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: pypi: TreeTime
https://packages.ecosyste.ms/registries/pypi.org/packages/TreeTime
TreeTime is a to-do list manager, test report tool, project manager, family ancestry editor,mind-mapping tool, etc. Using TreeTime you can categorise and organise any data in tree structures.You can define several trees, each with a different structure, on the same data. You can use functions(sums, ratios and means) recursively up the branches of a tree.
12 versions
Latest release: about 1 year ago
39 downloads last month
Papers Mentioning TreeTime 82
10.1371/journal.ppat.1009374
SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering eventCited by: 31
Author(s): Madlen Stange, Alfredo Mari, Tim Roloff, Helena M. B. Seth-Smith, Michael Schweitzer, Myrta Brunner, Karoline Leuzinger, Kirstine Kobberøe Søgaard, Alexander Gensch, Sarah Tschudin‐Sutter, Simon Fuchs, Julia Bielicki, Hans Pargger, Martin Siegemund, Christian H. Nickel, Roland Bingisser, Michael Osthoff, Stefano Bassetti, Rita Schneider-Sliwa, Manuel Battegay, Hans H. Hirsch, Adrian Egli
Software Mentions: 9
Published: over 3 years ago
10.3390/pathogens10080988
Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021Cited by: 11
Author(s): Vinícius Bonetti Franceschi, Gabriel Dickin Caldana, Christiano Perin, Alexandre Horn, Camila Peter, Gabriela Bettella Cybis, Patrícia Aline Gröhs Ferrareze, Liane Nanci Rotta, Flavio Cadegiani, Ricardo Ariel Zimerman, Claudia Elizabeth Thompson
Software Mentions: 8
Published: about 3 years ago
10.1002/cpz1.60
Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhyloCited by: 24
Author(s): Xavier Didelot, Michaela Kendall, Yuanwei Xu, Peter J White, Noel D. McCarthy
Software Mentions: 7
Published: over 3 years ago
10.7554/eLife.58931
Recurrent evolution of high virulence in isolated populations of a DNA virusCited by: 11
Author(s): Tom Hill, Robert L. Unckless
Software Mentions: 6
Published: almost 4 years ago
10.1371/journal.ppat.1008686
Helicobacter pylori diversification during chronic infection within a single host generates sub-populations with distinct phenotypesCited by: 7
Author(s): Laura Jackson, Barney Potter, Sean E. Schneider, Matthew Fitzgibbon, Kris M. Blair, Hajirah Farah, U. Murali Krishna, Trevor Bedford, Richard M. Peek, Nina R. Salama
Software Mentions: 6
Published: over 3 years ago
10.3389/fmicb.2021.655567
Molecular Evolution of Human Norovirus GII.2 ClustersCited by: 7
Author(s): Xingguang Li, Haizhou Liu, Brittany Rife Magalis, Sergei L. Kosakovsky Pond, Erik Volz
Software Mentions: 5
Published: over 3 years ago
10.1128/mSphere.00511-17
Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticusCited by: 9
Author(s): Tatum D Mortimer, Douglas S. Annis, Mary O’Neill, Lindsey L. Bohr, Tracy M. Smith, Hendrik N. Poinar, Deane F. Mosher, Caitlin S. Pepperell
Software Mentions: 5
Published: over 6 years ago
10.1371/journal.pone.0243265
Genomic variation and epidemiology of SARS-CoV-2 importation and early circulation in IsraelCited by: 4
Author(s): Neta S. Zuckerman, Efrat Bucris, Yaron Drori, Oran Erster, Danit Sofer, Rakefet Pando, Ella Mendelson, Orna Mor, Michal Mandelboim
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pgen.1009820
Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into natureCited by: 7
Author(s): Mark Achtman, Frederik Van den Broeck, Kerry K. Cooper, Philippe Lemey, Craig T. Parker, Zhemin Zhou
Software Mentions: 5
Published: almost 3 years ago
10.1093/ve/vex042
TreeTime: Maximum-likelihood phylodynamic analysisCited by: 786
Author(s): Pavel Sagulenko, Vadim Puller, Richard A. Neher
Software Mentions: 5
Published: over 6 years ago
10.4269/ajtmh.18-0980
Global Outbreaks and Origins of a Chikungunya Virus Variant Carrying Mutations Which May Increase Fitness for Aedes aegypti: Revelations from the 2016 Mandera, Kenya OutbreakCited by: 40
Author(s): Irina Maljkovic Berry, Fredrick Eyase, Simon Pollett, Samson L. Konongoi, Michael Joyce, Katherine Figueroa, Victor Ofula, Helen Koka, Edith Koskei, Albert Nyunja, James D. Mancuso, Richard G. Jarman, Rosemary Sang
Software Mentions: 4
Published: over 5 years ago
10.7717/peerj.8272
Evaluating probabilistic programming and fast variational Bayesian inference in phylogeneticsCited by: 18
Author(s): Mathieu Fourment, Aaron E. Darling
Software Mentions: 4
Published: over 4 years ago
10.1186/s13059-021-02483-z
Trycycler: consensus long-read assemblies for bacterial genomesCited by: 128
Author(s): Ryan R. Wick, Louise M. Judd, Louise Cerdeira, Jane Hawkey, Guillaume Méric, Ben Vezina, Kelly L. Wyres, Kathryn E. Holt
Software Mentions: 4
Published: about 3 years ago
10.7554/eLife.60197
Effects of domestication on the gut microbiota parallel those of human industrializationCited by: 37
Author(s): Aspen T. Reese, Katia S. Chadaideh, Caroline E. Diggins, Laura D. Schell, Mark Beckel, Peggy Callahan, Roberta Ryan, Melissa Emery Thompson, Rachel N. Carmody
Software Mentions: 4
Published: over 3 years ago
10.1186/s13059-020-02198-7
The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elementsCited by: 17
Author(s): Pingli Liu, Xi Zhang, Jian‐Feng Mao, Yan-Ming Hong, Rengang Zhang, E Yilan, Shuai Nie, Kai‐Hua Jia, Chen-Kun Jiang, Jian He, Weiwei Shen, Qizouhong He, Wenqing Zheng, Samar H. Abbas, Pawan Kumar Jewaria, Xue Tian, Changjun Liu, Xueyu Jiang, Yafang Yin, Bo Liu, Li Wang, Biao Jin, Yongpeng Ma, Zongbo Qiu, Frantǐsek Baluška, Jozef Šamaj, Xin-Qiang He, Shihui Niu, Jianbo Xie, Lei Xie, Huimin Xu, Hongzhi Kong, Song Ge, Richard A. Dixon, Yuannian Jiao, Jinxing Lin
Software Mentions: 4
Published: almost 4 years ago
10.3390/v13091801
Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in UruguayCited by: 6
Author(s): Natalia Rego, Cecilia Salazar, Mercedes Paz, Alicia Costábile, Álvaro Fajardo, Ignacio Ferrés, Paula Perbolianachis, Tamara Fernández-Calero, Verónica Noya, Matías Machado, Mariana Brandes, Rodrigo Arce, Mailén Arleo, Tania Possi, Natalia Reyes, María Noel Bentancor, Andrés Lizasoain, Viviana Bortagaray, Ana Moller, Odhille Chappos, Nicolás Nín, Javier Hurtado, Melissa Duquía, María Paula González, Luciana Griffero, Mauricio Méndez, Maria Pía Techera, J. E. Zanetti, Emiliano Pereira, Bernardina Rivera, Matías Maidana, Martina Alonso, Pablo Smircich, Ighor Arantes, Daiana Mir, Cecilia Alonso, Julio C. Medina, Henry Albornoz, Rodney Colina, Gonzalo Bello, Pilar Moreno, Gonzalo Moratorio, Gregorio Iraola, Lucía Spangenberg
Software Mentions: 4
Published: about 3 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: over 3 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
10.1186/s12879-019-4566-2
Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in ColombiaCited by: 12
Author(s): Allison Black, Louise H. Moncla, Katherine Laiton‐Donato, Barney Potter, Lissethe Pardo, Angélica Rico, Catalina Tovar, Diana Patricia Rojas, Ira M. Longini, M. Elizabeth Halloran, Dioselina Peláez-Carvajal, Juan David Ramírez, Marcela Mercado-Reyes, Trevor Bedford
Software Mentions: 3
Published: almost 5 years ago
10.3390/life11030219
SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic WaveCited by: 7
Author(s): Maria Bousali, Aristea Dimadi, Evangelia Georgia Kostaki, Sotirios Tsiodras, Georgios K. Nikolopoulos, Dionyssios N. Sgouras, Gkikas Magiorkinis, George V. Papatheodoridis, Vasiliki Pogka, Giota Lourida, Aikaterini Argyraki, Emmanouil Angelakis, George Sourvinos, Apostolos Beloukas, Dimitrios Paraskevis, Timokratis Karamitros
Software Mentions: 3
Published: over 3 years ago
10.3390/microorganisms8030373
The Nature and Extent of Plasmid Variation in Chlamydia trachomatisCited by: 9
Author(s): Charlotte Jones, James Hadfield, Nicholas R. Thomson, David W. Cleary, Peter Marsh, Ian N. Clarke, Colette O’Neill
Software Mentions: 3
Published: over 4 years ago
10.3390/vaccines9060616
A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in IsraelCited by: 20
Author(s): Neta S. Zuckerman, Shay Fleishon, Efrat Bucris, Dana Bar-Ilan, Michal Linial, Itay Bar-Or, Victoria Indenbaum, Merav Weil, Yaniv Lustig, Ella Mendelson, Michal Mandelboim, Orna Mor, Neta S. Zuckerman
Software Mentions: 3
Published: over 3 years ago
10.1093/ve/veaa010
Linking influenza virus evolution within and between human hostsCited by: 39
Author(s): Katherine S Xue, Jesse D. Bloom
Software Mentions: 3
Published: over 4 years ago
10.1093/ve/veaa084
Genomic epidemiology of coxsackievirus A16 in mainland of China, 2000–18Cited by: 20
Author(s): Zhaoxia Han, Yang Song, Jingwei Xiao, Lili Jiang, Wei E. Huang, Haiyan Wei, Jie Li, Hanri Zeng, Qingliang Yu, Jiameng Li, Deshan Yu, Yanjun Zhang, Chonghai Li, Zhifei Zhan, Yuanli Shi, Ying Xiong, Xianjun Wang, Tianjiao Ji, Qian Yang, Shuangli Zhu, Dongmei Yan, Wenbo Xu, Yong Zhang
Software Mentions: 3
Published: almost 4 years ago
10.3390/v10040192
Full Genome Sequencing Reveals New Southern African Territories Genotypes Bringing Us Closer to Understanding True Variability of Foot-and-Mouth Disease Virus in AfricaCited by: 22
Author(s): Lidia Lasecka-Dykes, Caroline F. Wright, Antonello Di Nardo, Greg Logan, Valérie Mioulet, Terry Jackson, Tobias J. Tuthill, Nick J. Knowles, Donald P. King
Software Mentions: 3
Published: over 6 years ago
10.3390/v12020182
In Search of Covariates of HIV-1 Subtype B Spread in the United States—A Cautionary Tale of Large-Scale Bayesian PhylogeographyCited by: 13
Author(s): Samuel L. Hong, Simon Dellicour, Bram Vrancken, Marc A. Suchard, Michael T. Pyne, David R. Hillyard, Philippe Lemey, Guy Baele
Software Mentions: 3
Published: over 4 years ago
10.7717/peerj.6663
Complete plastome sequence of <i>Iodes cirrhosa</i> Turcz., the first in the Icacinaceae, comparative genomic analyses and possible split of <i>Idoes</i> species in response to climate changesCited by: 10
Author(s): Liqiang Wang, Hui Zhang, Mei Jiang, Haimei Chen, Linfang Huang, Chang Liu
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pcbi.1007046
A new method for inferring timetrees from temporally sampled molecular sequencesCited by: 14
Author(s): Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A Huuki, Sergei L. Kosakovsky Pond, Jessica Priest, Jiamin Deng, Sudhir Kumar
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pntd.0009327
Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon BasinCited by: 7
Author(s): Nathalia Ballesteros, Marina Muñoz, Luz Helena Patiño, Carolina Hernández, Felipe González-Casabianca, Iván Carroll, Mauricio Santos-Vega, Jaime Cascante, Andrés Ángel, Alejandro Feged-Rivadeneira, Mónica Palma-Cuero, Carolina Flórez, Sergio Gómez, Adriana van de Guchte, Zenab Khan, Jayeeta Dutta, Ajay Obla, Hala Alshammary, Ana S. González-Reiche, Matthew M. Hernandez, Emilia Mia Sordillo, Viviana Simon, Harm van Bakel, Alberto Paníz-Mondolfi, Juan David Ramírez
Software Mentions: 3
Published: over 3 years ago
10.1016/j.cell.2020.05.035
Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during InfectionCited by: 26
Author(s): Jessica Ho, Matthew Angel, Yixuan Ma, Elizabeth Sloan, Guojun Wang, Carles Martínez-Romero, Marta Alenquer, Vladimir Roudko, Liliane Chung, Simin Zheng, Max W. Chang, Yesai Fstkchyan, Sara Clohisey, Adam M. Dinan, James S. Gibbs, Robert J. Gifford, Rong Shen, Quan Gu, Nerea Irigoyen, Laura Campisi, Cheng Huang, Nan Zhao, Joshua D. Jones, Ingeborg van Knippenberg, Zeyu Zhu, Natasha Moshkina, Léa Meyer, Justine Noel, Zuleyma Peralta, Veronica V. Rezelj, Robyn M. Kaake, Brad R. Rosenberg, Bo Wang, Jiajie Wei, Slobodan Paessler, Helen Wise, Jeffrey R. Johnson, Alessandro Vannini, Maria João Amorim, J Kenneth Baillie, Emily R. Miraldi, Christopher Benner, Ian Brierley, Paul Digard, Marta Łuksza, Andrew E. Firth, Nevan J. Krogan, Benjamin Greenbaum, Megan K. L. MacLeod, Harm van Bakel, Adolfo Garcı́a-Sastre, Jonathan W. Yewdell, Edward Hutchinson, Ivan Marazzi
Software Mentions: 3
Published: over 4 years ago
10.3389/fgene.2021.586569
Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease EpidemiologyCited by: 27
Author(s): Madhvi Joshi, Apurvasinh Puvar, Dinesh Kumar, Afzal Ansari, Maharshi Pandya, Janvi Raval, Zarna Patel, Pinal Trivedi, Monika Gandhi, Labdhi Pandya, Komal Patel, Nitin Savaliya, S. B. Bagatharia, Sachin Kumar, Chaitanya Joshi
Software Mentions: 3
Published: over 3 years ago
10.3389/fmicb.2019.01708
Molecular Evolutionary Analysis of Potato Virus Y Infecting Potato Based on the VPg GeneCited by: 14
Author(s): Yanzhi Mao, Xuhong Sun, Jianguo Shen, Fangluan Gao, Guangwei Qiu, Teng Wang, Xianzhou Nie, Wei Zhang, Yanling Gao, Yuling Bai
Software Mentions: 3
Published: about 5 years ago
10.3389/fvets.2020.00176
Animal Disease Surveillance in the 21st Century: Applications and Robustness of Phylodynamic Methods in Recent U.S. Human-Like H3 Swine Influenza OutbreaksCited by: 1
Author(s): Moh A. Alkhamis, Chong Li, Montserrat Torremorell
Software Mentions: 3
Published: over 4 years ago
10.3390/genes12020239
Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya VirusCited by: 7
Author(s): Thomas Spicher, Markus Delitz, Adriano de Bernardi Schneider, Michael T. Wolfinger
Software Mentions: 3
Published: over 3 years ago
10.3906/biy-2005-35
Phylogenetic analysis of SARS-CoV-2 genomes in TurkeyCited by: 13
Author(s): Ogün Adebali, Aylin Bircan, Defne Circi, Burak İŞlek, Zeynep Kilinc, Berkay Selçuk, Berk Turhan
Software Mentions: 3
Published: about 4 years ago
10.1101/2021.01.18.427056
Model design for non-parametric phylodynamic inference and applications to pathogen surveillanceCited by: 3
Author(s): Xavier Didelot, Lily Geidelberg, Erik Volz
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0243412
Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of KarnatakaCited by: 25
Author(s): Chitra Pattabiraman, Farhat Habib, Pulleri Kandi Harsha, Risha Rasheed, Pramada Prasad, Vijayalakshmi Reddy, Prameela Dinesh, Tina Damodar, Kiran Hosallimath, Anson K. George, Nakka Vijay Kiran Reddy, Banerjee John, Amrita Pattanaik, Narendra Kumar, Reeta Subramaniam Mani, Manjunatha M. Venkataswamy, Shafeeq K Shahul Hameed, Brind Kumar, Anita Desai, Vasanthapuram Ravi
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0234671
Real-time tracking of Tomato brown rugose fruit virus (ToBRFV) outbreaks in the Netherlands using NextstrainCited by: 29
Author(s): Bart van de Vossenberg, M. Visser, Maaike Bruinsma, H. Koenraadt, Marcel Westenberg, Marleen Botermans
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0256451
Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in PakistanCited by: 22
Author(s): Najia Karim Ghanchi, Asghar Nasir, Kiran Iqbal Masood, Syed Hani Abidi, Syed Faisal Mahmood, Akbar Kanji, Safina Abdul Razzak, Waqasuddin Khan, Saba Shahid, Maliha Yameen, Ali Raza, Javaria Ashraf, Zeeshan Ansar, Mohammad Buksh Dharejo, Najmul Islam, Zahra Hasan, Rumina Hasan
Software Mentions: 2
Published: about 3 years ago
10.3390/vaccines9080937
The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452RCited by: 11
Author(s): Orna Mor, Michal Mandelboim, Shay Fleishon, Efrat Bucris, Dana Bar-Ilan, Michal Linial, Ital Nemet, Limor Kliker, Yaniv Lustig, Ella Mendelson, Neta S. Zuckerman
Software Mentions: 2
Published: about 3 years ago
10.1080/22221751.2020.1863747
SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in UruguayCited 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
10.1371/journal.pone.0221068
TreeCluster: Clustering biological sequences using phylogenetic treesCited by: 80
Author(s): Metin Balaban, Niema Moshiri, Uyen Mai, Xingfan Jia, Siavash Mirarab
Software Mentions: 2
Published: about 5 years ago
10.1093/molbev/msaa193
Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology PhylogeniesCited by: 26
Author(s): Xavier Didelot, Igor Siveroni, Erik Volz
Software Mentions: 2
Published: about 4 years ago
10.3390/v13081491
Rise and Fall of SARS-CoV-2 Lineage A.27 in GermanyCited by: 9
Author(s): Sébastien Calvignac‐Spencer, Matthias Budt, Matthew R. Huska, Hugues Richard, Luca Leipold, Linus Grabenhenrich, Torsten Semmler, Max von Kleist, Stefan Kröger, Thorsten Wolff, Martin Hölzer
Software Mentions: 2
Published: about 3 years ago
10.3390/v13081628
On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review StudyCited by: 9
Author(s): Kanika D Nahata, Nena Bollen, Mandev S. Gill, Maylis Layan, Hervé Bourhy, Simon Dellicour, Guy Baele
Software Mentions: 2
Published: about 3 years ago
10.3390/pathogens10070896
West Nile Virus in BrazilCited by: 15
Author(s): Érica Azevedo Costa, Marta Giovanetti, Lilian Silva Catenacci, Vagner Fonseca, Flávia Figueira Aburjaile, Flávia Löwen Levy Chalhoub, Joilson Xavier, Felipe Campos de Melo Iani, Marcelo Adriano da Cunha e Silva Vieira, Danielle Freitas Henriques, Daniele Barbosa de Almeida Medeiros, Maria Isabel Maldonado Coelho Guedes, Beatriz Senra Álvares da Silva Santos, Aila Solimar Gonçalves Silva, Renata de Pino Albuquerque Maranhão, Nieli Rodrigues da Costa Faria, Renata Farinelli de Siqueira, Túlio de Oliveira, Karina Ribeiro Leite Jardim Cavalcante, Noely Fabiana Oliveira de Moura, Alessandro Romano, Carlos Frederico Campelo de Albuquerque, Lauro César Soares Feitosa, José Joffre Martins Bayeux, Raffaella Bertoni Cavalcanti Teixeira, Osmaikon Lisboa Lobato, Silvokleio da Costa Silva, Ana María Bispo de Filippis, Rivaldo Venâncio da Cunha, José Lourenço, Luíz Carlos Júnior Alcântara
Software Mentions: 2
Published: about 3 years ago
10.3390/v13071359
Variant Analysis of SARS-CoV-2 Genomes from Belgian Military Personnel Engaged in Overseas Missions and OperationsCited by: 5
Author(s): Jean‐Paul Pirnay, Philippe Selhorst, Samuel L. Hong, Christel Cochez, Barney Potter, Piet Maes, Mauro Petrillo, Gytis Dudas, Vincent Claes, Yolien Van der Beken, Gilbert Verbeken, Julie Degueldre, Simon Dellicour, Lize Cuypers, France T’Sas, Guy Van den Eede, Bruno Verhasselt, Wouter Weuts, Cedric Smets, Jan Mertens, Philippe Geeraerts, Kevin K. Ariën, Emmanuel André, Pierre Neirinckx, Patrick Soentjens, Guy Baele
Software Mentions: 2
Published: about 3 years ago
10.7554/eLife.44205
Phylodynamic theory of persistence, extinction and speciation of rapidly adapting pathogensCited by: 27
Author(s): Le Yan, Richard A. Neher, Boris I. Shraiman
Software Mentions: 2
Published: almost 5 years ago
10.3389/fmicb.2021.722838
Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri LankaCited by: 8
Author(s): Chandima Jeewandara, Deshni Jayathilaka, D.M.S.H.K. Ranasinghe, Sharon Hsu, Dinuka Ariyaratne, Tibutius Jayadas, Deshan Madhusanka Panambara Arachchige, Benjamin B. Lindsey, Laksiri Gomes, Matthew Parker, Ananda Wijewickrama, Malika Karunaratne, Graham Ogg, Thushan I. de Silva, Gathsaurie Neelika Malavige
Software Mentions: 2
Published: about 3 years ago
10.3390/vaccines9060608
Phylogenetic Structure and Sequential Dominance of Sub-Lineages of PRRSV Type-2 Lineage 1 in the United StatesCited by: 29
Author(s): Igor Adolfo Dexheimer Paploski, Nakarin Pamornchainavakul, Dennis N. Makau, Albert Rovira, Cesar Corzo, Declan C. Schroeder, Maxim C.-J. Cheeran, Andrea Doeschl‐Wilson, Rowland R. Kao, Samantha Lycett, Kimberly VanderWaal
Software Mentions: 2
Published: over 3 years ago
10.1128/MRA.00697-20
Genome Sequences of SARS-CoV-2 Strains Detected in Hong KongCited by: 5
Author(s): Chun Hang Au, Wai Sing Chan, Ho Yin Lam, Dona N. Ho, Simon Y. M. Lam, Jonpaul Sze-Tsing Zee, Tsun Leung Chan, S. K. Edmond
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.ppat.1009453
A human coronavirus evolves antigenically to escape antibody immunityCited by: 166
Author(s): Rachel Eguia, Katharine H.D. Crawford, Terry Stevens-Ayers, Laurel Kelnhofer-Millevolte, Alexander L. Greninger, Janet A. Englund, Michael Boeckh, Jesse D. Bloom
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pntd.0008885
An epidemiological surveillance of hand foot and mouth disease in paediatric patients and in community: A Singapore retrospective cohort study, 2013–2018Cited by: 14
Author(s): Nyo Min, Y. H. Ong, Alvin X. Han, Si Xian Ho, Emmerie Wong Phaik Yen, Kenneth Ban, Sebastian Maurer‐Stroh, Chia Yin Chong, Justin Jang Hann Chu
Software Mentions: 2
Published: over 3 years ago
10.1093/molbev/msaa284
A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 LineagesCited by: 66
Author(s): Simon Dellicour, Keith Durkin, Samuel L. Hong, Bert Vanmechelen, Joan Martí-Carreras, Mandev S. Gill, Cécile Meex, Sébastien Bontems, Emmanuel André, Marius Gilbert, Conor R Walker, Nicola De Maio, Nuno Rodrigues Faria, James Hadfield, Marie Pierre Hayette, Vincent Bours, Tony Wawina-Bokalanga, Maria Artesi, Guy Baele, Piet Maes
Software Mentions: 1
Published: almost 4 years ago
10.1038/s41598-019-45752-5
A novel host-adapted strain of Salmonella Typhimurium causes renal disease in olive ridley turtles (Lepidochelys olivacea) in the PacificCited by: 10
Author(s): Thierry M. Work, Julie Dagenais, Brian A. Stacy, Jason T. Ladner, Jeffrey M. Lorch, George H. Balazs, Elías Barquero-Calvo, Brenda M. Berlowski-Zier, Renee Breeden, Natalia Corrales-Gómez, Rocío González-Barrientos, Heather Harris, Gabriela Hernández-Mora, Ángel Herrera-Ulloa, Shoreh Hesami, Timothy Jones, Juan Alberto Morales, Terry M. Norton, Robert A. Rameyer, Daniel R. Taylor, Thomas B. Waltzek
Software Mentions: 1
Published: about 5 years ago
10.1038/s41598-019-46509-w
Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infantCited by: 20
Author(s): Charles N. Agoti, My Phan, Patrick K. Munywoki, George Githinji, Graham F. Medley, Patricia A. Cane, Paul Kellam, Matthew Cotten, D. James Nokes
Software Mentions: 1
Published: about 5 years ago
10.1038/s41598-021-97667-9
Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020Cited by: 8
Author(s): Nena Bollen, Maria Artesi, Keith Durkin, Samuel L. Hong, Barney Potter, Bouchra Boujemla, Bert Vanmechelen, Joan Martí-Carreras, Tony Wawina-Bokalanga, Cécile Meex, Sébastien Bontems, Marie‐Pierre Hayette, Emmanuel André, Piet Maes, Vincent Bours, Guy Baele, Simon Dellicour
Software Mentions: 1
Published: almost 3 years ago
10.7554/eLife.66448
Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington StateCited by: 10
Author(s): Louise H. Moncla, Allison Black, Chase DeBolt, Misty Lang, Nicholas R. Graff, Ailyn C. Pérez-Osorio, Nicola F. Müller, Dirk Haselow, Scott Lindquist, Trevor Bedford
Software Mentions: 1
Published: over 3 years ago
10.3906/biy-2008-56
Current mutatome of SARS-CoV-2 in Turkey reveals mutations of interestCited by: 9
Author(s): Doğa Eskier, Evren Akalp, Özlem Dalan, Gökhan Karakülah, Yavuz Oktay
Software Mentions: 1
Published: over 3 years ago
10.1186/s12862-019-1567-0
The ability of single genes vs full genomes to resolve time and space in outbreak analysisCited by: 30
Author(s): Gytis Dudas, Trevor Bedford
Software Mentions: 1
Published: almost 5 years ago
10.1128/mSystems.00108-17
Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosisCited by: 31
Author(s): Tatum D Mortimer, Alexandra M. Weber, Caitlin S. Pepperell
Software Mentions: 1
Published: over 6 years ago
10.3390/v13060984
Epidemic Spread of SARS-CoV-2 Lineage B.1.1.7 in BrazilCited by: 14
Author(s): Filipe Romero Rebello Moreira, Diego Menezes, Danielle Alves Gomes Zauli, Joice P Silva, Aline Brito de Lima, Frederico Scott Varella Malta, Alexandre de Aguiar Ferreira, Victor Cavalcanti Pardini, Wagner C. S. Magalhães, Daniel Costa Queiroz, Rafael Marques de Souza, Victor Emmanuel Viana Geddes, Walyson Coelho Costa, Rennan Garcias Moreira, Nuno Rodrigues Faria, Carolina M Voloch, Renan Pedra de Souza, Renato Santana Aguiar
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pcbi.1007774
Estimating effective population size changes from preferentially sampled genetic sequencesCited by: 13
Author(s): Michael D. Karcher, Luiz Max Carvalho, Marc A. Suchard, Gytis Dudas, Vladimir N. Minin
Software Mentions: 1
Published: almost 4 years ago
10.1101/2020.07.09.20149104
Distinct patterns of SARS-CoV-2 transmission in two nearby communities in Wisconsin, USACited by: 6
Author(s): Gage K. Moreno, Katarina M. Braun, Kasen K. Riemersma, Michael A. Martin, Peter Halfmann, Chelsea M. Crooks, Trent M. Prall, David Baker, John J. Baczenas, Anna S. Heffron, Mitchell D. Ramuta, Manjeet Khubbar, Andrea M. Weiler, Molly A. Accola, William M. Rehrauer, Shelby L. O’Connor, Nasia Safdar, Caitlin S. Pepperell, Trivikram Dasu, Sanjib Bhattacharyya, Yoshihiro Kawaoka, Katia Koelle, David H. O’Connor, Thomas C. Friedrich
Software Mentions: 1
Published: about 4 years ago
10.3390/v13040592
Limited Genetic Diversity Detected in Middle East Respiratory Syndrome-Related Coronavirus Variants Circulating in Dromedary Camels in JordanCited by: 4
Author(s): Stephanie N. Seifert, Jonathan Schulz, Stacy Ricklefs, Michael Letko, Elangeni Yabba, Zaidoun S.K. Hijazeen, Peter J. Holloway, Bilal Al-Omari, Hani A. Talafha, Markos Tibbo, Danielle R. Adney, Javier Guitian, Nadim Mukhles Amarin, Jüergen A. Richt, Chester McDowell, John Steel, Ehab A. Abu‐Basha, Ahmad M. Al-Majali, Neeltje van Doremalen, Vincent J. Munster
Software Mentions: 1
Published: over 3 years ago
10.7554/eLife.68353
Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assayCited by: 52
Author(s): Joshua Batson, Gytis Dudas, Eric J. Haas-Stapleton, Amy Kistler, Lucy M Li, Phoenix Logan, Kalani Ratnasiri, Hanna Retallack
Software Mentions: 1
Published: over 3 years ago
10.3390/v13030526
Multiple Early Introductions of SARS-CoV-2 to Cape Town, South AfricaCited by: 20
Author(s): Susan Engelbrecht, Kayla Eileen Delaney, Bronwyn Kleinhans, Eduan Wilkinson, Houriiyah Tegally, Tania Stander, Gert van Zyl, Wolfgang Preiser, Túlio de Oliveira
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0245584
In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in BangladeshCited by: 25
Author(s): Tushar Ahmed Shishir, Iftekhar Bin Naser, Shah M. Faruque
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0241405
SARS-CoV-2 transmission routes from genetic data: A Danish case studyCited by: 16
Author(s): Andreas Bluhm, Matthias Christandl, Fulvio Gesmundo, Frederik Ravn Klausen, Laura Mančinska, Vincent Steffan, Daniel Stilck França, Albert H. Werner
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pone.0234010
Origin of HAV strains responsible for 2016–2017 outbreak among MSM: Viral phylodynamics in Lazio regionCited by: 5
Author(s): Claudia Minosse, Francesco Messina, Anna Rosa Garbuglia, Silvia Meschi, Paola Scognamiglio, Maria Rosaria Capobianchi, Giuseppe Ippolito, Simone Lanini
Software Mentions: 1
Published: over 4 years ago
10.3390/v13010116
Molecular Epidemiological Analysis of the Origin and Transmission Dynamics of the HIV-1 CRF01_AE Sub-Epidemic in BulgariaCited by: 6
Author(s): Ivailo Alexiev, Ellsworth Campbell, S. P. Knyazev, Y. Pan, Lyubomira Grigorova, Reneta Dimitrova, Aleksandra Partsuneva, Anna Gancheva, Asya Kostadinova, Carole Seguin-Devaux, Ivaylo Elenkov, Nina Yancheva, William M. Switzer
Software Mentions: 1
Published: over 3 years ago
10.1080/22221751.2021.1943540
Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutationsCited by: 17
Author(s): Lishuang Shen, Jennifer Dien Bard, Timothy J. Triche, Alexander R. Judkins, Jaclyn A. Biegel, Xiaowu Gai
Software Mentions: 1
Published: over 3 years ago
10.1080/22221751.2021.1922097
Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implicationsCited by: 41
Author(s): Lishuang Shen, Jennifer Dien Bard, Timothy J. Triche, Alexander R. Judkins, Jaclyn A. Biegel, Xiaowu Gai
Software Mentions: 1
Published: over 3 years ago
10.7554/eLife.60067
Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolutionCited by: 25
Author(s): John Huddleston, John Barnes, Thomas Rowe, Xinhua Xu, Rebecca Kondor, David E. Wentworth, Lynne Whittaker, Burcu Ermetal, Rodney S. Daniels, John W. McCauley, Seiichiro Fujisaki, Kenzo Nakamura, Noriko Kishida, Shinji Watanabe, Hideki Hasegawa, Ian G. Barr, Kanta Subbarao, Pierre Barrat-Charlaix, Richard A. Neher, Trevor Bedford
Software Mentions: 1
Published: about 4 years ago
10.1093/ve/veaa066
Efficient inference, potential, and limitations of site-specific substitution modelsCited by: 3
Author(s): Vadim Puller, Pavel Sagulenko, Richard A. Neher
Software Mentions: 1
Published: about 4 years ago
10.1186/1471-2148-9-151
Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizardsCited by: 67
Author(s): Christy A. Hipsley, Lin Himmelmann, Dirk Metzler, Johannes Müller
Software Mentions: 1
Published: about 15 years ago
10.7554/eLife.45079
Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humansCited by: 38
Author(s): Y. Q. Shirleen Soh, Louise H. Moncla, Rachel Eguia, Trevor Bedford, Jesse D. Bloom
Software Mentions: 1
Published: over 5 years ago
10.1093/ve/vey016
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10Cited by: 2,159
Author(s): Marc A. Suchard, Philippe Lemey, Guy Baele, Daniel L. Ayres, Alexei J. Drummond, Andrew Rambaut
Software Mentions: 1
Published: over 6 years ago
10.1186/s40249-021-00853-0
Epidemiology and evolution of Middle East respiratory syndrome coronavirus, 2012–2020Cited by: 31
Author(s): Anran Zhang, Wenqiang Shi, Kun Liu, Xin-Lou Li, Mingjin Liu, Wenhui Zhang, Guoping Zhao, Jinjin Chen, Xiao-Ai Zhang, Dong Miao, Wei Ma, Wei Liu, Yang Yang, Li‐Qun Fang
Software Mentions: 1
Published: over 3 years ago
10.1001/jamanetworkopen.2020.24191
Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 PandemicCited by: 30
Author(s): Wenjuan Zhang, John Paul Govindavari, Brian D. Davis, Stephanie S Chen, Jong Taek Kim, Jianbo Song, Jean Lopategui, Jasmine T Plummer, Eric Vail
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.ppat.1008042
Twenty years of West Nile virus spread and evolution in the Americas visualized by NextstrainCited by: 80
Author(s): James Hadfield, Anderson F. Brito, Daniele M. Swetnam, Chantal B.F. Vogels, Ryan E. Tokarz, Kristian G. Andersen, Ryan C. Smith, Trevor Bedford, Nathan D. Grubaugh
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.ppat.1008191
Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in CambodiaCited by: 18
Author(s): Louise H. Moncla, Trevor Bedford, Philippe Dussart, Srey Viseth Horm, Sareth Rith, Philippe Buchy, Erik A. Karlsson, Lifeng Li, Yongmei Liu, Hua Zhu, Yi Guan, Thomas C. Friedrich, Paul F. Horwood
Software Mentions: 1
Published: over 4 years ago