Fengzhu Sun

Kevin S. Blake, JooHee Choi, Gautam Dantas

Shuai Wang, Yiqi Jiang, Shuaicheng Li

Yancong Zhang, Kelsey N. Thompson, Tobyn Branck, Yan Yan, Long H. Nguyen, Eric A. Franzosa, Curtis Huttenhower

Victoria R. Carr, Andrey Shkoporov, Colin Hill, Peter Mullany, David L. Moyes

Teresa Gil-Gil, Luz Edith Ochoa-Sánchez, Fernando Baquero, José Luis Martínez

Teng Wang, Andrea Weiss, Yuanchi Ha, Lingchong You

Alyssa G. Kent, Albert C. Vill, Qiaojuan Shi, Michael J. Satlin, Ilana Lauren Brito

Augusto Dulanto Chiang, John P Dekker

Matthew Z. DeMaere, Michael Y. Z. Liu, Enmoore Lin, Steven P. Djordjevic, Ian G. Charles, Paul Worden, Catherine M. Burke, Leigh G. Monahan, Melissa Gardiner, Thomas J. Borody, Aaron E. Darling

Bram van Dijk, Paulien Hogeweg, Hilje M Doekes, Nobuto Takeuchi

Thea Van Rossum, Pamela Ferretti, Oleksandr M. Maistrenko, Peer Bork

Zhichao Xu, Jesse R Dixon

Aravind Natarajan, Ami S. Bhatt

Christina C Saak, Cong B Dinh, Rachel J Dutton

C. Titus Brown, Dominik Moritz, Michael P. O’Brien, Felix Reidl, Taylor Reiter, Blair D. Sullivan

Thijs De Mulder, Geertrui Rasschaert, Els Van Coillie, Tina Van den Meersche, Annelies Haegeman, Tom Ruttink, Tom Van de Wiele, Marc Heyndrickx

Kostas Koutsoumanis, Ana Allende, Avelino Alvarez‐Ordóñez, Declan Bolton, Sara Bover‐Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Luisa Peixe, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Claire Jenkins, Burkhard Malorny, Ana Sofia Ribeiro Duarte, Mia Torpdahl, Maria Teresa da Silva Felício, Beatriz Guerra, Mirko Rossi, Lieve Herman

Thibault Stalder, Maximilian O Press, Shawn Sullivan, Ivan Liachko, Eva M Top

Lyam Baudry, Théo Foutel-Rodier, Agnès Thierry, Romain Koszul, Martial Marbouty

Matthew Z. DeMaere, Aaron E. Darling

Eitan Yaffe, David A. Relman

Sharon A. Huws, Christopher J. Creevey, Linda B. Oyama, Itzhak Mizrahi, Stuart E. Denman, Milka Popova, Rafael Muñoz-Tamayo, Evelyne Forano, Sinead M. Waters, Matthias Hess, Ilma Tapio, Hauke Smidt, Sophie J. Krizsan, David R. Yáñez-Ruiz, Alejandro Belanche, Leluo Guan, Robert J. Gruninger, Tim A. McAllister, C. Jamie Newbold, Rainer Roehe, Richard J. Dewhurst, Tim J. Snelling, Mick Watson, Garret Suen, Elizabeth H. Hart, Alison H. Kingston-Smith, Nigel D. Scollan, Rodolpho M. do Prado, Eduardo J. Pilau, Hilario C. Mantovani, Graeme T. Attwood, Joan E. Edwards, Neil R. McEwan, Steven Morrisson, Olga L. Mayorga, Christopher Elliott, Diego P. Morgavi

Caiti Smukowski Heil, Joshua N. Burton, Ivan Liachko, Anne Friedrich, Noah A. Hanson, Cody L. Morris, Joseph Schacherer, Jay Shendure, James H. Thomas, Maitreya J. Dunham

Federica Gigliucci, F. A. Bastiaan von Meijenfeldt, Arnold Knijn, Valeria Michelacci, Gaia Scavia, Fabio Minelli, Bas E. Dutilh, Hamideh M. Ahmad, Gerwin C. Raangs, Alex W. Friedrich, John W. A. Rossen, Stefano Morabito

Théo Foutel-Rodier, Agnès Thierry, Romain Koszul, Martial Marbouty

Kyle Fletcher, Richard Michelmore

Matthew Z DeMaere, Aaron E Darling

Sivan Oddes, Aviv Zelig, Noam Kaplan

Eric C. Keen, Gautam Dantas

Robert D. Stewart, Marc D. Auffret, Amanda Warr, Andrew H. Wiser, Maximilian O. Press, Kyle W. Langford, Ivan Liachko, Timothy J. Snelling, Richard J. Dewhurst, Alan W. Walker, Rainer Roehe, Mick Watson

Cecilia Noecker, Colin P. McNally, Alexander Eng, Elhanan Borenstein

Vittorio Tracanna, Anne de Jong, Marnix H. Medema, Oscar P. Kuipers

Krupa M. Parmar, Saurabh L. Gaikwad, Prashant K. Dhakephalkar, Ramesh Kothari, Ravindra Pal Singh

Ian Miller, Marc Chevrette, Jason Kwan

José L. Martínez, Teresa M. Coque, Val F. Lanza, Fernando de la Cruz, Fernando Baquero

Martial Marbouty, Lyam Baudry, Axel Cournac, Romain Koszul

Xuegong Zhang, Shansong Liu, Hongfei Cui, Ting Chen

Ilana L. Brito, Eric J. Alm

Annette Denker, Wouter de Laat

Richard Allen White, Eric M. Bottos, Taniya Roy Chowdhury, Jeremy D. Zucker, Colin J. Brislawn, Carrie D. Nicora, Sarah J. Fansler, Kurt R. Glaesemann, Kevin Glass, Janet K. Jansson

Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, Bas E. Dutilh

Matthew Z. DeMaere, Aaron E. Darling

Anthony D. Schmitt, Ming Hu, Bing Ren

Jean-François Flot, Hervé Marie-Nelly, Romain Koszul

Nicholas J. Loman, Mark J. Pallen

Jason A. O’Rawe, Scott Ferson, Gholson J. Lyon

Siddarth Selvaraj, Anthony D. Schmitt, Jesse R. Dixon, Bing Ren

Kornelia Smalla, Sven Jechalke, Eva M. Top

Martial Marbouty, Romain Koszul

Chengwei Luo, Rob Knight, Heli Siljander, Mikael Knip, Ramnik J Xavier, Dirk Gevers

Michael Liu, Aaron Darling

N. Varoquaux, I. Liachko, F. Ay, J. N. Burton, J. Shendure, M. J. Dunham, J.-P. Vert, W. S. Noble

Daniel R. Garza, Bas E. Dutilh

Kornelia Smalla, Sven Jechalke, Eva M. Top

Bryan R. Lajoie, Job Dekker, Noam Kaplan

Joshua N Burton, Ivan Liachko, Maitreya J Dunham, Jay Shendure

Martial Marbouty, Axel Cournac, Jean-François Flot, Hervé Marie-Nelly, Julien Mozziconacci, Romain Koszul

Ohad Manor, Roie Levy, Elhanan Borenstein

2025	Targeted analysis of metagenomes: divide and conquer Biotechnology Advances Marios I. Valmas, Konstantinos Kormas, Dimitrios G. Karpouzas, Konstantinos T. Konstantinidis, Svjetlana Dekić Rozman, Nikolina Udiković-Kolić, Mitja N.P. Remus-Emsermann, Sotirios Vasileiadis
2025	Freshwater snail faecal metagenomes reveal environmental reservoirs of antimicrobial resistance genes across two continents Microbial Genomics Angus M. O'Ferrall, Alexandra Juhász, Sam Jones, Peter Makaula, Gladys Namacha, Shaali Ame, David Oguttu, Aidan Foo, Sekeleghe A. Kayuni, E. James LaCourse, Janelisa Musaya, J. Russell Stothard, Adam P. Roberts
2025	Analysis of metagenomic data Nature Reviews Methods Primers Shaopeng Liu, Judith S. Rodriguez, Viorel Munteanu, Cynthia Ronkowski, Nitesh Kumar Sharma, Mohammed Alser, Francesco Andreace, Ran Blekhman, Dagmara Błaszczyk, Rayan Chikhi, Keith A. Crandall, Katja Della Libera, Dallace Francis, Alina Frolova, Abigail Shahar Gancz, Naomi E. Huntley, Pooja Jaiswal, Tomasz Kosciolek, Pawel P. Łabaj, Wojciech Łabaj, Tu Luan, Christopher Mason, Ahmed M. Moustafa, Harihara Subrahmaniam Muralidharan, Onur Mutlu, Nika Mansouri Ghiasi, Ali Rahnavard, Fengzhu Sun, Shuchang Tian, Braden T. Tierney, Emily Van Syoc, Riccardo Vicedomini, Joseph P. Zackular, Alex Zelikovsky, Kinga Zielińska, Erika Ganda, Emily R. Davenport, Mihai Pop, David Koslicki, Serghei Mangul
2025	Using genomics to explore the epidemiology of vancomycin resistance in a sewage system Microbiology Spectrum Emilie Egholm Bruun Jensen, Saria Otani, Ivan Liachko, Benjamin Auch, Frank M. Aarestrup
2025	Shotgun and Hi-C Sequencing Datasets for Binning Wheat Rhizosphere Microbiome Scientific Data Roshan Regmi, Jonathan Anderson, Lauren Burgess, Hayley Mangelson, Ivan Liachko, Gupta Vadakattu
2025	Microbiome Single Cell Atlases Generated with a Commercial Instrument Advanced Science Xiangpeng Li, Linfeng Xu, Benjamin Demaree, Cecilia Noecker, Jordan E. Bisanz, Daniel W. Weisgerber, Cyrus Modavi, Peter J. Turnbaugh, Adam R. Abate
2024	Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Random Walk with Restart Journal of Computational Biology Yuxuan Du, Wenxuan Zuo, Fengzhu Sun
2024	Orchestrating chromosome conformation capture analysis with Bioconductor Nature Communications Jacques Serizay, Cyril Matthey-Doret, Amaury Bignaud, Lyam Baudry, Romain Koszul
2024	Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing Genome Biology Mir Henglin, Maryam Ghareghani, William T. Harvey, David Porubsky, Sergey Koren, Evan E. Eichler, Peter Ebert, Tobias Marschall
2024	CRISPR spacers acquired from plasmids primarily target backbone genes, making them valuable for predicting potential hosts and host range Microbiology Spectrum Lucy Androsiuk, Sivan Maane, Shay Tal
2024	Advances of high-throughput sequencing for unraveling biotechnological potential of microalgal-bacterial communities Journal of Applied Phycology Petr A. Zaytsev, Vladimir A. Rodin, Anna A. Zaytseva, Maria I. Zvereva, Alexei E. Solovchenko
2023	Methods in Molecular Biology Bram Danneels, Aurélien Carlier
2023	Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome Current Opinion in Microbiology Stephen R Stockdale, Colin Hill
2023	Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning PeerJ Harrison Ho, Mansi Chovatia, Rob Egan, Guifen He, Yuko Yoshinaga, Ivan Liachko, Ronan O’Malley, Zhong Wang
2023	Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria Microbiome Quentin Lamy-Besnier, Amaury Bignaud, Julian R. Garneau, Marie Titecat, Devon E. Conti, Alexandra Von Strempel, Marc Monot, Bärbel Stecher, Romain Koszul, Laurent Debarbieux, Martial Marbouty
2023	MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data Nature Communications Yuxuan Du, Fengzhu Sun
2023	ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data Nature Communications Yuxuan Du, Jed A. Fuhrman, Fengzhu Sun
2023	Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts Microbial Genomics Gregory E. McCallum, Amanda E. Rossiter, Mohammed Nabil Quraishi, Tariq H. Iqbal, Sarah A. Kuehne, Willem van Schaik
2022	Methods in Molecular Biology Martial Marbouty, Romain Koszul
2022	HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities PLOS Genetics Lajos Kalmar, Srishti Gupta, Iain R. L. Kean, Xiaoliang Ba, Nazreen Hadjirin, Elizabeth M. Lay, Stefan P. W. de Vries, Michael Bateman, Harriet Bartlet, Juan Hernandez-Garcia, Alexander W. Tucker, Olivier Restif, Mark P. Stevens, James L. N. Wood, Duncan J. Maskell, Andrew J. Grant, Mark A. Holmes
2022	Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity The ISME Journal Elizabeth G Wilbanks, Hugo Doré, Meredith H Ashby, Cheryl Heiner, Richard J Roberts, Jonathan A Eisen
2022	Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression Journal of Computational Biology Yuxuan Du, Sarah M. Laperriere, Jed Fuhrman, Fengzhu Sun
2022	Antibiotic Resistance Genes in River Biofilms: A Metagenomic Approach toward the Identification of Sources and Candidate Hosts Environmental Science & Technology David Kneis, Thomas U. Berendonk, Sofia K. Forslund, Stefanie Hess
2022	Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors Genome Research Nitan Shalon, David A. Relman, Eitan Yaffe
2022	Emerging technologies in the study of the virome Current Opinion in Virology Sophie E Smith, Wanqi Huang, Kawtar Tiamani, Magdalena Unterer, Mohammadali Khan Mirzaei, Li Deng
2022	HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs Bioinformatics Yuxuan Du, Fengzhu Sun
2022	Introduction to the principles and methods underlying the recovery of metagenome‐assembled genomes from metagenomic data MicrobiologyOpen Gleb Goussarov, Mohamed Mysara, Peter Vandamme, Rob Van Houdt
2022	Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians Nature Communications Jean-Sebastien Gounot, Minghao Chia, Denis Bertrand, Woei-Yuh Saw, Aarthi Ravikrishnan, Adrian Low, Yichen Ding, Amanda Hui Qi Ng, Linda Wei Lin Tan, Yik-Ying Teo, Henning Seedorf, Niranjan Nagarajan
2022	Novel canine high-quality metagenome-assembled genomes, prophages and host-associated plasmids provided by long-read metagenomics together with Hi-C proximity ligation Microbial Genomics Anna Cuscó, Daniel Pérez, Joaquim Viñes, Norma Fàbregas, Olga Francino
2022	HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps Genome Biology Yuxuan Du, Fengzhu Sun
2021	Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria Cellular and Molecular Life Sciences Kevin S. Blake, JooHee Choi, Gautam Dantas
2021	PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data Bioinformatics Shuai Wang, Yiqi Jiang, Shuaicheng Li
2021	Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling Annual Review of Biomedical Data Science Yancong Zhang, Kelsey N. Thompson, Tobyn Branck, Yan Yan, Long H. Nguyen, Eric A. Franzosa, Curtis Huttenhower
2021	Examining horizontal gene transfer in microbial communities Nature Reviews Microbiology Ilana Lauren Brito
2021	Computational methods for chromosome-scale haplotype reconstruction Genome Biology Shilpa Garg
2021	Probing the Mobilome: Discoveries in the Dynamic Microbiome Trends in Microbiology Victoria R. Carr, Andrey Shkoporov, Colin Hill, Peter Mullany, David L. Moyes
2021	Antibiotic resistance: Time of synthesis in a post-genomic age Computational and Structural Biotechnology Journal Teresa Gil-Gil, Luz Edith Ochoa-Sánchez, Fernando Baquero, José Luis Martínez
2021	Predicting plasmid persistence in microbial communities by coarse‐grained modeling BioEssays Teng Wang, Andrea Weiss, Yuanchi Ha, Lingchong You
2020	Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C Nature Communications Alyssa G. Kent, Albert C. Vill, Qiaojuan Shi, Michael J. Satlin, Ilana Lauren Brito
2020	From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics The Journal of Infectious Diseases Augusto Dulanto Chiang, John P Dekker
2020	Metagenomic Hi-C of a Healthy Human Fecal Microbiome Transplant Donor Microbiology Resource Announcements Matthew Z. DeMaere, Michael Y. Z. Liu, Enmoore Lin, Steven P. Djordjevic, Ian G. Charles, Paul Worden, Catherine M. Burke, Leigh G. Monahan, Melissa Gardiner, Thomas J. Borody, Aaron E. Darling
2020	Slightly beneficial genes are retained by bacteria evolving DNA uptake despite selfish elements eLife Bram van Dijk, Paulien Hogeweg, Hilje M Doekes, Nobuto Takeuchi
2020	Diversity within species: interpreting strains in microbiomes Nature Reviews Microbiology Thea Van Rossum, Pamela Ferretti, Oleksandr M. Maistrenko, Peer Bork
2020	Genome reconstruction and haplotype phasing using chromosome conformation capture methodologies Briefings in Functional Genomics Zhichao Xu, Jesse R Dixon
2020	Microbes and microbiomes in 2020 and beyond Nature Communications Aravind Natarajan, Ami S. Bhatt
2020	Experimental approaches to tracking mobile genetic elements in microbial communities FEMS Microbiology Reviews Christina C Saak, Cong B Dinh, Rachel J Dutton
2020	Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity Genome Biology C. Titus Brown, Dominik Moritz, Michael P. O’Brien, Felix Reidl, Taylor Reiter, Blair D. Sullivan
2019	Impact of Cross-Contamination Concentrations of Doxycycline Hyclate on the Microbial Ecosystem in anEx VivoModel of the Pig's Cecum Microbial Drug Resistance Thijs De Mulder, Geertrui Rasschaert, Els Van Coillie, Tina Van den Meersche, Annelies Haegeman, Tom Ruttink, Tom Van de Wiele, Marc Heyndrickx
2019	Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms EFSA Journal Kostas Koutsoumanis, Ana Allende, Avelino Alvarez‐Ordóñez, Declan Bolton, Sara Bover‐Cid, Marianne Chemaly, Robert Davies, Alessandra De Cesare, Friederike Hilbert, Roland Lindqvist, Maarten Nauta, Luisa Peixe, Giuseppe Ru, Marion Simmons, Panagiotis Skandamis, Elisabetta Suffredini, Claire Jenkins, Burkhard Malorny, Ana Sofia Ribeiro Duarte, Mia Torpdahl, Maria Teresa da Silva Felício, Beatriz Guerra, Mirko Rossi, Lieve Herman
2019	Linking the resistome and plasmidome to the microbiome The ISME Journal Thibault Stalder, Maximilian O Press, Shawn Sullivan, Ivan Liachko, Eva M Top
2019	MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries Frontiers in Genetics Lyam Baudry, Théo Foutel-Rodier, Agnès Thierry, Romain Koszul, Martial Marbouty
2019	bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes Genome Biology Matthew Z. DeMaere, Aaron E. Darling
2019	Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation Nature Microbiology Eitan Yaffe, David A. Relman
2018	Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future Frontiers in Microbiology Sharon A. Huws, Christopher J. Creevey, Linda B. Oyama, Itzhak Mizrahi, Stuart E. Denman, Milka Popova, Rafael Muñoz-Tamayo, Evelyne Forano, Sinead M. Waters, Matthias Hess, Ilma Tapio, Hauke Smidt, Sophie J. Krizsan, David R. Yáñez-Ruiz, Alejandro Belanche, Leluo Guan, Robert J. Gruninger, Tim A. McAllister, C. Jamie Newbold, Rainer Roehe, Richard J. Dewhurst, Tim J. Snelling, Mick Watson, Garret Suen, Elizabeth H. Hart, Alison H. Kingston-Smith, Nigel D. Scollan, Rodolpho M. do Prado, Eduardo J. Pilau, Hilario C. Mantovani, Graeme T. Attwood, Joan E. Edwards, Neil R. McEwan, Steven Morrisson, Olga L. Mayorga, Christopher Elliott, Diego P. Morgavi
2018	Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context Trends in Microbiology Alvaro San Millan
2018	Genomic Approaches in Earth and Environmental Sciences
2018	Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi‐C Yeast Caiti Smukowski Heil, Joshua N. Burton, Ivan Liachko, Anne Friedrich, Noah A. Hanson, Cody L. Morris, Joseph Schacherer, Jay Shendure, James H. Thomas, Maitreya J. Dunham
2018	Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients Frontiers in Cellular and Infection Microbiology Federica Gigliucci, F. A. Bastiaan von Meijenfeldt, Arnold Knijn, Valeria Michelacci, Gaia Scavia, Fabio Minelli, Bas E. Dutilh, Hamideh M. Ahmad, Gerwin C. Raangs, Alex W. Friedrich, John W. A. Rossen, Stefano Morabito
2018	Methods in Enzymology Théo Foutel-Rodier, Agnès Thierry, Romain Koszul, Martial Marbouty
2018	Methods in Molecular Biology Kyle Fletcher, Richard Michelmore
2018	Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies GigaScience Matthew Z DeMaere, Aaron E Darling
2018	Three invariant Hi-C interaction patterns: Applications to genome assembly Methods Sivan Oddes, Aviv Zelig, Noam Kaplan
2018	Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity Trends in Microbiology Eric C. Keen, Gautam Dantas
2018	Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen Nature Communications Robert D. Stewart, Marc D. Auffret, Amanda Warr, Andrew H. Wiser, Maximilian O. Press, Kyle W. Langford, Ivan Liachko, Timothy J. Snelling, Richard J. Dewhurst, Alan W. Walker, Rainer Roehe, Mick Watson
2017	High-resolution characterization of the human microbiome Translational Research Cecilia Noecker, Colin P. McNally, Alexander Eng, Elhanan Borenstein
2017	Mining prokaryotes for antimicrobial compounds: from diversity to function FEMS Microbiology Reviews Vittorio Tracanna, Anne de Jong, Marnix H. Medema, Oscar P. Kuipers
2017	Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics Frontiers in Microbiology Krupa M. Parmar, Saurabh L. Gaikwad, Prashant K. Dhakephalkar, Ramesh Kothari, Ravindra Pal Singh
2017	Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations Marine Drugs Ian Miller, Marc Chevrette, Jason Kwan
2017	Genomic and metagenomic technologies to explore the antibiotic resistance mobilome Annals of the New York Academy of Sciences José L. Martínez, Teresa M. Coque, Val F. Lanza, Fernando de la Cruz, Fernando Baquero
2017	Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay Science Advances Martial Marbouty, Lyam Baudry, Axel Cournac, Romain Koszul
2016	Reading the Underlying Information From Massive Metagenomic Sequencing Data Proceedings of the IEEE Xuegong Zhang, Shansong Liu, Hongfei Cui, Ting Chen
2016	Tracking Strains in the Microbiome: Insights from Metagenomics and Models Frontiers in Microbiology Ilana L. Brito, Eric J. Alm
2016	The second decade of 3C technologies: detailed insights into nuclear organization Genes & Development Annette Denker, Wouter de Laat
2016	Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes mSystems Richard Allen White, Eric M. Bottos, Taniya Roy Chowdhury, Jeremy D. Zucker, Colin J. Brislawn, Carrie D. Nicora, Sarah J. Fansler, Kurt R. Glaesemann, Kevin Glass, Janet K. Jansson
2016	Computational approaches to predict bacteriophage–host relationships FEMS Microbiology Reviews Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, Bas E. Dutilh
2016	Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C) PeerJ Matthew Z. DeMaere, Aaron E. Darling
2016	Genome-wide mapping and analysis of chromosome architecture Nature Reviews Molecular Cell Biology Anthony D. Schmitt, Ming Hu, Bing Ren
2015	Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures FEBS Letters Jean-François Flot, Hervé Marie-Nelly, Romain Koszul
2015	Twenty years of bacterial genome sequencing Nature Reviews Microbiology Nicholas J. Loman, Mark J. Pallen
2015	Accounting for uncertainty in DNA sequencing data Trends in Genetics Jason A. O’Rawe, Scott Ferson, Gholson J. Lyon
2015	Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq BMC Genomics Siddarth Selvaraj, Anthony D. Schmitt, Jesse R. Dixon, Bing Ren
2015	Plasmids Kornelia Smalla, Sven Jechalke, Eva M. Top
2015	Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data Trends in Genetics Martial Marbouty, Romain Koszul
2015	ConStrains identifies microbial strains in metagenomic datasets Nature Biotechnology Chengwei Luo, Rob Knight, Heli Siljander, Mikael Knip, Ramnik J Xavier, Dirk Gevers
2015	Metagenomic Chromosome Conformation Capture (3C): techniques, applications, and challenges F1000Research Michael Liu, Aaron Darling
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2015	Plasmid Detection, Characterization, and Ecology Microbiology Spectrum Kornelia Smalla, Sven Jechalke, Eva M. Top
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2014	Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps G3 Genes\|Genomes\|Genetics Joshua N Burton, Ivan Liachko, Maitreya J Dunham, Jay Shendure
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2014	Mapping the Inner Workings of the Microbiome: Genomic- and Metagenomic-Based Study of Metabolism and Metabolic Interactions in the Human Microbiome Cell Metabolism Ohad Manor, Roie Levy, Elhanan Borenstein
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