Ecosyste.ms: Papers

10.3390/genes11030257

mRNAsi Index: Machine Learning in Mining Lung Adenocarcinoma Stem Cell Biomarkers
Cited by: 61
Author(s): Yitong Zhang, Joseph T. Tseng, I-Chia Lien, Fenglan Li, Wei Wu, Hui Li
Software Mentions: 20
Published: over 4 years ago

10.1186/s12864-020-06832-3

Seamless integration of image and molecular analysis for spatial transcriptomics workflows
Cited by: 121
Author(s): Joseph Bergenstråhle, Ludvig Larsson, Joakim Lundeberg
Software Mentions: 20
Published: over 4 years ago

10.1098/rsos.202050

Experiments confirm a dispersive phenotype associated with a natural gene drive system
Cited by: 7
Author(s): Jan‐Niklas Runge, Anna K. Lindholm
Software Mentions: 19
Published: over 3 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: almost 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

10.1038/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

10.1371/journal.pone.0247002

Chainchecker: An application to visualise and explore transmission chains for Ebola virus disease
Cited by: 2
Author(s): Katy A. M. Gaythorpe, Aaron Morris, Natsuko Imai, Miles Stewart, Jeffrey S. Freeman, Mary J. Choi
Software Mentions: 19
Published: almost 4 years ago

10.1186/s12866-021-02282-3

Associations between the gut microbiome and metabolome in early life
Cited by: 14
Author(s): Quang P. Nguyen, Margaret R. Karagas, Juliette C. Madan, Erika Dade, Thomas J. Palys, Hilary G. Morrison, Wimal Pathmasiri, Susan McRitche, Susan Sumner, H. Robert Frost, Anne G. Hoen
Software Mentions: 19
Published: about 3 years ago

10.1093/molbev/msaa311

A Two-Locus System with Strong Epistasis Underlies Rapid Parasite-Mediated Evolution of Host Resistance
Cited by: 15
Author(s): Camille Ameline, Yann Bourgeois, Felix Vögtli, Eevi Savola, Jason P. Andras, Jan Engelstädter, Dieter Ebert
Software Mentions: 19
Published: almost 4 years ago

10.3390/plants10020247

Machine Learning Applications and Optimization of Clustering Methods Improve the Selection of Descriptors in Blackberry Germplasm Banks
Cited by: 5
Author(s): Juan Camilo Henao-Rojas, María Gladis Rosero-Alpala, Carolina Ortiz-Muñoz, Carlos Enrique Velásquez-Arroyo, William A. León-Rueda, Joaquín Guillermo Ramírez‐Gil
Software Mentions: 19
Published: almost 4 years ago

10.1007/s00122-020-03716-8

Linear models for diallel crosses: a review with R functions
Cited by: 11
Author(s): Andrea Onofri, Niccolò Terzaroli, Luigi Russi
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

10.1371/journal.pcbi.1007664

Tximeta: Reference sequence checksums for provenance identification in RNA-seq
Cited by: 122
Author(s): Michael I. Love, Charlotte Soneson, Peter Hickey, Lisa K. Johnson, Nicholas Pierce, Lori Shepherd, Martin Morgan, Rob Patro
Software Mentions: 19
Published: over 4 years ago

10.1371/journal.pone.0061217

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
Cited by: 11,386
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 19
Published: over 11 years ago

10.3390/cancers12040948

Reconstruction of Ewing Sarcoma Developmental Context from Mass-Scale Transcriptomics Reveals Characteristics of EWSR1-FLI1 Permissibility
Cited by: 23
Author(s): Henry E. Miller, Aparna Gorthi, Nicklas Bassani, Liesl A. Lawrence, Brian S. Iskra, Alexander J.R. Bishop
Software Mentions: 19
Published: over 4 years ago

10.3390/ijms21186652

Identification of Gastritis Subtypes by Convolutional Neuronal Networks on Histological Images of Antrum and Corpus Biopsies
Cited by: 15
Author(s): Georg Steinbuß, Katharina Kriegsmann, Mark Kriegsmann
Software Mentions: 19
Published: about 4 years ago

10.1084/jem.20201795

Diagnostic blood RNA profiles for human acute spinal cord injury
Cited by: 21
Author(s): Nikos Kyritsis, Abel Torres-Espín, Patrick G. Schupp, J. Russell Huie, Austin Chou, Xuan Duong Fernandez, Libby Thomas, Rachel Tsolinas, Debra D. Hemmerle, Lisa U. Pascual, Vineeta Singh, Jonathan Z. Pan, Jason F. Talbott, William D. Whetstone, John F. Burke, Anthony M DiGiorgio, Philip Weinstein, Geoffrey T. Manley, Sanjay S. Dhall, Adam R. Ferguson, Michael C. Oldham, Jacqueline C. Bresnahan, Michael S. Beattie
Software Mentions: 19
Published: almost 4 years ago

10.12688/gatesopenres.12832.2

DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis
Cited by: 7
Author(s): Greg Finak, Bryan T. Mayer, William J. Fulp, Paul Obrecht, Alicia Sato, Eva Yin-han Chung, Drienna Holman, Raphaël Gottardo
Software Mentions: 19
Published: over 6 years ago

10.3390/s19204551

Assessing Older Adults’ Daily Mobility: A Comparison of GPS-Derived and Self-Reported Mobility Indicators
Cited by: 24
Author(s): Michelle Pasquale Fillekes, Eun Kyeong Kim, Rieke Trumpf, Wiebren Zijlstra, Eleftheria Giannouli, Robert Weibel
Software Mentions: 19
Published: about 5 years ago

10.15252/msb.20209438

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics
Cited by: 49
Author(s): Carmen Bravo González-Blas, Xiao‐Jiang Quan, Ramon Duran-Romaña, Ibrahim Ihsan Taskiran, Duygu Koldere, Kristofer Davie, Valerie Christiaens, Samira Makhzami, Gert Hulselmans, Maxime De Waegeneer, David Mauduit, Suresh Poovathingal, Sara Aibar, Stein Aerts
Software Mentions: 19
Published: over 4 years ago

10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment
Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: about 8 years ago

10.1371/journal.pone.0169748

SoilGrids250m: Global gridded soil information based on machine learning
Cited by: 2,126
Author(s): Tomislav Hengl, Jorge Mendes de Jesus, G.B.M. Heuvelink, M. Ruiperez González, Milorad Kilibarda, Aleksandar Blagotić, Wei Shangguan, Marvin N. Wright, Xiaoyuan Geng, Bernhard Bauer-Marschallinger, Mário Guevara, Rodrigo Vargas, R.A. MacMillan, N.H. Batjes, J.G.B. Leenaars, Eloi Ribeiro, Ichsani Wheeler, S. Mantel
Software Mentions: 19
Published: almost 8 years ago

10.1016/j.cub.2020.12.047

A sex-specific switch between visual and olfactory inputs underlies adaptive sex differences in behavior
Cited by: 32
Author(s): Tetsuya Nojima, Annika Rings, Annette D. Allen, Nils Otto, Thomas A. Verschut, Jean‐Christophe Billeter, Megan C Neville, Stephen F. Goodwin
Software Mentions: 19
Published: over 3 years ago

10.1155/2021/6613151

Genomic and Transcriptome Analysis to Identify the Role of the mTOR Pathway in Kidney Renal Clear Cell Carcinoma and Its Potential Therapeutic Significance
Cited by: 6
Author(s): Xiangyu Che, Xiaochen Qi, Yingkun Xu, Qifei Wang, Guangzhen Wu
Software Mentions: 19
Published: over 3 years ago

10.1186/s12942-019-0181-0

Towards a comprehensive set of GPS-based indicators reflecting the multidimensional nature of daily mobility for applications in health and aging research
Cited by: 47
Author(s): Michelle Pasquale Fillekes, Eleftheria Giannouli, Eun Kyeong Kim, Wiebren Zijlstra, Robert Weibel
Software Mentions: 18
Published: over 5 years ago

10.15252/emmm.202012640

Mithramycin induces promoter reprogramming and differentiation of rhabdoid tumor
Cited by: 7
Author(s): Maggie H. Chassé, Benjamin K. Johnson, Elissa A. Boguslawski, Katie M. Sorensen, Jessica E Rosien, Min H. Kang, C. Patrick Reynolds, Lyong Heo, Zachary Madaj, Ian Beddows, Gabrielle E. Foxa, Susan M. Kitchen-Goosen, Bart O. Williams, Timothy J. Triche, Patrick J. Grohar
Software Mentions: 18
Published: almost 4 years ago

10.1111/eva.13237

A machine learning approach to integrating genetic and ecological data in tsetse flies ( <i>Glossina pallidipes</i> ) for spatially explicit vector control planning
Cited by: 5
Author(s): Anusha P Bishop, Giuseppe Amatulli, Chaz Hyseni, Evlyn Pless, Rosemary Bateta, Winnie A. Okeyo, Paul O. Mireji, Sylvance Okoth, Imna Malele, Grace Murilla, Serap Aksoy, Adalgisa Caccone, Norah P. Saarman
Software Mentions: 18
Published: over 3 years ago

10.1186/s12889-021-11267-w

Influence of chronic hepatitis C infection on the monocyte-to-platelet ratio: data analysis from the National Health and Nutrition Examination Survey (2009–2016)
Cited by: 1
Author(s): Aidan M. Nikiforuk, Mohammad Ehsanul Karim, David M. Patrick, Agatha Jassem
Software Mentions: 18
Published: over 3 years ago

10.3389/fimmu.2021.620270

Non-Genomic AhR-Signaling Modulates the Immune Response in Endotoxin-Activated Macrophages After Activation by the Environmental Stressor BaP
Cited by: 18
Author(s): Henning Großkopf, Katharina Walter, Isabel Karkossa, Martin von Bergen, Kristin Schubert
Software Mentions: 18
Published: over 3 years ago

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

10.3389/fimmu.2021.700501

Interferon-γ-Producing CD4+ T Cells Drive Monocyte Activation in the Bone Marrow During Experimental Leishmania donovani Infection
Cited by: 6
Author(s): Audrey Romano, Najmeeyah Brown, Helen Ashwin, Johannes S. P. Doehl, Jonathan Hamp, Mohamed Osman, Nidhi Sharma Dey, Gulab Fatima Rani, Tiago Luiz Ferreira, Paul M. Kaye
Software Mentions: 18
Published: about 3 years ago

10.3390/ijms22105385

Deep Learning in Pancreatic Tissue: Identification of Anatomical Structures, Pancreatic Intraepithelial Neoplasia, and Ductal Adenocarcinoma
Cited by: 15
Author(s): Mark Kriegsmann, Katharina Kriegsmann, Georg Steinbuß, Christiane Zgorzelski, Anne Kraft, Matthias M. Gaida
Software Mentions: 18
Published: over 3 years ago

10.3389/fonc.2021.646267

Exploring MRI Characteristics of Brain Diffuse Midline Gliomas With the H3 K27M Mutation Using Radiomics
Cited by: 13
Author(s): Qian Li, Fei Dong, Biao Jiang, Minming Zhang
Software Mentions: 18
Published: over 3 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

10.3390/genes12030413

Spt4 Promotes Pol I Processivity and Transcription Elongation
Cited by: 5
Author(s): Abigail K. Huffines, Yvonne J. K. Edwards, David A. Schneider
Software Mentions: 18
Published: over 3 years ago

10.1093/bioinformatics/bty947

SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data
Cited by: 19
Author(s): Jamie Soul, Timothy E. Hardingham, Raymond P. Boot-Handford, Jean-Marc Schwartz
Software Mentions: 18
Published: almost 6 years ago

10.1371/journal.pbio.3000673

“Frozen evolution” of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence
Cited by: 15
Author(s): David Pascall, Kyriaki Nomikou, Emmanuel Bréard, Stéphan Zientara, Ana da Silva Filipe, Bernd Hoffmann, Maude Jacquot, Joshua B. Singer, Kris De Clercq, Anette Bøtner, Corinne Sailleau, Cyril Viarouge, Carrie Batten, Giantonella Puggioni, Ciriaco Ligios, Giovanni Savini, Piet A. van Rijn, Peter Mertens, Roman Biek, Massimo Palmarini
Software Mentions: 18
Published: over 4 years ago

10.1093/gigascience/giaa010

Interpretable and accurate prediction models for metagenomics data
Cited by: 29
Author(s): Edi Prifti, Yann Chevaleyre, Blaise Hanczar, Eugeni Belda, Antoine Danchin, Karine Clément, Jean-Daniel Zucker
Software Mentions: 18
Published: over 4 years ago

10.3389/fonc.2020.607727

Gene Panel of Persister Cells as a Prognostic Indicator for Tumor Repopulation After Radiation
Cited by: 3
Author(s): Yucui Zhao, Yanwei Song, Ruyi Zhao, Minghui Zhao, Qian Huang
Software Mentions: 18
Published: about 4 years ago

10.1371/journal.pone.0244384

Metropolitan age-specific mortality trends at borough and neighborhood level: The case of Mexico City
Cited by: 2
Author(s): Karol Baca-López, Cristóbal Fresno, Jesús Espinal-Enríquez, Miriam V. Flores-Merino, Miguel A. Camacho-López, Enrique Hernández‐Lemus
Software Mentions: 18
Published: almost 4 years ago

10.3389/fonc.2021.605810

A Novel Risk Factor Model Based on Glycolysis-Associated Genes for Predicting the Prognosis of Patients With Prostate Cancer
Cited by: 6
Author(s): Kaixuan Guo, Cong Lai, Juan Shi, Zhuang Tang, Cheng Liu, Kuiqing Li, Kailin Xu
Software Mentions: 18
Published: about 3 years ago

10.1186/s12862-020-01717-1

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa
Cited by: 7
Author(s): Zhongning Zhao, Neil Heideman, Phillip Armand Bester, Adriaan Jordaan, Margaretha D. Hofmeyr
Software Mentions: 18
Published: about 4 years ago

10.1186/s12859-019-2879-1

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
Cited by: 146
Author(s): Fédérico Marini, Harald Binder
Software Mentions: 18
Published: over 5 years ago

10.1186/s13059-019-1805-1

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation
Cited by: 65
Author(s): Amanda J. Price, Leonardo Collado‐Torres, Н. А. Иванов, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Software Mentions: 18
Published: about 5 years ago

10.1002/1878-0261.12960

KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix
Cited by: 6
Author(s): Jin K. Kim, Michael R. Marco, Seo‐Hyun Choi, Xuan Qu, Chin-Tung Chen, Moshe Elkabets, Lauren Fairchild, Oliver Chow, Francisco M. Barriga, Lukas E. Dow, Kevin P. O’Rourke, Bryan Szeglin, Dmitry Yarilin, Sho Fujisawa, Katia Manova‐Todorova, Philip B. Paty, Jinru Shia, Christina Leslie, J. Joshua Smith, Scott W. Lowe, Raphael Pelossof, Francisco Sánchez-Vega, Julio García-Aguilar
Software Mentions: 18
Published: over 3 years ago

10.3390/ijms21228837

Machine Learning Identifies Robust Matrisome Markers and Regulatory Mechanisms in Cancer
Cited by: 6
Author(s): Anni Kääriäinen, Vilma Pesola, Annalena Dittmann, Juho A. J. Kontio, Jarkko Koivunen, Taina Pihlajaniemi, Valerio Izzi
Software Mentions: 18
Published: almost 4 years ago

10.3390/cancers13102419

Deep Learning for the Classification of Non-Hodgkin Lymphoma on Histopathological Images
Cited by: 16
Author(s): Georg Steinbuß, Mark Kriegsmann, Christiane Zgorzelski, Alexander Brobeil, Benjamin Goeppert, Sascha Dietrich, Gunhild Mechtersheimer, Katharina Kriegsmann
Software Mentions: 18
Published: over 3 years ago

10.20517/jtgg.2020.51

Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq
Cited by: 2
Author(s): Brandon Lieberman, Meena Kusi, Chia-Nung Hung, Chih-Wei Chou, Ning He, Yen‐Yi Ho, Josephine A. Taverna, Tim Hui-Ming Huang, Chun-Liang Chen
Software Mentions: 18
Published: almost 5 years ago

10.1186/s12859-019-3059-z

HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data
Cited by: 28
Author(s): Anh Tran, Alex M. Dussaq, Timothy Kennell, Christopher D. Willey, Anita B. Hjelmeland
Software Mentions: 18
Published: about 5 years ago

10.1371/journal.pone.0238665

Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains
Cited by: 19
Author(s): Anastasis Oulas, Maria Zanti, Marios Tomazou, Margarita Zachariou, George Minadakis, Marilena M. Bourdakou, Margarita Zachariou, George M. Spyrou
Software Mentions: 18
Published: almost 4 years ago

10.1186/s13059-021-02295-1

gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
Cited by: 77
Author(s): Johannes Zimmermann, Christoph Kaleta, Silvio Waschina
Software Mentions: 18
Published: over 3 years ago

10.1016/j.cell.2020.12.016

Spatiotemporal analysis of human intestinal development at single-cell resolution
Cited by: 215
Author(s): David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren J. Fowler, Edward Morrissey, Christine M. Cunningham, Johnson Prv., Hashem Koohy, Alison Simmons
Software Mentions: 18
Published: almost 4 years ago

10.1186/s12859-019-3152-3

flowEMMi: an automated model-based clustering tool for microbial cytometric data
Cited by: 16
Author(s): Joachim Ludwig, Christian Höner zu Siederdissen, Zishu Liu, Peter F. Stadler, Susann Müller
Software Mentions: 18
Published: almost 5 years ago

10.1093/bioinformatics/bty149

NanoPack: visualizing and processing long-read sequencing data
Cited by: 1,423
Author(s): Wouter De Coster, Svenn D’Hert, Darrin T. Schultz, Marc Cruts, Christine Van Broeckhoven
Software Mentions: 18
Published: over 6 years ago

10.1016/j.scitotenv.2020.140792

ESPRES: A web application for interactive analysis of multiple pressures in aquatic ecosystems
Cited by: 4
Author(s): Ángel Údias, Alberto Pistocchi, Olga Vigiak, Bruna Grizzetti, F. Bouraoui, César Alfaro
Software Mentions: 18
Published: about 4 years ago

10.1371/journal.pone.0195970

The importance of regional models in assessing canine cancer incidences in Switzerland
Cited by: 4
Author(s): Gianluca Boo, Stefan Leyk, Chris Brunsdon, Ricarda Graf, Andreas Pospischil, Sara Irina Fabrikant
Software Mentions: 18
Published: over 6 years ago

10.1128/mBio.01054-19

Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures
Cited by: 28
Author(s): Miles Richardson, Neil Gottel, Jack A. Gilbert, Simon Lax
Software Mentions: 18
Published: about 5 years ago

10.1093/bioinformatics/btab039

mlr3proba: an R package for machine learning in survival analysis
Cited by: 38
Author(s): Raphael Sonabend, Franz J. Király, Andreas Bender, Bernd Bischl, Michel Lang
Software Mentions: 18
Published: almost 4 years ago

10.1371/journal.pbio.3001296

Tapping into non-English-language science for the conservation of global biodiversity
Cited by: 79
Author(s): Tatsuya Amano, Violeta Berdejo‐Espinola, Alec P. Christie, Kate Willott, Munemitsu Akasaka, András Báldi, Anna Berthinussen, Sandro Bertolino, Andrew J. Bladon, Min Chen, Chang Yong Choi, Magda Bou Dagher Kharrat, Luís Guilherme de Oliveira, Perla Farhat, Marina Golivets, Nataly Hidalgo Aranzamendi, Kerstin Jantke, Joanna Kajzer‐Bonk, M. Çisel Kemahlı Aytekin, Igor Khorozyan, Kensuke Kito, Ko Konno, Da Li Lin, Nick A. Littlewood, Yang Liu, Yifan Liu, Matthias Claudio Loretto, Valentina Marconi, Philip A. Martin, William H. Morgan, Juan Pablo Narváez-Gómez, Pablo José Negret, Elham Nourani, José Manuel Ochoa Quintero, Nancy Ockendon, Rachel Rui Ying Oh, Silviu O. Petrovan, Ana Cláudia Piovezan-Borges, Ingrid L. Pollet, Danielle Leal Ramos, Ana L. Reboredo Segovia, A. Nayelli Rivera‐Villanueva, Ricardo Rocha, Marie Morgane Rouyer, Katherine A. Sainsbury, Richard Schuster, Dominik Schwab, Çaǧan H. Şekercioǧlu, Hae Min Seo, Gorm E. Shackelford, Yushin Shinoda, Rebecca K. Smith, Shan Dar Tao, Ming-shan Tsai, Elizabeth Tyler, Flóra Vajna, José O. Valdebenito, Svetlana Vozykova, Paweł Waryszak, Veronica Zamora‐Gutiérrez, Rafael Dudeque Zenni, Wenjun Zhou, William J. Sutherland
Software Mentions: 18
Published: about 3 years ago

10.3389/fimmu.2020.01691

Leveraging Public Single-Cell and Bulk Transcriptomic Datasets to Delineate MAIT Cell Roles and Phenotypic Characteristics in Human Malignancies
Cited by: 22
Author(s): Tony Yao, Parisa Shooshtari, S. M. Mansour Haeryfar
Software Mentions: 18
Published: over 4 years ago

10.18632/aging.103499

Multi-omics network analysis reveals distinct stages in the human aging progression in epidermal tissue
Cited by: 16
Author(s): Nicholas Holzscheck, Jörn Söhle, Boris Kristof, Elke Grönniger, Stefan Gallinat, Horst Wenck, Marc Winnefeld, Cassandra Falckenhayn, Lars Kaderali
Software Mentions: 18
Published: over 4 years ago

10.1007/s10734-020-00674-4

Lights, camera, active! appreciation of active learning predicts positive attitudes towards lecture capture
Cited by: 6
Author(s): Emily Nordmann, Anne L. Clark, Elliott Spaeth, Jill R D MacKay
Software Mentions: 18
Published: almost 4 years ago

10.1186/s40168-019-0702-x

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

10.1016/j.molcel.2021.05.023

Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection
Cited by: 87
Author(s): Wael Kamel, Marko Noerenberg, Berati Cerikan, Honglin Chen, Aino I Järvelin, Mohamed Kammoun, Young Seok Lee, Shuai Ni, Manuel García-Moreno, Anna Andrejeva, Michael J. Deery, Natasha Johnson, Christopher J Neufeldt, Mirko Cortese, Michael Knight, Kathryn S. Lilley, Javier Martı̂nez, Ilan Davis, Ralf Bartenschlager, Shabaz Mohammed, Alfredo Castelló
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/s12880-021-00551-1

Sensitivity analysis for interpretation of machine learning based segmentation models in cardiac MRI
Cited by: 14
Author(s): Markus J. Ankenbrand, Liliia Shainberg, Michael Hock, David Lohr, Laura M. Schreiber
Software Mentions: 18
Published: almost 4 years ago

10.1002/ece3.5763

Sex matters: Otolith shape and genomic variation in deacon rockfish (<i>Sebastes diaconus</i>)
Cited by: 18
Author(s): Felix Vaux, Leif K. Rasmuson, Lisa A. Kautzi, Polly S. Rankin, Matthew T. O. Blume, Kelly Lawrence, Sandra Bohn, Kathleen G. O’Malley
Software Mentions: 17
Published: about 5 years ago

10.1038/s41598-020-58274-2

Pollen defenses negatively impact foraging and fitness in a generalist bee (Bombus impatiens: Apidae)
Cited by: 34
Author(s): Kristen Brochu, Maria T. van Dyke, Nelson J. Milano, Jessica D. Petersen, Scott H. McArt, Brian A. Nault, André Kessler, Bryan N. Danforth
Software Mentions: 17
Published: almost 5 years ago

10.1371/journal.pcbi.1006245

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
Cited by: 213
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 17
Published: over 6 years ago

10.1016/j.stem.2019.07.008

Defining the Identity and Dynamics of Adult Gastric Isthmus Stem Cells
Cited by: 85
Author(s): Seungmin Han, J. Lynn Fink, David J. Jörg, Eunmin Lee, Min Kyu Yum, Lemonia Chatzeli, Sebastian R. Merker, Manon Josserand, Teodora Trendafilova, Amanda Andersson-Rolf, Catherine Dabrowska, Hyunki Kim, Ronald Naumann, Ji–Hyun Lee, Nobuo Sasaki, Richard L. Mort, Onur Basak, Hans Clevers, Daniel E. Stange, Anna Philpott, Jong Kim, Benjamin D. Simons, Bon‐Kyoung Koo
Software Mentions: 17
Published: about 5 years ago

10.1186/s12859-020-03577-4

NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
Cited by: 38
Author(s): Ayman Yousif, Nizar Drou, Jillian Rowe, Mohammed Khalfan, Kristin C. Gunsalus
Software Mentions: 17
Published: over 4 years ago

10.12688/f1000research.15666.3

A systematic performance evaluation of clustering methods for single-cell RNA-seq data
Cited by: 33
Author(s): Angelo Duò, Mark D. Robinson, Charlotte Soneson
Software Mentions: 17
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

10.7717/peerj.5457

Global mapping of potential natural vegetation: an assessment of machine learning algorithms for estimating land potential
Cited by: 84
Author(s): Tomislav Hengl, Markus Walsh, Jonathan Sanderman, Ichsani Wheeler, Sandy P. Harrison, Iain Colin Prentice
Software Mentions: 17
Published: over 6 years ago

10.3390/brainsci11081017

Facial Signals and Social Actions in Multimodal Face-to-Face Interaction
Cited by: 14
Author(s): Naomi Nota, James P. Trujillo, Judith Holler
Software Mentions: 17
Published: over 3 years ago

10.3389/fvets.2021.620327

Detection of Mycobacterium avium ssp. paratuberculosis in Cultures From Fecal and Tissue Samples Using VOC Analysis and Machine Learning Tools
Cited by: 6
Author(s): Philipp Vitense, Elisa Kasbohm, Anne Klassen, Peter Gierschner, Phillip Trefz, M. Weber, Wolfram Miekisch, Jochen K. Schubert, Petra Möbius, Petra Reinhold, Volkmar Liebscher, Heike Köhler
Software Mentions: 17
Published: almost 4 years ago

10.1371/journal.pone.0200653

Cryopreservation of human mucosal tissues
Cited by: 13
Author(s): Sean M. Hughes, April L. Ferre, Sarah E Yandura, Cory Shetler, Chris A. R. Baker, Fernanda Calienes, Claire Levy, Rena D. Astronomo, Zhiquan Shu, Gretchen M. Lentz, Michael Fialkow, Anna C. Kirby, M. Juliana McElrath, Elizabeth Sinclair, Lisa C. Rohan, Peter L. Anderson, Barbara L. Shacklett, Charlene S. Dezzutti, Dayong Gao, Florian Hladik
Software Mentions: 17
Published: over 6 years ago

10.1016/j.cell.2015.01.006

Enhancer Evolution across 20 Mammalian Species
Cited by: 626
Author(s): Diego Villar, Camille Berthelot, Sarah Aldridge, Tim Rayner, Margus Lukk, Miguel Pignatelli, Thomas J. Park, Robert Deaville, Jonathan Thor Erichsen, Anna J. Jasinska, James M. A. Turner, Mads F. Bertelsen, Elizabeth P. Murchison, Paul Flicek, Duncan T. Odom
Software Mentions: 17
Published: almost 10 years ago

10.1016/j.cell.2019.12.013

Identification of a Master Regulator of Differentiation in Toxoplasma
Cited by: 154
Author(s): Benjamin S. Waldman, Dominic Schwarz, Marc H. Wadsworth, Jeroen P. J. Saeij, Alex K. Shalek, Sebastian Lourido
Software Mentions: 17
Published: almost 5 years ago

10.1038/s42003-021-02025-0

SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy
Cited by: 23
Author(s): Marta Giovanetti, Eleonora Cella, Francesca Benedetti, Brittany Rife Magalis, Vagner Fonseca, Silvia Fabris, Giovanni Campisi, Alessandra Ciccozzi, Silvia Angeletti, Alessândra Borsetti, Vittoradolfo Tambone, Caterina Sagnelli, Stefano Pascarella, Alberto Riva, Giancarlo Ceccarelli, Alessandro Marcello, Taj Azarian, Eduan Wilkinson, Túlio de Oliveira, Luiz Carlos Júnior Alcântara, Roberto Cauda, Arnaldo Caruso, Natalie E. Dean, Cameron J. Browne, José Lourenço, Marco Salemi, Davide Zella, Massimo Ciccozzi
Software Mentions: 17
Published: over 3 years ago

10.1073/pnas.2006024117

Diel variability of methane emissions from lakes
Cited by: 46
Author(s): Anna Sieczko, Nguyen Thanh Duc, Jonathan Schenk, Gustav Pajala, David Rudberg, Henrique O. Sawakuchi, David Bastviken
Software Mentions: 17
Published: over 4 years ago

10.3389/fmicb.2019.01726

Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System
Cited by: 66
Author(s): Hai-Zhen Zhu, Z.F. Zhang, Nan Zhou, Cheng‐Ying Jiang, Baojun Wang, Lei Cai, Shuang‐Jiang Liu
Software Mentions: 17
Published: over 5 years ago

10.12688/wellcomeopenres.16458.2

MethylDetectR: a software for methylation-based health profiling
Cited by: 14
Author(s): Robert F. Hillary, Riccardo E. Marioni
Software Mentions: 17
Published: over 3 years ago

10.1186/s13059-019-1819-8

SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Cited by: 12
Author(s): Abraham Gihawi, Ghanasyam Rallapalli, Rachel Hurst, Colin S. Cooper, Richard M. Leggett, Daniel Brewer
Software Mentions: 17
Published: about 5 years ago

10.3389/fimmu.2020.565730

Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19
Cited by: 22
Author(s): Marco Antônio M. Pretti, Rômulo Gonçalves Galvani, Gustavo Fioravanti Vieira, Adriana Bonomo, Martín Bonamino, Mariana Boroni
Software Mentions: 17
Published: almost 4 years ago

10.1084/jem.20200920

Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment
Cited by: 57
Author(s): Kristen E. Pauken, Osmaan Shahid, Kaitlyn A. Lagattuta, Kelly Mahuron, Jacob M. Luber, Margaret M. Lowe, Lüping Huang, Conor P. Delaney, Jaclyn M. Long, Megan E. Fung, Kathleen Newcomer, Katy K. Tsai, Melissa Chow, Samantha Guinn, Juhi R. Kuchroo, Kelly P. Burke, Jason M. Schenkel, Michael D. Rosenblum, Adil Daud, Arlene H. Sharpe, Meromit Singer
Software Mentions: 17
Published: over 3 years ago

10.15252/msb.20188636

Unsupervised identification of disease states from high‐dimensional physiological and histopathological profiles
Cited by: 11
Author(s): Kenichi Shimada, Timothy J. Mitchison
Software Mentions: 17
Published: almost 6 years ago

10.3389/fgene.2019.00499

ABioTrans: A Biostatistical Tool for Transcriptomics Analysis
Cited by: 6
Author(s): Zou Yutong, Thuy Tien Bui, Kumar Selvarajoo
Software Mentions: 17
Published: over 5 years ago

10.1186/s12920-015-0114-0

Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma
Cited by: 12
Author(s): Vinay Randhawa, Vishal Acharya
Software Mentions: 17
Published: over 9 years ago

10.1186/s12913-019-4105-2

Testing the psychometric properties of the Finnish version of the cross-cultural competence instrument of healthcare professionals (CCCHP)
Cited by: 5
Author(s): Laura Hietapakka, Marko Elovainio, Karolina Wesołowska, Anna-Mari Aalto, Anu‐Marja Kaihlanen, Timo Sinervo, Tarja Heponiemi
Software Mentions: 17
Published: over 5 years ago

10.1371/journal.pone.0232822

SimSurvey: An R package for comparing the design and analysis of surveys by simulating spatially-correlated populations
Cited by: 5
Author(s): Paul M. Regular, Gregory J. Robertson, Keith P. Lewis, Jonathan Babyn, Brian Healey, Fran Mowbray
Software Mentions: 17
Published: over 4 years ago

10.7717/peerj.9539

The importance of open science for biological assessment of aquatic environments
Cited by: 15
Author(s): Marcus W. Beck, Casey C. O’Hara, Julia S. Stewart Lowndes, Raphael D. Mazor, Susanna Theroux, David J. Gillett, Belize Lane, Gregory Gearheart
Software Mentions: 17
Published: over 4 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: almost 8 years ago

10.1038/s41598-020-75345-6

High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae)
Cited by: 9
Author(s): Sara L. Martin, Leshawn Benedict, Wei Wei, Connie A. Sauder, Hugh J. Beckie, Linda M. Hall
Software Mentions: 17
Published: about 4 years ago

10.12688/f1000research.8923.2

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
Cited by: 105
Author(s): Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D’Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Software Mentions: 17
Published: almost 8 years ago

10.1186/s13059-020-02104-1

Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
Cited by: 57
Author(s): Matteo Calgaro, Chiara Romualdi, Levi Waldron, Davide Risso, Nicola Vitulo
Software Mentions: 17
Published: over 4 years ago

10.1186/s12859-021-04054-2

CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data
Cited by: 13
Author(s): Yuting Dai, Aining Xu, Jianfeng Li, Liang Wu, Shanhe Yu, Jun Chen, Wei‐Li Zhao, Xiao Jian Sun, Jinyan Huang
Software Mentions: 17
Published: over 3 years ago

10.3389/fonc.2021.658165

Using Tumor-Infiltrating Immune Cells and a ceRNA Network Model to Construct a Prognostic Analysis Model of Thyroid Carcinoma
Cited by: 11
Author(s): Fan Zhang, Xiao‐Juan Yu, Zheyu Lin, Xichang Wang, Tengteng Gao, Di Teng, Weiping Teng
Software Mentions: 17
Published: over 3 years ago

10.7554/eLife.53350

The natverse, a versatile toolbox for combining and analysing neuroanatomical data
Cited by: 128
Author(s): Alexander Shakeel Bates, James D. Manton, Sridhar R. Jagannathan, Marta Costa, Philipp Schlegel, Torsten Rohlfing, Gregory Jefferis
Software Mentions: 17
Published: over 4 years ago

10.1371/journal.pone.0135831

CoGA: An R Package to Identify Differentially Co-Expressed Gene Sets by Analyzing the Graph Spectra
Cited by: 18
Author(s): Suzana de Siqueira Santos, Thais Fernanda de Almeida Galatro, Rodrigo Akira Watanabe, Sueli Mieko Oba-Shinjo, Suely Kazue Nagahashi Marie, André Fujita
Software Mentions: 17
Published: about 9 years ago