cran: tree | Projects | Ecosyste.ms: Papers

10.1093/gigascience/giaa039

Biospytial: spatial graph-based computing for ecological Big Data
Cited 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 algorithms
Cited 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 structure
Cited 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 Transcripts
Cited 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 networks
Cited 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 simulator
Cited 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 Gasteracantha cancriformis (Araneae: Araneidae) in Northern South America
Cited 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:Rhinichthys osculus) of the Greater Death Valley ecosystem
Cited 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 Detection
Cited 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 Sea
Cited 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 arabica
Cited 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, Musca domestica
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 sequencing
Cited 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 genome
Cited 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 Sinorhizobium meliloti to Symbiotically Important, Defensin-Like Host Peptides
Cited 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 retraction
Cited 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 R
Cited 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 Mice
Cited 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 Andes
Cited 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 pathogens
Cited 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 Maintenance
Cited 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 phylogenies
Cited 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 Spain
Cited by: 36
Author(s): Antony Morgan, Francisco Rivera, Carmen Moreno, Bo J.A. Haglund
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-14-807

A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi
Cited 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 research
Cited 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 System
Cited 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 diversity
Cited 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 polyps
Cited 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 Benin
Cited 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 Review
Cited 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 Disease
Cited 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 children
Cited 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 individuals
Cited 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 knowledge
Cited 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 Learning
Cited 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 Landscape
Cited 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 harveyi
Cited 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 Patients
Cited 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, Borneo
Cited 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 infection
Cited 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 Species
Cited 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 proteome
Cited 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 insects
Cited 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-1
Cited 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 Bagasse
Cited 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 GCDFP15
Cited 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 species
Cited 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 Antagonists
Cited 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 distachyon
Cited 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 Patients
Cited 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 Cohorts
Cited 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

Projects: cran: tree

Papers Mentioning tree 53