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: phylogram
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/phylogram
Dendrograms for Evolutionary Analysis
5 versions
Latest release: over 6 years ago
5 dependent packages
616 downloads last month
Papers Mentioning phylogram 44
10.3390/v12101142
A Diverse Virome of Leafroll-Infected Grapevine Unveiled by dsRNA SequencingCited by: 24
Author(s): Mamadou L. Fall, De-Xiang Xu, Pierre Lemoyne, Issam Moussa, Carole Beaulieu, Odile Carisse
Software Mentions: 19
Published: about 4 years ago
10.1371/journal.pbio.3000534
The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation responseCited by: 112
Author(s): Omri M. Finkel, Isai Salas-González, Gabriel Castrillo, Stijn Spaepen, Theresa F. Law, Paulo José Pereira Lima Teixeira, Corbin D. Jones, Jeffery L. Dangl
Software Mentions: 6
Published: about 5 years ago
10.3390/genes5040957
High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data AnalysisCited by: 57
Author(s): Vahan Simonyan, Raja Mazumder
Software Mentions: 5
Published: about 10 years ago
10.1371/journal.pone.0153925
Molecular Characterization and Global Expression Analysis of Lectin Receptor Kinases in Bread Wheat (Triticum aestivum)Cited by: 66
Author(s): . Shumayla, Shailesh Sharma, Ajay Kumar Pandey, Kashmir Singh, Santosh Kumar Upadhyay
Software Mentions: 5
Published: over 8 years ago
10.1371/journal.pone.0241231
A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa RicaCited by: 7
Author(s): Joel H. Nitta, Atsushi Ebihara, Alan Р. Smith
Software Mentions: 5
Published: about 4 years ago
10.1111/j.1755-0998.2011.03041.x
DNA barcoding of oomycetes with cytochrome <i>c</i> oxidase subunit I and internal transcribed spacerCited by: 459
Author(s): G.P. Robideau, A. W. A. M. de Cock, Michael D. Coffey, Hermann Voglmayr, Henk J. Brouwer, Kanak Bala, David W. Chitty, N. L. Désaulniers, Quinn Eggertson, Claire M. M. Gachon, Chia-Hui Hu, Frithjof C. Küpper, Tara L. Rintoul, Ehab Sarhan, E.C.P. Verstappen, Yonghong Zhang, P.J.M. Bonants, Jean Beagle Ristaino, C. André Lévesque
Software Mentions: 4
Published: over 13 years ago
10.1186/gb-2008-9-1-r11
CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationshipsCited by: 36
Author(s): Wei-Cheng Lo, Ping Lyu
Software Mentions: 4
Published: almost 17 years ago
10.1186/1471-2148-13-208
Integration of molecules and new fossils supports a Triassic origin for Lepidosauria (lizards, snakes, and tuatara)Cited by: 161
Author(s): Marc E. H. Jones, Cajsa Lisa Anderson, Christy A. Hipsley, Johannes Müller, SE Evans, Rainer R. Schoch
Software Mentions: 3
Published: almost 12 years ago
10.3390/microorganisms9020299
What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard BarcodesCited by: 4
Author(s): Angela Conti, Laura Della Corte, Debora Casagrande Pierantoni, Vincent Robert, Gianluigi Cardinali
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41598-017-10376-0
Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceusCited by: 28
Author(s): Juan Chen, Zhiai Xu, Yan Yang, Yong Xing, Qi Zhang, Jia Mei Li, Ke Ma, Hong Wei Liu, Shun Guo
Software Mentions: 3
Published: about 7 years ago
10.1186/s12862-021-01797-7
Museomics and phylogenomics with protein-encoding ultraconserved elements illuminate the evolution of life history and phallic morphology of flesh flies (Diptera: Sarcophagidae)Cited by: 10
Author(s): Eliana Buenaventura
Software Mentions: 3
Published: over 3 years ago
10.1186/s12864-020-07108-6
Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformisCited by: 12
Author(s): Juan Chen, Jiamei Li, Yanjing Tang, Ke Ma, Bing Li, Zhiai Xu, Xiaobin Liu, Yang Li, Zhu‐Liang Yang, Weinan Xu, Baogui Xie, Hongwei Liu, Shunxing Guo
Software Mentions: 3
Published: about 4 years ago
10.1371/journal.pone.0082615
Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory StudyCited by: 89
Author(s): Adam L. Bazinet, Michael P. Cummings, Kim T. Mitter, Charles Mitter
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0021031
Improved Phylogenetic Analyses Corroborate a Plausible Position of Martialis heureka in the Ant Tree of LifeCited by: 25
Author(s): Patrick Kück, Francisco Hita Garcia, Bernhard Misof, Karen Meusemann
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0249354
Partial DnaK protein expression from Coxiella-like endosymbiont of Rhipicephalus annulatus tickCited by: 1
Author(s): Pornpiroon Nooroong, Wachareeporn Trinachartvanit, Visut Baimai, Panat Anuracpreeda, Arunee Ahantarig
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0126124
Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial SpeciesCited by: 88
Author(s): Ana Gutiérrez-Preciado, Alfredo G. Torres, Enrique Merino, Hernán Ruy Bonomi, Fernando A. Goldbaum, Víctor Antonio García-Angulo
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2105-7-398
PhyloPat: phylogenetic pattern analysis of eukaryotic genesCited by: 16
Author(s): Tim Hulsen, Jacob de Vlieg, Peter M.A. Groenen
Software Mentions: 2
Published: about 18 years ago
10.3389/fmicb.2019.00983
Characterization of the Castanopsis carlesii Deadwood Mycobiome by Pacbio Sequencing of the Full-Length Fungal Nuclear Ribosomal Internal Transcribed Spacer (ITS)Cited by: 17
Author(s): Witoon Purahong, Ausana Mapook, Yuting Wu, Chaur-Tzuhn Chen
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0084012
Tracing the Rise of Ants - Out of the GroundCited by: 59
Author(s): Andrea Lucky, Michelle Trautwein, Benoit Guénard, Michael D. Weiser, Robert R. Dunn
Software Mentions: 2
Published: almost 11 years ago
10.3389/fgene.2019.01172
The Local South American Chicken Populations Are a Melting-Pot of Genomic DiversityCited by: 1
Author(s): Agusto Luzuriaga-Neira, L. Pérez‐Pardal, Sean O’Rourke, Gustavo Villacís-Rivas, Freddy Cueva-Castillo, Galo Escudero-Sánchez, Juan Aguirre-Pabón, Amarilis Ulloa-Núñez, Makarena Rubilar-Quezada, Marcelo Vallinoto, Michael R. Miller, Albano Beja‐Pereira
Software Mentions: 1
Published: about 5 years ago
10.3389/fmicb.2021.579920
Antagonistic Activity of Trichoderma spp. Against Fusarium oxysporum in Rhizosphere of Radix pseudostellariae Triggers the Expression of Host Defense Genes and Improves Its Growth Under Long-Term Monoculture SystemCited by: 21
Author(s): Jun Chen, Liuting Zhou, Israr Ud Din, Yasir Arafat, Qian Li, Juanying Wang, Tingting Wu, Linkun Wu, Hongmiao Wu, Xianjin Qin, Ganga Raj Pokhrel, Shan Lin, Wenxiong Lin
Software Mentions: 1
Published: over 3 years ago
10.3389/fmicb.2016.00002
Developmental Peculiarities and Seed-Borne Endophytes in Quinoa: Omnipresent, Robust Bacilli Contribute to Plant FitnessCited by: 75
Author(s): Andrea Pitzschke
Software Mentions: 1
Published: almost 9 years ago
10.3389/fmicb.2021.631140
Low Bifidobacterium Abundance in the Lower Gut Microbiota Is Associated With Helicobacter pylori-Related Gastric Ulcer and Gastric CancerCited by: 27
Author(s): T. Barani Devi, Krishnadas Devadas, Meekha George, A. Gandhimathi, Deepak Chouhan, R. J. Retnakumar, Sneha Mary Alexander, Jijo Varghese, Sanjai Dharmaseelan, Sivakumar Krishnankutty Chandrika, V T Jissa, Bhabatosh Das, G. Balakrish Nair, Santanu Chattopadhyay
Software Mentions: 1
Published: over 3 years ago
10.1038/s41598-019-44481-z
A comparative genomics approach for identifying host-range determinants in Streptococcus thermophilus bacteriophagesCited by: 23
Author(s): Paula Szymczak, Martin Holm Rau, João M. Monteiro, Mariana G. Pinho, Sérgio R. Filipe, Finn K. Vogensen, Ahmad A. Zeidan, Thomas Janzen
Software Mentions: 1
Published: over 5 years ago
10.1186/s12859-019-3149-y
CLINE: a web-tool for the comparison of biological dendrogram structuresCited by: 0
Author(s): Rodolfo S. Allendes Osorio, Lokesh P. Tripathi, Kenji Mizuguchi
Software Mentions: 1
Published: about 5 years ago
10.1093/sysbio/syz066
Continued Adaptation of C4 Photosynthesis After an Initial Burst of Changes in the Andropogoneae GrassesCited by: 25
Author(s): Matheus E Bianconi, Jan Hackel, Maria S. Vorontsova, Adriana Alberti, Watchara Arthan, Sean V. Burke, Melvin R. Duvall, Elizabeth A. Kellogg, Sébastien Lavergne, Michael R. McKain, Alexandre Meunier, Colin P. Osborne, Paweena Traiperm, Pascal‐Antoine Christin, Guillaume Besnard
Software Mentions: 1
Published: about 5 years ago
10.1186/1471-2148-9-280
Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular studyCited by: 205
Author(s): Jerome C. Regier, Andreas Zwick, Michael P. Cummings, Akito Y. Kawahara, Soowon Cho, Susan J. Weller, Amanda D. Roe, Joaquín Baixeras, John W. Brown, Cynthia Parr, Donald R. Davis, Marc E. Epstein, Winifred Hallwachs, Axel Hausmann, Daniel H. Janzen, Ian J. Kitching, M. Alma Solís, Shen Horn Yen, Adam L. Bazinet, Charles Mitter
Software Mentions: 1
Published: almost 15 years ago
10.3897/mycokeys.62.47854
Discovery of Cytospora species associated with canker disease of tree hosts from Mount Dongling of ChinaCited by: 11
Author(s): Hucheng Zhu, Meng Pan, Jadson Diogo Pereira Bezerra, Chengming Tian
Software Mentions: 1
Published: almost 5 years ago
10.3897/zookeys.729.20615
Distribution of endangered Italian gudgeon Romanogobio benacensis (Cypriniformes, Cyprinidae, Gobioninae) with remarks on distinguishing morphological charactersCited by: 3
Author(s): Dušan Jelić, Mišel Jelić, Petar Žutinić, Ivana Šimunović, Primož Zupančić, Alexander M. Naseka
Software Mentions: 1
Published: almost 7 years ago
10.1186/s13071-019-3825-9
Cryptic intermediate snail host of the liver fluke Fasciola hepatica in AfricaCited by: 12
Author(s): Anna Mahulu, Catharina Clewing, Björn Stelbrink, Fred D. Chibwana, Immaculate Tumwebaze, J. Russell Stothard, Christian Albrecht
Software Mentions: 1
Published: almost 5 years ago
10.1186/s13071-019-3463-2
Shared species of crocodilian trypanosomes carried by tabanid flies in Africa and South America, including the description of a new species from caimans, Trypanosoma kaiowa n. sp.Cited by: 21
Author(s): Bruno R. Fermino, Fernando Paiva, Laerte B. Viola, Carla Monadeli Filgueira Rodrigues, Herakles A. García, Marta Campaner, Carmen S. A. Takata, Desie Sheferaw, John Joseph M. Kisakye, Agapitus Kato, Carlos Jared, Marta Maria Geraldes Teixeira, Erney P. Camargo
Software Mentions: 1
Published: over 5 years ago
10.1186/1756-3305-2-27
In silico analysis of the cyclophilin repertoire of apicomplexan parasitesCited by: 29
Author(s): Jürgen Krücken, Gisela Greif, Georg von Samson‐Himmelstjerna
Software Mentions: 1
Published: almost 16 years ago
10.7717/peerj.2051
The masquerade game: marine mimicry adaptation between egg-cowries and octocoralsCited by: 10
Author(s): Juan A. Sánchez, Angela P. Fuentes‐Pardo, Íde Ní Almhain, Néstor E. Ardila, Jaime Ricardo Cantera Kintz, Manu Forero-Shelton
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pone.0009950
CO I Barcoding Reveals New Clades and Radiation Patterns of Indo-Pacific Sponges of the Family Irciniidae (Demospongiae: Dictyoceratida)Cited by: 54
Author(s): Judith Pöppe, Patricia Sutcliffe, John N. A. Hooper, Gert Wörheide, Dirk Erpenbeck
Software Mentions: 1
Published: over 14 years ago
10.1371/journal.pone.0134328
Comprehensive Evolutionary and Expression Analysis of FCS-Like Zinc finger Gene Family Yields Insights into Their Origin, Expansion and DivergenceCited by: 20
Author(s): Muhammed Jamsheer K, Chanchal Thomas Mannully, Nandu Gopan, Ashverya Laxmi
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pone.0031559
Macro and Micro Diversity of Clostridium difficile Isolates from Diverse Sources and Geographical LocationsCited by: 114
Author(s): Richard A. Stabler, Lisa F. Dawson, Esmeralda Valiente, M. D. Cairns, Melissa J. Martin, Elizabeth H. Donahue, Thomas V. Riley, J. Glenn Songer, Ed J. Kuijper, Kate E. Dingle, Brendan W. Wren
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0033479
Traditional Taxonomic Groupings Mask Evolutionary History: A Molecular Phylogeny and New Classification of the Chromodorid NudibranchsCited by: 67
Author(s): Rebecca F. Johnson, Terrence M. Gosliner
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0099074
DUF581 Is Plant Specific FCS-Like Zinc Finger Involved in Protein-Protein InteractionCited by: 29
Author(s): Muhammed Jamsheer K, Ashverya Laxmi
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pone.0016580
Exploring the Evolutionary Relationship of Insulin Receptor Substrate Family Using Computational BiologyCited by: 27
Author(s): Chiranjib Chakraborty, Govindasamy Agoramoorthy, Minna J. Hsu
Software Mentions: 1
Published: over 13 years ago
10.1371/journal.pone.0004961
Coordinated Activation of Candidate Proto-Oncogenes and Cancer Testes Antigens via Promoter Demethylation in Head and Neck Cancer and Lung CancerCited by: 104
Author(s): Ian Smith, Chad A. Glazer, Suhail K. Mithani, Michael F. Ochs, Wenyue Sun, Sheetal Bhan, Alexander A. Vostrov, Ziedulla Abdullaev, Victor Lobanenkov, Andrew Gray, Chunyan Liu, Steven S. Chang, Kimberly Laskie Ostrow, William H. Westra, Shahnaz Begum, Mousumi Dhara, Joseph A. Califano
Software Mentions: 1
Published: over 15 years ago
10.1371/journal.pone.0024820
Characterization of Leishmania donovani Aquaporins Shows Presence of Subcellular Aquaporins Similar to Tonoplast Intrinsic Proteins of PlantsCited by: 16
Author(s): Neha Biyani, Suvra Mandal, Chandan Seth, Malika Saint, Krishnamurthy Natarajan, Indira Ghosh, Rentala Madhubala
Software Mentions: 1
Published: about 13 years ago
10.1371/journal.pone.0103800
A Brazilian Population of the Asexual Fungus-Growing Ant Mycocepurus smithii (Formicidae, Myrmicinae, Attini) Cultivates Fungal Symbionts with Gongylidia-Like StructuresCited by: 17
Author(s): Virginia E. Masiulionis, Christian Rabeling, Henrik H. De Fine Licht, Ted R. Schultz, Maurício Bacci, Cintia Maria Santos Bezerra, Fernando Carlos Pagnocca
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pone.0120518
Molecular and Morphological Analyses Reveal Phylogenetic Relationships of Stingrays Focusing on the Family Dasyatidae (Myliobatiformes)Cited by: 25
Author(s): K. C. Lim, Phaik-Eem Lim, Ving Ching Chong, Kar‐Hoe Loh
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pone.0220477
Living on the edge: Assessing the diversity of South African Pocillopora on the margins of the Southwestern Indian OceanCited by: 4
Author(s): Brent Chiazzari, Hélène Magalon, Pauline Gélin, Angus H. H. Macdonald
Software Mentions: 1
Published: over 5 years ago