Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: cran: tree
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/tree
Classification and Regression Trees
45 versions
Latest release: almost 2 years ago
26 dependent packages
15,654 downloads last month
Papers Mentioning tree 53
10.1093/gigascience/giaa039
Biospytial: spatial graph-based computing for ecological Big DataCited by: 5
Author(s): Juan Manuel Escamilla Molgora, Luigi Sedda, Peter M. Atkinson
Software Mentions: 14
Published: over 4 years ago
10.1002/cam4.2786
FOLFOX treatment response prediction in metastatic or recurrent colorectal cancer patients via machine learning algorithmsCited by: 24
Author(s): Wei Lu, Dongliang Fu, Xianglong Kong, Zhiheng Huang, Maxwell Hwang, Yaowu Zhu, Liubo Chen, Kai Jiang, Xinlin Li, Yihua Wu, Jun Li, Ying Yuan, Kefeng Ding
Software Mentions: 12
Published: almost 5 years ago
10.12688/f1000research.26669.2
TreeSummarizedExperiment: a S4 class for data with hierarchical structureCited by: 14
Author(s): Ronald Huang, Charlotte Soneson, Felix G.M. Ernst, Kévin Rue-Albrecht, Yu Guo, Stephanie C. Hicks, Mark D. Robinson
Software Mentions: 11
Published: over 3 years ago
10.3389/fimmu.2016.00372
SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell TranscriptsCited by: 52
Author(s): Chaim A. Schramm, Zizhang Sheng, Zhenhai Zhang, John R. Mascola, Peter D. Kwong, Lawrence Shapiro
Software Mentions: 10
Published: about 8 years ago
10.1080/0886022X.2020.1810068
Prediction models for acute kidney injury in patients with gastrointestinal cancers: a real-world study based on Bayesian networksCited by: 14
Author(s): Yang Li, Xiaohong Chen, Ziyan Shen, Yimei Wang, Jiayue Hu, Yunlu Zhang, Jiacheng Xu, Xiaoqiang Ding
Software Mentions: 7
Published: almost 5 years ago
10.3389/fninf.2013.00028
Reaction-diffusion in the NEURON simulatorCited by: 52
Author(s): Robert A. McDougal, Michael L. Hines, William W. Lytton
Software Mentions: 7
Published: almost 12 years ago
10.1002/ece3.4237
Gene flow and Andean uplift shape the diversification of <i>Gasteracantha cancriformis</i> (Araneae: Araneidae) in Northern South AmericaCited by: 19
Author(s): Fabian C. Salgado-Roa, Carolina Pardo‐Díaz, Eloisa Lasso, Carlos F. Arias, Vera Nisaka Solferini, Camilo Salazar
Software Mentions: 6
Published: over 6 years ago
10.1002/ece3.6736
Defining relictual biodiversity: Conservation units in speckled dace (Leuciscidae:<i>Rhinichthys osculus</i>) of the Greater Death Valley ecosystemCited by: 11
Author(s): Steven M. Mussmann, Michael E. Douglas, David D. Oakey
Software Mentions: 6
Published: about 4 years ago
10.1155/2018/6275435
A Framework of Rebalancing Imbalanced Healthcare Data for Rare Events’ Classification: A Case of Look-Alike Sound-Alike Mix-Up Incident DetectionCited by: 31
Author(s): Yang Zhao, Zoie Shui-Yee Wong, Kwok Leung Tsui
Software Mentions: 6
Published: almost 7 years ago
10.1371/journal.pone.0221408
Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow SeaCited by: 16
Author(s): Jong-Geol Kim, Joo-Han Gwak, Man‐Young Jung, Sung‐Uk An, Jung‐Ho Hyun, Sanghoon Kang, Sung‐Keun Rhee
Software Mentions: 6
Published: about 5 years ago
10.1371/journal.pone.0245298
Machine learning and statistics to qualify environments through multi-traits in Coffea arabicaCited by: 2
Author(s): Weverton Gomes da Costa, Ivan de Paiva Barbosa, Jacqueline Enequio de Souza, Cosme Damião Cruz, Moysés Nascimento, A. C. B. de Oliveira
Software Mentions: 5
Published: almost 4 years ago
10.1093/molbev/msw285
Rapid expansion of immune-related gene families in the house fly, <i>Musca domestica</i>Cited by: 23
Author(s): Timothy B. Sackton, Brian P. Lazzaro, Andrew G. Clark
Software Mentions: 5
Published: almost 8 years ago
10.1186/1471-2105-14-326
snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencingCited by: 6
Author(s): Ali Al‐Shahib, Anthony Underwood
Software Mentions: 4
Published: about 11 years ago
10.1093/gigascience/giy034
Improving the annotation of the Heterorhabditis bacteriophora genomeCited by: 15
Author(s): Florence McLean, Duncan Berger, Dominik R. Laetsch, Hillel T. Schwartz, Mark Blaxter
Software Mentions: 4
Published: over 6 years ago
10.1128/mBio.01060-17
Genome-Wide Sensitivity Analysis of the Microsymbiont <i>Sinorhizobium meliloti</i> to Symbiotically Important, Defensin-Like Host PeptidesCited by: 47
Author(s): Markus F. F. Arnold, Mohammed Shabab, Jon Penterman, Kevin L. Boehme, Joel S. Griffitts, Graham C. Walker
Software Mentions: 4
Published: about 7 years ago
10.1038/s41396-019-0508-7
Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)Cited by: 53
Author(s): Adrien Assié, Nikolaus Leisch, Dimitri V. Meier, Harald R. Gruber‐Vodicka, Halina E. Tegetmeyer, Anke Meyerdierks, Manuel Kleiner, Tjorven Hinzke, Samantha B. Joye, Matthew Saxton, Nicole Dubilier, Jillian M. Petersen
Software Mentions: 4
Published: about 5 years ago
10.7554/eLife.60920
Achieving functional neuronal dendrite structure through sequential stochastic growth and retractionCited by: 21
Author(s): André Ferreira Castro, Lothar Baltruschat, Tomke Stürner, Amirhoushang Bahrami, Paul Jedlicka, Gaia Tavosanis, Hermann Cuntz
Software Mentions: 4
Published: almost 4 years ago
10.1186/1471-2105-14-125
Random forest methodology for model-based recursive partitioning: the mobForest package for RCited by: 65
Author(s): Nikhil Garge, Georgiy Bobashev, Barry Eggleston
Software Mentions: 4
Published: over 11 years ago
10.3389/fnbeh.2019.00121
Large-Scale Validation of the Paddling Pool Task in the Clockmaze for Studying Hippocampus-Based Spatial Cognition in MiceCited by: 6
Author(s): Roman Sankowski, T. Huerta, Rishi Kalra, Toby J Klein, Joshua J. Strohl, Yousef Al‐Abed, Sergio Robbiati, Patricio T. Huerta
Software Mentions: 4
Published: over 5 years ago
10.1111/eva.12176
New host and lineage diversity of avian haemosporidia in the northern AndesCited by: 52
Author(s): Ryan J. Harrigan, Raúl Ernesto Sedano-Cruz, Anthony Chasar, Jaime A. Chaves, Jennifer T. Nguyen, Alexis Whitaker, Thomas B. Smith
Software Mentions: 4
Published: over 10 years ago
10.21105/joss.02906
Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogensCited by: 101
Author(s): John Huddleston, James Hadfield, Thomas H. Sibley, Jover Lee, Kairsten Fay, Misja Ilcisin, Elias Harkins, Trevor Bedford, Richard A. Neher, Emma B. Hodcroft
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pone.0137969
Ant Colonies Do Not Trade-Off Reproduction against MaintenanceCited by: 30
Author(s): Boris H. Kramer, Alexandra Schrempf, Alexander Scheuerlein, Jürgen Heınze
Software Mentions: 3
Published: about 9 years ago
10.1038/s41598-019-47954-3
Widespread Wolbachia infection in an insular radiation of damselflies (Odonata, Coenagrionidae)Cited by: 15
Author(s): M. Olalla Lorenzo-Carballa, Yusdiel Torres‐Cambas, K. Heaton, Gregory D. D. Hurst, Sylvain Charlat, Thomas N. Sherratt, Hans Van Gossum, Adolfo Cordero‐Rivera, Christopher D. Beatty
Software Mentions: 3
Published: over 5 years ago
10.1002/ecy.2788
For common community phylogenetic analyses, go ahead and use synthesis phylogeniesCited by: 63
Author(s): Daijiang Li, Lauren B. Trotta, Hannah E. Marx, Julie M. Allen, Miao Sun, Douglas E. Soltis, Pamela S. Soltis, Robert Guralnick, Benjamin Baiser
Software Mentions: 3
Published: over 5 years ago
10.1186/1471-2458-12-138
Does social capital travel? Influences on the life satisfaction of young people living in England and SpainCited by: 36
Author(s): Antony Morgan, Francisco Rivera, Carmen Moreno, Bo J.A. Haglund
Software Mentions: 2
Published: almost 13 years ago
10.1186/1471-2164-14-807
A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungiCited by: 27
Author(s): Jana Sperschneider, Donald M. Gardiner, Jennifer Taylor, James K. Hane, Karam B. Singh, John M. Manners
Software Mentions: 2
Published: almost 12 years ago
10.1093/database/baz110
RiceRelativesGD: a genomic database of rice relatives for rice researchCited by: 10
Author(s): Limin Mao, Meihong Chen, Qinjie Chu, Jia Lu, Most. Humaira Sultana, Dongya Wu, Xiang-Dong Kong, Jie Qiu, Chu-Yu Ye, Qian‐Hao Zhu, Xi Chen
Software Mentions: 2
Published: almost 6 years ago
10.3389/fmicb.2016.01006
Insights into Abundant Rumen Ureolytic Bacterial Community Using Rumen Simulation SystemCited by: 44
Author(s): Di Jin, Shengguo Zhao, Pengpeng Wang, Nan Zheng, Dengpan Bu, Yves Beckers, Jiaqi Wang
Software Mentions: 2
Published: over 8 years ago
10.1186/2047-217X-2-17
Galaxy tools to study genome diversityCited by: 19
Author(s): Oscar C. Bedoya-Reina, Aakrosh Ratan, Richard Burhans, Hie Lim Kim, Belinda Giardine, Cathy Riemer, Qunhua Li, Thomas L. Olson, Thomas P. Loughran, Bridgett M. vonHoldt, George H. Perry, Stephan C. Schuster, Webb Miller
Software Mentions: 2
Published: almost 11 years ago
10.1038/s41598-018-34345-3
Phosphoinositide 3-kinase-delta could be a biomarker for eosinophilic nasal polypsCited by: 0
Author(s): Jong Seung Kim, Jae Seok Jeong, Kyung Bae Lee, So Ri Kim, Yeong Hun Choe, Sam Hyun Kwon, Seong Ho Cho, Yong Chul Lee
Software Mentions: 2
Published: about 6 years ago
10.1038/s41598-021-88323-3
New species and a new record of Phylloporia from BeninCited by: 1
Author(s): Boris Armel Olou, Nourou S. Yorou, Ewald Langer
Software Mentions: 2
Published: over 3 years ago
10.3390/s18010160
Recognition of Activities of Daily Living Based on Environmental Analyses Using Audio Fingerprinting Techniques: A Systematic ReviewCited by: 21
Author(s): Ivan Miguel Pires, Rui Santos, Nuno Pombo, Francisco Flórez-Revuelta, Susanna Spinsante, Rossitza Goleva, Eftim Zdravevski
Software Mentions: 2
Published: almost 7 years ago
10.3389/fmicb.2017.01163
Oropharyngeal and Sputum Microbiomes Are Similar Following Exacerbation of Chronic Obstructive Pulmonary DiseaseCited by: 21
Author(s): Haiyue Liu, Shiyu Zhang, Wu Yang, Xiao-Fang Su, Yan He, Hongwei Zhou, Jin Su
Software Mentions: 1
Published: over 7 years ago
10.1186/1471-2431-12-81
Systematic literature review assessing tobacco smoke exposure as a risk factor for serious respiratory syncytial virus disease among infants and young childrenCited by: 59
Author(s): Joseph R. DiFranza, Anthony Masaquel, Amy Barrett, Ann Colosia, Parthiv J. Mahadevia
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0226372
Analysis of gut microbiota of obese individuals with type 2 diabetes and healthy individualsCited by: 92
Author(s): Aftab Ahmad, Wei Yang, Guofang Chen, Muhammad Shafiq, Sundus Javed, Syed Shujaat Ali Zaidi, Ramla Shahid, Chao Liu, Habib Bokhari
Software Mentions: 1
Published: almost 5 years ago
10.1093/genetics/iyab002
Robust modeling of additive and nonadditive variation with intuitive inclusion of expert knowledgeCited by: 3
Author(s): Ingeborg Gullikstad Hem, Maria Lie Selle, Gregor Gorjanc, Geir‐Arne Fuglstad, Andrea Riebler
Software Mentions: 1
Published: almost 4 years ago
10.2196/medinform.9960
Predicting the Reasons of Customer Complaints: A First Step Toward Anticipating Quality Issues of In Vitro Diagnostics Assays with Machine LearningCited by: 5
Author(s): Stéphane Aris‐Brosou, James Kim, Li Li, Liu Hui
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0038800
Influence of Landscape Structure and Human Modifications on Insect Biomass and Bat Foraging Activity in an Urban LandscapeCited by: 65
Author(s): Caragh G. Threlfall, Bradley Law, Peter B. Banks
Software Mentions: 1
Published: over 12 years ago
10.3390/pathogens9121051
Biological and Genomic Characterization of a Novel Jumbo Bacteriophage, vB_VhaM_pir03 with Broad Host Lytic Activity against Vibrio harveyiCited by: 18
Author(s): Gerald N. Misol, Constantina Kokkari, Pantelis Katharios
Software Mentions: 1
Published: almost 4 years ago
10.1155/2016/5741518
Urinary Extracellular Vesicles: Potential Biomarkers of Renal Function in Diabetic PatientsCited by: 27
Author(s): Agnieszka Kamińska, Mark Platt, Joanna Kasprzyk, Beata Kuśnierz-Cabała, Agnieszka Gala-Błądzińska, Olga Woźnicka, Benedykt R. Jany, Franciszek Krok, Wojciech Piekoszewski, Marek Kuźniewski, Ewa Stępień
Software Mentions: 1
Published: almost 9 years ago
10.3897/zookeys.556.6174
Depreissia decipiens, an enigmatic canopy spider from Borneo revisited (Araneae, Salticidae), with remarks on the distribution and diversity of canopy spiders in Sabah, BorneoCited by: 2
Author(s): Christa Deeleman-Reinhold, Jeremy A. Miller, Andreas Floren
Software Mentions: 1
Published: almost 9 years ago
10.1186/s12864-018-5007-0
Transcriptional response of honey bee (Apis mellifera) to differential nutritional status and Nosema infectionCited by: 28
Author(s): Farida Azzouz-Olden, Arthur G. Hunt, Gloria DeGrandi-Hoffman
Software Mentions: 1
Published: over 6 years ago
10.3390/v12080866
Aedes aegypti from Amazon Basin Harbor High Diversity of Novel Viral SpeciesCited by: 9
Author(s): Geovani de Oliveira Ribeiro, Vanessa dos Santos Morais, Fred Júlio Costa Monteiro, Edcelha Soares D’Athaide Ribeiro, Márlisson Octávio da Silva Rêgo, Raimundo Nonato Picanço Souto, Fabiola Villanova, Roozbeh Tahmasebi, Philip Michael Hefford, Xutao Deng, Eric Delwart, Éster Cerdeira Sabino, Lícia Natal Fernandes, Antônio Charlys da Costa, Élcio Leal
Software Mentions: 1
Published: over 4 years ago
10.7554/eLife.23717
Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteomeCited by: 113
Author(s): Richard G. Dorrell, Gillian H. Gile, Giselle McCallum, Raphaël Méheust, Éric Bapteste, Christen M. Klinger, Loraine Brillet-Guéguen, Katalina D Freeman, Daniel J. Richter, Chris Bowler
Software Mentions: 1
Published: over 7 years ago
10.1186/s12862-020-01623-6
MtOrt: an empirical mitochondrial amino acid substitution model for evolutionary studies of Orthoptera insectsCited by: 6
Author(s): Huihui Chang, Yimeng Nie, Nan Zhang, Xue Zhang, Haichun Sun, Ying Mao, Zhongying Qiu, Yuan Huang
Software Mentions: 1
Published: over 4 years ago
10.4056/sigs.2615838
Complete genome sequence of Treponema pallidum strain DAL-1Cited by: 36
Author(s): Marie Zobaníková, Pavol Mikolka, Darina Čejková, Petra Pospíšilová, Lei Chen, Michal Strouhal, Xiang Qin, George M. Weinstock, David Šmajs
Software Mentions: 1
Published: about 12 years ago
10.3390/molecules24193614
Matrix Discriminant Analysis Evidenced Surface-Lithium as an Important Factor to Increase the Hydrolytic Saccharification of Sugarcane BagasseCited by: 1
Author(s): Ana Sílvia de Almeida Scarcella, Alexandre Favarin Somera, Christiane da Costa Carreira Nunes, Eleni Gomes, Ana Cláudia Vici, Marcos Silveira Buckeridge, Maria de Lourdes Teixeira de Moraes Polizeli
Software Mentions: 1
Published: about 5 years ago
10.1186/bcr3421
Molecular apocrine breast cancers are aggressive estrogen receptor negative tumors overexpressing either HER2 or GCDFP15Cited by: 85
Author(s): Jacqueline Lehmann-Che, Anne-Sophie Hamy, Raphaël Porcher, Marc Barritault, Fatiha Bouhidel, Hanadi Habuellelah, Solenne Leman-Detours, Anne de Roquancourt, Laurence Cahen-Doidy, E. Bourstyn, Patricia de Crémoux, Cédric de Bazelaire, M. Albiter, Sylvie Giacchetti, C. Cuvier, Anne Janin, Marc Espié, Philippe Bertheau
Software Mentions: 1
Published: over 11 years ago
10.1016/j.dib.2021.106820
A dataset composed of multiangular spectral libraries and auxiliary data at tree, leaf, needle, and bark level for three common European tree speciesCited by: 3
Author(s): Aarne Hovi, Petri Forsström, Giulia Ghielmetti, Michael E. Schaepman, Miina Rautiainen
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0032839
Enabling Large-Scale Design, Synthesis and Validation of Small Molecule Protein-Protein AntagonistsCited by: 89
Author(s): David Ryan Koes, Kareem Khoury, Yijun Huang, Wei Wang, Michal Bista, Grzegorz M. Popowicz, Siglinde Wolf, Tad A. Holak, Alexander Dömling, Carlos J. Camacho
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0065503
A TILLING Platform for Functional Genomics in Brachypodium distachyonCited by: 73
Author(s): Marion Dalmais, Sébastien Antelme, Séverine Ho-Yue-Kuang, Yin Wang, Olivier Darracq, Madeleine Bouvier d’Yvoire, Laurent Cézard, Frédéric Legée, Eddy Blondet, Nicolas Oria, Christelle Troadec, Véronique Brunaud, Lise Jouanin, Monica Höfte, Abdelhafid Bendahmane, Catherine Lapierre, Richard Sibout
Software Mentions: 1
Published: over 11 years ago
10.3389/fcimb.2017.00302
Molecular Characterization of the Human Stomach Microbiota in Gastric Cancer PatientsCited by: 101
Author(s): Guoqin Yu, Javier Torres, Nan Hu, Rafael Medrano-Guzmán, Roberto Herrera‐Goepfert, Michael S. Humphrys, Lemin Wang, Chaoyu Wang, Ti Ding, Jacques Ravel, Philip R. Taylor, Christian C. Abnet, Alisa M. Goldstein
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pone.0093581
Overweight in Adolescence Can Be Predicted at Age 6 Years: A CART Analysis in German CohortsCited by: 16
Author(s): Christina Riedel, Rüdiger von Kries, Anette E. Buyken, Katharina Diethelm, Thomas Keil, Linus Grabenhenrich, Manfred J. Müller, Sandra Plachta-Danielzik
Software Mentions: 1
Published: over 10 years ago