cran: dendextend | Projects | Ecosyste.ms: Papers

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago

Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes
Cited by: 11
Author(s): Kristian Peters, Gerd Ulrich Balcke, Niklas Kleinenkuhnen, Hendrik Treutler, Steffen Neumann
Software Mentions: 31
Published: over 3 years ago

10.3389/fonc.2020.617890

Comparative Proteome Identifies Complement Component 3-Mediated Immune Response as Key Difference of Colon Adenocarcinoma and Rectal Adenocarcinoma
Cited by: 9
Author(s): Jun-Ze Liang, Xiaoling Liang, Liye Zhong, Chutian Wu, Jing Zhang, Yang Wang
Software Mentions: 30
Published: almost 4 years ago

10.3389/fimmu.2021.616967

A Multi-Omics Analysis of Mucosal-Associated-Invariant T Cells Reveals Key Drivers of Distinct Modes of Activation
Cited by: 12
Author(s): Kristin Schubert, Isabel Karkossa, Jana Schor, Beatrice Engelmann, Lisa Maria Steinheuer, Tony Bruns, Ulrike Rolle-Kampczyk, Jörg Hackermüller, Martin von Bergen
Software Mentions: 24
Published: over 3 years ago

10.1038/s41598-020-78469-x

Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions
Cited by: 14
Author(s): Jacob Cardenas, Uthra Balaji, Jin Gu
Software Mentions: 23
Published: almost 4 years ago

10.1038/s41598-019-55469-0

Minor compositional alterations in faecal microbiota after five weeks and five months storage at room temperature on filter papers
Cited by: 6
Author(s): Sebastian von Huth, Louise B. Thingholm, Corinna Bang, Malte Rühlemann, André Franke, Uffe Holmskov
Software Mentions: 20
Published: almost 5 years ago

10.3390/v12101142

A Diverse Virome of Leafroll-Infected Grapevine Unveiled by dsRNA Sequencing
Cited by: 24
Author(s): Mamadou L. Fall, De-Xiang Xu, Pierre Lemoyne, Issam Moussa, Carole Beaulieu, Odile Carisse
Software Mentions: 19
Published: about 4 years ago

10.3390/microorganisms7110547

Linking Soil Fungal Generality to Tree Richness in Young Subtropical Chinese Forests
Cited by: 9
Author(s): Christina Weißbecker, Anna Heintz‐Buschart, Helge Bruelheide, François Buscot, Tesfaye Wubet
Software Mentions: 19
Published: about 5 years ago

10.1038/s41598-020-73413-5

The macroevolutionary landscape of short-necked plesiosaurians
Cited by: 13
Author(s): Valentin Fischer, Jamie A. MacLaren, Laura C. Soul, Rebecca Bennion, Patrick S. Druckenmiller, Roger Benson
Software Mentions: 19
Published: about 4 years ago

10.1038/sdata.2018.179

Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes
Cited by: 13
Author(s): Kristian Peters, Karin Gorzolka, Helge Bruelheide, Steffen Neumann
Software Mentions: 17
Published: about 6 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

10.1093/gbe/evab127

Genome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome
Cited by: 4
Author(s): Jeffery S. McMullen, Eduardo Bueno, Frances Blow, Angela E. Douglas
Software Mentions: 16
Published: over 3 years ago

10.1038/s41419-021-03909-z

Diagnostic and prognostic potential of the proteomic profiling of serum-derived extracellular vesicles in prostate cancer
Cited by: 14
Author(s): Michele Signore, Romina Alfonsi, Giulia Federici, Simona Nanni, Antonio Addario, Lucia Bertuccini, Aurora Aiello, Anna Pace, Isabella Sperduti, Giovanni Muto, Alessandro Giacobbe, Devis Collura, Lidia Brunetto, Giuseppe Simone, Manuela Costantini, Lucio Crinò, Stefania Rossi, Claudio Tabolacci, Marco Diociaiuti, Tania Merlino, Michele Gallucci, Steno Sentinelli, Rocco Papalia, Ruggero De Maria, Dèsirèe Bonci
Software Mentions: 16
Published: over 3 years ago

10.1002/ece3.4361

Seasonal variation of secondary metabolites in nine different bryophytes
Cited by: 28
Author(s): Kristian Peters, Karin Gorzolka, Helge Bruelheide, Steffen Neumann
Software Mentions: 16
Published: over 6 years ago

10.1128/mBio.00034-20

Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes
Cited by: 98
Author(s): Laura M. Carroll, Martin Wiedmann, Jasna Kovač
Software Mentions: 15
Published: over 4 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

10.3389/fmicb.2020.580691

No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods
Cited by: 20
Author(s): Laura M. Carroll, Rachel A. Cheng, Jasna Kovač
Software Mentions: 15
Published: about 4 years ago

10.3390/metabo9100222

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species
Cited by: 29
Author(s): Kristian Peters, Hendrik Treutler, Stefanie Döll, Alida Kindt, Thomas Hankemeier, Steffen Neumann
Software Mentions: 15
Published: about 5 years ago

10.1038/s41598-020-69361-9

Effects of different intracranial volume correction methods on univariate sex differences in grey matter volume and multivariate sex prediction
Cited by: 28
Author(s): Carles Sanchis‐Segura, M.V. Ibáñez-Gual, Naiara Aguirre, Álvaro Javier Cruz-Gómez, Cristina Forn
Software Mentions: 14
Published: over 4 years ago

10.1093/molbev/msab063

Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus
Cited by: 42
Author(s): Olena Meleshko, Michael D. Martin, Thorfinn Sand Korneliussen, C. Schluechter, P. Lamkowski, Jeremy Schmutz, Adam Healey, Bryan Piatkowski, A. Jonathan Shaw, David J. Weston, Kjell Ivar Flatberg, Péter Szövényi, Kristian Hassel, Hans K. Stenøien
Software Mentions: 14
Published: over 3 years ago

10.3390/microorganisms9061167

Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad
Cited by: 10
Author(s): Amanda C. Ramdass, Sephra N. Rampersad
Software Mentions: 14
Published: over 3 years ago

10.1093/bioinformatics/btx657

heatmaply: an R package for creating interactive cluster heatmaps for online publishing
Cited by: 334
Author(s): Tal Galili, Alan O’Callaghan, Jonathan Savage, Carson Sievert
Software Mentions: 14
Published: about 7 years ago

10.3389/fcimb.2021.688256

Machine Learning Uses Chemo-Transcriptomic Profiles to Stratify Antimalarial Compounds With Similar Mode of Action
Cited by: 1
Author(s): Ashleigh van Heerden, Roelof van Wyk, Lyn-Marié Birkholtz
Software Mentions: 13
Published: over 3 years ago

10.1186/s12864-021-07542-0

Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn
Cited by: 8
Author(s): Songlin Guo, Shouxiong Huang, Xi Jiang, Haiyang Hu, Dingding Han, Carlos S. Moreno, Genevieve Fairbrother, David A. Hughes, Mark Stoneking, Philipp Khaitovich
Software Mentions: 13
Published: over 3 years ago

10.3389/fpls.2021.651936

Unraveling the Relationship Between Seed Yield and Yield-Related Traits in a Diversity Panel of Brassica juncea Using Multi-Traits Mixed Model
Cited by: 13
Author(s): Ranjit Saroj, S. L. Soumya, S. P. Singh, Surya Sankar, Rajat Chaudhary, . Yashpal, Neeru Saini, Sujata Vasudev, Devendra K. Yadava
Software Mentions: 12
Published: over 3 years ago

10.1093/g3journal/jkab104

Strongyloides RNA-seq Browser: a web-based software platform for on-demand bioinformatics analyses of Strongyloides species
Cited by: 2
Author(s): Astra S. Bryant, Stephanie F. DeMarco, Elissa A. Hallem
Software Mentions: 11
Published: over 3 years ago

10.1038/s41598-021-94324-z

Modest changes in Spi1 dosage reveal the potential for altered microglial function as seen in Alzheimer’s disease
Cited by: 17
Author(s): Ruth Jones, Robert Andrews, Peter Holmans, Matthew Hill, Philip R. Taylor
Software Mentions: 11
Published: over 3 years ago

10.3390/genes12091443

Breeding Tomato Hybrids for Flavour: Comparison of GWAS Results Obtained on Lines and F1 Hybrids
Cited by: 8
Author(s): Estelle Bineau, José L. Rambla, Santiago Priego-Cubero, Alexandre Hereil, Frédérique Bitton, Clémence Plissonneau, Antonio Granell, Mathilde Causse
Software Mentions: 11
Published: about 3 years ago

10.7717/peerj.11222

The postcranial skeleton of Cerrejonisuchus improcerus (Crocodyliformes: Dyrosauridae) and the unusual anatomy of dyrosaurids
Cited by: 1
Author(s): Isaure Scavezzoni, Valentin Fischer
Software Mentions: 10
Published: over 3 years ago

10.1093/plankt/fbaa017

Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea
Cited by: 11
Author(s): Laura Käse, Alexandra Kraberg, Katja Metfies, Stefan Neuhaus, Pim Sprong, Bernhard M. Fuchs, Maarten Boersma, Karen Helen Wiltshire
Software Mentions: 10
Published: over 4 years ago

10.3390/plants10091921

UHPLC-Orbitrap-MS Tentative Identification of 51 Oleraceins (Cyclo-Dopa Amides) in Portulaca oleracea L. Cluster Analysis and MS2 Filtering by Mass Difference
Cited by: 2
Author(s): Yulian Voynikov, Paraskev Nedialkov, Reneta Gevrenova, Dimitrina Zheleva‐Dimitrova, Vessela Balabanova, Иван Димитров
Software Mentions: 10
Published: about 3 years ago

10.1093/bioinformatics/btv428

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
Cited by: 1,079
Author(s): Tal Galili
Software Mentions: 10
Published: over 9 years ago

10.1038/s41598-020-76881-x

Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis
Cited by: 81
Author(s): Luis A. Corchete, Elizabeta A. Rojas, Diego Alonso-López, Javier De Las Rivas, Norma C. Gutiérrez, F.J. Burguillo
Software Mentions: 10
Published: about 4 years ago

10.1534/g3.120.401534

A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts
Cited by: 3
Author(s): Matthew Chung, Preston J. Basting, Rayanna S. Patkus, Alexandra Grote, Ashley N. Luck, Elodie Ghedin, Barton E. Slatko, Michelle L. Michalski, Jeremy M. Foster, Casey M. Bergman, Julie C. Dunning Hotopp
Software Mentions: 10
Published: about 4 years ago

10.3389/fmicb.2018.01598

Microbiome Composition in Both Wild-Type and Disease Model Mice Is Heavily Influenced by Mouse Facility
Cited by: 60
Author(s): Kristopher D. Parker, Shannon E. Albeke, Jason P. Gigley, Allan M. Goldstein, Naomi Ward
Software Mentions: 10
Published: over 6 years ago

10.1186/s12864-021-07388-6

Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential
Cited by: 3
Author(s): Niels A. Zondervan, Vítor A. P. Martins dos Santos, María Suárez-Diez, Edoardo Saccenti
Software Mentions: 10
Published: almost 4 years ago

10.1038/s41598-021-86272-5

Distributions of Arctic and Northwest Atlantic killer whales inferred from oxygen isotopes
Cited by: 0
Author(s): Cory J. D. Matthews, Fred J. Longstaffe, James S. Lawson, Steven H. Ferguson
Software Mentions: 10
Published: over 3 years ago

10.3390/genes12040503

Genomic and Phenotypic Diversity of Cultivated and Wild Tomatoes with Varying Levels of Heat Tolerance
Cited by: 10
Author(s): Mathieu Anatole Tele Ayenan, Agyemang Danquah, Paterne A. Agre, Peter Hanson, Isaac Asante, Eric Danquah
Software Mentions: 10
Published: over 3 years ago

10.1002/brb3.2174

Co‐activation pattern alterations in autism spectrum disorder–A volume‐wise hierarchical clustering fMRI study
Cited by: 2
Author(s): Jyri‐Johan Paakki, Jukka S. Rahko, Aija Kotila, Marja‐Leena Mattila, Helena Miettunen, Tuula Hurtig, Katja Jussila, Sanna Kuusikko‐Gauffin, Irma Moilanen, Osmo Tervonen, Vesa Kiviniemi
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

10.1002/1878-0261.12595

Aberrant expression of RSK1 characterizes high‐grade gliomas with immune infiltration
Cited by: 14
Author(s): Glaucia Noeli Maroso Hajj, Fernanda F. da Silva, Bárbara de Bellis, Fernanda C. S. Lupinacci, Hermano Martins Bellato, Juvanier R. Cruz, Claudionor Nogueira Costa Segundo, Igor Vilela Faquini, Leuridan Cavalcante Torres, Paulo Sanematsu, María Dirlei Begnami, Vilma R. Martins, Martín Roffé
Software Mentions: 9
Published: almost 5 years ago

10.1038/s41598-021-98542-3

A differential DNA methylome signature of pulmonary immune cells from individuals converting to latent tuberculosis infection
Cited by: 11
Author(s): Lovisa Karlsson, Jyotirmoy Das, Moa Nilsson, Amanda Tyrén, Isabelle Pehrson, Nina Idh, Shumaila Sayyab, Jakob Paues, César Ugarte-Gil, Melissa Méndez-Aranda, Maria Lerm
Software Mentions: 9
Published: about 3 years ago

10.1186/s12864-019-5692-3

Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains
Cited by: 14
Author(s): Marc Lorentzen, Hugo Campbell-Sills, Tue Sparholt Jørgensen, Tue Kjærgaard Nielsen, Monika Coton, Emmanuel Coton, Lars Hansen, Patrick Lucas
Software Mentions: 9
Published: over 5 years ago

10.1172/jci.insight.141683

CD84 is a regulator of the immunosuppressive microenvironment in Multiple Myeloma
Cited by: 15
Author(s): Hadas Lewinsky, Emine Gulsen Gunes, Keren David, Lihi Radomir, Matthias P. Kramer, Bianca Pellegrino, Michal Perpinial, Jing Chen, Ting He, Anthony G. Mansour, Kun yu Teng, Supriyo Bhattacharya, Enrico Caserta, Estelle Troadec, Peter Lee, Mingye Feng, Jonathan J. Keats, Amrita Krishnan, Michael Rosenzweig, Jianhua Yu, Michael A. Caligiuri, Yosef Cohen, Olga Shevetz, Shirly Becker-Herman, Flavia Pichiorri, Steven T. Rosen, Idit Shachar
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12864-021-07995-3

Neurogenomic divergence during speciation by reinforcement of mating behaviors in chorus frogs (Pseudacris)
Cited by: 4
Author(s): Oscar E. Ospina, Alan R. Lemmon, Mysia Dye, Christopher Zdyrski, Sean Holland, Daniel Stribling, Michelle L Kortyna, Emily Moriarty Lemmon
Software Mentions: 9
Published: about 3 years ago

10.3389/fimmu.2019.00413

Transcriptional Profiles of California Sea Lion Peripheral NK and CD+8 T Cells Reflect Ecological Regionalization and Infection by Oncogenic Viruses
Cited by: 4
Author(s): Ignacio Peñín, Mónica Eugenia Figueroa-Cabañas, Fabiola Guerrero-de la Rosa, Luis A. Soto-García, Roberto Álvarez-Martínez, Adriana Flores-Morán, Karina Acevedo‐Whitehouse
Software Mentions: 9
Published: over 5 years ago

10.3389/fmicb.2021.649517

Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST
Cited by: 15
Author(s): Carlus Deneke, Laura Uelze, Holger Brendebach, Simon H. Tausch, Burkhard Malorny
Software Mentions: 9
Published: over 3 years ago

10.3390/microorganisms9091814

Presence of Human Pathogens of the Borrelia burgdorferi sensu lato Complex Shifts the Sequence Read Abundances of Tick Microbiomes in Two German Locations
Cited by: 7
Author(s): Angeline Hoffmann, Thomas Müller, Volker Fingerle, Matthias Noll
Software Mentions: 9
Published: about 3 years ago

10.3390/toxins11100612

Lipophilic Toxins in Galicia (NW Spain) between 2014 and 2017: Incidence on the Main Molluscan Species and Analysis of the Monitoring Efficiency
Cited by: 21
Author(s): Juan Blanco, Fabiola Arévalo, Jorge Correa, Á. Moroño
Software Mentions: 8
Published: about 5 years ago

10.1002/ece3.6390

Can ancestry and morphology be used as surrogates for species niche relationships?
Cited by: 5
Author(s): Friedrich W. Keppeler, Kirk O. Winemiller
Software Mentions: 8
Published: over 4 years ago

10.1002/ece3.4535

Determining social and population structures requires multiple approaches: A case study of the desert antCataglyphis israelensis
Cited by: 3
Author(s): Tali Reiner Brodetzki, Abraham Hefetz
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41598-019-38483-0

Metabotyping as a Stopover in Genome-to-Phenome Mapping
Cited by: 31
Author(s): Pubudu Handakumbura, Bryan Stanfill, Albert Rivas‐Ubach, Dan Fortin, John P. Vogel, Christer Jansson
Software Mentions: 8
Published: almost 6 years ago

10.1186/s40168-019-0716-4

The association between pneumococcal vaccination, ethnicity, and the nasopharyngeal microbiota of children in Fiji
Cited by: 11
Author(s): Laura K. Boelsen, Eileen M. Dunne, Moana Mika, Stefanie Eggers, Cattram Nguyen, Felisita Tupou Ratu, Fiona M. Russell, E. Kim Mulholland, Markus Hilty, Catherine Satzke
Software Mentions: 8
Published: over 5 years ago

10.1016/j.immuni.2019.02.006

Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative Colitis
Cited by: 121
Author(s): Tomas Castro‐Dopico, Thomas W. Dennison, John R. Ferdinand, Rebeccah J. Mathews, Aaron Fleming, Dean Clift, Benjamin J Stewart, Chenzhi Jing, Konstantina Strongili, Larisa I. Labzin, Edward J M Monk, Kourosh Saeb‐Parsy, Clare E. Bryant, Simon Clare, Miles Parkes, Menna R. Clatworthy
Software Mentions: 8
Published: over 5 years ago

10.1186/s13059-019-1747-7

Cell type-specific epigenetic links to schizophrenia risk in the brain
Cited by: 65
Author(s): Isabel Mendizabal, Stefano Berto, Noriyoshi Usui, Kazuya Toriumi, Paramita Chatterjee, Connor Douglas, Iksoo Huh, Hyeonsoo Jeong, Thomas S. Layman, Carol A. Tamminga, Todd M. Preuss, Genevieve Konopka, Soojin V. Yi
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0246491

Trophic structure of a nektobenthic community exploited by a multispecific bottom trawling fishery in Northeastern Brazil
Cited by: 3
Author(s): Alex Souza Lira, Flávia Lucena‐Frédou, Frédéric Ménard, Thierry Frédou, Júlio Guazzelli Gonzalez, Valdimere Ferreira, José Souto Rosa Filho, Jean-Marie Munaron, François Le Loc’h
Software Mentions: 8
Published: almost 4 years ago

10.3390/cancers12113089

CT-Based Radiomics Analysis to Predict Malignancy in Patients with Intraductal Papillary Mucinous Neoplasm (IPMN) of the Pancreas
Cited by: 28
Author(s): David Tobaly, João Santinha, Riccardo Sartoris, Marco Dioguardi Burgio, Celso Matos, Jérôme Cros, Anne Couvelard, Vinciane Rebours, Alain Sauvanet, Maxime Ronot, Nikolaos Papanikolaou, Valérie Vilgrain
Software Mentions: 8
Published: about 4 years ago

10.3389/fmicb.2019.02359

Annual Protist Community Dynamics in a Freshwater Ecosystem Undergoing Contrasted Climatic Conditions: The Saint-Charles River (Canada)
Cited by: 21
Author(s): Perrine Cruaud, Adrien Vigneron, Marie‐Stéphanie Fradette, Caetano C. Dorea, Alexander I. Culley, Manuel J. Rodriguez, Steve J. Charette
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2017.02351

An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes
Cited by: 54
Author(s): Clémentine Henri, Pimlapas Leekitcharoenphon, Heather Carleton, Nicolas Radomski, Rolf Sommer Kaas, Jean-François Mariet, Arnaud Felten, Frank Møller Aarestrup, Peter Gerner Smidt, Sophie Roussel, Laurent Guillier, Michel‐Yves Mistou, René S. Hendriksen
Software Mentions: 7
Published: almost 7 years ago

10.1242/dmm.049068

A mechanism linking perinatal 2,3,7,8 tetrachlorodibenzo-p-dioxin exposure to lower urinary tract dysfunction in adulthood
Cited by: 4
Author(s): Anne E. Turco, S. G. Oakes, Kimberly P. Keil Stietz, Cheryl L. Dunham, Diya B. Joseph, Thrishna S Chathurvedula, Nicholas M Girardi, Andrew J. Schneider, Joseph Gawdzik, Celeste M Sheftel, Peiqing Wang, Zunyi Wang, Dale E. Bjorling, William A. Ricke, Weiping Tang, Laura Hernández, Janet R. Keast, Adrian D. Bonev, Matthew D Grimes, Douglas W. Strand, Nathan R. Tykocki, Robyn L Tanguay, Richard E. Peterson, Chad M. Vezina
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2018.02520

Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms
Cited by: 63
Author(s): Claire Bertelli, Sophie Courtois, Marta Rosikiewicz, P. Piriou, Sébastien Aeby, Robert Salais, Jean-François Loret, Gilbert Greub
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0209231

Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents
Cited by: 11
Author(s): Christopher Cheleuitte-Nieves, Christopher A. Gulvik, John R. McQuiston, Ben W. Humrighouse, Melissa Bell, Aaron Villarma, Vincent A. Fischetti, Lars F. Westblade, Neil S Lipman
Software Mentions: 7
Published: almost 6 years ago

10.3390/plants10050998

Sources of Resistance to Common Bacterial Blight and Charcoal Rot Disease for the Production of Mesoamerican Common Beans in the Southern United States
Cited by: 5
Author(s): Daniel Ambachew, Jacqueline Joshua, Margaret T. Mmbaga, Matthew W. Blair
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pbio.3000792

Heritable gene expression variability and stochasticity govern clonal heterogeneity in circadian period
Cited by: 12
Author(s): K. L. Nikhil, Sandra Korge, Achim Kramer
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pbio.3001390

Identifying and prioritizing potential human-infecting viruses from their genome sequences
Cited by: 43
Author(s): Nardus Mollentze, Simon A. Babayan, Daniel G. Streicker
Software Mentions: 7
Published: about 3 years ago

10.1186/s13195-020-00709-z

TREM2 Alzheimer’s variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages
Cited by: 25
Author(s): Hazel Hall‐Roberts, Devika Agarwal, Juliane Obst, Thomas B. Smith, Jimena Monzón‐Sandoval, Elena Di Daniel, Caleb Webber, William James, Emma Mead, John B. Davis, Sally A. Cowley
Software Mentions: 7
Published: about 4 years ago

10.3390/nu12051288

Cluster Analysis of Physical Activity Patterns, and Relationship with Sedentary Behavior and Healthy Lifestyles in Prepubertal Children: Genobox Cohort
Cited by: 20
Author(s): Rosaura Leis, José Manuel Jurado-Castro, Francisco Jesús Llorente-Cantarero, Augusto Anguita‐Ruiz, Azahara Iris-Rupérez, Juan José Bedoya-Carpente, Rocío Vázquez-Cobela, Concepción M. Aguilera, Gloria Bueno, Mercedes Gil-Campos
Software Mentions: 7
Published: over 4 years ago

10.7717/peerj.5319

Comparative chemical analysis of army ant mandibular gland volatiles (Formicidae: Dorylinae)
Cited by: 11
Author(s): Adrian Brückner, Philipp O. Hoenle, Christoph von Beeren
Software Mentions: 7
Published: over 6 years ago

10.1111/1462-2920.15314

Metagenomic assessment of the global diversity and distribution of bacteria and fungi
Cited by: 39
Author(s): Mohammad Bahram, Tarquin Netherway, Clémence Frioux, Pamela Ferretti, Luís Pedro Coelho, Stefan Geisen, Peer Bork, Falk Hildebrand
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12862-020-01708-2

The evolution of fruit scent: phylogenetic and developmental constraints
Cited by: 13
Author(s): Omer Nevo, Kim Valenta, Annemarie Kleiner, Diary Razafimandimby, Juan Antonio James Jeffrey, Colin A. Chapman, Manfred Ayasse
Software Mentions: 7
Published: about 4 years ago

10.7717/peerj.3051

Taxonomic and functional trait diversity of wild bees in different urban settings
Cited by: 97
Author(s): Étienne Normandin, Nicolas J. Vereecken, Christopher M. Buddle, Valérie Fournier
Software Mentions: 6
Published: over 7 years ago

10.34133/2020/1925495

Soybean Root System Architecture Trait Study through Genotypic, Phenotypic, and Shape-Based Clusters
Cited by: 30
Author(s): Kevin G. Falk, Talukder Z. Jubery, Jamie A. O’Rourke, Arti Singh, Soumik Sarkar, Baskar Ganapathysubramanian
Software Mentions: 6
Published: almost 5 years ago

10.3390/plants8120559

Identification of Stem Rust Resistance Genes in the Winter Wheat Collection from Southern Russia
Cited by: 5
Author(s): А. В. Алабушев, Н. Н. Вожжова, N. T. Kupreyshvili, Н. В. Шишкин, Д. М. Марченко, Е. В. Ионова
Software Mentions: 6
Published: almost 5 years ago

10.1136/bmj.m3249

Clinical characteristics of children and young people admitted to hospital with covid-19 in United Kingdom: prospective multicentre observational cohort study
Cited by: 445
Author(s): Olivia Swann, Karl Holden, Lance Turtle, Louisa Pollock, Cameron J Fairfield, Thomas M Drake, Sohan Seth, Conor Egan, Hayley Hardwick, Sophie Halpin, Michelle Girvan, Chloe Donohue, Mark G Pritchard, Latifa Patel, Shamez Ladhani, Louise Sigfrid, Ian Sinha, Piero Olliaro, Jonathan S Nguyen‐Van‐Tam, Peter Horby, Laura Merson, Gail Carson, Jake Dunning, Peter Openshaw, J Kenneth Baillie, Ewen M Harrison, Annemarie B Docherty, Malcolm G Semple
Software Mentions: 6
Published: about 4 years ago

10.1186/s12903-021-01832-5

The effects of removing dead bacteria by propidium monoazide on the profile of salivary microbiome
Cited by: 5
Author(s): Qidi Ren, Fangqiao Wei, Chao Yuan, Ce Zhu, Qian Zhang, Junkang Quan, Xiangyu Sun, Shuguo Zheng
Software Mentions: 6
Published: about 3 years ago

10.3390/plants9111446

The Genetic Diversity of Cranberry Crop Wild Relatives, Vaccinium macrocarpon Aiton and V. oxycoccos L., in the US, with Special Emphasis on National Forests
Cited by: 12
Author(s): Lorraine Rodríguez-Bonilla, Karen A. Williams, Fabian Rodríguez Bonilla, Daniel Matusinec, Andrew J. Maule, Kevin Coe, Eric Wiesman, Luis Díaz-Garcia, Juan Zalapa
Software Mentions: 6
Published: about 4 years ago

10.3389/fmicb.2020.01405

Denosumab Regulates Gut Microbiota Composition and Cytokines in Dinitrobenzene Sulfonic Acid (DNBS)-Experimental Colitis
Cited by: 7
Author(s): Azin Khafipour, Nour Eissa, Peris M. Munyaka, Mohammad Fazle Rabbi, Kunal Kapoor, Laëtitia Kermarrec, Ehsan Khafipour, Çharles N. Bernstein, Jean–Eric Ghia
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0204542

NOJAH: NOt Just Another Heatmap for genome-wide cluster analysis
Cited by: 9
Author(s): Manali Rupji, Bhakti Dwivedi, Jeanne Kowalski
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2018.01888

Infection-Induced Changes Within the Endocytic Recycling Compartment Suggest a Roadmap of Human Cytomegalovirus Egress
Cited by: 16
Author(s): William L. Close, James Glassbrook, Stephen J. Gurczynski, Philip E. Pellett
Software Mentions: 6
Published: over 6 years ago

10.3390/cancers12061461

PDX1 DNA Methylation Distinguishes Two Subtypes of Pancreatic Neuroendocrine Neoplasms with a Different Prognosis
Cited by: 19
Author(s): Gitta Boons, Timon Vandamme, Joe Ibrahim, Geert Roeyen, Ann Driessen, Dieter Peeters, Ben Lawrence, Cristin G. Print, Maria C. W. Peeters, Guy Van Camp, Ken Op de Beeck
Software Mentions: 6
Published: over 4 years ago

10.3390/cancers12113380

Cancer-Associated Angiogenesis: The Endothelial Cell as a Checkpoint for Immunological Patrolling
Cited by: 69
Author(s): Antonio Giovanni Solimando, Simona De Summa, Angelo Vacca, Doménico Ribatti
Software Mentions: 6
Published: about 4 years ago

10.3390/jpm10040210

Association of UBE3C Variants with Reduced Kidney Function in Patients with Diabetic Kidney Disease
Cited by: 3
Author(s): Ying Chun Chen, Mei Yi Wu, Zhi Yu, Wan Hsuan Chou, Yi Ting Lai, Chih-Chin Kao, Imaniar Noor Faridah, Mai Szu Wu, Wei Chiao Chang
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-021-84407-2

Premating barriers in young sympatric snail species
Cited by: 6
Author(s): Arina L. Maltseva, Marina A. Varfolomeeva, Arseniy Lobov, Polina Tikanova, Egor A. Repkin, Irina Y. Babkina, Marina Panova, Natalia A. Mikhailova, Andrei I. Granovitch
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-016-3228-7

RNA-seq based transcriptomic map reveals new insights into mouse salivary gland development and maturation
Cited by: 30
Author(s): Christian Gluck, Sang‐Won Min, Akinsola Oyelakin, Kirsten Smalley, Satrajit Sinha, Rose‐Anne Romano
Software Mentions: 5
Published: about 8 years ago

10.1186/s12864-019-5887-7

Refinement of breast cancer molecular classification by miRNA expression profiles
Cited by: 59
Author(s): Rolf Søkilde, Helena Persson, Anna Ehinger, Anna Chiara Pirona, Mårten Fernö, Cecilia Hegardt, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Lao H. Saal, Åke Borg, Johan Vallon-Christerson, Carlos Rovira
Software Mentions: 5
Published: over 5 years ago

10.1186/s12889-021-11760-2

Brazilian Longitudinal Study of Adult Health (ELSA-Brasil) participant’s profile regarding self-rated health: a multiple correspondence analysis
Cited by: 6
Author(s): Thaís Lopes de Oliveira, Raquel Vasconcellos Carvalhaes de Oliveira, Rosane Härter Griep, Arlinda B. Moreno, Maria da Conceição Chagas de Almeida, Ylva B. Almquist, Maria de Jesus Mendes da Fonseca
Software Mentions: 5
Published: about 3 years ago

10.1186/s40168-018-0586-1

Association of bovine major histocompatibility complex (BoLA) gene polymorphism with colostrum and milk microbiota of dairy cows during the first week of lactation
Cited by: 34
Author(s): Hooman Derakhshani, J.C. Plaizier, Jeroen De Buck, Herman W. Barkema, Ehsan Khafipour
Software Mentions: 5
Published: about 6 years ago

10.3390/v11080694

Prediction of the Spatial Origin of Puumala Virus Infections Using L Segment Sequences Derived from a Generic Screening PCR
Cited by: 6
Author(s): Sabrina Weiß, Boris Klempa, Beate Tenner, Detlev H. Krüger, Jörg Hofmann
Software Mentions: 5
Published: over 5 years ago

10.3390/v12121424

NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index
Cited by: 3
Author(s): Joan Martí-Carreras, Alejandro Rafael Gener, Sierra Miller, Anderson F. Brito, Christiam Camacho, Ryan Connor, Ward Deboutte, Cody Glickman, David M. Kristensen, Wynn K. Meyer, Sejal Modha, Alexis L. Norris, Surya Saha, Anna K. Belford, Evan Biederstedt, J. Rodney Brister, Jan P. Buchmann, Nicholas P. Cooley, Robert A. Edwards, Kiran Javkar, Michael Muchow, Harihara Subrahmaniam Muralidharan, Charles Pepe-Ranney, Nidhi Shah, Migun Shakya, Michael J. Tisza, Benjamin J. Tully, Bert Vanmechelen, Valerie Christine Virta, Jake L. Weissman, Vadim Zalunin, Alexandre Efremov, Ben Busby
Software Mentions: 5
Published: almost 4 years ago

10.7717/peerj.8546

Proteomic similarity of the Littorinid snails in the evolutionary context
Cited by: 13
Author(s): Arina L. Maltseva, Marina A. Varfolomeeva, Arseniy Lobov, Polina Tikanova, Marina Panova, Natalia Mikhailova, Andrei I. Granovitch
Software Mentions: 5
Published: almost 5 years ago

10.3390/ph14020087

Identification of 37 Heterogeneous Drug Candidates for Treatment of COVID-19 via a Rational Transcriptomics-Based Drug Repurposing Approach
Cited by: 4
Author(s): Andrea Gelemanović, Tinka Vidović, Višnja Stepanić, Katarina Trajković
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0212365

Mycobacteriophage CRB2 defines a new subcluster in mycobacteriophage classification
Cited by: 4
Author(s): Cristian Alejandro Suárez, Jorgelina Judith Franceschelli, Héctor Ricardo Morbidoni
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers13030365

Genome-Wide Circular RNA Expression Patterns Reflect Resistance to Immunomodulatory Drugs in Multiple Myeloma Cells
Cited by: 18
Author(s): Theresa Jakobsen, Mette Dahl, Konstantinos Dimopoulos, Kirsten Grønbæk, Jørgen Kjems, Lasse Sommer Kristensen
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.celrep.2019.04.098

The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer
Cited by: 85
Author(s): Leticia De Mattos-Arruda, Stephen‐John Sammut, Edith Ross, Rachael Bashford-Rogers, Erez Greenstein, Havell Markus, Sandro Morganella, Yvonne H. F. Teng, Yosef E. Maruvka, Bernard Pereira, Oscar M. Rueda, Suet-Feung Chin, Tania Contente-Cuomo, Regina Mayor, Alexandra Arias, H. Raza Ali, Wei Cope, Daniel Guimarães Tiezzi, Aliakbar Dariush, Tauanne Dias Amarante, Dan Reshef, Nikaoly Ciriaco, Elena Martinez-Saez, Vicente Peg, Santiago Ramón y Cajal, Javier Cortés, George S. Vassiliou, Gad Getz, Serena Nik-Zainal, Muhammed Murtaza, Nir Friedman, Florian Markowetz, Joan Seoane, Carlos Caldas
Software Mentions: 5
Published: over 5 years ago

10.3389/fbioe.2020.604838

Response of Microbial Community to Induced Failure of Anaerobic Digesters Through Overloading With Propionic Acid Followed by Process Recovery
Cited by: 15
Author(s): Azin Khafipour, Elsie M. Jordaan, Daniel Flores-Orozco, Ehsan Khafipour, David B. Levin, Richard Sparling
Software Mentions: 5
Published: almost 4 years ago

10.3389/fmicb.2019.02944

Evidence for Co-evolutionary History of Early Diverging Lycopodiaceae Plants With Fungi
Cited by: 12
Author(s): Gian Maria Niccolò Benucci, Delaney Burnard, Lara D. Shepherd, Gregory Bonito, Andrew B. Munkacsi
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2016.02143

Linking Peripartal Dynamics of Ruminal Microbiota to Dietary Changes and Production Parameters
Cited by: 37
Author(s): Hooman Derakhshani, Hein Min Tun, F.C. Cardoso, J.C. Plaizier, Ehsan Khafipour, Juan J. Loor
Software Mentions: 5
Published: almost 8 years ago

10.3390/genes12020292

Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea)
Cited by: 5
Author(s): Francesco Zapelloni, José A. Jurado‐Rivera, Damià Jaume, Carlos Juan, Joan Pons
Software Mentions: 5
Published: almost 4 years ago

10.1093/gbe/evaa062

The Origin and Composition of Korean Ethnicity Analyzed by Ancient and Present-Day Genome Sequences
Cited by: 16
Author(s): Jung-Eun Kim, Sungwon Jeon, Jae-Pil Choi, Asta Blažytė, Yeonsu Jeon, Jong‐Il Kim, Jun Ohashi, Katsushi Tokunaga, Sumio Sugano, Suthat Fucharoen, Fahd Al-Mulla, Jong Bhak
Software Mentions: 5
Published: over 4 years ago

10.1038/s41438-021-00465-7

Genetic characterization of an almond germplasm collection and volatilome profiling of raw and roasted kernels
Cited by: 10
Author(s): Mario Di Guardo, Brian Farneti, Iuliia Khomenko, Giulia Modica, A. Mosca, Gaetano Distefano, Luca Bianco, Michela Troggio, Francesco Sottile, Stefano La Malfa, Franco Biasioli, Alessandra Gentile
Software Mentions: 5
Published: almost 4 years ago

Projects: cran: dendextend

Papers Mentioning dendextend 201