pypi: scikit-bio | Projects | Ecosyste.ms: Papers

10.1038/s41396-020-00814-9

Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere
Cited by: 96
Author(s): Robyn J. Wright, Morgan G. I. Langille, Tony R. Walker
Software Mentions: 23
Published: about 4 years ago

10.1186/s40168-019-0702-x

Understanding microbial community dynamics to improve optimal microbiome selection
Cited by: 193
Author(s): Robyn J. Wright, Matthew I. Gibson, Joseph Alexander Christie-Oleza
Software Mentions: 18
Published: over 5 years ago

10.1186/s12859-018-2367-z

Biotite: a unifying open source computational biology framework in Python
Cited by: 54
Author(s): Patrick Kunzmann, Kay Hamacher
Software Mentions: 12
Published: about 6 years ago

10.1186/s40679-018-0060-y

An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data
Cited by: 11
Author(s): Laurent P. René de Cotret, Martin Otto, Mark J. Stern, Bradley J. Siwick
Software Mentions: 12
Published: about 6 years ago

10.3389/fcimb.2020.00137

Microbiotyping the Sinonasal Microbiome
Cited by: 15
Author(s): Ahmed Bassiouni, S. Paramasivan, Arron Shiffer, Matthew R. Dillon, Emily K. Cope, Clare Cooksley, Mahnaz Ramezanpour, Sophia Moraitis, Mohammad Javed Ali, Benjamin S. Bleier, Claudio Callejas, Marjolein Cornet, Richard Douglas, Daniel Lorena Dutra, Christos Georgalas, Richard J. Harvey, Peter H. Hwang, Amber U. Luong, Rodney J. Schlosser, Pongsakorn Tantilipikorn, Marc A. Tewfik, Sarah Vreugde, Peter John Wormald, J. Gregory Caporaso, Alkis James Psaltis
Software Mentions: 9
Published: over 4 years ago

10.1186/s13059-018-1616-9

Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana
Cited by: 61
Author(s): Matthew E.B. Hansen, Meagan A Rubel, Aubrey Bailey, Alessia Ranciaro, S. R. Thompson, Michael C. Campbell, William Beggs, Jaanki R. Dave, Gaonyadiwe George Mokone, Sununguko Wata Mpoloka, Thomas Nyambo, Christian C. Abnet, Stephen J. Chanock, Frederic D. Bushman, Sarah A. Tishkoff
Software Mentions: 8
Published: almost 6 years ago

10.1371/journal.pcbi.1005727

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
Cited by: 40
Author(s): Kevin Murray, Christfried Webers, Cheng Soon Ong, Justin O. Borevitz, Norman Warthmann
Software Mentions: 8
Published: about 7 years ago

10.1128/mSystems.00269-18

Calour: an Interactive, Microbe-Centric Analysis Tool
Cited by: 24
Author(s): Zhenjiang Zech Xu, Amir Almasi‐Hashiani, Jon G. Sanders, Quanyin Zhu, James T. Morton, Molly C. Bletz, Anupriya Tripathi, Shi Huang, Daniel McDonald, Lingjing Jiang, Rob Knight
Software Mentions: 6
Published: over 5 years ago

10.3389/fendo.2021.626359

Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes
Cited by: 25
Author(s): Laila Silamiķele, Ivars Silamiķelis, Monta Ustinova, Zane Kalniņa, Ilze Elbere, Ramona Petrovska, Ineta Kalniņa, Jānis Kloviņš
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0229001

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome
Cited by: 45
Author(s): Samuel J. Bowers, Fernando Vargas, Antonio González, Shannon He, Peng Jiang, Pieter C. Dorrestein, Rob Knight, Kenneth P. Wright, Christopher A. Lowry, Monika Fleshner, Martha Hotz Vitaterna, Fred W. Turek
Software Mentions: 6
Published: almost 5 years ago

10.1128/mSystems.00016-19

A Novel Sparse Compositional Technique Reveals Microbial Perturbations
Cited by: 255
Author(s): Cameron Martino, James T. Morton, Clarisse Marotz, Luke R. Thompson, Anupriya Tripathi, Rob Knight, Karsten Zengler
Software Mentions: 6
Published: over 5 years ago

10.2196/15371

Transfer Learning for Risk Classification of Social Media Posts: Model Evaluation Study
Cited by: 21
Author(s): Derek Howard, Marta M. Maslej, Justin Lee, Jacob Ritchie, Geoffrey Woollard, Leon French
Software Mentions: 5
Published: over 4 years ago

10.1128/mSystems.00093-19

Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry
Cited by: 14
Author(s): Peter Rubbens, Marian L. Schmidt, Ruben Props, Bopaiah A. Biddanda, Nico Boon, Willem Waegeman, Vincent J. Denef
Software Mentions: 5
Published: about 5 years ago

10.3389/fcimb.2021.714162

Characterization of the Oral and Esophageal Microbiota in Esophageal Precancerous Lesions and Squamous Cell Carcinoma
Cited by: 12
Author(s): Zhengqi Li, Lizhou Dou, Yueming Zhang, Shasha He, Di Zhao, Cui Hao, Gonghua Song, Wei Zhang, Yong Liu, Guiqi Wang
Software Mentions: 5
Published: about 3 years ago

10.3389/fpubh.2019.00241

Evaluation of Rapid Library Preparation Protocols for Whole Genome Sequencing Based Outbreak Investigation
Cited by: 28
Author(s): Helena M. B. Seth-Smith, Ferdinando Bonfiglio, Aline Cuénod, Josiane Reist, Adrian Egli, Daniel Wüthrich
Software Mentions: 5
Published: about 5 years ago

10.1016/j.chom.2018.06.005

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome
Cited by: 714
Author(s): Pamela Ferretti, Edoardo Pasolli, Adrian Tett, Francesco Asnicar, Valentina Gorfer, Sabina Fedi, Federica Armanini, Duy Tin Truong, Serena Manara, Moreno Zolfo, Francesco Beghini, Roberto Bertorelli, Veronica De Sanctis, Ilaria Bariletti, Rosarita Canto, Rosanna Clementi, Marina Cologna, Tiziana Crifò, Giuseppina Cusumano, Stefania Gottardi, Claudia Innamorati, Caterina Masè, Daniela Postai, Daniela Savoi, Sabrina Duranti, Gabriele Andrea Lugli, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Christian Milani, Marta Mangifesta, Rosaria Anzalone, Alice Viappiani, Moran Yassour, Hera Vlamakis, Ramnik J. Xavier, María Carmen Collado, Omry Koren, Saverio Tateo, Massimo Soffiati, Anna Pedrotti, Marco Ventura, Curtis Huttenhower, Peer Bork, Nicola Segata
Software Mentions: 4
Published: over 6 years ago

10.1128/mSystems.00162-16

Balance Trees Reveal Microbial Niche Differentiation
Cited by: 217
Author(s): James T. Morton, Jon G. Sanders, Robert A. Quinn, Daniel McDonald, Antonio González, Yoshiki Vázquez-Baeza, José A. Navas-Molina, Se Jin Song, Jessica L. Metcalf, Embriette R. Hyde, Manuel E. Lladser, Pieter C. Dorrestein, Rob Knight
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-016-0930-z

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments
Cited by: 150
Author(s): Jeff Daily
Software Mentions: 4
Published: almost 9 years ago

10.1186/s13059-021-02304-3

Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression
Cited by: 54
Author(s): Pan Gao, Qing Lyu, Amr R. Ghanam, Cícera R. Lazzarotto, Gregory A. Newby, Wei Zhang, Mi-Hyun Choi, Orazio J. Slivano, Kevin Holden, John Walker, Anastasia P. Kadina, Rob J. Munroe, Christian Abratte, John C. Schimenti, David R. Liu, Shengdar Q. Tsai, Xiaochun Long, Joseph M. Miano
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0241253

CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing
Cited by: 16
Author(s): Amelia D. Wallace, Thomas A Sasani, Jordan Swanier, Brooke L. Gates, Jeff Greenland, Brent S. Pedersen, Katherine E. Varley, Aaron R. Quinlan
Software Mentions: 4
Published: over 3 years ago

10.1186/s40168-019-0645-2

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month
Cited by: 99
Author(s): Nina Iszatt, Stefan Janssen, Virissa Lenters, Cecilie Dahl, Hein Stigum, Rob Knight, Siddhartha Mandal, Shyamal Peddada, Antonio González, Tore Midtvedt, Merete Eggesbø
Software Mentions: 4
Published: over 5 years ago

10.21105/joss.02076

fqfa: A pure Python package for genomic sequence files
Cited by: 0
Author(s): Alan F. Rubin
Software Mentions: 3
Published: over 4 years ago

10.1186/s12915-020-00804-5

The rise of diversity in metabolic platforms across the Candidate Phyla Radiation
Cited by: 37
Author(s): Alexander L. Jaffe, Cindy J. Castelle, Paula B. Matheus Carnevali, Simonetta Gribaldo, Jillian F. Banfield
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0228338

Effect of Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in drinking water on chicken crop and caeca microbiome
Cited by: 24
Author(s): Alessandra De Cesare, Claudia Sala, Gastone Castellani, Annalisa Astolfi, Valentina Indio, A. Giardini, Gerardo Manfreda
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0227006

Association between baseline abundance of Peptoniphilus, a Gram-positive anaerobic coccus, and wound healing outcomes of DFUs
Cited by: 19
Author(s): Kyung Rok Min, Adriana Galvis, Katherine L. Baquerizo Nole, Rohita Sinha, Jennifer Clarke, Robert S. Kirsner, Dragana Ajdić
Software Mentions: 3
Published: almost 5 years ago

10.3389/fmicb.2020.01847

Oceanographic Fronts Shape Phaeocystis Assemblages: A High-Resolution 18S rRNA Gene Survey From the Ice-Edge to the Equator of the South Pacific
Cited by: 14
Author(s): Swan Li San Sow, Thomas W. Trull, Levente Bodrossy
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2021.653314

Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial Communities
Cited by: 5
Author(s): Stanislav N. Iablokov, Pavel S. Novichkov, Andrei L. Osterman, Dmitry A. Rodionov
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-78511-y

Microbe-set enrichment analysis facilitates functional interpretation of microbiome profiling data
Cited by: 9
Author(s): Yan Kou, Xiaomin Xu, Zhengnong Zhu, Lei Dai, Yan Tan
Software Mentions: 3
Published: almost 4 years ago

10.1128/mSystems.00031-18

American Gut: an Open Platform for Citizen Science Microbiome Research
Cited by: 519
Author(s): Daniel McDonald, Embriette R. Hyde, Justine W. Debelius, James T. Morton, Antonio González, Gail Ackermann, Alexander A. Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C. Dorrestein, Robert R. Dunn, Ashkaan K. Fahimipour, James Gaffney, Jack A. Gilbert, Grant Gogul, Jessica L. Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A. Jackson, Stefan Janssen, Dilip V. Jeste, Lingjing Jiang, Scott T. Kelley, Dan Knights, Tomasz Kościółek, Joshua Ladau, Jeff D. Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V. Melnik, Jessica L. Metcalf, Hosein Mohimani, Emmanuel Montassier, José A. Navas-Molina, Tanya Nguyen, Shyamal D. Peddada, Pavel A. Pevzner, Katherine S. Pollard, Gholamali Rahnavard, Adam Robbins‐Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy D. Spector, Austin D. Swafford, Varykina G. Thackray, Luke R. Thompson, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Alison Vrbanac, Paul E. Wischmeyer, Elaine Wolfe, Quanyin Zhu, Rob Knight
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-016-1086-x

Tiny microbes, enormous impacts: what matters in gut microbiome studies?
Cited by: 112
Author(s): Justine W. Debelius, Se Jin Song, Yoshiki Vázquez-Baeza, Zhenjiang Xu, Antonio González, Rob Knight
Software Mentions: 2
Published: about 8 years ago

10.3390/v10110602

CRISPRStudio: A User-Friendly Software for Rapid CRISPR Array Visualization
Cited by: 35
Author(s): Moïra B. Dion, Simon J. Labrie, Shiraz A. Shah, Sylvain Moineau
Software Mentions: 2
Published: about 6 years ago

10.1264/jsme2.ME19037

The Earth Is Small for “Leviathans”: Long Distance Dispersal of Giant Viruses across Aquatic Environments
Cited by: 11
Author(s): Yanze Li, Hisashi Endo, Yasuhiro Gotoh, Hiroyasu Watai, Nana Ogawa, Romain Blanc-Mathieu, Takashi Yoshida, Hiroyuki Ogata
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-67443-2

Bladder cancer-related microbiota: examining differences in urine and tissue samples
Cited by: 57
Author(s): Bassel Mansour, Ádám Monyók, Nóra Makra, Márió Gajdács, István Vadnay, Balázs Ligeti, János Juhász, Dóra Szabó, Eszter Ostorházi
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-57450-8

Oropharyngeal microbiome of a college population following a meningococcal disease outbreak
Cited by: 6
Author(s): Adam C. Retchless, Cécilia B. Kretz, Lorraine D. Rodriguez‐Rivera, Alexander Chen, Heidi M. Soeters, Melissa Whaley, Xin Wang
Software Mentions: 2
Published: almost 5 years ago

10.1128/mSystems.00375-19

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis
Cited by: 23
Author(s): Alexey V. Melnik, Yoshiki Vázquez-Baeza, Alexander A. Aksenov, Embriette R. Hyde, Andrew C. McAvoy, Mingxun Wang, Ricardo R. da Silva, Ivan Protsyuk, Jason V. Wu, Amina Bouslimani, Yan Wei Lim, Tal Luzzatto-Knaan, William Comstock, Robert A. Quinn, Richard L. Wong, Greg Humphrey, Gail Ackermann, Timothy Spivey, Sharon S. Brouha, Nuno Bandeira, Grace Lin, Forest Rohwer, Douglas Conrad, Theodore Alexandrov, Rob Knight, Pieter C. Dorrestein, Neha Garg
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-52445-6

Comparison of oral microbiome profiles in stimulated and unstimulated saliva, tongue, and mouth-rinsed water
Cited by: 30
Author(s): Ryutaro Jo, Yuichiro Nishimoto, Kouta Umezawa, Kazuma Yama, Yuto Aita, Yuko Ichiba, S. Murakami, Yasushi Kakizawa, Toru Kumagai, Takuji Yamada, Shinji Fukuda
Software Mentions: 2
Published: about 5 years ago

10.21105/jose.00027

An Introduction to Applied Bioinformatics: a free, open, and interactive text.
Cited by: 12
Author(s): Evan Bolyen, Jai Ram Rideout, John Chase, T. Anders Pitman, Arron Shiffer, Willow Mercurio, Matthew R. Dillon, J. Gregory Caporaso
Software Mentions: 1
Published: about 6 years ago

10.1186/s12915-019-0660-6

The impact of skin care products on skin chemistry and microbiome dynamics
Cited by: 91
Author(s): Amina Bouslimani, Ricardo R. da Silva, Tomasz Kościółek, Stefan Janssen, Chris Callewaert, Amir Almasi‐Hashiani, Kathleen Dorrestein, Alexey V. Melnik, Livia S. Zaramela, Ji-Nu Kim, Gregory Humphrey, Tara Schwartz, Karenina Sanders, Caitriona Brennan, Tal Luzzatto-Knaan, Gail Ackermann, Daniel McDonald, Karsten Zengler, Rob Knight, Pieter C. Dorrestein
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms8111634

Microbial Reference Frames Reveal Distinct Shifts in the Skin Microbiota after Cleansing
Cited by: 6
Author(s): Riccardo Sfriso, Joshua T. Claypool
Software Mentions: 1
Published: about 4 years ago

10.3390/jof7090767

Using High-Throughput Amplicon Sequencing to Evaluate Intragenomic Variation and Accuracy in Species Identification of Cordyceps Species
Cited by: 3
Author(s): Soumitra Paloi, Wuttichai Mhuantong, J. Jennifer Luangsa‐ard, Noppol Kobmoo
Software Mentions: 1
Published: about 3 years ago

10.7554/eLife.61504

Freshwater monitoring by nanopore sequencing
Cited by: 54
Author(s): Lara Urban, Andre Holzer, J. Jotautas Baronas, Michael B. Hall, Philipp Braeuninger‐Weimer, Michael J. Scherm, Daniel J. Kunz, Surangi Perera, Daniel E. Martin‐Herranz, Edward T. Tipper, Susannah J. Salter, Maximilian R Stammnitz
Software Mentions: 1
Published: almost 4 years ago

Projects: pypi: scikit-bio

Papers Mentioning scikit-bio 41