cran: mclust | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1006361

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Cited by: 92
Author(s): Tian Li, Shian Su, Xueyi Dong, Daniela Amann‐Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J. Hilton, Shalin H. Naik, Matthew E. Ritchie
Software Mentions: 21
Published: over 6 years ago

10.7717/peerj.5794

beadplexr: reproducible and automated analysis of multiplex bead assays
Cited by: 4
Author(s): Ulrik Stervbo, Timm H. Westhoff, Nina Babel
Software Mentions: 20
Published: about 6 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: about 4 years ago

10.1186/s13059-020-02132-x

A systematic evaluation of single-cell RNA-sequencing imputation methods
Cited by: 156
Author(s): Wenpin Hou, Zhicheng Ji, Hongkai Ji, Stephanie Hicks
Software Mentions: 15
Published: over 4 years ago

10.1371/journal.pone.0219892

Quantification and isolation of Bacillus subtilis spores using cell sorting and automated gating
Cited by: 18
Author(s): Marianna Karava, Felix Bracharz, Johannes Kabisch
Software Mentions: 15
Published: over 5 years ago

10.1038/s42003-019-0554-8

Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome
Cited by: 37
Author(s): Weiyan Chen, Samuel Morabito, Kai Kessenbrock, Tariq Enver, Kerstin B. Meyer, Andrew E. Teschendorff
Software Mentions: 14
Published: over 5 years ago

10.1186/s13059-019-1739-7

CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data
Cited by: 33
Author(s): Rebekka Wegmann, Marilisa Neri, Sven Schuierer, Bilada Bilican, Huyen Hartkopf, Florian Nigsch, Felipa Mapa, Annick Waldt, Rachel Cuttat, Max R. Salick, Joe Raymond, Ajamete Kaykas, Guglielmo Roma, Caroline Gubser Keller
Software Mentions: 13
Published: over 5 years ago

10.12688/f1000research.19236.3

Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures
Cited by: 11
Author(s): Dharmesh D. Bhuva, Momeneh Foroutan, Yi Xie, Ruqian Lyu, Joseph Cursons, Melissa J. Davis
Software Mentions: 13
Published: about 5 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

10.1186/s12937-021-00692-7

A review of statistical methods for dietary pattern analysis
Cited by: 103
Author(s): Junkang Zhao, Zhiyao Li, Qian Gao, Haifeng Zhao, Shuting Chen, Ling-Qiao Huang, Yiyun Wang, Tong Wang
Software Mentions: 12
Published: over 3 years ago

10.1186/s12859-021-04028-4

scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data
Cited by: 12
Author(s): Bobby Ranjan, Florian Schmidt, Wenjie Sun, Jinyu Park, Mohammad Amin Honardoost, Joanna H.J. Tan, Nirmala Arul Rayan, Shyam Prabhakar
Software Mentions: 12
Published: over 3 years ago

10.1016/j.isci.2021.102882

Integrated analysis of glycan and RNA in single cells
Cited by: 22
Author(s): Fumi Minoshima, Haruka Ozaki, Haruki Odaka, Hiroaki Tateno
Software Mentions: 11
Published: over 3 years ago

10.1016/j.cell.2016.08.041

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds
Cited by: 359
Author(s): Alejandra Bruna, Oscar M. Rueda, Wendy Greenwood, Ankita Batra, Maurizio Callari, R N Batra, Katherine Pogrebniak, José Luís Sandoval, John W. Cassidy, Ana Tufegdžić Vidaković, Stephen‐John Sammut, Linda Jones, Elena Provenzano, Richard D. Baird, Peter Eirew, James Hadfield, Matthew Eldridge, Anne McLaren-Douglas, Andrew Barthorpe, Howard Lightfoot, Mark J. O’Connor, Joe W. Gray, Javier Cortés, José Baselga, Elisabetta Marangoni, Alana L. Welm, Samuel Aparicio, Violeta Serra, Mathew J. Garnett, Carlos Caldas
Software Mentions: 11
Published: over 8 years ago

10.1038/s41598-021-88698-3

In-depth transcriptomic analysis of human retina reveals molecular mechanisms underlying diabetic retinopathy
Cited by: 23
Author(s): Kolja Becker, H. Klein, Eric J. Simon, Coralie Viollet, Christian Haslinger, Germán Leparc, Christian Schultheis, Victor Chong, Markus H. Kuehn, Francesc Fernández-Albert, Remko A. Bakker
Software Mentions: 11
Published: over 3 years ago

10.1111/jcmm.16773

Peripheral blood transcriptome heterogeneity and prognostic potential in lung cancer revealed by RNA‐Seq
Cited by: 3
Author(s): Qi Zhang, Manchao Kuang, Haiyin An, Yajing Zhang, Kai Zhang, Feng Li, Lei Zhang, Shujun Cheng
Software Mentions: 11
Published: over 3 years ago

10.1186/s12859-020-03795-w

optimalFlow: optimal transport approach to flow cytometry gating and population matching
Cited by: 11
Author(s): Eustasio del Barrio, Hristo Inouzhe, Jean-Michel Loubès, Carlos Matrán, Agustín Mayo-Íscar
Software Mentions: 10
Published: about 4 years ago

10.1371/journal.pone.0095753

A Comparison of Supervised Machine Learning Algorithms and Feature Vectors for MS Lesion Segmentation Using Multimodal Structural MRI
Cited by: 41
Author(s): Elizabeth Sweeney, Joshua T. Vogelstein, Jennifer L. Cuzzocreo, Peter A. Calabresi, Daniel S. Reich, Ciprian M. Crainiceanu, Russell T. Shinohara
Software Mentions: 10
Published: over 10 years ago

10.1007/s10705-017-9870-x

Soil nutrient maps of Sub-Saharan Africa: assessment of soil nutrient content at 250 m spatial resolution using machine learning
Cited by: 170
Author(s): Tomislav Hengl, J.G.B. Leenaars, Keith D. Shepherd, Markus Walsh, G.B.M. Heuvelink, Tekalign Mamo, H. Tilahun, Ezra Berkhout, Matthew Cooper, Eric Fegraus, Ichsani Wheeler, Nketia A. Kwabena
Software Mentions: 10
Published: over 7 years ago

10.1371/journal.pone.0131435

Limitations of Climatic Data for Inferring Species Boundaries: Insights from Speckled Rattlesnakes
Cited by: 30
Author(s): Jesse M. Meik, Jeffrey W. Streicher, A. Michelle Lawing, Oscar Flores‐Villela, Matthew K. Fujita
Software Mentions: 10
Published: over 9 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

10.1186/1471-2105-11-503

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/s12885-017-3726-2

Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer
Cited by: 26
Author(s): Melissa Quintero, Douglas Adamóski, Larissa Menezes dos Reis, Carolline Fernanda Rodrigues Ascenção, Krishina Ratna Sousa de Oliveira, Kaliandra de Almeida Gonçalves, Milton Dias, Marcelo Falsarella Carazzolle, Sandra Martha Gomes Dias
Software Mentions: 9
Published: about 7 years ago

10.1186/s12915-018-0518-3

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3
Cited by: 21
Author(s): Angelika Schmidt, Francesco Marabita, Narsis A. Kiani, Catharina C. Groß, Henrik J. Johansson, Szabolcs Éliás, Sini Rautio, Matilda Eriksson, Sunjay Jude Fernandes, Gilad Silberberg, Ubaid Ullah, Urvashi Bhatia, Harri Lähdesmäki, Janne Lehtiö, David Gomez-Cabrero, Heinz Wiendl, Riitta Lahesmaa, Jesper Tegnér
Software Mentions: 9
Published: over 6 years ago

10.1016/j.comppsych.2019.152143

Longitudinal population subgroups of CRP and risk of depression in the ALSPAC birth cohort
Cited by: 11
Author(s): Emanuele F. Osimo, Jan S̆tochl, Stanley Zammit, Glyn Lewis, Peter B. Jones, Golam M. Khandaker
Software Mentions: 9
Published: almost 5 years ago

10.1186/s13059-020-02008-0

scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
Cited by: 24
Author(s): Wenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen, Kai Tan
Software Mentions: 9
Published: over 4 years ago

10.3389/fpsyg.2020.533593

Students’ Motivation and Affection Profiles and Their Relation to Mathematics Achievement, Persistence, and Behaviors
Cited by: 7
Author(s): Feiya Xiao, Li Sun
Software Mentions: 9
Published: almost 4 years ago

10.1186/1471-2164-15-139

Unique features of the transcriptional response to model aneuploidy in human cells
Cited by: 85
Author(s): Milena Dürrbaum, Anastasia Yurievna Kuznetsova, Verena Passerini, Silvia Stingele, Gabriele Stoehr, Zuzana Storchová
Software Mentions: 9
Published: almost 11 years ago

10.1186/s13059-020-02075-3

Single-cell ATAC-seq signal extraction and enhancement with SCATE
Cited by: 29
Author(s): Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji
Software Mentions: 8
Published: over 4 years ago

10.1038/s41392-021-00729-7

Technological advances in cancer immunity: from immunogenomics to single-cell analysis and artificial intelligence
Cited by: 34
Author(s): Ying Xu, Guan-Hua Su, Ding Ma, Yi Xiao, Zhi-Ming Shao
Software Mentions: 8
Published: over 3 years ago

10.3390/cancers13071561

NF2 and Canonical Hippo-YAP Pathway Define Distinct Tumor Subsets Characterized by Different Immune Deficiency and Treatment Implications in Human Pleural Mesothelioma
Cited by: 19
Author(s): Haitang Yang, Sean Hall, Beibei Sun, Liang Zhao, Yanyun Gao, Ralph A. Schmid, Swee T. Tan, Ren‐Wang Peng, Feng Yao
Software Mentions: 8
Published: over 3 years ago

10.1002/ece3.7211

Investigating the morphological and genetic divergence of arctic char ( Salvelinus alpinus) populations in lakes of arctic Alaska
Cited by: 3
Author(s): Stephen L. Klobucar, Jessica A. Rick, Elizabeth G. Mandeville, Catherine E. Wagner, Phaedra Budy
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12859-017-1998-9

Thresher: determining the number of clusters while removing outliers
Cited by: 36
Author(s): Min Wang, Zachary B. Abrams, Steven M. Kornblau, Kevin R. Coombes
Software Mentions: 8
Published: almost 7 years ago

10.1038/s41598-019-40503-y

Sequential conditioning-stimulation reveals distinct gene- and stimulus-specific effects of Type I and II IFN on human macrophage functions
Cited by: 23
Author(s): Quen J. Cheng, Faraz Behzadi, Supriya Sen, Sho Ohta, Roberto Spreafico, Rosane M. B. Teles, Robert L. Modlin, Alexander Hoffmann
Software Mentions: 8
Published: over 5 years ago

10.1002/ece3.4535

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

10.1371/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: almost 10 years ago

10.1186/s12864-019-6308-7

Human gene expression variability and its dependence on methylation and aging
Cited by: 23
Author(s): Nasser Bashkeel, Theodore J. Perkins, Mads Kærn, Jonathan M. Lee
Software Mentions: 7
Published: about 5 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

10.1371/journal.pbio.3000792

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

10.3390/nu13062081

Effects of a Diet Based on Foods from Symbiotic Agriculture on the Gut Microbiota of Subjects at Risk for Metabolic Syndrome
Cited by: 4
Author(s): Silvia Turroni, Elisabetta Petracci, Valeria Edefonti, Anna Maria Giudetti, Federica D’Amico, Lisa Paganelli, Giusto Giovannetti, Laura Del Coco, Francesco Paolo Fanizzi, Simone Rampelli, Débora Antoniazi Del Guerra, Claudia Rengucci, Jenny Bulgarelli, Marcella Tazzari, Nicoletta Pellegrini, Monica Ferraroni, Oriana Nanni, Patrizia Serra
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pgen.1008855

Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits
Cited by: 8
Author(s): Wei Cheng, Sohini Ramachandran, Lorin Crawford
Software Mentions: 7
Published: over 4 years ago

10.1186/s13059-015-0675-4

Extensive rewiring of epithelial-stromal co-expression networks in breast cancer
Cited by: 42
Author(s): Eunsun Oh, Stephen M Christensen, Sindhu Ghanta, Jong Cheol Jeong, Octavian Bucur, Benjamin Glass, Laleh Montaser‐Kouhsari, Nicholas W. Knoblauch, Nicholas Bertos, Sadiq M.I. Saleh, Benjamin Haibe‐Kains, Morag Park, Andrew H. Beck
Software Mentions: 7
Published: over 9 years ago

10.1186/s13075-016-1120-0

A discrete cluster of urinary biomarkers discriminates between active systemic lupus erythematosus patients with and without glomerulonephritis
Cited by: 25
Author(s): Carolina Landolt-Marticorena, Stephenie D. Prokopec, Stacey Morrison, Babak Noamani, Dennisse Bonilla, Heather N. Reich, James W. Scholey, Carmen Ávila-Casado, Paul R. Fortin, Paul C. Boutros, Joan E. Wither
Software Mentions: 7
Published: about 8 years ago

10.1534/g3.120.401579

High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus
Cited by: 19
Author(s): Thomas W. R. Harrop, Joseph Guhlin, Gemma M. McLaughlin, Elizabeth Permina, Peter A. Stockwell, Josh Gilligan, Marissa F. Le Lec, Monica A. M. Gruber, Oliver Quinn, Mackenzie Lovegrove, Elizabeth J. Duncan, Emily J. Remnant, Jens Van Eeckhoven, Brittany Graham, Rosemary A Knapp, Kyle W. Langford, Zev Kronenberg, Maximilian O. Press, Stephen Eacker, Erin E. Wilson Rankin, Jessica Purcell, Philip J. Lester, Peter K. Dearden
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0187735

Transcriptome profile of lung dendritic cells after in vitro porcine reproductive and respiratory syndrome virus (PRRSV) infection
Cited by: 16
Author(s): Maren Pröll, Christiane Neuhoff, K. Schellander, Muhammad Jasim Uddin, Mehmet Ulaş Çınar, Sudeep Sahadevan, Xuecheng Qu, M. S. Islam, Mikhaël Poirier, Marcel A. Müller, Christian Drosten, Dawit Tesfaye, Ernst Tholen, Christine Große‐Brinkhaus
Software Mentions: 7
Published: about 7 years ago

10.1136/bmj.m3249

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

10.1038/s41598-020-67016-3

Recursive Consensus Clustering for novel subtype discovery from transcriptome data
Cited by: 5
Author(s): Pranali Sonpatki, Nameeta Shah
Software Mentions: 6
Published: over 4 years ago

10.1002/ece3.6182

Isotopic niche differs between seal and fish‐eating killer whales ( Orcinus orca ) in northern Norway
Cited by: 24
Author(s): Eve Jourdain, Clare Andvik, Richard Karoliussen, Anders Ruus, Dag Vongraven, Katrine Borgå
Software Mentions: 6
Published: over 4 years ago

10.1186/1471-2105-10-145

flowClust: a Bioconductor package for automated gating of flow cytometry data
Cited by: 165
Author(s): Kenneth Lo, Florian Hahne, Ryan R. Brinkman, Raphaël Gottardo
Software Mentions: 6
Published: over 15 years ago

10.1038/srep26454

GBIQ: a non-arbitrary, non-biased method for quantification of fluorescent images
Cited by: 2
Author(s): Youichirou Ninomiya, Wei Zhao, Yumiko Saga
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.ppat.1006668

Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesis
Cited by: 78
Author(s): Jingwei Cheng, Donglim Esther Park, Christian Berrios, Elizabeth White, Reety Arora, Rosa Yoon, Timothy Branigan, Tengfei Xiao, Thomas Westerling, Alexander Federation, Rhamy Zeid, Benjamin J. Strober, Selene K. Swanson, Laurence Florens, James E. Bradner, Myles Brown, Peter M. Howley, Megha Padi, Michael P. Washburn, James A. DeCaprio
Software Mentions: 6
Published: about 7 years ago

10.1038/s41598-019-48118-z

Mapping behaviorally relevant light pollution levels to improve urban habitat planning
Cited by: 16
Author(s): Aaron E. Schirmer, Caleb Gallemore, Ting Liu, Seth B. Magle, Elisabeth DiNello, Humerah Ahmed, Thomas Gilday
Software Mentions: 6
Published: over 5 years ago

10.1186/1471-2105-11-279

Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liver
Cited by: 12
Author(s): Tung Nguyen, Richard R. Almon, Debra C. DuBois, William J. Jusko, Ioannis P. Androulakis
Software Mentions: 6
Published: over 14 years ago

10.1186/gm496

A robust prognostic signature for hormone-positive node-negative breast cancer
Cited by: 18
Author(s): Obi L. Griffith, François Pépin, Oana Enache, Laura M. Heiser, Eric A. Collisson, Paul T. Spellman, Joe W. Gray
Software Mentions: 6
Published: almost 12 years ago

10.3390/metabo11060361

Opposing Effects of Ceanothus velutinus Phytochemistry on Herbivore Communities at Multiple Scales
Cited by: 2
Author(s): Casey S. Philbin, M. J. Paulsen, Lora A. Richards
Software Mentions: 6
Published: over 3 years ago

10.3390/ijms22105322

The Detection and Bioinformatic Analysis of Alternative 3′ UTR Isoforms as Potential Cancer Biomarkers
Cited by: 4
Author(s): Nitika Kandhari, Calvin A. Kraupner-Taylor, Paul F. Harrison, David Powell, Traude H. Beilharz
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0210236

Clustering algorithms: A comparative approach
Cited by: 275
Author(s): Mayra Z. Rodriguez, César H. Comin, Dalcimar Casanova, Odemir Martinez Bruno, Diego R. Amancio, Luciano da Fontoura Costa, Francisco A. Rodrigues
Software Mentions: 6
Published: almost 6 years ago

10.1093/gigascience/giy059

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs
Cited by: 244
Author(s): Swati Parekh, Christoph Ziegenhain, Beate Vieth, Wolfgang Enard, Ines Hellmann
Software Mentions: 6
Published: over 6 years ago

10.3389/fimmu.2021.627036

Single Cell RNA-Seq and Machine Learning Reveal Novel Subpopulations in Low-Grade Inflammatory Monocytes With Unique Regulatory Circuits
Cited by: 8
Author(s): Jiyoung Lee, Shuo Geng, Song Li, Liwu Li
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0138726

The Relationship of Immune Cell Signatures to Patient Survival Varies within and between Tumor Types
Cited by: 24
Author(s): Peter S. Linsley, Damien Chaussabel, Cate Speake
Software Mentions: 5
Published: about 9 years ago

10.1186/s12889-021-11441-0

Introducing an efficient sampling method for national surveys with limited sample sizes: application to a national study to determine quality and cost of healthcare
Cited by: 5
Author(s): Mahboubeh Parsaeian, Mahdi Mahdavi, Mojdeh Saadati, Parinaz Mehdipour, Ali Sheidaei, Shahab Khatibzadeh, Farshad Farzadfar, Saeid Shahraz
Software Mentions: 5
Published: over 3 years ago

10.1002/ece3.6380

Exploring the functional meaning of head shape disparity in aquatic snakes
Cited by: 10
Author(s): Marion Segall, Raphaël Cornette, Ramiro Godoy-Diana, Anthony Herrel
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-019-45950-1

The Interplay between Incipient Species and Social Polymorphism in the Desert Ant Cataglyphis
Cited by: 9
Author(s): Tali Reiner Brodetzki, Shani Inbar, Pnina Cohen, Serge Aron, Eyal Privman, Abraham Hefetz
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0207250

Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes
Cited by: 12
Author(s): Maxime Caron, Pascal St-Onge, Simon Drouin, Chantal Richer, Thomas Sontag, Stephan Busche, Guillaume Bourque, Tomi Pastinen, Daniel Sinnett
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-021-07872-z

Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information
Cited by: 5
Author(s): Pattarapol Sumreddee, El Hamidi Hay, Sajjad Toghiani, Andrew Roberts, Samuel E. Aggrey, Romdhane Rekaya
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-018-2115-4

Notos - a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types
Cited by: 6
Author(s): Ingo Bulla, Benoît Aliaga, Virginia Lacal, Jan Bulla, Christoph Grunau, Cristian Chaparro
Software Mentions: 5
Published: over 6 years ago

10.1038/srep41393

Tree cover in Central Africa: determinants and sensitivity under contrasted scenarios of global change
Cited by: 11
Author(s): Julie C. Aleman, Olivier Blarquez, Sylvie Gourlet‐Fleury, Laurent Brémond, Charly Favier
Software Mentions: 5
Published: almost 8 years ago

10.7717/peerj.11898

Biogeography, diversity and environmental relationships of shelf and deep-sea benthic Amphipoda around Iceland
Cited by: 7
Author(s): Anne‐Nina Lörz, Stefanie Kaiser, Jens Oldeland, Caroline Stolter, Karlotta Kürzel, Saskia Brix
Software Mentions: 5
Published: over 3 years ago

10.3390/jcm9040993

Assessing ICD-11 Gaming Disorder in Adolescent Gamers: Development and Validation of the Gaming Disorder Scale for Adolescents (GADIS-A)
Cited by: 43
Author(s): Kerstin Paschke, Maria Isabella Austermann, Rainer Thomasius
Software Mentions: 5
Published: over 4 years ago

10.1186/s12862-019-1570-5

Adaptive divergence in shell morphology in an ongoing gastropod radiation from Lake Malawi
Cited by: 6
Author(s): Bert Van Bocxlaer, Claudia M Ortiz-Sepulveda, Pieter Gurdebeke, Xavier Vekemans
Software Mentions: 5
Published: almost 5 years ago

10.1002/ece3.1015

Crater lake cichlids individually specialize along the benthic–limnetic axis
Cited by: 39
Author(s): Henrik Kusche, Hans Recknagel, Axel Meyer
Software Mentions: 5
Published: almost 11 years ago

10.1186/s13059-015-0716-z

Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays
Cited by: 191
Author(s): Matteo Dell’Acqua, Daniel M. Gatti, G. Pea, Federica Cattonaro, Frederik Coppens, Gabriele Magris, Aye L. Hlaing, Htay Htay Aung, Hilde Nelissen, Joke Baute, Elisabetta Frascaroli, Gary A. Churchill, Dirk Inzé, Michèle Morgante, Mario Enrico Pè
Software Mentions: 5
Published: over 9 years ago

10.3389/fonc.2019.01479

Integrative Transcriptomic Analysis Reveals a Multiphasic Epithelial–Mesenchymal Spectrum in Cancer and Non-tumorigenic Cells
Cited by: 24
Author(s): Nicholas Panchy, Cassandra Azeredo-Tseng, Michael Luo, Natalie Randall, Tian Hong
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-018-27047-3

Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy
Cited by: 17
Author(s): Nina Marchi, Philippe Mennecier, Myriam Georges, Sophie Lafosse, Tatyana Hegay, Choduraa Dorzhu, Boris Chichlo, Laure Ségurel, Évelyne Heyer
Software Mentions: 5
Published: over 6 years ago

10.1186/s40164-020-00165-3

Microenvironment characterization and multi-omics signatures related to prognosis and immunotherapy response of hepatocellular carcinoma
Cited by: 45
Author(s): Furong Liu, Lu Qin, Zhibin Liao, Jia Song, Chaoyi Yuan, Yachong Liu, Yu Wang, Heze Xu, Qiaofeng Zhang, Yigang Pei, Hongwei Zhang, Yonglong Pan, Xiaoping Chen, Zhanguo Zhang, Wanguang Zhang, Bixiang Zhang
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2021.630215

Comparing Statistical Tests for Differential Network Analysis of Gene Modules
Cited by: 2
Author(s): Jaron Arbet, Yaxu Zhuang, Elizabeth Litkowski, Laura Saba, Katerina Kechris
Software Mentions: 4
Published: over 3 years ago

10.3758/s13428-017-0987-2

PredPsych: A toolbox for predictive machine learning-based approach in experimental psychology research
Cited by: 27
Author(s): Atesh Koul, Cristina Becchio, Andrea Cavallo
Software Mentions: 4
Published: about 7 years ago

10.1002/evl3.167

Ecological speciation in European whitefish is driven by a large‐gaped predator
Cited by: 13
Author(s): Gunnar Öhlund, Mats Bodin, Karin Nilsson, Sven‐Ola Öhlund, Kenyon B. Mobley, Alan G. Hudson, Mikael Peedu, Åke Brännström, Pia Bartels, Kim Præbel, Catherine L. Hein, Petter Johansson, Göran Englund
Software Mentions: 4
Published: over 4 years ago

10.1186/s12866-020-02052-7

MALDI-TOF mass spectrometry for sub-typing of Streptococcus pneumoniae
Cited by: 6
Author(s): Sivkheng Kann, Sena Sao, Chanleakhena Phoeung, Youlet By, Juliet E. Bryant, Florence Komurian-Pradel, Vonthanak Saphonn, Monidarin Chou, Paul Turner
Software Mentions: 4
Published: about 4 years ago

10.1016/j.envsoft.2018.02.011

Modelling background air pollution exposure in urban environments: Implications for epidemiological research
Cited by: 27
Author(s): Álvaro Gómez-Losada, José C.M. Pires, Rafael Pino‐Mejías
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-47046-2

SMAC, a computational system to link literature, biomedical and expression data
Cited by: 2
Author(s): S. Pirro, Emanuela Gadaleta, Andrea Galgani, Vittorio Colizzi, Claude Chelala
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1006295

Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster
Cited by: 35
Author(s): Hangnoh Lee, Dong-Yeon Cho, Cale Whitworth, Robert C. Eisman, Melissa A. S. Phelps, John Roote, Thomas C. Kaufman, Kevin R. Cook, Steven Russell, Teresa M. Przytycka, Brian Oliver
Software Mentions: 4
Published: over 8 years ago

10.1007/s13280-014-0601-0

Mapping bundles of ecosystem services reveals distinct types of multifunctionality within a Swedish landscape
Cited by: 194
Author(s): Cibele Queiroz, Megan Meacham, Kristina Richter, Albert V. Norström, Erik Andersson, Jon Norberg, Garry D. Peterson
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12859-016-1184-5

Stepwise iterative maximum likelihood clustering approach
Cited by: 12
Author(s): Alok Sharma, Daichi Shigemizu, Keith A. Boroevich, Yosvany López, Yoichiro Kamatani, Michiaki Kubo, Tatsuhiko Tsunoda
Software Mentions: 4
Published: over 8 years ago

10.1017/S0950268820002757

Community movement and COVID-19: a global study using Google's Community Mobility Reports
Cited by: 76
Author(s): Mihály Sulyok, Mark Walker
Software Mentions: 4
Published: almost 5 years ago

10.1093/sleep/zsab035

Sleep health and cognitive function among people with and without HIV: the use of different machine learning approaches
Cited by: 10
Author(s): Davide De Francesco, Caroline Sabin, Alan Winston, Michael Rueschman, Nicki Doyle, Jane Anderson, Jaime H. Vera, Marta Boffito, Memory Sachikonye, Patrick Mallon, Lewis Haddow, Frank A. Post, Susan Redline, Ken M. Kunisaki
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-019-3243-1

M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data
Cited by: 8
Author(s): Yu Zhang, Chunli Wan, Pengcheng Wang, Wennan Chang, Yan Huo, Jian Chen, Qin Ma, Sha Cao, Chi Zhang
Software Mentions: 4
Published: about 5 years ago

10.1038/s42003-021-02499-y

Modeling the effects of EMT-immune dynamics on carcinoma disease progression
Cited by: 2
Author(s): Daniel Bergman, Matthew Karikomi, Min Yu, Qing Nie, Adam L. MacLean
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0131697

Spatial and Temporal Characteristics of Pastoral Mobility in the Far North Region, Cameroon: Data Analysis and Modeling
Cited by: 20
Author(s): Ningchuan Xiao, Shanshan Cai, Mark Moritz, Rebecca Garabed, Laura W. Pomeroy
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.ppat.1002949

Identification of FAM111A as an SV40 Host Range Restriction and Adenovirus Helper Factor
Cited by: 54
Author(s): Debrah A. Fine, Orit Rozenblatt-Rosen, Megha Padi, Anna Korkhin, Robert James, Guillaume Adelmant, Rosa Yoon, Lifei Guo, Christian Berrios, Ying Zhang, Michael A. Calderwood, Soundarapandian Velmurgan, Jingwei Cheng, Jarrod A. Marto, David E. Hill, Michael E. Cusick, Marc Vidal, Laurence Florens, Michael P. Washburn, Larisa Litovchick, James A. DeCaprio
Software Mentions: 4
Published: about 12 years ago

10.7717/peerj.3334

pathVar:a new method for pathway-based interpretation of gene expression variability
Cited by: 6
Author(s): Laurence de Torrenté, Stephanie M. Zimmerman, Deanne Taylor, Yu Hasegawa, Christine A. Wells, Jessica C. Mar
Software Mentions: 4
Published: over 7 years ago

10.1002/1878-0261.12490

Solid pseudopapillary neoplasms of the pancreas are dependent on the Wnt pathway
Cited by: 14
Author(s): Pier Selenica, Nitya Raj, Rahul Kumar, David Brown, Oriol Arqués, Diane Lauren Reidy, David S. Klimstra, Matija Snuderl, Jonathan Serrano, Héctor G. Pálmer, Britta Weigelt, Jorge S. Reis‐Filho, Maurizio Scaltriti
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0137181

Biomechanical Diversity of Mating Structures among Harvestmen Species Is Consistent with a Spectrum of Precopulatory Strategies
Cited by: 23
Author(s): Mercedes Burns, Jeffrey W. Shultz
Software Mentions: 4
Published: over 9 years ago

10.1038/srep24204

Colony-Level Differences in the Scaling Rules Governing Wood Ant Compound Eye Structure
Cited by: 17
Author(s): Craig D. Perl, Jeremy E. Niven
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-017-18205-0

Tissue Tropism in Host Transcriptional Response to Members of the Bovine Respiratory Disease Complex
Cited by: 26
Author(s): Susanta K. Behura, P. C. Tizioto, JaeWoo Kim, Natália Vinhal Grupioni, Christopher M. Seabury, Robert D. Schnabel, Laurel J. Gershwin, Alison L. Van Eenennaam, Rachel L. Toaff-Rosenstein, Holly L. Neibergs, Luciana Correia de Almeida Regitano, Jeremy F. Taylor
Software Mentions: 4
Published: about 7 years ago

10.1016/j.molmet.2019.12.006

Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures
Cited by: 91
Author(s): Vivek Rai, Daniel Quang, Michael R. Erdos, Darren A. Cusanovich, Riza M. Daza, Narisu Narisu, Luli S. Zou, John P. Didion, Yuanfang Guan, Jay Shendure, Stephen C. J. Parker, Francis S. Collins
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13059-020-02163-4

Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis
Cited by: 55
Author(s): Ranjith Papareddy, Katalin Páldi, Subramanian Paulraj, Ping Kao, Stefan Lutzmayer, Michael D. Nodine
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-020-02119-8

Methods for copy number aberration detection from single-cell DNA-sequencing data
Cited by: 63
Author(s): Xian Mallory, Mohammadamin Edrisi, Nicholas E. Navin, Luay Nakhleh
Software Mentions: 4
Published: over 4 years ago

10.1186/s13073-016-0297-9

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet
Cited by: 144
Author(s): Douglas Mahana, Chad M. Trent, Zachary Kurtz, Nicholas A. Bokulich, Thomas Battaglia, Jennifer Chung, Christian L. Müller, Huilin Li, Richard Bonneau, Martin J. Blaser
Software Mentions: 4
Published: over 8 years ago

10.1093/bib/bbaa014

Regression on imperfect class labels derived by unsupervised clustering
Cited by: 1
Author(s): Rasmus Froberg Brøndum, Thomas Yssing Michaelsen, Martin Bøgsted
Software Mentions: 4
Published: almost 5 years ago

Projects: cran: mclust

Papers Mentioning mclust 297