cran: phylogram | Projects | Ecosyste.ms: Papers

10.3390/v12101142

A Diverse Virome of Leafroll-Infected Grapevine Unveiled by dsRNA Sequencing
Cited by: 24
Author(s): Mamadou L. Fall, De-Xiang Xu, Pierre Lemoyne, Issam Moussa, Carole Beaulieu, Odile Carisse
Software Mentions: 19
Published: over 3 years ago

10.1371/journal.pbio.3000534

The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response
Cited 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: over 4 years ago

10.3390/genes5040957

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis
Cited by: 57
Author(s): Vahan Simonyan, Raja Mazumder
Software Mentions: 5
Published: over 9 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: about 8 years ago

10.1371/journal.pone.0241231

A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica
Cited by: 7
Author(s): Joel H. Nitta, Atsushi Ebihara, Alan Р. Smith
Software Mentions: 5
Published: over 3 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 spacer
Cited 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: almost 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 relationships
Cited by: 36
Author(s): Wei-Cheng Lo, Ping Lyu
Software Mentions: 4
Published: over 16 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: over 11 years ago

10.3390/microorganisms9020299

What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes
Cited by: 4
Author(s): Angela Conti, Laura Della Corte, Debora Casagrande Pierantoni, Vincent Robert, Gianluigi Cardinali
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-017-10376-0

Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus
Cited 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: almost 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: about 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 filiformis
Cited 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: over 3 years ago

10.1371/journal.pone.0082615

Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study
Cited by: 89
Author(s): Adam L. Bazinet, Michael P. Cummings, Kim T. Mitter, Charles Mitter
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0021031

Improved Phylogenetic Analyses Corroborate a Plausible Position of Martialis heureka in the Ant Tree of Life
Cited by: 25
Author(s): Patrick Kück, Francisco Hita Garcia, Bernhard Misof, Karen Meusemann
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0249354

Partial DnaK protein expression from Coxiella-like endosymbiont of Rhipicephalus annulatus tick
Cited by: 1
Author(s): Pornpiroon Nooroong, Wachareeporn Trinachartvanit, Visut Baimai, Panat Anuracpreeda, Arunee Ahantarig
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0126124

Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial Species
Cited 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: about 9 years ago

10.1186/1471-2105-7-398

PhyloPat: phylogenetic pattern analysis of eukaryotic genes
Cited by: 16
Author(s): Tim Hulsen, Jacob de Vlieg, Peter M.A. Groenen
Software Mentions: 2
Published: almost 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: about 5 years ago

10.1371/journal.pone.0084012

Tracing the Rise of Ants - Out of the Ground
Cited by: 59
Author(s): Andrea Lucky, Michelle Trautwein, Benoit Guénard, Michael D. Weiser, Robert R. Dunn
Software Mentions: 2
Published: over 10 years ago

10.3389/fgene.2019.01172

The Local South American Chicken Populations Are a Melting-Pot of Genomic Diversity
Cited 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: over 4 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 System
Cited 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: about 3 years ago

10.3389/fmicb.2016.00002

Developmental Peculiarities and Seed-Borne Endophytes in Quinoa: Omnipresent, Robust Bacilli Contribute to Plant Fitness
Cited by: 75
Author(s): Andrea Pitzschke
Software Mentions: 1
Published: over 8 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 Cancer
Cited 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 bacteriophages
Cited 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: about 5 years ago

10.1186/s12859-019-3149-y

CLINE: a web-tool for the comparison of biological dendrogram structures
Cited by: 0
Author(s): Rodolfo S. Allendes Osorio, Lokesh P. Tripathi, Kenji Mizuguchi
Software Mentions: 1
Published: over 4 years ago

10.1093/sysbio/syz066

Continued Adaptation of C4 Photosynthesis After an Initial Burst of Changes in the Andropogoneae Grasses
Cited 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: over 4 years ago

10.1186/1471-2148-9-280

Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study
Cited 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: over 14 years ago

10.3897/mycokeys.62.47854

Discovery of Cytospora species associated with canker disease of tree hosts from Mount Dongling of China
Cited by: 11
Author(s): Hucheng Zhu, Meng Pan, Jadson Diogo Pereira Bezerra, Chengming Tian
Software Mentions: 1
Published: over 4 years ago

10.3897/zookeys.729.20615

Distribution of endangered Italian gudgeon Romanogobio benacensis (Cypriniformes, Cyprinidae, Gobioninae) with remarks on distinguishing morphological characters
Cited by: 3
Author(s): Dušan Jelić, Mišel Jelić, Petar Žutinić, Ivana Šimunović, Primož Zupančić, Alexander M. Naseka
Software Mentions: 1
Published: over 6 years ago

10.1186/s13071-019-3825-9

Cryptic intermediate snail host of the liver fluke Fasciola hepatica in Africa
Cited by: 12
Author(s): Anna Mahulu, Catharina Clewing, Björn Stelbrink, Fred D. Chibwana, Immaculate Tumwebaze, J. Russell Stothard, Christian Albrecht
Software Mentions: 1
Published: over 4 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: about 5 years ago

10.1186/1756-3305-2-27

In silico analysis of the cyclophilin repertoire of apicomplexan parasites
Cited by: 29
Author(s): Jürgen Krücken, Gisela Greif, Georg von Samson‐Himmelstjerna
Software Mentions: 1
Published: over 15 years ago

10.7717/peerj.2051

The masquerade game: marine mimicry adaptation between egg-cowries and octocorals
Cited 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: almost 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: about 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 Divergence
Cited by: 20
Author(s): Muhammed Jamsheer K, Chanchal Thomas Mannully, Nandu Gopan, Ashverya Laxmi
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0031559

Macro and Micro Diversity of Clostridium difficile Isolates from Diverse Sources and Geographical Locations
Cited 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 Nudibranchs
Cited by: 67
Author(s): Rebecca F. Johnson, Terrence M. Gosliner
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0099074

DUF581 Is Plant Specific FCS-Like Zinc Finger Involved in Protein-Protein Interaction
Cited by: 29
Author(s): Muhammed Jamsheer K, Ashverya Laxmi
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0016580

Exploring the Evolutionary Relationship of Insulin Receptor Substrate Family Using Computational Biology
Cited 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 Cancer
Cited 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: about 15 years ago

10.1371/journal.pone.0024820

Characterization of Leishmania donovani Aquaporins Shows Presence of Subcellular Aquaporins Similar to Tonoplast Intrinsic Proteins of Plants
Cited by: 16
Author(s): Neha Biyani, Suvra Mandal, Chandan Seth, Malika Saint, Krishnamurthy Natarajan, Indira Ghosh, Rentala Madhubala
Software Mentions: 1
Published: over 12 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 Structures
Cited 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: almost 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: about 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 Ocean
Cited by: 4
Author(s): Brent Chiazzari, Hélène Magalon, Pauline Gélin, Angus H. H. Macdonald
Software Mentions: 1
Published: almost 5 years ago

Projects: cran: phylogram

Papers Mentioning phylogram 44