Ecosyste.ms: Papers

10.3389/fmicb.2018.01474

Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current
Cited by: 24
Author(s): Flavia Flaviani, Declan C. Schroeder, Karen Lebret, Cecilia Balestreri, Andrea Highfield, Joanna L. Schroeder, Sally Thorpe, Karen Moore, Konrad Pasckiewicz, Maya C. Pfaff, Edward P. Rybicki
Software Mentions: 27
Published: over 6 years ago

10.1186/1751-0473-8-1

MmPalateMiRNA, an R package compendium illustrating analysis of miRNA microarray data
Cited by: 11
Author(s): Guy Brock, Partha Mukhopadhyay, Vasyl Pihur, Cynthia L. Webb, Robert M. Greene, M. Michele Pisano
Software Mentions: 24
Published: almost 12 years ago

10.1038/s41421-020-00226-1

Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo
Cited by: 68
Author(s): Hang‐Ping Yao, Xiangyun Lu, Qiong Chen, Kaijin Xu, Yu Chen, Ming-Hui Cheng, Keda Chen, Linfang Cheng, Tian-Hao Weng, Danrong Shi, Fumin Liu, Zhigang Wu, Mingjie Xie, Haibo Wu, Changzhong Jin, Min Zheng, Nanping Wu, Chao Jiang, Lanjuan Li
Software Mentions: 21
Published: about 4 years ago

10.3389/fgene.2021.667936

Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During Infections
Cited by: 9
Author(s): Matineh Rahmatbakhsh, Alla Gagarinova, Mohan Babu
Software Mentions: 21
Published: over 3 years ago

10.1186/s13104-019-4179-2

TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data
Cited by: 75
Author(s): Wei Su, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 20
Published: almost 6 years ago

10.1186/1756-0500-3-277

EMA - A R package for Easy Microarray data analysis
Cited by: 45
Author(s): Nicolas Servant, Eléonore Gravier, Pierre Gestraud, Cécile Laurent, Caroline Paccard, Anne Biton, Isabel Martínez Brito, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupé
Software Mentions: 20
Published: about 14 years ago

10.1371/journal.pntd.0005121

Seasonal and Spatial Environmental Influence on Opisthorchis viverrini Intermediate Hosts, Abundance, and Distribution: Insights on Transmission Dynamics and Sustainable Control
Cited by: 20
Author(s): Christina Sunyoung Kim, Pierre Echaubard, Apiporn Suwannatrai, Sasithorn Kaewkes, Bruce A. Wilcox, Banchob Sripa
Software Mentions: 19
Published: about 8 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

10.1093/gigascience/giz028

Rice Galaxy: an open resource for plant science
Cited by: 13
Author(s): Venice Margarette Juanillas, Alexis Dereeper, Nicolas Beaume, Gaëtan Droc, Joshua Gregor A. Dizon, J. Mendoza, Jon Peter Perdon, Locedie Mansueto, Lindsay R. Triplett, Jillian M. Lang, Gabriel Zhou, Kunalan Ratharanjan, Beth Plale, Jason Haga, Jan E. Leach, Manuel Ruiz, Michael J. Thomson, Nickolai Alexandrov, Pierre Larmande, Tobias Kretzschmar, Ramil Mauleon
Software Mentions: 18
Published: over 5 years ago

10.1371/journal.pone.0151935

Novel and Lost Forests in the Upper Midwestern United States, from New Estimates of Settlement-Era Composition, Stem Density, and Biomass
Cited by: 48
Author(s): Simon Goring, David J. Mladenoff, Charles V. Cogbill, Sydne Record, Christopher J. Paciorek, Stephen T. Jackson, Michael C. Dietze, Andria Dawson, Jaclyn Hatala Matthes, J. S. McLachlan, John W. Williams
Software Mentions: 17
Published: about 8 years ago

10.1371/journal.pcbi.1003531

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
Cited by: 2,083
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 17
Published: over 10 years ago

10.1038/s41598-020-71344-9

Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State
Cited by: 9
Author(s): Laura M. Carroll, Jana S. Huisman
Software Mentions: 17
Published: over 4 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

10.1038/s41598-017-11514-4

Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles
Cited by: 121
Author(s): Lindsay A. Parnell, Catherine Briggs, Bin Cao, Omar Delannoy-Bruno, Andrew E. Schrieffer, Indira U. Mysorekar
Software Mentions: 16
Published: over 7 years ago

10.1371/journal.pone.0183417

Association of gene expression with biomass content and composition in sugarcane
Cited by: 23
Author(s): Nam V. Hoang, Agnelo Furtado, Angela O'Keeffe, Frederik C. Botha, Robert J. Henry
Software Mentions: 15
Published: over 7 years ago

10.2196/24889

A Novel Machine Learning Framework for Comparison of Viral COVID-19–Related Sina Weibo and Twitter Posts: Workflow Development and Content Analysis
Cited by: 7
Author(s): Shi Chen, Lina Zhou, Yunya Song, Qian Xu, Ping Wang, Kanlun Wang, Yaorong Ge, Daniel Janies
Software Mentions: 15
Published: almost 4 years ago

10.12688/f1000research.11622.3

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
Cited by: 205
Author(s): Małgorzata Nowicka, Carsten Krieg, Helena L. Crowell, Lukas M. Weber, Felix J. Hartmann, Silvia Guglietta, Burkhard Becher, Mitchell P. Levesque, Mark D. Robinson
Software Mentions: 15
Published: over 5 years ago

10.1038/s41396-020-00798-6

Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations
Cited by: 48
Author(s): Kali M. Pruss, Ángela Marcobal, Audrey Southwick, Dylan Dahan, Sam Smits, Jessica A. Ferreyra, Steven K. Higginbottom, Erica D. Sonnenburg, Purna C. Kashyap, Biswa Choudhury, Lars Bode, Justin L. Sonnenburg
Software Mentions: 14
Published: about 4 years ago

10.1007/s00401-021-02343-x

Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy body diseases
Cited by: 23
Author(s): Rahel Feleke, Regina H. Reynolds, Amy M. Smith, Bension S. Tilley, Sarah A. Gagliano Taliun, John Hardy, Paul M. Matthews, Steve Gentleman, David R. Owen, Michael R. Johnson, Prashant K. Srivastava, Mina Ryten
Software Mentions: 14
Published: over 3 years ago

10.1523/ENEURO.0328-20.2020

Group II Metabotropic Glutamate Receptors Modulate Sound Evoked and Spontaneous Activity in the Mouse Inferior Colliculus
Cited by: 1
Author(s): Inga Kristaponyte, Nichole L. Beebe, Jesse W. Young, Sharad J. Shanbhag, Brett R. Schofield, Alexander V. Galazyuk
Software Mentions: 14
Published: about 4 years ago

10.1007/s43032-020-00438-6

Changes in the Vaginal Microbiome during the Pregnancy to Postpartum Transition
Cited by: 24
Author(s): Kenetta L. Nunn, Steven S. Witkin, Gudrun Schneider, Allison Boester, Dimitrios Nasioudis, Evelyn Minis, Karol Gliniewicz, Larry J. Forney
Software Mentions: 14
Published: almost 4 years ago

10.3390/ijerph18179227

Multivariate Analysis of Risk Factors of the COVID-19 Pandemic in the Community of Madrid, Spain
Cited by: 2
Author(s): Víctor Pérez-Segura, Raquel Caro Carretero, António Rua
Software Mentions: 14
Published: over 3 years ago

10.1371/journal.pone.0243467

Predicting self-harm within six months after initial presentation to youth mental health services: A machine learning study
Cited by: 16
Author(s): Frank Iorfino, Nicholas Ho, Joanne S. Carpenter, Shane Cross, Tracey A Davenport, Daniel F. Hermens, Hannah Yee, Alissa Nichles, Natalia Zmicerevska, Adam J. Guastella, Elizabeth Scott, Ian B. Hickie
Software Mentions: 14
Published: almost 4 years ago

10.3389/fgene.2021.723360

Species and Phenotypic Distribution Models Reveal Population Differentiation in Ethiopian Indigenous Chickens
Cited by: 7
Author(s): Fasil Getachew Kebede, Hans Komen, Tadelle Dessie, Setegn Worku Alemu, Olivier Hanotte, J.W.M. Bastiaansen
Software Mentions: 14
Published: over 3 years ago

10.1186/s13073-020-00823-5

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients
Cited by: 169
Author(s): Anna C. Aschenbrenner, Maria Mouktaroudi, Benjamin Krämer, Marie Oestreich, Nikolaos Antonakos, Melanie Nuesch-Germano, Konstantina Gkizeli, Lorenzo Bonaguro, Nico Reusch, Kevin Baßler, Maria Saridaki, Rainer Knoll, Tal Pecht, Theodore S. Kapellos, Sarandia Doulou, Charlotte Kröger, Miriam Herbert, Lisa Holsten, Arik Horne, Ioanna Gemünd, Nikoletta Rovina, Shobhit Agrawal, K. Dahm, Martina van Uelft, Anna Drews, Lena Lenkeit, Niklas Bruse, Jelle Gerretsen, Jannik Gierlich, Matthias Becker, Kristian Händler, Michael Kraut, Heidi Theis, Simachew Abebe Mengiste, Elena De Domenico, Jonas Schulte-Schrepping, Lea Seep, Jan Raabe, Christoph Hoffmeister, Michael ToVinh, Verena Keitel, Gereon J Rieke, Valentina Talevi, Dirk Skowasch, N. Ahmad Aziz, Peter Pickkers, Frank L. van de Veerdonk, Mihai G. Netea, Joachim L. Schultze, Matthijs Kox, Monique M.B. Breteler, Jacob Nattermann, Antonia Koutsoukou, Evangelos J. Giamarellos‐Bourboulis, Thomas Ulas
Software Mentions: 13
Published: almost 4 years ago

10.1128/AEM.01096-17

Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data
Cited by: 58
Author(s): Laura M. Carroll, Jasna Kovač, Robert W. Miller, Martin Wiedmann
Software Mentions: 13
Published: over 7 years ago

10.7717/peerj.1668

Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution
Cited by: 26
Author(s): Tsung Fei Khang, Oi Yoon Michelle Soo, Wooi Boon Tan, L. H. S. Lim
Software Mentions: 13
Published: almost 9 years ago

10.1007/s00248-020-01635-1

Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral Composition
Cited by: 12
Author(s): Irina Tanuwidjaja, Cordula Vogel, Geertje Johanna Pronk, Anne Schöler, Susanne Kublik, Gisle Vestergaard, Ingrid Kögel‐Knabner, Mirna Mrkonjić Fuka, Michael Schloter, Stefanie Schulz
Software Mentions: 13
Published: about 4 years ago

10.3390/ijms21134674

The Inflammasome Adaptor Protein ASC in Mild Cognitive Impairment and Alzheimer’s Disease
Cited by: 37
Author(s): Xavier O. Scott, Marisa E. Stephens, Marie C. Desir, W. Dalton Dietrich, Robert W. Keane, Juan Pablo de Rivero Vaccari
Software Mentions: 13
Published: over 4 years ago

10.1038/s41598-019-49160-7

Early life determinants induce sustainable changes in the gut microbiome of six-year-old children
Cited by: 27
Author(s): Silvia Gschwendtner, Hani Kang, Elisabeth Thiering, Susanne Kublik, Bärbel U. Foesel, Holger Schulz, Susanne Krauss‐Etschmann, Joachim Heinrich, Anne Schöler, Michael Schloter, Marie Standl
Software Mentions: 13
Published: over 5 years ago

10.1038/srep26451

Glycosyltransferase Gene Expression Profiles Classify Cancer Types and Propose Prognostic Subtypes
Cited by: 52
Author(s): Jahanshah Ashkani, Kevin J. Naidoo
Software Mentions: 12
Published: over 8 years ago

10.1084/jem.20160553

Egr2 and 3 control adaptive immune responses by temporally uncoupling expansion from T cell differentiation
Cited by: 46
Author(s): Tizong Miao, Alistair L. J. Symonds, Randeep Singh, Janine D. Symonds, Ane Ogbe, Becky Omodho, Bo Zhu, Suling Li, Ping Wang
Software Mentions: 12
Published: over 7 years ago

10.1200/PO.20.00158

Breakthrough Cancer Pain Clinical Features and Differential Opioids Response: A Machine Learning Approach in Patients With Cancer From the IOPS-MS Study
Cited by: 9
Author(s): Francesco Pantano, Tea Zeppola, Angelo Onorato, Michele Iuliani, Sonia Simonetti, Bruno Vincenzi, Daniele Santini, Sebastiano Mercadante, Paolo Marchetti, Arturo Cuomo, Augusto Caraceni, Rocco Domenico Mediati, Renato Vellucci, Massimo Mammucari, Silvia Natoli, Marzia Lazzari, Mario Dauri, Claudio Adile, Mario Airoldi, Giuseppe Azzarello, Livio Blasi, Bruno Chiurazzi, Daniela Degiovanni, Flavio Fusco, Vittorio Guardamagna, Simeone Liguori, Liana Palermo, Sergio Mameli, Francesco Masedu, Teresita Mazzei, Rita Maria Melotti, Valentino Menardo, Danilo Miotti, S. Moroso, Gaetano Pascoletti, Stefano De Santis, Remo Orsetti, Alfonso Papa, Sergio Ricci, E. Scelzi, Michele Sofia, Federica Aielli, Alessandro Valle, Giuseppe Tonini
Software Mentions: 12
Published: about 4 years ago

10.1038/s41396-018-0251-5

Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals
Cited by: 56
Author(s): Amanda C. Perofsky, Rebecca J. Lewis, Lauren Ancel Meyers
Software Mentions: 12
Published: over 6 years ago

10.1038/s41598-019-44765-4

Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression
Cited by: 35
Author(s): Ingrid Tarr, Emma McCann, Beben Benyamin, Timothy J. Peters, Natalie A. Twine, Katharine Y. Zhang, Qiongyi Zhao, Zong Hong Zhang, Dominic B. Rowe, Garth A. Nicholson, Denis C. Bauer, Susan J. Clark, Ian P. Blair, Kelly L. Williams
Software Mentions: 11
Published: over 5 years ago

10.1186/1471-2164-9-419

Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: Comparison of rat and mouse
Cited by: 74
Author(s): Paul C. Boutros, Rui Yan, Ivy D. Moffat, Raimo Pohjanvirta, Allan B. Okey
Software Mentions: 11
Published: almost 17 years ago

10.3389/fpls.2020.599228

Hormopriming to Mitigate Abiotic Stress Effects: A Case Study of N9-Substituted Cytokinin Derivatives With a Fluorinated Carbohydrate Moiety
Cited by: 17
Author(s): Magdaléna Bryksová, Andrea Hybenová, Alba E. Hernándiz, Ondřej Novák, Aleš Pěnčík, Lukáš Spíchal, Nuria De Diego, Karel Doležal
Software Mentions: 11
Published: about 4 years ago

10.1186/s12575-018-0067-8

Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results
Cited by: 23
Author(s): Shitao Zhao, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 10
Published: almost 7 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

10.1038/s41598-020-74909-w

Multi-strain volatile profiling of pathogenic and commensal cutaneous bacteria
Cited by: 19
Author(s): Shane Fitzgerald, Emer Duffy, Linda Holland, Aoife Morrin
Software Mentions: 10
Published: about 4 years ago

10.3389/fpls.2020.587426

Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces
Cited by: 13
Author(s): Victor Allan, Mani Vetriventhan, R. Senthil, S. Geetha, Santosh Deshpande, Abhishek Rathore, Vinod Kumar, Prabhat Kumar Singh, Surender Reddymalla, V. C. R. Azevedo
Software Mentions: 10
Published: about 4 years ago

10.3390/nu13061766

Multidimensional Approach to Assess Nutrition and Lifestyle in Breastfeeding Women during the First Month of Lactation
Cited by: 9
Author(s): Andrea Gila-Díaz, Nuria Díaz-Rullo Alcántara, Gloria Herranz Carrillo, Pratibha Singh, Silvia M. Arribas, David Ramiro-Cortijo
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pone.0127816

HIV-1 Coreceptor Usage Assessment by Ultra-Deep Pyrosequencing and Response to Maraviroc
Cited by: 3
Author(s): Christophe Rodriguez, Cathia Soulié, Anne–Geneviève Marcelin, Vincent Cálvez, Diane Descamps, Charlotte Charpentier, Philippe Flandre, Patrícia Recordon-Pinson, Pantxika Bellecave, Jean‐Michel Pawlotsky, Bernard Masquelier
Software Mentions: 10
Published: over 9 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: over 3 years ago

10.1186/s12864-021-07742-8

Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa
Cited by: 5
Author(s): Heidi Kaech, Alice B. Dennis, Christoph Vorburger
Software Mentions: 10
Published: over 3 years ago

10.3389/fonc.2020.526577

Patient Stratification of Clear Cell Renal Cell Carcinoma Using the Global Transcription Factor Activity Landscape Derived From RNA-Seq Data
Cited by: 7
Author(s): Yanyan Zhu, Shundong Cang, Bowang Chen, Ye Gu, Miaomiao Jiang, Junya Yan, Fengmin Shao, Xiaoyun Huang
Software Mentions: 10
Published: about 4 years ago

10.3390/ijerph18168271

Cluster Analysis of Urban Acoustic Environments on Barcelona Sensor Network Data
Cited by: 10
Author(s): Antonio Pita, Francisco Javier Iglesias Rodríguez, Juan M. Navarro
Software Mentions: 10
Published: over 3 years ago

10.1186/s11689-021-09360-7

Modeling familial predictors of proband outcomes in neurogenetic disorders: initial application in XYY syndrome
Cited by: 3
Author(s): Kathleen Wilson, Ari M. Fish, Catherine Mankiw, Anastasia Xenophontos, Allysa Warling, Ethan T. Whitman, Liv S. Clasen, Erin Torres, Jonathan D. Blumenthal, Armin Raznahan
Software Mentions: 10
Published: almost 4 years ago

10.1186/1472-6785-10-12

The world's richest tadpole communities show functional redundancy and low functional diversity: ecological data on Madagascar's stream-dwelling amphibian larvae
Cited by: 54
Author(s): Axel Strauß, Erik Reeve, Roger-Daniel Randrianiaina, Miguel Vences, Julian Glos
Software Mentions: 10
Published: almost 15 years ago

10.1371/journal.pone.0185171

Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes
Cited by: 29
Author(s): Tuulia Mali, Jaana Kuuskeri, Firoz Shah, Taina Lundell
Software Mentions: 10
Published: about 7 years ago

10.1186/1471-2105-11-503

Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering
Cited by: 54
Author(s): Eva Freyhult, Mattias Landfors, Jenny Önskog, Torgeir R. Hvidsten, Patrik Rydén
Software Mentions: 9
Published: about 14 years ago

10.1186/s42523-021-00118-z

Microbial composition differs between production systems and is associated with growth performance and carcass quality in pigs
Cited by: 5
Author(s): Christian Maltecca, Robert R. Dunn, Yuqing He, Nathan P. McNulty, Constantino Schillebeeckx, Charles V. Schwab, Caleb M Shull, Justin Fix, Francesco Tiezzi
Software Mentions: 9
Published: over 3 years ago

10.1186/s12859-020-3463-4

ORdensity: user-friendly R package to identify differentially expressed genes
Cited by: 0
Author(s): José María Martínez-Otzeta, Itziar Irigoien, Basilio Sierra, C. Arenas
Software Mentions: 9
Published: over 4 years ago

10.3390/insects12070646

Are There Personality Differences between Rural vs. Urban-Living Individuals of a Specialist Ground Beetle, Carabus convexus?
Cited by: 10
Author(s): Tibor Magura, Szabolcs Mizser, Roland Horváth, D Nagy, Mária Tóth, Réka Csicsek, Gábor L. Löveï
Software Mentions: 9
Published: over 3 years ago

10.1186/1472-6807-9-27

PTools: an opensource molecular docking library
Cited by: 34
Author(s): Adrien Saladin, Sébastien Fiorucci, Pierre Poulain, Chantal Prévost, Martin Zacharias
Software Mentions: 9
Published: over 15 years ago

10.1371/journal.pone.0137132

Clustering of Expression Data in Chronic Lymphocytic Leukemia Reveals New Molecular Subdivisions
Cited by: 7
Author(s): Sally Yepes, María Mercedes Torres, Rafael Andrade
Software Mentions: 9
Published: over 9 years ago

10.1371/journal.pone.0249858

Morpho-agronomic, biochemical and molecular analysis of genetic diversity in the Mesoamerican common bean panel
Cited by: 5
Author(s): Alexandre Simões Nogueira, Vânia Moda-Cirino, Jéssica Delfini, Luriam Aparecida Brandão, Silas Mian, Leonel Vinícius Constantino, Douglas Mariani Zeffa, José dos Santos Neto, Leandro Simões Azeredo Gonçalves
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-021-95185-2

The food patterns of a multicenter cohort of Brazilian nulliparous pregnant women
Cited by: 3
Author(s): Maria J Miele, Renato Teixeira Souza, Iracema de Mattos Paranhos Calderon, Francisco Edson de Lucena Feitosa, Débora Farias Batista Leite, Edilberto A. Rocha Filho, Janete Vettorazzi, Jussara Mayrink, Karayna Gil Fernandes, Matias C. Vieira, Rodolfo C. Pacagnella, José Guilherme Cecatti
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pone.0240462

The origins of money: Calculation of similarity indexes demonstrates the earliest development of commodity money in prehistoric Central Europe
Cited by: 11
Author(s): Maikel H.G. Kuijpers, Cătălin Nicolae Popa
Software Mentions: 9
Published: almost 4 years ago

10.1038/s41598-017-15525-z

Single-cell Co-expression Subnetwork Analysis
Cited by: 20
Author(s): Thomas E. Bartlett, Sören Müller, Aaron A. Diaz
Software Mentions: 9
Published: about 7 years ago

10.3390/nu12061779

Maternal Microbiota, Cortisol Concentration, and Post-Partum Weight Recovery Are Dependent on Mode of Delivery
Cited by: 7
Author(s): Marta Selma‐Royo, Izaskun García-Mantrana, Marta Calatayud, Anna Parra-Llorca, Cecilia Martínez‐Costa, María Carmen Collado
Software Mentions: 9
Published: over 4 years ago

10.1038/srep08508

No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls
Cited by: 64
Author(s): Aldona Dlugosz, Björn Winckler, E. Lundin, Katherina Zakikhany, Gunnar Sandström, Weimin Ye, Lars Engstrand, Greger Lindberg
Software Mentions: 9
Published: almost 10 years ago

10.1186/s40168-018-0592-3

Citizen science charts two major “stomatotypes” in the oral microbiome of adolescents and reveals links with habits and drinking water composition
Cited by: 73
Author(s): Jesse R. Willis, Pedro González-Torres, Alexandros A. Pittis, Luis A. Bejarano, Luca Cozzuto, Núria Andreu, Miriam Alloza-Trabado, Antònia Valentín, Ewa Księżopolska, Harris Onywera, Magda Montfort, Antonio Hermoso, Susana Iraola-Guzmán, Ester Saus, Annick Labeeuw, Carlo Carolis, Jochen Hecht, Julia Ponomarenko, Toni Gabaldón
Software Mentions: 9
Published: about 6 years ago

10.1186/1471-2407-14-130

Systematic analysis of 18F-FDG PET and metabolism, proliferation and hypoxia markers for classification of head and neck tumors
Cited by: 21
Author(s): Bianca A.W. Hoeben, Maud H.W. Starmans, Ralph T.H. Leijenaar, Ludwig Dubois, Albert J. van der Kogel, J.H.A.M. Kaanders, Paul C. Boutros, Johan Bussink
Software Mentions: 9
Published: almost 11 years ago

10.3389/fmicb.2019.01793

The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life
Cited by: 22
Author(s): Wentao Yang, Carola Petersen, Barbara Pees, Johannes Zimmermann, Silvio Waschina, Philipp Dirksen, Philip Rosenstiel, Andreas Tholey, Matthias Leippe, Katja Dierking, Christoph Kaleta, Hinrich Schulenburg
Software Mentions: 9
Published: over 5 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: almost 6 years ago

10.1186/s13058-019-1148-6

Identification of three subtypes of triple-negative breast cancer with potential therapeutic implications
Cited by: 70
Author(s): Pascal Jézéquel, Olivier Kerdraon, Hubert Hondermarck, Catherine Guérin‐Charbonnel, Hamza Lasla, Wilfried Gouraud, Jean-Luc Canon, Andrea Gombos, Florence Dalenc, Suzette Delaloge, Jérôme Lemonnier, Delphine Loussouarn, Véronique Verrièle, Mario Campone
Software Mentions: 9
Published: over 5 years ago

10.3389/fneur.2020.01021

Medical Informatics Platform (MIP): A Pilot Study Across Clinical Italian Cohorts
Cited by: 10
Author(s): Alberto Redolfi, Silvia De Francesco, Fulvia Palesi, Samantha Galluzzi, Cristina Muscio, Gloria Castellazzi, Pietro Tiraboschi, Giovanni Savini, Anna Nigri, Gabriella Bottini, Maria Grazia Bruzzone, Matteo Cotta Ramusino, Stefania Ferraro, C Wheeler-Kingshott, Fabrizio Tagliavini, Giovanni B. Frisoni, Philippe Ryvlin, Jean-François Demonet, Ferath Kherif, Stefano F. Cappa, Egidio D’Angelo
Software Mentions: 9
Published: about 4 years ago

10.3389/fpsyt.2019.00041

A Data Science-Based Analysis Points at Distinct Patterns of Lipid Mediator Plasma Concentrations in Patients With Dementia
Cited by: 6
Author(s): Robert Gurke, Semra Etyemez, David Prvulovic, Dominique Thomas, Stefanie C. Fleck, Andreas Reif, Gerd Geißlinger, Jörn Lötsch
Software Mentions: 9
Published: almost 6 years ago

10.1186/s13293-020-00296-6

Sex-specific clustering of metabolic risk factors and cancer risk: a longitudinal study in Iran
Cited by: 2
Author(s): Azra Ramezankhani, Fereidoun Azizi, Farzad Hadaegh
Software Mentions: 8
Published: over 4 years ago

10.1186/gm385

Exploiting the noise: improving biomarkers with ensembles of data analysis methodologies
Cited by: 14
Author(s): Maud H.W. Starmans, Melania Pintilie, Thomas John, Sandy D. Der, Frances A. Shepherd, Igor Jurišica, Philippe Lambin, Ming‐Sound Tsao, Paul C. Boutros
Software Mentions: 8
Published: almost 13 years ago

10.3389/fpsyg.2020.00359

Validation of the Czech Version of the Relational Needs Satisfaction Scale
Cited by: 3
Author(s): Martina Pourová, Tomáš Řiháček, Gregor Žvelc
Software Mentions: 8
Published: almost 5 years ago

10.1172/jci.insight.138751

In utero human intestine harbors unique metabolome, including bacterial metabolites
Cited by: 27
Author(s): Yujia Li, Jessica Toothaker, Shira Ben-Simon, Lital Ozeri, Ron Schweitzer, Blake McCourt, Collin C. McCourt, Lael Werner, Scott B. Snapper, Dror S. Shouval, Soliman Khatib, Omry Koren, Sameer Agnihorti, George C. Tseng, Liza Konnikova
Software Mentions: 8
Published: about 4 years ago

10.1186/s12967-021-02744-2

Combined lymphocyte/monocyte count, D-dimer and iron status predict COVID-19 course and outcome in a long-term care facility
Cited by: 20
Author(s): Flavia Biamonte, Cirino Botta, Maria Mazzitelli, Salvatore Rotundo, Enrico Maria Trecarichi, Daniela Foti, Carlo Torti, Giuseppe Viglietto, Daniele Torella, Francesco Costanzo
Software Mentions: 8
Published: almost 4 years ago

10.3390/microorganisms9020378

Differences in the Concentration of the Fecal Neurotransmitters GABA and Glutamate Are Associated with Microbial Composition among Healthy Human Subjects
Cited by: 18
Author(s): Hend Altaib, Kohei Nakamura, Mayuko Abe, Yassien Badr, Emiko Yanase, Izumi Nomura, Tomohiko Suzuki
Software Mentions: 8
Published: almost 4 years ago

10.3390/plants10030550

Phenolic Compounds and Biological Activity of Selected Mentha Species
Cited by: 51
Author(s): Sanja Ćavar Zeljković, Jana Šišková, Karolína Komzáková, Nuria De Diego, K. Kaffková, Petr Tarkowski
Software Mentions: 8
Published: almost 4 years ago

10.3389/fonc.2021.616133

Analysis of Autophagy-Related Signatures Identified Two Distinct Subtypes for Evaluating the Tumor Immune Microenvironment and Predicting Prognosis in Ovarian Cancer
Cited by: 11
Author(s): Xingyu Chen, Hua Lan, Dong He, Zhanwang Wang, Runshi Xu, Jing Yuan, Mengqing Xiao, Yao Zhang, Lian Gong, Songshu Xiao, Ke Cao
Software Mentions: 8
Published: over 3 years ago

10.1038/s41598-019-47117-4

Using a trait-based approach to understand the efficiency of a selective device in a multispecific fishery
Cited by: 7
Author(s): Maud Mouchet, Manon Poirson, Fabien Morandeau, Camille Vogel, Sonia Méhault, Dorothée Kopp
Software Mentions: 8
Published: over 5 years ago

10.1186/s40168-017-0371-6

Multi-level comparisons of cloacal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks
Cited by: 55
Author(s): H. Pieter J. van Veelen, Joana Falcão Salles, B. Irene Tieleman
Software Mentions: 8
Published: about 7 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

10.1371/journal.pone.0255190

The effect of risk at birth on breastfeeding duration and exclusivity: A cohort study at a Brazilian referral center for high-risk neonates and infants
Cited by: 1
Author(s): Maíra Domingues Bernardes Silva, Raquel Oliveira, Davi da Silveira Barroso Alves, Enirtes Caetano Prates Melo
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0250629

Epiphytic diatom community structure and richness is determined by macroalgal host and location in the South Shetland Islands (Antarctica)
Cited by: 3
Author(s): Andrea M. Burfeid-Castellanos, Rafael P. Martín–Martín, Michael Kloster, Carlos Angulo‐Preckler, Conxita Àvila, Bánk Beszteri
Software Mentions: 8
Published: over 3 years ago

10.3390/ijms22042102

Putative Circulating MicroRNAs Are Able to Identify Patients with Mitral Valve Prolapse and Severe Regurgitation
Cited by: 6
Author(s): Paola Songia, Mattia Chiesa, Valentina Alfieri, Ilaria Massaiu, Donato Moschetta, Veronika A. Myasoedova, Vincenza Valerio, Laura Fusini, Paola Gripari, Marco Zanobini, Paolo Poggio
Software Mentions: 8
Published: almost 4 years ago

10.1186/s13058-015-0550-y

Gene-expression molecular subtyping of triple-negative breast cancer tumours: importance of immune response
Cited by: 223
Author(s): Pascal Jézéquel, Delphine Loussouarn, Catherine Guérin‐Charbonnel, Loı̈c Campion, Antoine Vanier, Wilfried Gouraud, Hamza Lasla, Catherine Guette, Isabelle Valo, Véronique Verrièle, Mario Campone
Software Mentions: 8
Published: almost 10 years ago

10.1155/2021/8892849

Correlation Analysis between GDM and Gut Microbial Composition in Late Pregnancy
Cited by: 17
Author(s): Genxia Li, Pan Yin, Shuhui Chu, Wen Gao, Shihong Cui, Shuhua Guo, Yajuan Xu, Enwu Yuan, Texuan Zhu, Jie You, Junya Zhang, Manman Yang
Software Mentions: 8
Published: almost 4 years ago

10.3390/jcm9082530

Distinctive Tissue and Serum MicroRNA Profile of IgG4-Related Ophthalmic Disease and MALT Lymphoma
Cited by: 5
Author(s): Naoya Nezu, Yoshihiko Usui, Masaki Asakage, Hiroyuki Shimizu, Kinya Tsubota, Akitomo Narimatsu, Kazuhiko Umazume, Naoyuki Yamakawa, Shinya Ohno, Masakatsu Takanashi, Masahiko Kuroda, Hiroshi Gotô
Software Mentions: 8
Published: over 4 years ago

10.3390/biology9080199

Spatial Phylogenetics, Biogeographical Patterns and Conservation Implications of the Endemic Flora of Crete (Aegean, Greece) under Climate Change Scenarios
Cited by: 23
Author(s): Konstantinos Kougioumoutzis, Ioannis Kokkoris, Maria Panitsa, Panayiotis Trigas, Arne Strid, Panayotis Dimopoulos
Software Mentions: 8
Published: over 4 years ago

10.1186/1751-0473-7-13

MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads
Cited by: 4
Author(s): Alexander Tyakht, Anna Popenko, Maxim S. Belenikin, Ilya Altukhov, Alexander V. Pavlenko, Elena S. Kostryukova, Oksana V. Selezneva, Andrei K. Larin, Irina Y. Karpova, Dmitry Alexeev
Software Mentions: 7
Published: about 12 years ago

10.1186/1752-0509-6-63

Network methods for describing sample relationships in genomic datasets: application to Huntington’s disease
Cited by: 121
Author(s): Michael C. Oldham, Peter Langfelder, Steve Horvath
Software Mentions: 7
Published: almost 13 years ago

10.1128/mSphere.00806-20

Raman Spectroscopy-Based Measurements of Single-Cell Phenotypic Diversity in Microbial Populations
Cited by: 15
Author(s): Cristina García‐Timermans, Ruben Props, Boris Zacchetti, Myrsini Sakarika, Frank Delvigne, Nico Boon
Software Mentions: 7
Published: about 4 years ago

10.1186/1471-2105-14-S16-S14

RMaNI: Regulatory Module Network Inference framework
Cited by: 6
Author(s): Piyush B. Madhamshettiwar, Stefan Maetschke, Melissa J. Davis, Mark A. Ragan
Software Mentions: 7
Published: about 11 years ago

10.1186/s12862-016-0858-y

Cambrian suspension-feeding lobopodians and the early radiation of panarthropods
Cited by: 22
Author(s): Jean‐Bernard Caron, Cédric Aria
Software Mentions: 7
Published: almost 8 years ago

10.1186/cc11667

Identification of sepsis subtypes in critically ill adults using gene expression profiling
Cited by: 47
Author(s): David Maslove, Benjamin Tang, Anthony S. McLean
Software Mentions: 7
Published: almost 13 years ago

10.1371/journal.pone.0007225

MicroRNAs Show Mutually Exclusive Expression Patterns in the Brain of Adult Male Rats
Cited by: 94
Author(s): Line Olsen, Mikkel Klausen, Lone Helboe, Finn Cilius Nielsen, Thomas Werge
Software Mentions: 7
Published: about 15 years ago

10.3390/vetsci7030138

Cattle Manure Trade Network Analysis and the Relevant Spatial Pathways in an Endemic Area of Foot and Mouth Disease in Northern Thailand
Cited by: 0
Author(s): Chalutwan Sansamur, Anuwat Wiratsudakul, Arisara Charoenpanyanet, Veerasak Punyapornwithaya
Software Mentions: 7
Published: over 4 years ago

10.3389/fpsyg.2018.01748

The Semantic Content of Abstract Concepts: A Property Listing Study of 296 Abstract Words
Cited by: 57
Author(s): Marcel Harpaintner, Natalie M. Trumpp, Markus Kiefer
Software Mentions: 7
Published: over 6 years ago

10.1186/1471-2164-9-S1-S5

Transcription network construction for large-scale microarray datasets using a high-performance computing approach
Cited by: 14
Author(s): Mengxia Zhu, Qishi Wu
Software Mentions: 7
Published: almost 17 years ago

10.1002/ece3.7777

Fine‐scale movements and behaviors of coyotes (<i>Canis latrans</i>) during their reproductive period
Cited by: 5
Author(s): Michael J. Chamberlain, Bradley S. Cohen, Patrick H. Wightman, Emily Rushton, Joseph W. Hinton
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0196117

Identification of a neutrophil-related gene expression signature that is enriched in adult systemic lupus erythematosus patients with active nephritis: Clinical/pathologic associations and etiologic mechanisms
Cited by: 37
Author(s): Joan E. Wither, Stephenie D. Prokopec, Babak Noamani, Nan-Hua Chang, Dennisse Bonilla, Zahi Touma, Carmen Ávila-Casado, Heather N. Reich, James W. Scholey, Paul R. Fortin, Paul C. Boutros, Carolina Landolt-Marticorena
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-018-26930-3

Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period
Cited by: 64
Author(s): Shebl E. Salem, Thomas W. Maddox, Adam Berg, Philipp Antczak, Julian M. Ketley, Nicola Williams, Debra Archer
Software Mentions: 7
Published: over 6 years ago