bioconductor: DECIPHER | Projects

10.1186/s40168-021-01100-2

Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation
Cited by: 31
Author(s): Anna Cäcilia Ingham, Katrine Kielsen, Hanne Mordhorst, Marianne Ifversen, Frank Møller Aarestrup, Klaus Müller, Sünje Johanna Pamp
Software Mentions: 18
Published: over 3 years ago

10.1371/journal.pone.0194899

Investigation of the seasonal microbiome of Anopheles coluzzii mosquitoes in Mali
Cited by: 34
Author(s): Benjamin J Krajacich, Diana L. Huestis, Adama Dao, Alpha Seydou Yaro, Moussa Diallo, Asha Krishna, Jianchu Xu, Tovi Lehmann
Software Mentions: 18
Published: over 6 years ago

10.1186/s40168-019-0725-3

Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and host
Cited by: 43
Author(s): Aonghus Lavelle, Thomas Hoffmann, Hang-Phuong Pham, Philippe Langella, Éric Guédon, Harry Sokol
Software Mentions: 16
Published: over 5 years ago

10.12688/f1000research.27268.1

rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis
Cited by: 16
Author(s): Sébastien Theil, Étienne Rifa
Software Mentions: 16
Published: almost 4 years ago

10.3390/ijms22052244

The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis
Cited by: 4
Author(s): Anton E. Shikov, Yury V. Malovichko, Arseniy Lobov, Maria Belousova, Anton A. Nizhnikov, Kirill S. Antonets
Software Mentions: 16
Published: over 3 years ago

10.3390/biomedicines9020144

Dietary Rice Bran-Modified Human Gut Microbial Consortia Confers Protection against Colon Carcinogenesis Following Fecal Transfaunation
Cited by: 19
Author(s): Kristopher D. Parker, Akhilendra Kumar Maurya, Hend Ibrahim, Sangeeta Rao, Petronella R. Hove, Dileep Kumar, Rama Kant, B. L. Raina, Rajesh Agarwal, Kristine A. Kuhn, Komal Raina, Elizabeth P. Ryan
Software Mentions: 15
Published: almost 4 years ago

10.1098/rsos.191609

Spatial heterogeneity of the shorebird gastrointestinal microbiome
Cited by: 17
Author(s): Kirsten Grond, Hannah Guilani, Sarah M. Hird
Software Mentions: 15
Published: almost 5 years ago

10.3390/cells10061292

Effect of Differences in the Microbiome of Cyp17a1-Deficient Mice on Atherosclerotic Background
Cited by: 1
Author(s): Axel Künstner, Rédouane Aherrahrou, Misa Hirose, Petra Bruse, Saleh M. Ibrahim, Hauke Busch, Jeanette Erdmann, Zouhair Aherrahrou
Software Mentions: 15
Published: over 3 years ago

10.1186/s12859-021-04193-6

Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing
Cited by: 32
Author(s): Zachary D Wallen
Software Mentions: 14
Published: over 3 years ago

10.3390/microorganisms9061222

Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index—A Pilot Study
Cited by: 5
Author(s): Hend Alqaderi, Meganathan P. Ramakodi, Rasheeba Nizam, Sindhu Jacob, Sriraman Devarajan, Muthukrishnan Eaaswarkhanth, Fahd Al-Mulla
Software Mentions: 14
Published: over 3 years ago

10.12688/f1000research.8986.2

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
Cited by: 483
Author(s): Ben J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie, Susan Holmes
Software Mentions: 13
Published: about 8 years ago

10.3390/nu13082639

Infants’ First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental Cohorts
Cited by: 18
Author(s): Chiara-Maria Homann, Connor A J Rossel, Sara Dizzell, Liene Bervoets, Julia Simioni, Jenifer Li, Elizabeth Gunn, Michael G. Surette, Russell J. de Souza, Monique Mommers, Eileen K. Hutton, Katherine M. Morrison, John Penders, Niels van Best, Jennifer C. Stearns
Software Mentions: 12
Published: over 3 years ago

10.3389/fmicb.2021.624071

Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific
Cited by: 10
Author(s): Miguel Semedo, Eva Lopes, Mafalda S. Baptista, Ainhoa Oller-Ruiz, Javier Gilabert, Maria Paola Tomasino, Catarina Magalhães
Software Mentions: 11
Published: over 3 years ago

10.1371/journal.pone.0169662

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
Cited by: 171
Author(s): John Vollmers, Sandra Wiegand, Anne‐Kristin Kaster
Software Mentions: 11
Published: almost 8 years ago

10.3389/fmicb.2021.685263

Exploring the Potential of Micrococcus luteus Culture Supernatant With Resuscitation-Promoting Factor for Enhancing the Culturability of Soil Bacteria
Cited by: 9
Author(s): Marco Antonio Lopez Marin, Michal Strejcek, Petra Junková, Jáchym Šuman, Jiří Šantrůček, Ondřej Uhlík
Software Mentions: 10
Published: over 3 years ago

10.1038/s41396-020-00777-x

A network approach to elucidate and prioritize microbial dark matter in microbial communities
Cited by: 71
Author(s): Tatyana Zamkovaya, Jamie S. Foster, Valérie de Crécy‐Lagard, Ana Conesa
Software Mentions: 10
Published: about 4 years ago

10.1371/journal.pbio.2005396

Gut microbiome transition across a lifestyle gradient in Himalaya
Cited by: 109
Author(s): Aashish R. Jha, Emily Davenport, Yoshina Gautam, Dinesh Bhandari, Sarmila Tandukar, Katharine M. Ng, Gabriela K. Fragiadakis, Susan Holmes, Guru Prasad Gautam, Jeff D. Leach, Jeevan Bahadur Sherchand, Carlos D. Bustamante, Justin L. Sonnenburg
Software Mentions: 10
Published: about 6 years ago

10.1534/g3.120.401309

CeMbio - TheCaenorhabditis elegansMicrobiome Resource
Cited by: 71
Author(s): Philipp Dirksen, Adrien Assié, Johannes Zimmermann, Fan Zhang, Adina-Malin Tietje, Sarah Arnaud Marsh, Marie‐Anne Félix, Michael Y. Shapira, Christoph Kaleta, Hinrich Schulenburg, Buck S. Samuel
Software Mentions: 10
Published: about 4 years ago

10.1093/gbe/evab028

sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R
Cited by: 14
Author(s): Kuan-Hao Chao, Kirston Barton, Sarah Palmer, Robert Lanfear
Software Mentions: 10
Published: almost 4 years ago

10.1098/rspb.2020.0302

Mating changes the genital microbiome in both sexes of the common bedbug Cimex lectularius across populations
Cited by: 4
Author(s): Sara Bellinvia, Paul R. Johnston, Susan Mbedi, Oliver Otti
Software Mentions: 10
Published: over 4 years ago

10.1038/s41396-019-0546-1

Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus)
Cited by: 29
Author(s): Corey C. Holt, Mark van der Giezen, Carly L. Daniels, Grant D. Stentiford, David Bass
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pone.0241529

Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation
Cited by: 5
Author(s): Anita Silver, Sean Perez, Melanie Gee, Bethany Xu, Shreeya Garg, Kipling Will, Amanjit Gill
Software Mentions: 9
Published: over 3 years ago

10.3390/microorganisms8040485

Characterization of the Duodenal Mucosal Microbiome in Obese Adult Subjects by 16S rRNA Sequencing
Cited by: 33
Author(s): Carmela Nardelli, Ilaria Granata, Valeria D’Argenio, Salvatore Tramontano, Debora Compare, Mario Rosario Guarracino, Gerardo Nardone, Vincenzo Pilone, Lucia Sacchetti
Software Mentions: 8
Published: over 4 years ago

10.1038/s41598-020-57612-8

Long-term Proton Pump Inhibitor Administration Caused Physiological and Microbiota Changes in Rats
Cited by: 26
Author(s): Yuxing Yang, Hsuen-Wen Chang, I-Hsuan Lin, Li‐Nien Chien, Min-Ju Wu, Yun‐Ru Liu, Peiguo Chu, Guoxiang Xie, Fangcong Dong, Jia Wang, Vincent H.S. Chang, Yun Yen
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pone.0217804

Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons
Cited by: 12
Author(s): Kirsten Grond, Julie Perreau, Wesley T. Loo, A. James Spring, Colleen M. Cavanaugh, Sarah M. Hird
Software Mentions: 8
Published: over 5 years ago

10.3389/fmicb.2021.584676

Microbial Community Characteristics Largely Unaffected by X-Ray Computed Tomography of Sediment Cores
Cited by: 0
Author(s): Erica Ewton, Scott Klasek, Erin K. Peck, J. Wiest, Frederick S. Colwell
Software Mentions: 8
Published: over 3 years ago

10.3389/fmicb.2021.676615

Attributes of Drying Define the Structure and Functioning of Microbial Communities in Temperate Riverbed Sediment
Cited by: 7
Author(s): José Schreckinger, Michael Mutz, Clara Mendoza‐Lera, Aline Frossard
Software Mentions: 8
Published: over 3 years ago

10.3390/pathogens10010066

Contamination Sources and Transmission Routes for Campylobacter on (Mixed) Broiler Farms in Belgium, and Comparison of the Gut Microbiota of Flocks Colonized and Uncolonized with Campylobacter
Cited by: 8
Author(s): Karolien Hertogs, Annelies Haegeman, Dries Schaumont, Philippe Gelaude, Lieven De Zutter, Jeroen Dewulf, Marc Heyndrickx, Geertrui Rasschaert
Software Mentions: 7
Published: almost 4 years ago

10.1093/gigascience/giaa135

Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology
Cited by: 33
Author(s): Christina Weißbecker, Beatrix Schnabel, Anna Heintz‐Buschart
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41396-020-0690-7

Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice
Cited by: 20
Author(s): Meriem Belheouane, Marie Vallier, Aleksa Čepić, Chin-Wan Chung, Saleh M. Ibrahim, John F. Baines
Software Mentions: 7
Published: over 4 years ago

10.3389/fmicb.2020.572931

Hydrocarbon-Degrading Bacteria Alcanivorax and Marinobacter Associated With Microalgae Pavlova lutheri and Nannochloropsis oculata
Cited by: 30
Author(s): Tatyana Chernikova, Rafael Bargiela, Stepan V. Toshchakov, Vignesh Shivaraman, Evgenii A. Lunev, Michail M. Yakimov, David N. Thomas, Peter N. Golyshin
Software Mentions: 7
Published: about 4 years ago

10.7717/peerj.11865

ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences
Cited by: 2
Author(s): Dylan Catlett, Kevin Son, Connie Liang
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2021.685937

Metagenomic Survey of the Highly Polyphagous Anastrepha ludens Developing in Ancestral and Exotic Hosts Reveals the Lack of a Stable Microbiota in Larvae and the Strong Influence of Metamorphosis on Adult Gut Microbiota
Cited by: 10
Author(s): Martı́n Aluja, Jesús Alejandro Zamora‐Briseño, Vicente Pérez‐Brocal, Alma Altúzar-Molina, Larissa Guillén, Damaris Desgarennes, Mirna Vázquez-Rosas-Landa, Enrique Ibarra-Laclette, Alexandro Alonso-Sánchez, Andrés Moya
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2021.645784

Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure
Cited by: 1
Author(s): Scott Klasek, Marcus T. Brock, Hilary G. Morrison, Cynthia Weinig, Loïs Maignien
Software Mentions: 7
Published: over 3 years ago

10.1186/s40168-021-01070-5

Defining the resilience of the human salivary microbiota by a 520-day longitudinal study in a confined environment: the Mars500 mission
Cited by: 4
Author(s): Giovanni Bacci, Alessio Mengoni, Giovanni Emiliani, Carolina Chiellini, Edoardo Giovanni Cipriani, Giovanna Bianconi, Francesco Canganella, Renato Fani
Software Mentions: 6
Published: over 3 years ago

10.3390/microorganisms8030368

Optimization of Preservation Methods Allows Deeper Insights into Changes of Raw Milk Microbiota
Cited by: 8
Author(s): Alexandre J.K. Ouamba, Gisèle LaPointe, Simon Dufour, Denis Roy
Software Mentions: 6
Published: over 4 years ago

10.1007/s00784-020-03613-w

Limited antimicrobial efficacy of oral care antiseptics in microcosm biofilms and phenotypic adaptation of bacteria upon repeated exposure
Cited by: 22
Author(s): Sophia R. Schwarz, Stefanie Hirsch, Andreas Hiergeist, Christian Kirschneck, Denise Muehler, Karl‐Anton Hiller, Tim Maisch, Ali Al‐Ahmad, André Gessner, Wolfgang Buchalla, Fabian Cieplik
Software Mentions: 6
Published: about 4 years ago

10.1186/s12864-020-07182-w

nanotatoR: a tool for enhanced annotation of genomic structural variants
Cited by: 4
Author(s): Surajit Bhattacharya, Hayk Barseghyan, Emmanuèle C. Délot, Éric Vilain
Software Mentions: 6
Published: almost 4 years ago

10.1186/s40168-019-0711-9

Bacterial alkylquinolone signaling contributes to structuring microbial communities in the ocean
Cited by: 22
Author(s): Kristen E. Whalen, Jamie W. Becker, Anna M. Schrecengost, Yongjie Gao, Nicole Giannetti, Elizabeth L. Harvey
Software Mentions: 6
Published: over 5 years ago

10.1186/s12866-020-02031-y

Identifying candidate Aspergillus pathogenicity factors by annotation frequency
Cited by: 4
Author(s): Kayla K. Pennerman, Guohua Yin, Anthony E. Glenn, Joan W. Bennett
Software Mentions: 6
Published: about 4 years ago

10.1186/s40168-015-0069-6

Perturbation and restoration of the fathead minnow gut microbiome after low-level triclosan exposure
Cited by: 108
Author(s): Adrienne B. Narrowe, Munira Albuthi-Lantz, Erin P. Smith, Kimberly J Bower, Timberley M. Roane, Alan M. Vajda, Christopher S. Miller
Software Mentions: 6
Published: over 9 years ago

10.1186/s13023-019-1020-x

The mutational and phenotypic spectrum of TUBA1A-associated tubulinopathy
Cited by: 46
Author(s): Moritz Hebebrand, Ulrike Hüffmeier, Regina Trollmann, Ute Hehr, Steffen Uebe, Arif B. Ekici, Cornelia Kraus, Mandy Krumbiegel, André Reis, Christian T. Thiel, Bernt Popp
Software Mentions: 6
Published: almost 6 years ago

10.3390/plants9121801

The Role of Symbiotic Microorganisms, Nutrient Uptake and Rhizosphere Bacterial Community in Response of Pea (Pisum sativum L.) Genotypes to Elevated Al Concentrations in Soil
Cited by: 10
Author(s): Andrey A. Belimov, А. И. Шапошников, D. S. Syrova, Arina Kichko, Polina Guro, O. S. Yuzikhin, T. S. Azarova, Anna L Sazanova, E. A. Sekste, Vladimir A Litvinskiy, Vladimir V. Nosikov, А. А. Завалин, E. E. Andronov, Vera I. Safronova
Software Mentions: 6
Published: almost 4 years ago

10.1098/rstb.2019.0242

Phylogenetic conservation of soil bacterial responses to simulated global changes
Cited by: 41
Author(s): Kazuo Isobe, Nicholas J. Bouskill, Eoin L. Brodie, Erika A. Sudderth, Jennifer B. H. Martiny
Software Mentions: 6
Published: over 4 years ago

10.1128/mSystems.00446-21

Transmission of Seed and Soil Microbiota to Seedling
Cited by: 27
Author(s): Aude Rochefort, Marie Simonin, Coralie Marais, Anne‐Yvonne Guillerm‐Erckelboudt, Matthieu Barret, Alain Sarniguet
Software Mentions: 6
Published: over 3 years ago

10.1128/mSystems.00712-21

Activity-Based Cell Sorting Reveals Resistance of Functionally Degenerate Nitrospira during a Press Disturbance in Nitrifying Activated Sludge
Cited by: 4
Author(s): Maxwell B. W. Madill, Yaqian Luo, Pranav Sampara, Ryan M. Ziels
Software Mentions: 6
Published: about 3 years ago

10.3389/fmicb.2021.614957

Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains
Cited by: 34
Author(s): Camila Gazolla Volpiano, Fernando Hayashi Sant’Anna, Adriana Ambrosini, Jackson Freitas Brilhante de São José, Anelise Beneduzi, William B. Whitman, Emanuel Maltempi de Souza, Bruno Brito Lisboa, Luciano Kayser Vargas, Luciane Maria Pereira Passaglia
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0195534

Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis
Cited by: 34
Author(s): Daniel Hagenfeld, Raphael Koch, Sebastian Jünemann, Karola Prior, Inga Harks, Peter Eickholz, Thomas Hoffmann, Ti‐Sun Kim, Thomas Kocher, Jörg Meyle, Doğan Kaner, Ulrich Schlagenhauf, Benjamin Ehmke, Dag Harmsen
Software Mentions: 6
Published: over 6 years ago

10.3389/fmicb.2021.642197

Infant Feeding Alters the Longitudinal Impact of Birth Mode on the Development of the Gut Microbiota in the First Year of Life
Cited by: 25
Author(s): Modupe Coker, Hannah E. Laue, Anne G. Hoen, Margaret Hilliard, Erika Dade, Zhigang Li, Thomas J. Palys, Hilary G. Morrison, Emily Baker, Margaret R. Karagas, Juliette C. Madan
Software Mentions: 6
Published: over 3 years ago

10.3390/brainsci11081085

Maternal Immune Activation Causes Social Behavior Deficits and Hypomyelination in Male Rat Offspring with an Autism-Like Microbiota Profile
Cited by: 29
Author(s): Gilbert Lee, Yen Kuang Lin, Jing Lai, Yu Chun Lo, Yu Yang, Syuan You Ye, Chia-Jung Lee, Ching Chiung Wang, Yung Hsiao Chiang, Sung Hui Tseng
Software Mentions: 5
Published: over 3 years ago

10.1002/ece3.6196

Competition with insectivorous ants as a contributor to low songbird diversity at low elevations in the eastern Himalaya
Cited by: 12
Author(s): K. Supriya, Trevor D. Price, Corrie S. Moreau
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-018-24126-3

Metabarcoding analysis of strongylid nematode diversity in two sympatric primate species
Cited by: 31
Author(s): Barbora Pafčo, Dagmar Čížková, Jakub Kreisinger, Hideo Hasegawa, Peter Vallo, Kathryn Shutt, Angelique Todd, Klára J. Petrželková, David Modrý
Software Mentions: 5
Published: over 6 years ago

10.1038/s42003-021-02372-y

Function-adaptive clustered nanoparticles reverse Streptococcus mutans dental biofilm and maintain microbiota balance
Cited by: 9
Author(s): Fatemeh Ostadhossein, Parikshit Moitra, Esra Altun, Debapriya Dutta, Dinabandhu Sar, Indu Tripathi, Shih Hsuan Hsiao, Valeriya Kravchuk, Shuming Nie, Dipanjan Pan
Software Mentions: 5
Published: over 3 years ago

10.3390/nu12092570

Diet, Perceived Intestinal Well-Being and Compositions of Fecal Microbiota and Short Chain Fatty Acids in Oat-Using Subjects with Celiac Disease or Gluten Sensitivity
Cited by: 8
Author(s): Lotta Nylund, Salla Hakkola, Leo Lahti, Seppo Salminen, Marko Kalliomäki, Baoru Yang, Kaisa M. Linderborg
Software Mentions: 5
Published: about 4 years ago

10.1186/s40168-017-0392-1

Metabolic capability and in situ activity of microorganisms in an oil reservoir
Cited by: 61
Author(s): Yi Fan Liu, Daniela Domingos Galzerani, Serge Maurice Mbadinga, Livia S. Zaramela, Ji Dong Gu, Bo Zhong Mu, Karsten Zengler
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0115692

HPOSim: An R Package for Phenotypic Similarity Measure and Enrichment Analysis Based on the Human Phenotype Ontology
Cited by: 49
Author(s): Yue Deng, Lin Gao, Bingbo Wang, Guo Xia-zhen
Software Mentions: 5
Published: almost 10 years ago

10.3389/fmicb.2019.01204

Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria
Cited by: 22
Author(s): Laura Gómez‐Consarnau, David M. Needham, Peter K. Weber, Jed A. Fuhrman, Xavier Mayali
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1008640

Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa
Cited by: 7
Author(s): Verena Ras, Gerrit Botha, Shaun Aron, Katie Lennard, Imane Allali, Shantelle Claassen-Weitz, Kilaza Samson Mwaikono, Dane Kennedy, Jessica R. Holmes, Gloria Rendon, Sumir Panji, Christopher J. Fields, Nicola Mulder
Software Mentions: 5
Published: over 3 years ago

10.3390/plants10091870

The Arabinogalactan Protein Family of Centaurium erythraea Rafn
Cited by: 3
Author(s): Danijela M. Paunović, Katarina Ćuković, Milica Bogdanović, Slaðana Todorović, Milana Trifunović‐Momčilov, Angelina Subotić, Ana Simonović, Milan Dragićević
Software Mentions: 5
Published: about 3 years ago

10.7717/peerj.10424

Ixodes scapularis microbiome correlates with life stage, not the presence of human pathogens, in ticks submitted for diagnostic testing
Cited by: 14
Author(s): Joshua C Gil, Zeinab H. Helal, Guillermo R. Risatti, Sarah M. Hird
Software Mentions: 5
Published: almost 4 years ago

10.3390/ijms22157928

A Fork Trap in the Chromosomal Termination Area Is Highly Conserved across All Escherichia coli Phylogenetic Groups
Cited by: 3
Author(s): Daniel J. Goodall, Katie H. Jameson, Michelle Hawkins, Christian J. Rudolph
Software Mentions: 5
Published: over 3 years ago

10.3390/toxics9090215

Subacute Exposure to an Environmentally Relevant Dose of Di-(2-ethylhexyl) Phthalate during Gestation Alters the Cecal Microbiome, but Not Pregnancy Outcomes in Mice
Cited by: 4
Author(s): Karen Chiu, Shah Tauseef Bashir, Lei Gao, Jessica Gutiérrez, María R C de Godoy, Jenny Drnevich, Christopher J. Fields, Isaac Cann, Jodi A. Flaws, Romana A. Nowak
Software Mentions: 5
Published: about 3 years ago

10.1038/sdata.2018.154

Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments
Cited by: 73
Author(s): Paul M. Berube, Steven J. Biller, Thomas Hackl, Brandon M. Satinsky, Jamie W. Becker, Rogier Braakman, Sara B. Collins, Libusha Kelly, Jessie W Berta-Thompson, Allison Coe, Kristin Bergauer, Heather A. Bouman, Thomas J. Browning, Daniele De Corte, Christel Hassler, Yotam Hulata, Jeremy E. Jacquot, Elizabeth W. Maas, Thomas Reinthaler, Eva Sintes, Taichi Yokokawa, Debbie Lindell, Ramunas Stepanauskas, Sallie W. Chisholm
Software Mentions: 4
Published: about 6 years ago

10.1002/ece3.5992

Generalist Eimeria species in rodents: Multilocus analyses indicate inadequate resolution of established markers
Cited by: 13
Author(s): Víctor Hugo Jarquín‐Díaz, Alice Balard, Anna Mácová, Jenny Jost, Tabea Roth von Szepesbéla, Karin Berktold, Steffen Tank, Jana Kvičerová, Emanuel Heitlinger
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13073-021-00843-9

Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study
Cited by: 42
Author(s): Amy Langdon, Drew J. Schwartz, Christopher Bulow, Xiaoqing Sun, Tiffany Hink, Kimberly A. Reske, Courtney Jones, Carey-Ann D. Burnham, Erik R. Dubberke, Gautam Dantas
Software Mentions: 4
Published: almost 4 years ago

10.1016/j.cub.2017.04.057

Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2
Cited by: 76
Author(s): Thomas W. Marchant, Edward J. Johnson, Lynn McTeir, Craig Johnson, Adam Gow, Tiziana Liuti, Dana Kuehn, Karen L. Svenson, Mairead Lesley Bermingham, Michaela Drögemüller, Marc Nussbaumer, Megan Davey, David Argyle, Roger M. Powell, Sérgio Guilherme, Johann Lang, Gert ter Haar, Tosso Leeb, Tobias Schwarz, Richard J. Mellanby, Dylan Clements, Jeffrey J. Schoenebeck
Software Mentions: 4
Published: over 7 years ago

10.1093/bioinformatics/btaa1096

MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes
Cited by: 8
Author(s): Maria K. Sobczyk, Tom R. Gaunt, Lavinia Paternoster
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0199132

Effects of low dose silver nanoparticle treatment on the structure and community composition of bacterial freshwater biofilms
Cited by: 23
Author(s): Alexandra Grün, Constantin Benjamin App, Andreas Breidenbach, Jutta Meier, George Metreveli, Gabriele E. Schaumann, Werner Manz
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-46632-8

TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish
Cited by: 23
Author(s): Sanna Gudmundsson, Maria Wilbe, Beata Filipek-Górniok, Anna-Maja Molin, Sara Ekvall, Josefin Johansson, Amin Allalou, Hans Gylje, Vera M. Kalscheuer, Johan Ledin, Göran Annerén, Marie-Louise Bondeson
Software Mentions: 4
Published: over 5 years ago

10.3390/nu13051559

Maternal Vegetable and Fruit Consumption during Pregnancy and Its Effects on Infant Gut Microbiome
Cited by: 13
Author(s): Hsien Yu Fan, Yu Tang Tung, Yu Yang, Justin Bo-Kai Hsu, Cheng Yang Lee, Tzu Hao Chang, Emily Chia Yu Su, Rong Hong Hsieh, Yang Ching Chen
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0104355

Copy Number Variation in Thai Population
Cited by: 25
Author(s): Bhoom Suktitipat, Chaiwat Naktang, Wuttichai Mhuantong, Tularak Thitima, Paramita Artiwet, Pasomsap Ekawat, Wallaya Jongjaroenprasert, Suthat Fuchareon, Surakameth Mahasirimongkol, Wasun Chantratita, Boonsit Yimwadsana, Varodom Charoensawan, Natini Jinawath
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0195334

iCopyDAV: Integrated platform for copy number variations—Detection, annotation and visualization
Cited by: 38
Author(s): Prashanthi Dharanipragada, Sriharsha Vogeti, Nita Parekh
Software Mentions: 4
Published: over 6 years ago

10.1186/2049-2618-2-1

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants
Cited by: 314
Author(s): Brandon Brooks, Brian Firek, Christopher S. Miller, Itai Sharon, Brian C. Thomas, Robyn Baker, Michael J. Morowitz, Jillian F. Banfield
Software Mentions: 4
Published: almost 11 years ago

10.3389/fmicb.2021.684233

Maternal Antibiotic Treatment Disrupts the Intestinal Microbiota and Intestinal Development in Neonatal Mice
Cited by: 8
Author(s): Chung-Ming Chen, Hsiu Chu Chou, Yu Yang
Software Mentions: 4
Published: over 3 years ago

10.1093/molbev/msaa323

Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence
Cited by: 40
Author(s): Gemma G. R. Murray, Jane Charlesworth, Eric L. Miller, Michael J. Casey, Catrin Lloyd, Marcelo Gottschalk, Alexander W. Tucker, John J. Welch, Lucy A. Weinert
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pgen.1009054

Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases
Cited by: 13
Author(s): Elena Díaz-Santiago, Fernando M. Jabato, Elena Rojano, Pedro Seoane, Florencio Pazos, James R. Perkins, Juan A. G. Ranea
Software Mentions: 4
Published: about 4 years ago

10.3390/membranes10120415

Reducing the Impacts of Biofouling in RO Membrane Systems through In Situ Low Fluence Irradiation Employing UVC-LEDs
Cited by: 9
Author(s): Philipp Sperle, Christian Wurzbacher, Jörg E. Drewes, Bertram Skibinski
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2019.02257

Effects of Habitat Partitioning on the Distribution of Bacterioplankton in Deep Lakes
Cited by: 12
Author(s): Nico Salmaso
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2020.00912

Microbial Composition and Functional Diversity Differ Across Urban Green Infrastructure Types
Cited by: 25
Author(s): Amanjit Gill, Kai Purnell, Matthew I. Palmer, Jaime A. Stein, Krista L. McGuire
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2018.00537

SeqVItA: Sequence Variant Identification and Annotation Platform for Next Generation Sequencing Data
Cited by: 4
Author(s): Prashanthi Dharanipragada, Sampreeth Reddy Seelam, Nita Parekh
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.11956

Small-scale variation in a pristine montane cloud forest: evidence on high soil fungal diversity and biogeochemical heterogeneity
Cited by: 1
Author(s): Patricia Vélez, Yunuen Tapia-Torres, Felipe Garcı́a-Oliva, Jaime Gasca-Pineda
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-76161-8

Better understanding and prediction of antiviral peptides through primary and secondary structure feature importance
Cited by: 34
Author(s): Abu Sayed Chowdhury, Sarah Reehl, Kylene Kehn-Hall, Barney Bishop, Bobbie‐Jo Webb‐Robertson
Software Mentions: 4
Published: about 4 years ago

10.1007/s00401-019-02109-6

Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases
Cited by: 37
Author(s): Elena Perenthaler, Anita Nikoncuk, Soheil Yousefi, Woutje M. Berdowski, Maysoon Alsagob, Ivan Čapo, Herma C. van der Linde, Paul van den Berg, Edwin H. Jacobs, Darija Putar, Mehrnaz Ghazvini, Eleonora Aronica, Wilfred F. J. van IJcken, Walter G. de Valk, Evita Medici-van den Herik, Marjon van Slegtenhorst, Lauren Brick, Mariya Kozenko, Jennefer N. Kohler, Jonathan A. Bernstein, Kristin G. Monaghan, Amber Begtrup, Rebecca Torene, Amna Al Futaisi, Fathiya Al Murshedi, Renjith Mani, Faisal Al Azri, Erik‐Jan Kamsteeg, Majid Mojarrad, Atieh Eslahi, Zaynab Khazaei, Fateme Massinaei Darmiyan, Mohammad Doosti, Ehsan Ghayoor Karimiani, Jana Vandrovcová, Faisal Zafar, Nuzhat Rana, Krishna Kumar Kandaswamy, Jozef Hertecant, Péter Bauer, Mohammed A. AlMuhaizea, Mustafa A. Salih, Mazhor Aldosary, Rawan Almass, Laila AlQuait, Wafa Qubbaj, Serdar Coşkun, Khaled O. Alahmadi, Muddathir H. Hamad, Salem Alwadaee, Khalid Awartani, Anas Dababo, Futwan Al‐Mohanna, Dilek Çolak, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Murat Günel, A. Gülhan Ercan-Şençiçek, Gouri Rao Passi, Huma Arshad Cheema, Stéphanie Efthymiou, Henry Houlden, Aida M. Bertoli‐Avella, Alice S. Brooks, Kyle Retterer, Reza Maroofian, Namik Kaya, Tjakko J. van Ham, Tahsin Stefan Barakat
Software Mentions: 4
Published: almost 5 years ago

10.1038/ejhg.2017.32

Analysis of exome data for 4293 trios suggests GPI-anchor biogenesis defects are a rare cause of developmental disorders
Cited by: 60
Author(s): Alistair T. Pagnamenta, Yoshiko Murakami, John M. Taylor, Consuelo Anzilotti, Malcolm F. Howard, Venessa Miller, Diana Johnson, Shereen Tadros, Sahar Mansour, I. Karen Temple, Rachel Firth, Elisabeth Rosser, Rachel Harrison, B Kerr, Niko Popitsch, Taroh Kinoshita, Jenny C Taylor, Usha Kini
Software Mentions: 3
Published: over 7 years ago

10.1038/s41597-020-0427-5

Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample
Cited by: 35
Author(s): Joan Mas-Lloret, Mireia Obón-Santacana, Gemma Ibáñez‐Sanz, Elisabet Guinó, Miguel L Pato, Francisco Rodríguez-Moranta, Alfredo Mata, Ana García-Rodríguez, Vı́ctor Moreno, Ville N. Pimenoff
Software Mentions: 3
Published: over 4 years ago

10.3390/biom9100516

Fish Oil, but Not Olive Oil, Ameliorates Depressive-Like Behavior and Gut Microbiota Dysbiosis in Rats under Chronic Mild Stress
Cited by: 18
Author(s): Te-Hsuan Tung, Yen-Ting Tung, I-Hsuan Lin, Chun Kuang Shih, Ngan Thi Kim Nguyen, Amalina Shabrina, Shih‐Yi Huang
Software Mentions: 3
Published: about 5 years ago

10.1111/jam.12516

Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration
Cited by: 78
Author(s): Isabel Douterelo, Rebecca Sharpe, Joby Boxall
Software Mentions: 3
Published: over 10 years ago

10.1093/database/baw015

Wikidata as a semantic framework for the Gene Wiki initiative
Cited by: 47
Author(s): Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Elvira Mitraka, Julia Turner, Tim Putman, Justin Leong, Chinmay Naik, Paul Pavlidis, Lynn M. Schriml, Benjamin M. Good, Andrew I. Su
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13073-017-0452-y

Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability
Cited by: 28
Author(s): Claudio Reggiani, Sandra Coppens, Tayeb Sékhara, Ivan K. Dimov, Bruno Pichon, Nicolas Lufin, Marie Claude Addor, Elga Fabia Belligni, María Cristina Digilio, Flavio Faletra, Giovanni Battista Ferrero, Marion Gérard, Bertrand Isidor, Shelagh Joss, Florence Niel-Bütschi, Maria Dolores Perrone, Florence Petit, Alessandra Renieri, Serge Romana, Alexandra Topa, Joris Robert Vermeesch, Tom Lenaerts, Georges Casimir, Marc Abramowicz, Gianluca Bontempi, Catheline Vilain, Nicolas Deconinck, Guillaume Smits
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-6-124

Cited by: 80
Author(s): Björn Menten, Filip Pattyn, Katleen De Preter, Piet Robbrecht, Evi Michels, Karen Buysse, Geert Mortier, Anne De Paepe, Steven Van Vooren, Joris Robert Vermeesch, Yves Moreau, Bart De Moor, Stefan Vermeulen, Frank Speleman, Jo Vandesompele
Software Mentions: 3
Published: almost 20 years ago

10.1111/j.1399-0004.2011.01755.x

Corpus callosum abnormalities, intellectual disability, speech impairment, and autism in patients with haploinsufficiency of ARID1B
Cited by: 118
Author(s): Christina Halgren, Susanne Kjærgaard, Mads Bak, Christine Søholm Hansen, Zahra El-Schich, Claire Anderson, Karen Friis Henriksen, Helle Hjalgrim, Maria Kirchhoff, Emilia K. Bijlsma, Maartje Nielsen, Nicolette S. den Hollander, Claudia Ruivenkamp, Bertrand Isidor, Cédric Le Caignec, Raffaella Zannolli, Mafalda Mucciolo, Alessandra Renieri, Francesca Mari, Britt Marie Anderlid, J Andrieux, Anne Dieux, Niels Tommerup, Iben Bache
Software Mentions: 3
Published: about 13 years ago

10.1186/1471-2164-15-1107

Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms
Cited by: 60
Author(s): Nicholas B. Justice, Anders Norman, Christopher T. Brown, Anil K. Singh, Brian C. Thomas, Jillian F. Banfield
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13229-020-00407-5

Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank
Cited by: 9
Author(s): Chloe X. Yap, Gail A. Alvares, Anjali K. Henders, Lin Tian, Leanne Wallace, Alaina Farrelly, Tiana McLaren, Jolene Berry, Anna A. E. Vinkhuyzen, Maciej Trzaskowski, Jian Zeng, Yuanhao Yang, Dominique Cleary, Rachel Grove, Claire Hafekost, Alexis Harun, Helen Holdsworth, Rachel Jellett, Feroza Khan, Lauren P. Lawson, Jodie Leslie, Mira Levis Frenk, Anne Masi, Nisha E. Mathew, Melanie Muniandy, Michaela Nothard, Peter M. Visscher, Paul A. Dawson, Cheryl Dissanayake, Valsamma Eapen, Helen Heussler, Andrew J. O. Whitehouse, Naomi R. Wray, Jacob Gratten
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0173029

Exploring gastric bacterial community in young pigs
Cited by: 8
Author(s): Vincenzo Motta, Paolo Trevisi, Francesca Bertolini, Anisa Ribani, Giuseppina Schiavo, Luca Fontanesi, Paolo Bosi
Software Mentions: 3
Published: over 7 years ago

10.1038/s41436-018-0330-z

The ARID1B spectrum in 143 patients: from nonsyndromic intellectual disability to Coffin–Siris syndrome
Cited by: 73
Author(s): Pleuntje J. van der Sluijs, Sandra Jansen, Samantha A. Schrier Vergano, Miho Adachi-Fukuda, Yasemin Alanay, Adila Al-Kindy, Anwar Baban, Allan Bayat, Stefanie Beck-Wödl, Katherine Berry, Emilia K. Bijlsma, Levinus A. Bok, Alwin F.J. Brouwer, Ineke van der Burgt, Philippe M. Campeau, Natalie Canham, Krystyna Chrzanowska, Yoyo Wing-Yiu Chu, Brain H. Y. Chung, Karin Dahan, Marjan De Rademaeker, Anne Destrée, Tracy Dudding‐Byth, Rachel K. Earl, Nursel Elçioğlu, Ellen Roy Elias, Christina Fagerberg, Alice Gardham, Blanca Gener, Erica H. Gerkes, Ute Grasshoff, Arie van Haeringen, Karin R. Heitink, Johanna C. Herkert, Nicolette S. den Hollander, Denise Horn, David Hunt, Sarina G. Kant, Mitsuhiro Kato, Hülya Kayserili, Rogier Kersseboom, Esra Kılıç, M Krajewska‐Walasek, Kylin Lammers, Lone Walentin Laulund, Damien Lederer, Melissa Lees, Vanesa López‐González, Saskia M. Maas, Grazia M.S. Mancini, Carlo Marcelis, Francisco Martı́nez, Isabelle Maystadt, Marianne McGuire, Shane McKee, Sarju G. Mehta, Kay Metcalfe, Jeff M. Milunsky, Seiji Mizuno, John B. Moeschler, Christian Netzer, Charlotte W. Ockeloen, Barbara Oehl-Jaschkowitz, Nobuhiko Okamoto, Sharon N. M. Olminkhof, Carmen Orellana, Laurent Pasquier, Caroline Pottinger, Vera Riehmer, Stephen Robertson, Maian Roifman, Caroline Rooryck, Fabienne G. Ropers, Mónica Rosello, Claudia Ruivenkamp, Mahmut Şamil Sağıroğlu, Suzanne C E H Sallevelt, A. Sanchís Calvo, Pelin Özlem Şimşek‐Kiper, Gabriela Soares, Lucia Solaeche, Fatma Müjgan Sönmez, Miranda Splitt, Duco Steenbeek, Alexander P.A. Stegmann, Constance T. R. M. Stumpel, Saori Tanabe, Eyyüp Üçtepe, Gülen Eda Ütine, Hermine E. Veenstra‐Knol, Sunita Venkateswaran, Catheline Vilain, Catherine Vincent‐Delorme, Anneke T. Vulto-van Silfhout, Patricia G. Wheeler, Golder N. Wilson, Louise Wilson, Bernd Wollnik, Tomoki Kosho, Dagmar Wieczorek, Evan E. Eichler, Rolph Pfundt, Bert B.A. de Vries, Jill Clayton‐Smith, Gijs W.E. Santen
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0116230

Evaluation of Simultaneous Nutrient and COD Removal with Polyhydroxybutyrate (PHB) Accumulation Using Mixed Microbial Consortia under Anoxic Condition and Their Bioinformatics Analysis
Cited by: 10
Author(s): Jyotsnarani Jena, Ravindra Kumar, Anshuman Dixit, Satish Kumar Pandey, Trupti Das
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0093945

Uncoupling of Bacterial and Terrigenous Dissolved Organic Matter Dynamics in Decomposition Experiments
Cited by: 52
Author(s): Daniel P. R. Herlemann, Marcus Manecki, Christian Meeske, Falk Pollehne, Matthias Labrenz, Detlef E. Schulz‐Bull, Thorsten Dittmar, Klaus Jürgens
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2017.00472

Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning
Cited by: 47
Author(s): John Vollmers, Martinique Frentrup, Patrick Rast, Christian Jogler, Anne‐Kristin Kaster
Software Mentions: 3
Published: over 7 years ago

10.3389/fpsyt.2020.00354

A Novel LINS1 Truncating Mutation in Autosomal Recessive Nonsyndromic Intellectual Disability
Cited by: 2
Author(s): Babylakshmi Muthusamy, Anikha Bellad, Pramada Prasad, Aravind K. Bandari, G. Bhuvanalakshmi, R. M. Kiragasur, Satish Chandra Girimaji, Akhilesh Pandey
Software Mentions: 3
Published: over 4 years ago

10.1534/g3.119.400037

Evolution of Antibiotic Synthesis Gene Clusters in the Streptomyces globisporus TFH56, Isolated from Tomato Flower
Cited by: 6
Author(s): Gyeongjun Cho, Youn‐Sig Kwak
Software Mentions: 3
Published: over 5 years ago

Projects: bioconductor: DECIPHER

Papers Mentioning DECIPHER 415