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Muhammad Iqbal, M. Iqbal Rivai, Rini Suswita, Irwan Irwan, Avit Suchitra

Eleanor Wedell, Chengze Shen, Tandy Warnow

Fumihiko Nagano, Yoshihiro Yoshimura, Hidetaka Wakabayashi, Ayaka Matsumoto, Sayuri Shimazu, Ai Shiraishi, Takahiro Bise, Yoshifumi Kido, Takenori Hamada, Aomi Kuzuhara, Kouki Yoneda, Keisuke Maeda

Kathleen Zani, Joseph Hobeika, Yilun Sun, Christina Kohler, Anju Cherian, Trinity Fields, Qidong Jia, Li Tang, Nicholas D. Hysmith, Elisa B. Margolis

Grace Pold, Germán Bonilla-Rosso, Aurélien Saghaï, Marc Strous, Christopher M Jones, Sara Hallin

Sarah Leclaire, Mandar Bandekar, Melissah Rowe, Jarmo Ritari, Annalaura Jokiniemi, Jukka Partanen, Pia Allinen, Liisa Kuusipalo, Jukka Kekäläinen

Elisa B Margolis, Gabriela Maron, Yilun Sun, Ronald H Dallas, Kim J Allison, Jose Ferrolino, Hailey S Ross, Amy E Davis, Qidong Jia, Paige Turner, Victoria Mackay, Cara E Morin, Brandon M Triplett, Eileen J Klein, Janet A Englund, Li Tang, Randall T Hayden

Eleanor Wedell, Yirong Cai, Tandy Warnow

Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, Graeme J. Eamens, Linda Falconer, Toni A. Chapman, Steven Djordjevic, Aaron E. Darling

Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, Pierre Barbera

Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D. Sepich-Poore, Austin D. Swafford, Promi Das, Justin P. Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S. Havulinna, Guillaume Méric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A. Gilbert, Rob Knight

Amy D Willis, Bryan D Martin

Eleanor Wedell, Yirong Cai, Tandy Warnow

Hyunwook Koh, Susan Tuddenham, Cynthia L Sears, Ni Zhao

Andrew L. Neal, Timothy McLaren, Mariana Lourenço Campolino, David Hughes, Antônio Marcos Coelho, Ubiraci Gomes de Paula Lana, Eliane Aparecida Gomes, Sylvia Morais de Sousa

Sandipan Samaddar, Jaak Truu, Poulami Chatterjee, Kristjan Oopkaup, Marika Truu, Kiyoon Kim, Sookjin Kim, Radomir Schmidt, Aritra Roy Choudhury, Jeongyun Choi, Tongmin Sa

Alice Risely, Mark A. F. Gillingham, Arnaud Béchet, Stefan Brändel, Alexander C. Heni, Marco Heurich, Sebastian Menke, Marta B. Manser, Marco Tschapka, Wasimuddin, Simone Sommer

Meera Ongmu Bhutia, Namrata Thapa, H. Nakibapher Jones Shangpliang, Jyoti Prakash Tamang

Pierre Barbera, Lucas Czech, Sarah Lutteropp, Alexandros Stamatakis

Andrew L. Neal, David Hughes, Ian M. Clark, Janet K. Jansson, Penny R. Hirsch

Kathleen Beilsmith, Matthew Perisin, Joy Bergelson

Marika Truu, Hiie Nõlvak, Ivika Ostonen, Kristjan Oopkaup, Martin Maddison, Teele Ligi, Mikk Espenberg, Veiko Uri, Ülo Mander, Jaak Truu

Megan L Dillon, Ian Hawes, Anne D Jungblut, Tyler J Mackey, Jonathan A Eisen, Peter T Doran, Dawn Y Sumner

Hana Kahleova, Emilie Rembert, Jihad Alwarith, Willy N. Yonas, Andrea Tura, Richard Holubkov, Melissa Agnello, Robynne Chutkan, Neal D. Barnard

Maria Batool, Syed Baqir Ali, Ali Jaan, Kehkishan Khalid, Syeda Aba Ali, Kaynat Kamal, Afraz Ahmed Raja, Farzana Gul, Arshan Nasir

Valerie Cortez, David F. Boyd, Jeremy Chase Crawford, Bridgett Sharp, Brandi Livingston, Hannah M. Rowe, Amy Davis, Ramzi Alsallaq, Camenzind G. Robinson, Peter Vogel, Jason W. Rosch, Elisa Margolis, Paul G. Thomas, Stacey Schultz-Cherry

Cerano C. Da Silva, Michele A. Monteil, Elaine Monica Davis

Gregory J. Grosicki, Bryan L. Riemann, Andrew A. Flatt, Taylor Valentino, Michael S. Lustgarten

Molly S. Walkenhorst, Leticia Reyes, Gonzalo Perez, Ann Progulske-Fox, Mary B. Brown, Priscilla L. Phillips

Elisa Morales‐Marroquin, Blake Hanson, Leigh Greathouse, Nestor de la Cruz‐Munoz, Sarah E. Messiah

Andrew L. Neal, Margaret J. Glendining

Benjamin Linard, Krister Swenson, Fabio Pardi

Elisa Morales, Jun Chen, K. Leigh Greathouse

Hong-Hsing Liu, Yu-Chen Lin, Chen-Shuan Chung, Kevin Liu, Ya-Hui Chang, Chung-Hsiang Yang, Yun Chen, Yen-Hsuan Ni, Pi-Feng Chang

Manichanh Satdichanh, Huaixia Ma, Kai Yan, Gbadamassi G.O. Dossa, Leigh Winowiecki, Tor‐G. Vågen, Anja Gassner, Jianchu Xu, Rhett D. Harrison

Florent Lassalle, Matteo Spagnoletti, Matteo Fumagalli, Liam Shaw, Mark Dyble, Catherine Walker, Mark G. Thomas, Andrea Bamberg Migliano, Francois Balloux

Mikk Espenberg, Marika Truu, Ülo Mander, Kuno Kasak, Hiie Nõlvak, Teele Ligi, Kristjan Oopkaup, Martin Maddison, Jaak Truu

Zhigang Li, Katherine Lee, Margaret R. Karagas, Juliette C. Madan, Anne G. Hoen, A. James O’Malley, Hongzhe Li

Jonathan L Golob, Steven A Pergam, Sujatha Srinivasan, Tina L Fiedler, Congzhou Liu, Kristina Garcia, Marco Mielcarek, Daisy Ko, Sarah Aker, Sara Marquis, Tillie Loeffelholz, Anna Plantinga, Michael C Wu, Kevin Celustka, Alex Morrison, Maresa Woodfield, David N Fredricks

Nicolas Tromas, Nathalie Fortin, Larbi Bedrani, Yves Terrat, Pedro Cardoso, David Bird, Charles W Greer, B Jesse Shapiro

Luisa W. Hugerth, Anders F. Andersson

Virginie Lemieux-Labonté, Nicolas Tromas, B. Jesse Shapiro, François-Joseph Lapointe

T.C. Hsieh, Anne Chao

Joe D. Moore, John P. Stegemeier, Kyle Bibby, Stella M. Marinakos, Gregory V. Lowry, Kelvin B. Gregory

H.M. Poggi-Varaldo, K.M. Muñoz-Páez

Aaron E. Darling, Guillaume Jospin, Eric Lowe, Frederick A. Matsen, Holly M. Bik, Jonathan A. Eisen

2025	Alpha Diversity Analysis of Microbiota Dysbiosis in Normal and Colorectal Cancer of Mice Feces International Journal of Statistics in Medical Research Muhammad Iqbal, M. Iqbal Rivai, Rini Suswita, Irwan Irwan, Avit Suchitra
2025	BSCAMPP: Batch-Scaled Phylogenetic Placement on Large Trees IEEE Transactions on Computational Biology and Bioinformatics Eleanor Wedell, Chengze Shen, Tandy Warnow
2025	Gut microbiome diversity and nutrition intake in post‐stroke patients Geriatrics & Gerontology International Fumihiko Nagano, Yoshihiro Yoshimura, Hidetaka Wakabayashi, Ayaka Matsumoto, Sayuri Shimazu, Ai Shiraishi, Takahiro Bise, Yoshifumi Kido, Takenori Hamada, Aomi Kuzuhara, Kouki Yoneda, Keisuke Maeda
2025	Nasal microbiota predictors for methicillin resistant Staphylococcus colonization in critically ill children PLOS ONE Kathleen Zani, Joseph Hobeika, Yilun Sun, Christina Kohler, Anju Cherian, Trinity Fields, Qidong Jia, Li Tang, Nicholas D. Hysmith, Elisa B. Margolis
2024	Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases reveal their distinct functional and ecological roles ISME Communications Grace Pold, Germán Bonilla-Rosso, Aurélien Saghaï, Marc Strous, Christopher M Jones, Sara Hallin
2024	Female reproductive tract microbiota varies with MHC profile Proceedings of the Royal Society B: Biological Sciences Sarah Leclaire, Mandar Bandekar, Melissah Rowe, Jarmo Ritari, Annalaura Jokiniemi, Jukka Partanen, Pia Allinen, Liisa Kuusipalo, Jukka Kekäläinen
2023	Microbiota Predict Infections and Acute Graft-Versus-Host Disease After Pediatric Allogeneic Hematopoietic Stem Cell Transplantation The Journal of Infectious Diseases Elisa B Margolis, Gabriela Maron, Yilun Sun, Ronald H Dallas, Kim J Allison, Jose Ferrolino, Hailey S Ross, Amy E Davis, Qidong Jia, Paige Turner, Victoria Mackay, Cara E Morin, Brandon M Triplett, Eileen J Klein, Janet A Englund, Li Tang, Randall T Hayden
2023	SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees IEEE/ACM Transactions on Computational Biology and Bioinformatics Eleanor Wedell, Yirong Cai, Tandy Warnow
2023	Methods in Molecular Biology Youngchul Kim
2022	Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig PLOS ONE Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, Graeme J. Eamens, Linda Falconer, Toni A. Chapman, Steven Djordjevic, Aaron E. Darling
2022	Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade Frontiers in Bioinformatics Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, Pierre Barbera
2022	Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy mSystems Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D. Sepich-Poore, Austin D. Swafford, Promi Das, Justin P. Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S. Havulinna, Guillaume Méric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A. Gilbert, Rob Knight
2022	Estimating diversity in networked ecological communities Biostatistics Amy D Willis, Bryan D Martin
2021	Lecture Notes in Computer Science Eleanor Wedell, Yirong Cai, Tandy Warnow
2021	Meta‐analysis methods for multiple related markers: Applications to microbiome studies with the results on multiple α‐diversity indices Statistics in Medicine Hyunwook Koh, Susan Tuddenham, Cynthia L Sears, Ni Zhao
2021	Crop type exerts greater influence upon rhizosphere phosphohydrolase gene abundance and phylogenetic diversity than phosphorus fertilization FEMS Microbiology Ecology Andrew L. Neal, Timothy McLaren, Mariana Lourenço Campolino, David Hughes, Antônio Marcos Coelho, Ubiraci Gomes de Paula Lana, Eliane Aparecida Gomes, Sylvia Morais de Sousa
2021	Long‐term inorganic nitrogen application changes the ammonia‐oxidizing archaeal community composition in paddy soils European Journal of Soil Science Sandipan Samaddar, Jaak Truu, Poulami Chatterjee, Kristjan Oopkaup, Marika Truu, Kiyoon Kim, Sookjin Kim, Radomir Schmidt, Aritra Roy Choudhury, Jeongyun Choi, Tongmin Sa
2021	Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host Species Frontiers in Microbiology Alice Risely, Mark A. F. Gillingham, Arnaud Béchet, Stefan Brändel, Alexander C. Heni, Marco Heurich, Sebastian Menke, Marta B. Manser, Marco Tschapka, Wasimuddin, Simone Sommer
2021	Metataxonomic profiling of bacterial communities and their predictive functional profiles in traditionally preserved meat products of Sikkim state in India Food Research International Meera Ongmu Bhutia, Namrata Thapa, H. Nakibapher Jones Shangpliang, Jyoti Prakash Tamang
2021	SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements Molecular Ecology Resources Pierre Barbera, Lucas Czech, Sarah Lutteropp, Alexandros Stamatakis
2021	Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity mSystems Andrew L. Neal, David Hughes, Ian M. Clark, Janet K. Jansson, Penny R. Hirsch
2021	Natural Bacterial Assemblages in Arabidopsis thaliana Tissues Become More Distinguishable and Diverse during Host Development mBio Kathleen Beilsmith, Matthew Perisin, Joy Bergelson
2020	Soil Bacterial and Archaeal Communities and Their Potential to Perform N-Cycling Processes in Soils of Boreal Forests Growing on Well-Drained Peat Frontiers in Microbiology Marika Truu, Hiie Nõlvak, Ivika Ostonen, Kristjan Oopkaup, Martin Maddison, Teele Ligi, Mikk Espenberg, Veiko Uri, Ülo Mander, Jaak Truu
2020	Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica FEMS Microbiology Ecology Megan L Dillon, Ian Hawes, Anne D Jungblut, Tyler J Mackey, Jonathan A Eisen, Peter T Doran, Dawn Y Sumner
2020	Effects of a Low-Fat Vegan Diet on Gut Microbiota in Overweight Individuals and Relationships with Body Weight, Body Composition, and Insulin Sensitivity. A Randomized Clinical Trial Nutrients Hana Kahleova, Emilie Rembert, Jihad Alwarith, Willy N. Yonas, Andrea Tura, Richard Holubkov, Melissa Agnello, Robynne Chutkan, Neal D. Barnard
2020	Initial Sequencing and Characterization of the Gastrointestinal and Oral Microbiota in Urban Pakistani Adults Frontiers in Cellular and Infection Microbiology Maria Batool, Syed Baqir Ali, Ali Jaan, Kehkishan Khalid, Syeda Aba Ali, Kaynat Kamal, Afraz Ahmed Raja, Farzana Gul, Arshan Nasir
2020	Astrovirus infects actively secreting goblet cells and alters the gut mucus barrier Nature Communications Valerie Cortez, David F. Boyd, Jeremy Chase Crawford, Bridgett Sharp, Brandi Livingston, Hannah M. Rowe, Amy Davis, Ramzi Alsallaq, Camenzind G. Robinson, Peter Vogel, Jason W. Rosch, Elisa Margolis, Paul G. Thomas, Stacey Schultz-Cherry
2020	Overweight and Obesity in Children Are Associated with an Abundance of Firmicutes and Reduction of Bifidobacterium in Their Gastrointestinal Microbiota Childhood Obesity Cerano C. Da Silva, Michele A. Monteil, Elaine Monica Davis
2020	Self-reported sleep quality is associated with gut microbiome composition in young, healthy individuals: a pilot study Sleep Medicine Gregory J. Grosicki, Bryan L. Riemann, Andrew A. Flatt, Taylor Valentino, Michael S. Lustgarten
2020	A Uniquely Altered Oral Microbiome Composition Was Observed in Pregnant Rats With Porphyromonas gingivalis Induced Periodontal Disease Frontiers in Cellular and Infection Microbiology Molly S. Walkenhorst, Leticia Reyes, Gonzalo Perez, Ann Progulske-Fox, Mary B. Brown, Priscilla L. Phillips
2020	Cutaneous Bacteria in the Gut Microbiome as Biomarkers of Systemic Malodor and People Are Allergic to Me (PATM) Conditions: Insights From a Virtually Conducted Clinical Trial JMIR Dermatology Irene S Gabashvili
2020	Comparison of methodological approaches to human gut microbiota changes in response to metabolic and bariatric surgery: A systematic review Obesity Reviews Elisa Morales‐Marroquin, Blake Hanson, Leigh Greathouse, Nestor de la Cruz‐Munoz, Sarah E. Messiah
2019	Handbook of Statistical Genomics Hongzhe Li
2019	Calcium exerts a strong influence upon phosphohydrolase gene abundance and phylogenetic diversity in soil Soil Biology and Biochemistry Andrew L. Neal, Margaret J. Glendining
2019	Rapid alignment-free phylogenetic identification of metagenomic sequences Bioinformatics Benjamin Linard, Krister Swenson, Fabio Pardi
2019	Methods in Molecular Biology Elisa Morales, Jun Chen, K. Leigh Greathouse
2019	Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes Scientific Reports Hong-Hsing Liu, Yu-Chen Lin, Chen-Shuan Chung, Kevin Liu, Ya-Hui Chang, Chung-Hsiang Yang, Yun Chen, Yen-Hsuan Ni, Pi-Feng Chang
2019	Phylogenetic diversity correlated with above‐ground biomass production during forest succession: Evidence from tropical forests in Southeast Asia Journal of Ecology Manichanh Satdichanh, Huaixia Ma, Kai Yan, Gbadamassi G.O. Dossa, Leigh Winowiecki, Tor‐G. Vågen, Anja Gassner, Jianchu Xu, Rhett D. Harrison
2018	Oral microbiomes from hunter‐gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet Molecular Ecology Florent Lassalle, Matteo Spagnoletti, Matteo Fumagalli, Liam Shaw, Mark Dyble, Catherine Walker, Mark G. Thomas, Andrea Bamberg Migliano, Francois Balloux
2018	Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils Scientific Reports Mikk Espenberg, Marika Truu, Ülo Mander, Kuno Kasak, Hiie Nõlvak, Teele Ligi, Kristjan Oopkaup, Martin Maddison, Jaak Truu
2018	Conditional Regression Based on a Multivariate Zero-Inflated Logistic-Normal Model for Microbiome Relative Abundance Data Statistics in Biosciences Zhigang Li, Katherine Lee, Margaret R. Karagas, Juliette C. Madan, Anne G. Hoen, A. James O’Malley, Hongzhe Li
2018	An adaptive microbiome α-diversity-based association analysis method Scientific Reports Hyunwook Koh
2017	Stool Microbiota at Neutrophil Recovery Is Predictive for Severe Acute Graft vs Host Disease After Hematopoietic Cell Transplantation Clinical Infectious Diseases Jonathan L Golob, Steven A Pergam, Sujatha Srinivasan, Tina L Fiedler, Congzhou Liu, Kristina Garcia, Marco Mielcarek, Daisy Ko, Sarah Aker, Sara Marquis, Tillie Loeffelholz, Anna Plantinga, Michael C Wu, Kevin Celustka, Alex Morrison, Maresa Woodfield, David N Fredricks
2017	Characterising and predicting cyanobacterial blooms in an 8-year amplicon sequencing time course The ISME Journal Nicolas Tromas, Nathalie Fortin, Larbi Bedrani, Yves Terrat, Pedro Cardoso, David Bird, Charles W Greer, B Jesse Shapiro
2017	Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing Frontiers in Microbiology Luisa W. Hugerth, Anders F. Andersson
2016	Environment and host species shape the skin microbiome of captive neotropical bats PeerJ Virginie Lemieux-Labonté, Nicolas Tromas, B. Jesse Shapiro, François-Joseph Lapointe
2016	Rarefaction and Extrapolation: Making Fair Comparison of Abundance-Sensitive Phylogenetic Diversity among Multiple Assemblages Systematic Biology T.C. Hsieh, Anne Chao
2016	Impacts of Pristine and Transformed Ag and Cu Engineered Nanomaterials on Surficial Sediment Microbial Communities Appear Short-Lived Environmental Science & Technology Joe D. Moore, John P. Stegemeier, Kyle Bibby, Stella M. Marinakos, Gregory V. Lowry, Kelvin B. Gregory
2015	Phylogenetics and the Human Microbiome Systematic Biology Frederick A. Matsen
2015	Microbiome, Metagenomics, and High-Dimensional Compositional Data Analysis Annual Review of Statistics and Its Application Hongzhe Li
2015	WITHDRAWN: Evaluation of biohydrogen production at ambient temperature from cheese whey and assessment of the associated microbial community International Journal of Hydrogen Energy H.M. Poggi-Varaldo, K.M. Muñoz-Páez
2014	PhyloSift: phylogenetic analysis of genomes and metagenomes PeerJ Aaron E. Darling, Guillaume Jospin, Eric Lowe, Frederick A. Matsen, Holly M. Bik, Jonathan A. Eisen
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