Ecosyste.ms: Papers

10.1371/journal.pntd.0005223

MLST-Based Population Genetic Analysis in a Global Context Reveals Clonality amongst Cryptococcus neoformans var. grubii VNI Isolates from HIV Patients in Southeastern Brazil
Cited by: 55
Author(s): Kennio Ferreira‐Paim, Leonardo Andrade-Silva, Fernanda Machado Fonseca, Thatiana Bragine Ferreira, Delio José Mora, Juliana Andrade-Silva, Aziza Khan, Aiken Dao, Eduardo C. Reis, Margarete Teresa Gottardo de Almeida, André Luiz Maltos, R. Virmondes, Luciana Trilles, Volker Rickerts, Ariya Chindamporn, Jane E. Sykes, Massimo Cogliati, Kirsten Nielsen, Teun Boekhout, Matthew C. Fisher, June Kwon‐Chung, David M. Engelthaler, Márcia dos Santos Lazéra, Wieland Meyer, Mário León Silva-Vergara
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pcbi.1003107

Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples
Cited by: 125
Author(s): David R. Riley, Karsten B. Sieber, Kelly Robinson, James R. White, Ashwinkumar Ganesan, Syrus Nourbakhsh, Julie C. Dunning Hotopp
Software Mentions: 4
Published: over 11 years ago

10.3389/fnins.2018.00573

Detection and Distinction of Mild Brain Injury Effects in a Ferret Model Using Diffusion Tensor MRI (DTI) and DTI-Driven Tensor-Based Morphometry (D-TBM)
Cited by: 15
Author(s): Elizabeth Hutchinson, Susan C. Schwerin, Kryslaine L. Radomski, Neda Sadeghi, Michal E. Komlosh, M. Okan İrfanoğlu, Sharon L. Juliano, Carlo Pierpaoli
Software Mentions: 3
Published: about 6 years ago

10.1186/1752-0509-4-3

Deciphering chemotaxis pathways using cross species comparisons
Cited by: 66
Author(s): Rebecca Hamer, Pao‐Yang Chen, Judith P. Armitage, Gesine Reinert, Charlotte M. Deane
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0070396

Functional Divergence and Convergent Evolution in the Plastid-Targeted Glyceraldehyde-3-Phosphate Dehydrogenases of Diverse Eukaryotic Algae
Cited by: 8
Author(s): Daniel Gaston, Andrew J. Roger
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2164-8-1

Comparative genomic analysis of prion genes
Cited by: 152
Author(s): Marko Premzl, Vera Gamulin
Software Mentions: 2
Published: over 17 years ago

10.1186/s40679-017-0040-7

Trace: a high-throughput tomographic reconstruction engine for large-scale datasets
Cited by: 27
Author(s): Tekin Biçer, Doğa Gürsoy, Vincent De Andrade, Rajkumar Kettimuthu, William Scullin, Francesco De Carlo, Ian Foster
Software Mentions: 2
Published: over 7 years ago

10.1186/2040-2392-4-32

Expression of non-protein-coding antisense RNAs in genomic regions related to autism spectrum disorders
Cited by: 41
Author(s): Dmitry Velmeshev, Marco Magistri, Mohammad Ali Faghihi
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pcbi.1000488

A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence
Cited by: 25
Author(s): Julie Baussand, Alessandra Carbone
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pgen.1000538

Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution
Cited by: 87
Author(s): Lucia Carbone, R. Alan Harris, Gery M. Vessere, Alan R. Mootnick, Sean Humphray, Jane Rogers, Sung K. Kim, Jeffrey D. Wall, David I. K. Martin, Jerzy Jurka, Aleksandar Milosavljevic, Pieter J. de Jong
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pntd.0004861

MLST and Whole-Genome-Based Population Analysis of Cryptococcus gattii VGIII Links Clinical, Veterinary and Environmental Strains, and Reveals Divergent Serotype Specific Sub-populations and Distant Ancestors
Cited by: 45
Author(s): Carolina Firacative, Chandler C. Roe, Richard Malík, Kennio Ferreira‐Paim, Patricia Escandón, Jane E. Sykes, Laura Rocío Castañón-Olivares, Cudberto Contreras-Peres, Blanca Samayoa, Tania C. Sorrell, Elizabeth Castañeda, Shawn R. Lockhart, David M. Engelthaler, Wieland Meyer
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0016410

Abundant Human DNA Contamination Identified in Non-Primate Genome Databases
Cited by: 108
Author(s): Mark S. Longo, Michael O’Neill, Rachel J. O’Neill
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0123365

Distinctive Patterns of Evolution of the δ-Globin Gene (HBD) in Primates
Cited by: 5
Author(s): Ana Moleirinho, Alexandra M. Lopes, Susana Seixas, Ramiro Morales‐Hojas, Maria João Prata, António Amorim
Software Mentions: 2
Published: over 9 years ago

10.1016/j.csbj.2021.04.041

Structure and evolutionary trace-assisted screening of a residue swapping the substrate ambiguity and chiral specificity in an esterase
Cited by: 6
Author(s): Isabel Cea‐Rama, Cristina Coscolín, Panagiotis Katsonis, Rafael Bargiela, Peter N. Golyshin, Olivier Lichtarge, Manuel Ferrer, J. Sanz‐Aparicio
Software Mentions: 2
Published: over 3 years ago

10.1080/22221751.2020.1863747

SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay
Cited by: 29
Author(s): Victoria Elizondo, Gordon William Harkins, Batsirai Mabvakure, Sabine Smidt, Paul Zappile, Christian Marier, Matthew T. Maurano, Victoria Pérez, Natalia Mazza, Carolina Beloso, Silvana Ifrán, Mariana Fernández, Andrea Santini, Verónica López Pérez, Verónica Estevez, Matilde Nin, Gonzalo Manrique, Leticia Perez, Fabiana Ross, Susana Boschi, María Noel Zubillaga, Raquel Ballesté, Simon Dellicour, Adriana Heguy, Ralf Duerr
Software Mentions: 2
Published: over 3 years ago

10.1186/gb-2010-11-3-r28

Detection and correction of false segmental duplications caused by genome mis-assembly
Cited by: 81
Author(s): David R. Kelley, Steven L. Salzberg
Software Mentions: 2
Published: over 14 years ago

10.3390/s17102218

Clustered Multi-Task Learning for Automatic Radar Target Recognition
Cited by: 7
Author(s): Cong Liu, Weimin Bao, Luping Xu, Hua Zhang
Software Mentions: 2
Published: almost 7 years ago

10.3390/s21165560

Distributed Architecture for an Integrated Development Environment, Large Trace Analysis, and Visualization
Cited by: 2
Author(s): Yonni Chen Kuang Piao, Naser Ezzati‐Jivan, Michel R. Dagenais
Software Mentions: 2
Published: about 3 years ago

10.7554/eLife.48496

Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture
Cited by: 5
Author(s): Hemanth K. N. Reddy, Marta Carroni, János Hajdu, Martin Svenda
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2148-13-232

Multilocus phylogeny and cryptic diversity in Asian shrew-like moles (Uropsilus, Talpidae): implications for taxonomy and conservation
Cited by: 26
Author(s): Tao Wan, Kai He, Xuelong Jiang
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pgen.1001052

A Deviation from the Bipolar-Tetrapolar Mating Paradigm in an Early Diverged Basidiomycete
Cited by: 56
Author(s): Marco A. Coelho, José Paulo Sampaio, Paula Gonçalves
Software Mentions: 1
Published: about 14 years ago

10.3389/fcvm.2021.660246

A Neonatal Mouse Model for Pressure Overload: Myocardial Response Corresponds to Severity
Cited by: 6
Author(s): Jielei Gu, Xuke Chen, Yangshuo Jin, Mingke Liu, Qiong Xu, Xiaolin Liu, Zhenyu Luo, Sisi Ling, Ningning Liu, Shiming Liu
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-11-230

BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences
Cited by: 215
Author(s): Christian Rohde, Yingying Zhang, Richard Reinhardt, Albert Jeltsch
Software Mentions: 1
Published: over 14 years ago

10.1186/s12859-016-1216-1

Analysis of optimal alignments unfolds aligners’ bias in existing variant profiles
Cited by: 4
Author(s): Quang Tran, Shanshan Gao, Vinhthuy Phan
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0103806

Evolution of Oleosin in Land Plants
Cited by: 17
Author(s): Yuan Fang, Rui‐Liang Zhu, Brent D. Mishler
Software Mentions: 1
Published: about 10 years ago

10.3389/fpubh.2021.716421

Is My Cough a Cold or Covid? A Qualitative Study of COVID-19 Symptom Recognition and Attitudes Toward Testing in the UK
Cited by: 17
Author(s): Fiona Mowbray, Lisa Woodland, Louise Smith, Richard Amlôt, G. James Rubin
Software Mentions: 1
Published: about 3 years ago

10.1186/s12859-019-2949-4

SRAssembler: Selective Recursive local Assembly of homologous genomic regions
Cited by: 8
Author(s): Thomas McCarthy, Hsien-Chao Chou, Volker Brendel
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0140280

Molecular Phylogeny Supports Repeated Adaptation to Burrowing within Small-Eared Shrews Genus of Cryptotis (Eulipotyphla, Soricidae)
Cited by: 14
Author(s): Kai He, Neal Woodman, Sean Boaglio, Mariel Roberts, Sunjana Supekar, Jesús E. Maldonado
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0174712

Phylogeographic patterns of Lygus pratensis (Hemiptera: Miridae): Evidence for weak genetic structure and recent expansion in northwest China
Cited by: 10
Author(s): Lijuan Zhang, Wanzhi Cai, Junyu Luo, Shuai Zhang, Chunyi Wang, Limin Lv, Xiangzhen Zhu, Li Wang, Jinjie Cui
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-25664-6

Interplay of grounding-line dynamics and sub-shelf melting during retreat of the Bjørnøyrenna Ice Stream
Cited by: 6
Author(s): Michele Petrini, Florence Colleoni, Nina Kirchner, Anna L.C. Hughes, Angelo Camerlenghi, Michele Rebesco, Renata Giulia Lucchi, Emanuele Forte, Renato R. Colucci, Riko Noormets
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0232035

Performance evaluation of humpback whale-inspired shortboard surfing fins based on ocean wave fieldwork
Cited by: 4
Author(s): David Shormann, Marc in het Panhuis
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0160672

Phylodynamic Characterization of an Ocular-Tropism Coxsackievirus A24 Variant
Cited by: 8
Author(s): Yung-Chang Yen, Pei-Huan Chu, Po‐Liang Lu, Yen-Ting Lin, Yipeng Shi, Li-Chiu Chou, Chufeng Wang, Yi‐Ying Lin, Hui-Ju Su, Chien-Ching Lin, Jing-Yun Zeng, Yu‐Chang Tyan, Guan-Ming Ke, Pei‐Yu Chu
Software Mentions: 1
Published: about 8 years ago

10.1186/gb-2010-11-2-r12

Genomic and small RNA sequencing of Miscanthus × giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses
Cited by: 91
Author(s): Kankshita Swaminathan, Magdy S. Alabady, Kranthi Varala, Emanuele De Paoli, Isaac Ho, Daniel S. Rokhsar, Aru K. Arumuganathan, Ray Ming, Pamela J. Green, Blake C. Meyers, Stephen P. Moose, Matthew E. Hudson
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-10-79

The mitochondrial genomes of Ancylostoma caninum and Bunostomum phlebotomum – two hookworms of animal health and zoonotic importance
Cited by: 62
Author(s): Aaron R. Jex, Andrea Waeschenbach, Min Hu, J.A. Van Wyk, Ian Beveridge, D. Timothy J. Littlewood, Robin B. Gasser
Software Mentions: 1
Published: over 15 years ago

10.1186/s12889-015-1869-0

Study protocol: the effectiveness and cost effectiveness of a brief behavioural intervention to promote regular self-weighing to prevent weight regain after weight loss: randomised controlled trial (The LIMIT Study)
Cited by: 12
Author(s): Claire Madigan, Kate Jolly, Andrea Roalfe, Alexander Lewis, Laura Webber, Paul Aveyard, Amanda Daley
Software Mentions: 1
Published: over 9 years ago

10.1186/1756-0500-4-146

SNPmplexViewer--toward a cost-effective traceability system
Cited by: 0
Author(s): Yanir Seroussi, Andrey Shirak, Eyal Seroussi
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-11-420

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences
Cited by: 136
Author(s): Allen Kovach, Jill L. Wegrzyn, Genı́s Parra, Carson Holt, George Bruening, Carol A. Loopstra, James Hartigan, Mark Yandell, Charles H. Langley, Ian F Korf, David B. Neale
Software Mentions: 1
Published: about 14 years ago

10.1039/c5mt00312a

Behavior of platinum(<scp>iv</scp>) complexes in models of tumor hypoxia: cytotoxicity, compound distribution and accumulation
Cited by: 38
Author(s): Ekaterina Schreiber‐Brynzak, Verena Pichler, Petra Heffeter, Buck Hanson, Sarah Theiner, Irene Lichtscheidl, Christoph Kornauth, Luca Bamonti, Vineet Dhery, Diana Groza, David P. Berry, Walter Berger, Markus Galanski, Michael A. Jakupec, Bernhard K. Keppler
Software Mentions: 1
Published: over 8 years ago

10.15252/embj.201695861

<i>miR‐31</i> mutants reveal continuous glial homeostasis in the adult <i>Drosophila</i> brain
Cited by: 15
Author(s): Lynette C. Foo, Shilin Song, Stephen M. Cohen
Software Mentions: 1
Published: over 7 years ago

10.1017/S003118201700213X

Monophyly of the species of <i>Hepatozoon</i> (Adeleorina: Hepatozoidae) parasitizing (African) anurans, with the description of three new species from hyperoliid frogs in South Africa
Cited by: 23
Author(s): Edward C. Netherlands, Courtney A. Cook, Louis H. Du Preez, Maarten Pieterjan Vanhove, Luc Brendonck, Nico J. Smit
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13071-020-3933-6

Molecular characterisation and morphological description of two new species of Hepatozoon Miller, 1908 (Apicomplexa: Adeleorina: Hepatozoidae) infecting leukocytes of African leopards Panthera pardus pardus (L.)
Cited by: 7
Author(s): Michelle van As, Edward C. Netherlands, Nico J. Smit
Software Mentions: 1
Published: over 4 years ago

10.1186/s13071-016-1702-3

A new lizard malaria parasite Plasmodium intabazwe n. sp. (Apicomplexa: Haemospororida: Plasmodiidae) in the Afromontane Pseudocordylus melanotus (Sauria: Cordylidae) with a review of African saurian malaria parasites
Cited by: 3
Author(s): Johann Van As, Courtney A. Cook, Edward C. Netherlands, Nico J. Smit
Software Mentions: 1
Published: about 8 years ago

10.7717/peerj.6264

Intraspecific divergences and phylogeography of<i>Panzerina lanata</i>(Lamiaceae) in northwest China
Cited by: 9
Author(s): Yanfen Zhao, Hongxiang Zhang, Bo‐Rong Pan, Mingli Zhang
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.7342

Functional and evolutionary perspectives on gill structures of an obligate air-breathing, aquatic snail
Cited by: 13
Author(s): Cristian Rodriguez, Guido I. Prieto, Israel A. Vega, Alfredo Castro-Vázquez
Software Mentions: 1
Published: about 5 years ago

10.1186/s13742-016-0138-1

Transcriptome of the Caribbean stony coral Porites astreoides from three developmental stages
Cited by: 16
Author(s): Tamer Mansour, Joshua J. C. Rosenthal, C. Titus Brown, Loretta Roberson
Software Mentions: 1
Published: about 8 years ago