cran: rgl | 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

mixOmics: An R package for ‘omics feature selection and multiple data integration
Cited by: 1,902
Author(s): Florian Rohart, Benoît Gautier, Amrit Singh, Kim‐Anh Lê Cao
Software Mentions: 29
Published: almost 7 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: over 3 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: over 3 years ago

10.3389/fimmu.2017.00445

Integration of Immune Cell Populations, mRNA-Seq, and CpG Methylation to Better Predict Humoral Immunity to Influenza Vaccination: Dependence of mRNA-Seq/CpG Methylation on Immune Cell Populations
Cited by: 15
Author(s): Michael T. Zimmermann, Richard B. Kennedy, Diane E. Grill, Ann L. Oberg, Krista M. Goergen, Inna G. Ovsyannikova, Iana H. Haralambieva, Gregory A. Poland
Software Mentions: 16
Published: over 7 years ago

10.3389/fonc.2020.555632

Comprehensive Characterization of Alternative mRNA Splicing Events in Glioblastoma: Implications for Prognosis, Molecular Subtypes, and Immune Microenvironment Remodeling
Cited by: 8
Author(s): Liang Zhao, Jiayue Zhang, Zhiyuan Liu, Yu Wang, Shurui Xuan, Peng Zhao
Software Mentions: 16
Published: over 3 years ago

10.1186/1471-2105-13-133

Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling
Cited by: 30
Author(s): Julien Pelé, Jean Michel Bécu, Hervé Abdi, Marie Chabbert
Software Mentions: 14
Published: over 12 years ago

10.1007/s10875-020-00908-1

Targeted Proteomics Reveals Inflammatory Pathways that Classify Immune Dysregulation in Common Variable Immunodeficiency
Cited by: 13
Author(s): Roos-Marijn Berbers, Julia Drylewicz, Pauline M. Ellerbroek, Joris M. van Montfrans, Virgil A. S. H. Dalm, P. Martin van Hagen, Baerbel Keller, Klaus Warnatz, Annick van de Ven, J.M. van Laar, Stefan Nierkens, Helen L. Leavis
Software Mentions: 13
Published: almost 4 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: over 8 years ago

10.1186/s12915-016-0258-1

The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model
Cited by: 283
Author(s): Philipp Dirksen, Sarah Arnaud Marsh, Ines Braker, Nele Heitland, Sophia Wagner, Rania Nakad, Sebastian Mäder, Carola Petersen, Vienna Kowallik, Philip Rosenstiel, Marie‐Anne Félix, Hinrich Schulenburg
Software Mentions: 12
Published: over 8 years ago

10.12688/f1000research.12122.1

Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference
Cited by: 14
Author(s): Fanny Perraudeau, Davide Risso, Kelly Street, Elizabeth Purdom, Sandrine Dudoit
Software Mentions: 12
Published: about 7 years ago

10.1002/ece3.6784

Ecomorphology of the pectoral girdle in anurans (Amphibia, Anura): Shape diversity and biomechanical considerations
Cited by: 10
Author(s): Karolin Engelkes, Lena Kath, Thomas Kleinteich, Jörg U. Hammel, André Beerlink, Alexander Haas
Software Mentions: 12
Published: about 4 years ago

10.1016/j.ccell.2017.08.017

Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma
Cited by: 662
Author(s): Alan Mackay, Anna Burford, Diana Carvalho, Elisa Izquierdo, Janat Fazal-Salom, Kathryn R. Taylor, Lynn Bjerke, Matthew Clarke, Maria Vinci, Meera Nandhabalan, Sara Temelso, Sergey Popov, Valeria Molinari, Pichai Raman, Angela J. Waanders, Harry Han, Saumya Gupta, Lynley V. Marshall, Stergios Zacharoulis, Sucheta Vaidya, Henry Mandeville, Leslie Bridges, Andrew Martin, Safa Al‐Sarraj, Christopher Chandler, Ho Keung Ng, Xingang Li, Kun Mu, Saoussen Trabelsi, Dorra H’mida-Ben Brahim, Alexei N. Kisljakov, Д. М. Коновалов, Andrew S. Moore, Ángel M. Carcaboso, Mariona Suñol, Carmen de Torres, Ofelia Cruz, Jaume Mora, Л. И. Шац, João N. Stávale, Lucas Tadeu Bidinotto, Rui Manuel Reis, Natacha Entz‐Werlé, Michael Farrell, Jane Cryan, Darach Crimmins, John Caird, Jane Pears, Michelle Monje, Marie‐Anne Debily, David Castel, Jacques Grill, Cynthia Hawkins, Hamid Nikbakht, Nada Jabado, Suzanne J. Baker, Stefan M. Pfister, David Jones, Maryam Fouladi, André O. von Bueren, Michael Baudis, Adam Resnick, Chris Jones
Software Mentions: 11
Published: almost 7 years ago

10.1371/journal.pone.0089470

Analytic Programming with fMRI Data: A Quick-Start Guide for Statisticians Using R
Cited by: 9
Author(s): Ani Eloyan, Shanshan Li, John Muschelli, James J. Pekar, Stewart H. Mostofsky, Brian Caffo
Software Mentions: 11
Published: over 10 years ago

10.3389/fimmu.2021.602539

Single-Cell Transcriptomic Analyses Define Distinct Peripheral B Cell Subsets and Discrete Development Pathways
Cited by: 60
Author(s): Alexander Stewart, Joseph C.F. Ng, Gillian A. Wallis, Vasiliki Tsioligka, Franca Fraternali, Deborah K. Dunn‐Walters
Software Mentions: 10
Published: over 3 years ago

10.1186/s12918-015-0169-8

Increased robustness of early embryogenesis through collective decision-making by key transcription factors
Cited by: 8
Author(s): Ali Sharifi-Zarchi, Mehdi Totonchi, Keynoush Khaloughi, Razieh Karamzadeh, Marcos J. Araúzo-Bravo, Hossein Baharvand, Ruzbeh Tusserkani, Hamid Pezeshk, Hamidreza Chitsaz, Mehdi Sadeghi
Software Mentions: 10
Published: over 9 years ago

10.1038/s42003-021-02137-7

The lexicon of antimicrobial peptides: a complete set of arginine and tryptophan sequences
Cited by: 33
Author(s): Sam Clark, Thomas A. Jowitt, Lynda K. Harris, Christopher G. Knight, Curtis B. Dobson
Software Mentions: 10
Published: over 3 years ago

10.1038/s41396-019-0546-1

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

10.1186/s12859-017-1936-x

Software for rapid time dependent ChIP-sequencing analysis (TDCA)
Cited by: 1
Author(s): Mike Myschyshyn, Marco Farren-Dai, Tien-Jui Chuang, David J. Vocadlo
Software Mentions: 9
Published: almost 7 years ago

10.3389/fnbeh.2019.00036

Prolonged Bat Call Exposure Induces a Broad Transcriptional Response in the Male Fall Armyworm (Spodoptera frugiperda; Lepidoptera: Noctuidae) Brain
Cited by: 13
Author(s): Scott D Cinel, Steven J. Taylor
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0204990

Blaunet: An R-based graphical user interface package to analyze Blau space
Cited by: 4
Author(s): Michael Genkin, Cheng Wang, George Berry, Matthew E. Brashears
Software Mentions: 9
Published: almost 6 years ago

10.1186/s13007-021-00795-6

Open source 3D phenotyping of chickpea plant architecture across plant development
Cited by: 6
Author(s): William T. Salter, Arjina Shrestha, Margaret M. Barbour
Software Mentions: 9
Published: about 3 years ago

10.7717/peerj.11370

Ecosystem services show variable responses to future climate conditions in the Colombian páramos
Cited by: 4
Author(s): Mauricio Diazgranados, Carolina Tovar, Thomas R. Etherington, Paula A. Rodríguez‐Zorro, Carolina Castellanos-Castro, Manuel Galvis Rueda, Suzette G. A. Flantua
Software Mentions: 8
Published: over 3 years ago

10.12688/f1000research.14361.1

freesurfer: Connecting the Freesurfer software with R
Cited by: 7
Author(s): John Muschelli, Elizabeth Sweeney, Ciprian M. Crainiceanu
Software Mentions: 8
Published: over 6 years ago

10.1186/1471-2164-13-556

Proteome remodelling during development from blood to insect-form Trypanosoma brucei quantified by SILAC and mass spectrometry
Cited by: 117
Author(s): Kapila Gunasekera, Daniel Wüthrich, Sophie Braga-Lagache, Manfred Heller, Torsten Ochsenreiter
Software Mentions: 8
Published: almost 12 years ago

10.3389/fpls.2021.675760

Genotype-Specific Expression and NLR Repertoire Contribute to Phenotypic Resistance Diversity in Plantago lanceolata
Cited by: 4
Author(s): Pezhman Safdari, Layla Höckerstedt, Mikael Brosché, Jarkko Salojärvi, Anna‐Liisa Laine
Software Mentions: 8
Published: about 3 years ago

10.3389/fpls.2020.00820

Biological Nitrification Inhibition (BNI): Phenotyping of a Core Germplasm Collection of the Tropical Forage Grass Megathyrsus maximus Under Greenhouse Conditions
Cited by: 28
Author(s): Daniel Villegas, Ashly Arévalo, Jonathan Nùñez, Johanna Mazabel, G. V. Subbarao, Idupulapati M. Rao, Jose J De Vega, Jacobo Arango
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0086986

Revealing Individual Signatures of Human T Cell CDR3 Sequence Repertoires with Kidera Factors
Cited by: 9
Author(s): Michael Epstein, Martino Barenco, Nigel Klein, Michael Hubank, Robin E. Callard
Software Mentions: 7
Published: over 10 years ago

10.1186/s12859-017-1914-3

bcROCsurface: an R package for correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests
Cited by: 6
Author(s): Khanh To Duc
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pone.0232682

A chronological model for the Late Paleolithic at Shuidonggou Locality 2, North China
Cited by: 10
Author(s): Fei Peng, Sam C. Lin, Ilaria Patania, Vladimir Levchenko, Jialong Guo, Huimin Wang, Xing Gao
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0116508

Large Scale Aggregate Microarray Analysis Reveals Three Distinct Molecular Subclasses of Human Preeclampsia
Cited by: 90
Author(s): Katherine Leavey, Shannon Bainbridge, Brian Cox
Software Mentions: 7
Published: over 9 years ago

10.1186/1471-2105-11-44

The curvHDR method for gating flow cytometry samples
Cited by: 29
Author(s): Ulrike Naumann, George Luta, M. P. Wand
Software Mentions: 7
Published: over 14 years ago

10.1016/j.immuni.2020.07.003

Differential IRF8 Transcription Factor Requirement Defines Two Pathways of Dendritic Cell Development in Humans
Cited by: 130
Author(s): Urszula Cytlak, Anastasia Resteu, Sarah Pagan, Kile Green, Paul Milne, Sheetal Maisuria, David McDonald, Gillian Hulme, Andrew Filby, Benjamin Carpenter, Rachel Queen, Sophie Hambleton, Rosie Hague, Hana Lango Allen, James Thaventhiran, Gina M. Doody, Matthew Collin, Venetia Bigley
Software Mentions: 6
Published: about 4 years ago

10.7717/peerj.1417

Tools for quantitative form description; an evaluation of different software packages for semi-landmark analysis
Cited by: 28
Author(s): Léo Botton‐Divet, Alexandra Houssaye, Anthony Herrel, Anne‐Claire Fabre, Raphaël Cornette
Software Mentions: 6
Published: almost 9 years ago

10.3390/plants10061033

Metabolic Alterations in Pisum sativum Roots during Plant Growth and Arbuscular Mycorrhiza Development
Cited by: 13
Author(s): O. Y. Shtark, Roman Puzanskiy, G. S. Avdeeva, Vladislav V. Yemelyanov, А. Л. Шаварда, Daria A. Romanyuk, Marina S. Kliukova, А. А. Кирпичникова, И. А. Тихонович, Vladimir A. Zhukov, М. Ф. Шишова
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0052884

Wrangling Phosphoproteomic Data to Elucidate Cancer Signaling Pathways
Cited by: 17
Author(s): Mark L. Grimes, Wan-Jui Lee, Laurens van der Maaten, Paul Shannon
Software Mentions: 6
Published: over 11 years ago

10.1007/s10710-018-9328-1

Visualising the global structure of search landscapes: genetic improvement as a case study
Cited by: 12
Author(s): Nadarajen Veerapen, Gabriela Ochoa
Software Mentions: 6
Published: about 6 years ago

10.18632/oncotarget.10962

Epigenetic reprogramming and aberrant expression of PRAME are associated with increased metastatic risk in Class 1 and Class 2 uveal melanomas
Cited by: 85
Author(s): Matthew G. Field, Michael A. Durante, Christina L. Decatur, Berçin Tarlan, Kristen M. Oelschlager, John F. Stone, Jeffim N. Kuznetsov, Anne M. Bowcock, Stefan Kurtenbach, J. William Harbour
Software Mentions: 6
Published: about 8 years ago

10.3390/metabo4020433

Influence of Missing Values Substitutes on Multivariate Analysis of Metabolomics Data
Cited by: 139
Author(s): Piotr S. Gromski, Yun Xu, Helen L. Kotze, Elon Correa, David I. Ellis, Emily G. Armitage, Michael L. Turner, Royston Goodacre
Software Mentions: 6
Published: over 10 years ago

10.3389/fimmu.2020.00851

Gene Expression Profiling of PDGFRA Mutant GIST Reveals Immune Signatures as a Specific Fingerprint of D842V Exon 18 Mutation
Cited by: 10
Author(s): Valentina Indio, Gloria Ravegnini, Annalisa Astolfi, Milena Urbini, Maristella Saponara, Antonio De Leo, Elisa Gruppioni, Giuseppe Tarantino, Sabrina Angelini, Andrea Pession, Maria Abbondanza Pantaleo, Margherita Nannini
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-017-06880-y

A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis
Cited by: 29
Author(s): Fiona Fouhy, N.J. Ronan, Órla O’Sullivan, Yvonne McCarthy, Aaron M. Walsh, Desmond M. Murphy, Mary B. Daly, Evelyn Flanagan, C. Fleming, M. McCarthy, C. Shortt, Joseph A. Eustace, Fergus Shanahan, Mary C. Rea, R. Paul Ross, Catherine Stanton, Barry J. Plant
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pone.0219072

Defining ecological regions in Italy based on a multivariate clustering approach: A first step towards a targeted vector borne disease surveillance
Cited by: 21
Author(s): Carla Ippoliti, Luca Candeloro, Marius Gilbert, Maria Goffredo, Giuseppe Mancini, Gabriele Curci, Serena Falasca, Susanna Tora, Alessio Di Lorenzo, Michela Quaglia, Annamaria Conte
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0053544

Visualising the Cross-Level Relationships between Pathological and Physiological Processes and Gene Expression: Analyses of Haematological Diseases
Cited by: 13
Author(s): M. Ono, Reiko Tanaka, Manabu Kano, Toshio Sugiman
Software Mentions: 6
Published: over 11 years ago

10.1371/journal.pone.0207051

A comparative venomic fingerprinting approach reveals that galling and non-galling fig wasp species have different venom profiles
Cited by: 4
Author(s): Leonardo Abdala Elias, Denise Brentan Silva, Ricardo Silva, Yan‐Qiong Peng, Da‐Rong Yang, Norberto P. Lopes, Rodrigo Augusto Santinelo Pereira
Software Mentions: 6
Published: almost 6 years ago

10.1038/srep30388

Smoking, pregnancy and the subgingival microbiome
Cited by: 31
Author(s): Akshay D. Paropkari, Binnaz Leblebicioğlu, Lisa M. Christian, Purnima Kumar
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pone.0117605

Gender-Dependent Differences in Plasma Matrix Metalloproteinase-8 Elevated in Pulmonary Tuberculosis
Cited by: 27
Author(s): Tarangini Sathyamoorthy, Gurjinder Sandhu, Liku B. Tezera, Richard Thomas, Akul Singhania, Christopher H. Woelk, Borislav D. Dimitrov, Dan Agranoff, Carlton A. Evans, Jon S. Friedland, Paul Elkington
Software Mentions: 5
Published: over 9 years ago

10.1016/j.celrep.2021.109119

Integrated OMICs unveil the bone-marrow microenvironment in human leukemia
Cited by: 13
Author(s): Diana Passaro, Manuel Garcia-Albornoz, Giovanni Diana, Probir Chakravarty, Linda Ariza‐McNaughton, Antoniana Batsivari, Clara Borràs-Eroles, Ander Abarrategi, Alexander Waclawiczek, Luigi Ombrato, Ilaria Malanchi, John G. Gribben, Dominique Bonnet
Software Mentions: 5
Published: over 3 years ago

10.12688/f1000research.10411.2

A Bioconductor workflow for processing and analysing spatial proteomics data
Cited by: 23
Author(s): Lisa M. Breckels, Claire M. Mulvey, Kathryn S. Lilley, Laurent Gatto
Software Mentions: 5
Published: about 6 years ago

10.3389/fonc.2020.01119

Identification of RNA: 5-Methylcytosine Methyltransferases-Related Signature for Predicting Prognosis in Glioma
Cited by: 23
Author(s): Peng Wang, Minxian Wu, Zewei Tu, Chuming Tao, Qing Hu, Kuangxun Li, Xingen Zhu, Kai Huang
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-020-67897-4

New methodology to process shifted excitation Raman difference spectroscopy data: a case study of pollen classification
Cited by: 15
Author(s): Florian Korinth, Abdullah Saif Mondol, Clara Stiebing, Iwan W. Schie, Christoph Krafft, Jürgen Popp
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-020-62782-6

Exploring the configuration spaces of surface materials using time-dependent diffraction patterns and unsupervised learning
Cited by: 4
Author(s): Daniel M. Packwood
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-58433-5

Hybridization between subterranean tuco-tucos (Rodentia, Ctenomyidae) with contrasting phylogenetic positions
Cited by: 11
Author(s): Bruno Busnello Kubiak, Rafael Kretschmer, Leonardo Trindade Leipnitz, Renan Maestri, Thamara Santos de Almeida, Leandro Rodrigues Borges, Daniel Galiano, Jorge C. Pereira, Edivaldo Herculano Corrêa de Oliveira, Malcolm A. Ferguson-Smith, Thales Renato Ochotorena de Freitas
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-018-29677-z

Automated analysis of lipid drug-response markers by combined fast and high-resolution whole cell MALDI mass spectrometry biotyping
Cited by: 18
Author(s): David Weigt, Denis A. Sammour, Timon Ulrich, Bogdan Munteanu, Carsten Hopf
Software Mentions: 5
Published: about 6 years ago

10.1016/j.mex.2020.100820

A statistical and numerical modeling approach for spatiotemporal reconstruction of glaciations in the Central Asian mountains
Cited by: 1
Author(s): Sourav Saha, Lewis A. Owen, Elizabeth N. Orr, Marc W. Caffee
Software Mentions: 5
Published: over 4 years ago

10.1038/srep24362

Perceptual drifts of real and artificial limbs in the rubber hand illusion
Cited by: 43
Author(s): Xaver Fuchs, Martin Riemer, Martin Diers, Herta Flor, Jörg Trojan
Software Mentions: 5
Published: over 8 years ago

10.1021/acs.jcim.0c01382

Use of the Complementarity Principle in Docking Procedures: A New Approach for Evaluating the Correctness of Binding Poses
Cited by: 12
Author(s): Hrvoje Rimac, Maria Grishina, В. А. Потемкин
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0103514

Identification of a Novel Luminal Molecular Subtype of Breast Cancer
Cited by: 14
Author(s): Anna Dvorkin‐Gheva, John A. Hassell
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pone.0239541

Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.)
Cited by: 14
Author(s): Nikolaj Vendelbo, Pernille Sarup, Jihad Orabi, Peter Skov Kristensen, A. Jahoor
Software Mentions: 5
Published: almost 4 years ago

10.14814/phy2.13133

Hypothalamic transcriptomic alterations in male and female California mice (Peromyscus californicus) developmentally exposed to bisphenol A or ethinyl estradiol
Cited by: 25
Author(s): Sarah A. Johnson, William G. Spollen, Lindsey K. Manshack, Nathan J. Bivens, Scott A. Givan, Cheryl S. Rosenfeld
Software Mentions: 4
Published: over 7 years ago

10.18632/oncotarget.7442

Distinct lncRNA transcriptional fingerprints characterize progressive stages of multiple myeloma
Cited by: 75
Author(s): Domenica Ronchetti, Luca Agnelli, Elisa Taìana, S. Galletti, Martina Manzoni, Katia Todoerti, Pellegrino Musto, Francesco Strozzi, Antonino Neri
Software Mentions: 4
Published: over 8 years ago

10.1038/s41396-021-00953-7

Nutrient complexity triggers transitions between solitary and colonial growth in bacterial populations
Cited by: 30
Author(s): Glen D’Souza, Vanessa R. Povolo, Johannes M. Keegstra, Roman Stocker, Martin Ackermann
Software Mentions: 4
Published: over 3 years ago

10.3390/vaccines9060664

In Vitro Characterization of the Innate Immune Pathways Engaged by Live and Inactivated Tick-Borne Encephalitis Virus
Cited by: 3
Author(s): Aurora Signorazzi, Jeroen L. A. Pennings, Marilena P. Etna, Malou Noya, Eliana M. Coccia, Anke Huckriede
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2105-11-45

NeatMap - non-clustering heat map alternatives in R
Cited by: 77
Author(s): Satwik Rajaram, Yoshitsugu Oono
Software Mentions: 4
Published: over 14 years ago

10.1186/s13073-020-00824-4

The identification of novel immunogenic antigens as potential Shigella vaccine components
Cited by: 8
Author(s): Ruklanthi de Alwis, Li Liang, Omid Taghavian, Emma Werner, Trang Nguyen Hoang Thu, Vu Thuy Duong, D. Huw Davies, Philip L. Felgner, Stephen Baker
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2105-14-S16-S4

cellXpress: a fast and user-friendly software platform for profiling cellular phenotypes
Cited by: 25
Author(s): Danai Laksameethanasan, Rui Zhen Tan, Geraldine Wei-Ling Toh, Lit‐Hsin Loo
Software Mentions: 4
Published: almost 11 years ago

10.1016/j.omto.2020.04.001

A Cross-Reactive Small Protein Binding Domain Provides a Model to Study Off-Tumor CAR-T Cell Toxicity
Cited by: 6
Author(s): Joanne A. Hammill, Jacek M. Kwiecień, Anna Dvorkin‐Gheva, Vivian Wing Chong Lau, Christopher L. Baker, Ying Wu, Ksenia Bezverbnaya, Craig Aarts, Christopher W. Heslen, Galina Denisova, Heather Derocher, Katy Milne, Brad H. Nelson, Jonathan L. Bramson
Software Mentions: 4
Published: over 4 years ago

10.3390/microorganisms8040513

Relationships between Gut Microbiota, Metabolome, Body Weight, and Glucose Homeostasis of Obese Dogs Fed with Diets Differing in Prebiotic and Protein Content
Cited by: 15
Author(s): Emmanuelle Apper, Lisa Privet, Bernard Taminiau, Cindy Le Bourgot, Ljubica Svilar, Jean‐Charles Martin, Marianne Diez
Software Mentions: 4
Published: over 4 years ago

10.1128/mBio.03348-19

An Advanced Human Intestinal Coculture Model Reveals Compartmentalized Host and Pathogen Strategies during Salmonella Infection
Cited by: 21
Author(s): Leon N. Schulte, Matthias Schweinlin, Alexander J. Westermann, Harshavardhan Janga, Sara Correia Santos, Silke Appenzeller, Heike Walles, Jörg Vogel, Marco Metzger
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2017.01351

Critical Role of Plasmacytoid Dendritic Cells in Regulating Gene Expression and Innate Immune Responses to Human Rhinovirus-16
Cited by: 11
Author(s): Xi Yang, Niamh M. Troy, Denise Anderson, Olga M. Pena, Jason P. Lynch, Simon Phipps, Anthony Bosco, John W. Upham
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41416-019-0558-7

Evaluating radiological response in pancreatic neuroendocrine tumours treated with sunitinib: comparison of Choi versus RECIST criteria (CRIPNET_ GETNE1504 study)
Cited by: 15
Author(s): María Pilar Solis-Hernández, A. Fernández del Valle, Alberto Carmona-Bayonas, Rocío Garcia-Carbonero, Ana Custodio, Marta Benavent, Teresa Alonso Gordoa, Bárbara Nuñez-Valdovino, Manuel Sánchez Cánovas, Ignacio Matos, Vicente Alonso, Carlos López, A. Viúdez, M. Izquierdo, David Calvo-Temprano, Enrique Grande, Jaume Capdevila, Paula Jiménez‐Fonseca
Software Mentions: 4
Published: about 5 years ago

10.1038/bcj.2016.77

lncRNA profiling in early-stage chronic lymphocytic leukemia identifies transcriptional fingerprints with relevance in clinical outcome
Cited by: 40
Author(s): Domenica Ronchetti, Martina Manzoni, Luca Agnelli, Cristina Vinci, Sonia Fabris, Giovanna Cutrona, Serena Matis, Monica Colombo, S. Galletti, Elisa Taìana, Anna Grazia Recchia, Sabrina Bossio, Massimo Gentile, Caterina Musolino, Francesco Di Raimondo, Andrea Grilli, Silvio Bicciato, Agostino Cortelezzi, Pierfrancesco Tassone, Fortunato Morabito, Manlio Ferrarini, Antonino Neri
Software Mentions: 4
Published: about 8 years ago

10.1186/s12920-018-0378-2

Identification of differential gene expression profile from peripheral blood cells of military pilots with hypertension by RNA sequencing analysis
Cited by: 10
Author(s): Xiaohu Zhao, Shaohua Yang, Yi-Shang Yan, Xin Zhang, Lin Zhang, Bo Jiao, Shuai Jiang, Zhi‐Bin Yu
Software Mentions: 4
Published: about 6 years ago

10.1186/s13395-016-0115-5

Skeletal muscle characteristics are preserved in hTERT/cdk4 human myogenic cell lines
Cited by: 53
Author(s): Matthew Thorley, Stéphanie Duguez, Emilia Maria Cristina Mazza, Sara Valsoni, Anne Bigot, Kamel Mamchaoui, Brennan Harmon, Thomas Voït, Vincent Mouly, William Duddy
Software Mentions: 4
Published: almost 8 years ago

10.3390/jcm9051418

Circulating MicroRNAs as Potential Predictors of Anthracycline-Induced Troponin Elevation in Breast Cancer Patients: Diverging Effects of Doxorubicin and Epirubicin
Cited by: 27
Author(s): Sonia Gioffré, Mattia Chiesa, Daniela Cardinale, Veronica Ricci, Chiara Vavassori, Carlo M. Cipolla, Serge Masson, Maria Teresa Sandri, Michela Salvatici, Fabio Ciceri, Roberto Latini, Lidia Staszewsky, Giulio Pompilio, Gualtiero I. Colombo, Yuri D’Alessandra
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.ppat.1005168

The White-Nose Syndrome Transcriptome: Activation of Anti-fungal Host Responses in Wing Tissue of Hibernating Little Brown Myotis
Cited by: 90
Author(s): Kenneth A. Field, Joseph S. Johnson, Thomas M. Lilley, Sophia Reeder, Elizabeth J. Rogers, Melissa Behr, DeeAnn M. Reeder
Software Mentions: 4
Published: almost 9 years ago

10.1534/g3.120.401824

A Novel Mapping Strategy Utilizing Mouse Chromosome Substitution Strains Identifies Multiple Epistatic Interactions That Regulate Complex Traits
Cited by: 3
Author(s): Anna Miller, Anlu Chen, Jacquelaine Bartlett, Li Wang, Scott M. Williams, David A. Buchner
Software Mentions: 4
Published: almost 4 years ago

10.1021/acs.jpcb.1c00304

Oligomannose N-Glycans 3D Architecture and Its Response to the FcγRIIIa Structural Landscape
Cited by: 7
Author(s): Carl A Fogarty, Elisa Fadda
Software Mentions: 3
Published: over 3 years ago

10.1186/s12920-020-0712-3

MyoMiner: explore gene co-expression in normal and pathological muscle
Cited by: 7
Author(s): Apostolos Malatras, Ioannis Michalopoulos, Stéphanie Duguez, Gillian Butler‐Browne, Simone Spuler, William Duddy
Software Mentions: 3
Published: over 4 years ago

10.1186/1755-8794-7-28

Integrative analysis of the transcriptome profiles observed in type 1, type 2 and gestational diabetes mellitus reveals the role of inflammation
Cited by: 27
Author(s): Adriane Feijó Evangelista, Cristhianna V. A. Collares, Deise Ferreira Xavier, Cristiana Santos de Macedo, Fernanda S. Manoel-Caetano, Diane Meyre Rassi, Maria Cristina Foss‐Freitas, Milton César Foss, Elza T. Sakamoto-Hojo, Catherine Nguyen, Denis Puthier, Geraldo A. S. Passos, Eduardo Antônio Donadi
Software Mentions: 3
Published: over 10 years ago

10.1186/s12943-021-01392-w

Using single-cell sequencing technology to detect circulating tumor cells in solid tumors
Cited by: 32
Author(s): Jiasheng Xu, Kaili Liao, Yang Xi, Chengfeng Wu, Wei Wu, Shuwen Han
Software Mentions: 3
Published: about 3 years ago

10.3897/zookeys.560.6264

Taxonomic revision of the tarantula genus Aphonopelma Pocock, 1901 (Araneae, Mygalomorphae, Theraphosidae) within the United States
Cited by: 53
Author(s): Chris A. Hamilton, Brent E. Hendrixson, Jason E. Bond
Software Mentions: 3
Published: over 8 years ago

10.7717/peerj.7355

Intraspecific variation and symmetry of the inner-ear labyrinth in a population of wild turkeys: implications for paleontological reconstructions
Cited by: 13
Author(s): Donald G. Cerio, Lawrence M. Witmer
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0212120

Molecular fungal community and its decomposition activity in sapwood and heartwood of 13 temperate European tree species
Cited by: 51
Author(s): Sabrina Leonhardt, Björn Hoppe, Elisa Stengel, Lisa Noll, Julia Moll, Claus Bässler, Andreas Dahl, François Buscot, Martin Hofrichter, Harald Kellner
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0078835

Depth-Dependent Differences in Community Structure of the Human Colonic Microbiota in Health
Cited by: 21
Author(s): Aonghus Lavelle, Gráinne Lennon, Neil G. Docherty, Áine Balfe, Hugh Mulcahy, Glen Doherty, Diarmuid O’Donoghue, John Hyland, Fergus Shanahan, Kieran Sheahan, J. Calvin Coffey, Desmond C. Winter, P. R. O’Connell
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0039752

Convergence and Divergence in the Evolution of Cat Skulls: Temporal and Spatial Patterns of Morphological Diversity
Cited by: 54
Author(s): Manabu Sakamoto, Marcello Ruta
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0245501

Balancing time use for children’s fitness and adiposity: Evidence to inform 24-hour guidelines for sleep, sedentary time and physical activity
Cited by: 16
Author(s): Dorothea Dumuid, Melissa Wake, David Burgner, Mark S. Tremblay, Anthony D. Okely, Ben Edwards, Terence Dwyer, Tim Olds
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0101777

Rapid Phenotypic and Genomic Change in Response to Therapeutic Pressure in Prostate Cancer Inferred by High Content Analysis of Single Circulating Tumor Cells
Cited by: 123
Author(s): Angel E. Dago, Asya Stepansky, Anders Carlsson, Madelyn Luttgen, Jude Kendall, Timour Baslan, Anand Kolatkar, Michael Wigler, Kelly Bethel, Mitchell E. Gross, James Hicks, Peter Kühn
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0118528

A Cell-Based Systems Biology Assessment of Human Blood to Monitor Immune Responses after Influenza Vaccination
Cited by: 73
Author(s): Kristen L. Hoek, Parimal Samir, Leigh M. Howard, Xinnan Niu, Nripesh Prasad, Allison C. Galassie, Qi Liu, Tara M. Allos, Kyle A. Floyd, Yan Guo, Yu Shyr, Shawn Levy, Sebastian Joyce, Kathryn M. Edwards, Andrew J. Link
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0118201

A Combined Gene Signature of Hypoxia and Notch Pathway in Human Glioblastoma and Its Prognostic Relevance
Cited by: 45
Author(s): Khushboo Irshad, Saroj Kant Mohapatra, Chitrangda Srivastava, Harshit Garg, Seema Mishra, Bhawana Dikshit, Chitra Sarkar, Deepak Gupta, P. Sarat Chandra, Parthaprasad Chattopadhyay, Subrata Sinha, Kunzang Chosdol
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0255168

FFPE samples from cavitational ultrasonic surgical aspirates are suitable for RNA profiling of gliomas
Cited by: 2
Author(s): Cristina Alenda, Estefanía Rojas, Luis M. Valor
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0229956

Trajectories toward maximum power and inequality in resource distribution networks
Cited by: 2
Author(s): Natalie Davis, Andrew Jarvis, Matt Aitkenhead, Gary Polhill
Software Mentions: 3
Published: over 4 years ago

10.3390/cancers13030550

Extracellular miRNAs as Predictive Biomarkers for Glypican-3-Derived Peptide Vaccine Therapy Response in Ovarian Clear Cell Carcinoma
Cited by: 6
Author(s): Makoto Ukai, Akira Yokoi, Kosuke Yoshida, Shiro Suzuki, Kiyosumi Shibata, Fumitaka Kikkawa, Tetsuya Nakatsura, Hiroaki Kajiyama
Software Mentions: 3
Published: over 3 years ago

10.1002/ece3.5779

Novel tri‐isotope ellipsoid approach reveals dietary variation in sympatric predators
Cited by: 11
Author(s): Christina Skinner, Aileen C. Mill, Steven P. Newman, Jason Newton, Matthew R. D. Cobain, Nicholas Polunin
Software Mentions: 3
Published: almost 5 years ago

10.3390/jcm10051057

Gene Expression Landscape of SDH-Deficient Gastrointestinal Stromal Tumors
Cited by: 9
Author(s): Valentina Indio, Angela Schipani, Margherita Nannini, Milena Urbini, Alessandro Rizzo, Antonio De Leo, Annalisa Altimari, Valerio Di Scioscio, Daria Messelodi, Giuseppe Tarantino, Annalisa Astolfi, Maria Abbondanza Pantaleo
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1008010

The Klebsiella pneumoniae citrate synthase gene, gltA, influences site specific fitness during infection
Cited by: 25
Author(s): Jay Vornhagen, Yuang Sun, Paul A. Breen, Valerie Forsyth, Lili Zhao, Harry L. T. Mobley, Michael A. Bachman
Software Mentions: 3
Published: about 5 years ago

10.1186/s12284-021-00481-0

Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam
Cited by: 11
Author(s): Janet Higgins, Bruno Santos, Tran Dang Khanh, Khuất Hữu Trung, Tran Duy Duong, Nguyen Thi Phuong Doai, Nguyen Truong Khoa, Dang Thi Thanh Ha, Nguyen Thuy Diep, Kieu Thi Dung, Cong Nguyen Phi, Trần Thị Thu Thủy, Nguyễn Thành Tuấn, Hoang-Dung Tran, Nguyễn Thành Trung, Hoang Thi Nam Giang, Ta Kim Nhung, Cuong Tran, Son Lang, La Tuan Nghia, Nguyễn Văn Giảng, Tran Dang Xuan, Anthony Hall, Sarah Dyer, Lê Huy Hàm, Mario Cáccamo, Jose J De Vega
Software Mentions: 3
Published: over 3 years ago

10.1038/srep10035

Atlas of tissue renin-angiotensin-aldosterone system in human: A transcriptomic meta-analysis
Cited by: 50
Author(s): Ali Nehme, Catherine Cerutti, Nedra Dhaouadi, Marie Paule Gustin, Pierre‐Yves Courand, Kazem Zibara, Giampiero Bricca
Software Mentions: 3
Published: over 9 years ago

10.1155/2013/232143

Computational Representation of White Matter Fiber Orientations
Cited by: 0
Author(s): Adelino R. Ferreira da Silva
Software Mentions: 3
Published: over 11 years ago

10.7554/eLife.37621

Strong biomechanical relationships bias the tempo and mode of morphological evolution
Cited by: 34
Author(s): Martha M. Muñoz, Yinan Hu, Philip S. L. Anderson, S. N. Patek
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.21715

Spinal microcircuits comprising dI3 interneurons are necessary for motor functional recovery following spinal cord transection
Cited by: 41
Author(s): Tuan V. Bui, Nicolas Stifani, Turgay Akay, Robert M. Brownstone
Software Mentions: 3
Published: almost 8 years ago

Projects: cran: rgl

Papers Mentioning rgl 156