cran: LSD | Projects | Ecosyste.ms: Papers

10.1128/mBio.01105-19

Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent
Cited by: 42
Author(s): Eike J. Steinig, Sebastián Duchêne, D. Ashley Robinson, Stefan Monecke, Maho Yokoyama, Maisem Laabei, Peter Slickers, Patiyan Andersson, Deborah A. Williamson, Angela Kearns, Richard V. Goering, Elizabeth Dickson, Ralf Ehricht, Margaret Ip, Matthew V. N. O’Sullivan, Geoffrey W. Coombs, Andreas Petersen, Gráinne I. Brennan, Anna C. Shore, David C. Coleman, Annalisa Pantosti, Hermı́nia de Lencastre, Henrik Westh, Nobumichi Kobayashi, Helen Heffernan, Birgit Strommenger, Franziska Layer, Stefan Weber, Hege Vangstein Aamot, Leila Skakni, Sharon J. Peacock, Derek S. Sarovich, Simon R. Harris, Julian Parkhill, Ruth C. Massey, Matthew T. G. Holden, Stephen D. Bentley, Steven Y. C. Tong
Software Mentions: 10
Published: almost 5 years ago

10.1093/ve/vey039

Evidence for a recombinant origin of HIV-1 Group M from genomic variation
Cited by: 7
Author(s): Abayomi S Olabode, Mariano Avino, Garway T Ng, Faisal Abu-Sardanah, David W Dick, Art F. Y. Poon
Software Mentions: 7
Published: almost 6 years ago

10.1002/cpz1.60

Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo
Cited by: 24
Author(s): Xavier Didelot, Michaela Kendall, Yuanwei Xu, Peter J White, Noel D. McCarthy
Software Mentions: 7
Published: almost 4 years ago

10.1002/pld3.279

Gene expression changes occurring at bolting time are associated with leaf senescence in Arabidopsis
Cited by: 12
Author(s): Will E. Hinckley, Judy A. Brusslan
Software Mentions: 6
Published: about 4 years ago

10.1186/s12920-018-0358-6

Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability
Cited by: 5
Author(s): Ute Scheller, Kathrin Pfisterer, Steffen Uebe, Arif B. Ekici, André Reis, Rami Abou Jamra, Fulvia Ferrazzi
Software Mentions: 6
Published: over 6 years ago

10.1093/ve/vew029

Reconstructing contact network parameters from viral phylogenies
Cited by: 11
Author(s): Rosemary M. McCloskey, Richard Liang, Art F. Y. Poon
Software Mentions: 6
Published: over 8 years ago

10.1534/g3.116.032276

Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in<i>Saccharomyces cerevisiae</i>
Cited by: 39
Author(s): Benjamin Neymotin, Victoria M. Ettorre, David Gresham
Software Mentions: 5
Published: about 8 years ago

10.3389/fmicb.2021.655567

Molecular Evolution of Human Norovirus GII.2 Clusters
Cited 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

10.1038/s41598-018-22725-8

Erosion of natural darkness in the geographic ranges of cacti
Cited by: 6
Author(s): M. Correa-Cano, Bárbara Goettsch, James P. Duffy, Jonathan Bennie, Richard Inger, Kevin J. Gaston
Software Mentions: 5
Published: over 6 years ago

10.1093/molbev/msw124

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution
Cited by: 107
Author(s): Michaela Kendall, Caroline Colijn
Software Mentions: 5
Published: over 8 years ago

10.1093/ve/veaa089

Simulating within host human immunodeficiency virus 1 genome evolution in the persistent reservoir
Cited by: 5
Author(s): Bradley R. Jones, Jeffrey B. Joy
Software Mentions: 5
Published: over 4 years ago

10.1093/ve/vex042

TreeTime: Maximum-likelihood phylodynamic analysis
Cited by: 786
Author(s): Pavel Sagulenko, Vadim Puller, Richard A. Neher
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0175330

Genomic analyses of the ancestral Manila family of Mycobacterium tuberculosis
Cited by: 8
Author(s): Xuehua Wan, Kent J. Koster, Lishi Qian, Edward Desmond, Richard Brostrom, Shaobin Hou, James T. Douglas
Software Mentions: 5
Published: over 7 years ago

10.3390/microorganisms8040559

Comparative Transcriptomics Reveals Distinct Gene Expressions of a Model Ciliated Protozoan Feeding on Bacteria-Free Medium, Digestible, and Digestion-Resistant Bacteria
Cited by: 9
Author(s): Songbao Zou, Qianqian Zhang, Jun Gong
Software Mentions: 5
Published: over 4 years ago

10.1093/molbev/msaa222

Log Transformation Improves Dating of Phylogenies
Cited by: 4
Author(s): Uyen Mai, Siavash Mirarab
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pgen.1002604

Gene Reactivation by 5-Aza-2′-Deoxycytidine–Induced Demethylation Requires SRCAP–Mediated H2A.Z Insertion to Establish Nucleosome Depleted Regions
Cited by: 52
Author(s): Xiaojing Yang, Houtan Noushmehr, Han Han, Claudia Andreu-Vieyra, Gangning Liang, Peter A. Jones
Software Mentions: 4
Published: over 12 years ago

10.15252/msb.20156198

Single‐cell polyadenylation site mapping reveals 3′ isoform choice variability
Cited by: 54
Author(s): Lars Velten, Simon Anders, Aleksandra Pękowska, Aino I Järvelin, Wolfgang Huber, Vicent Pelechano, Lars M. Steinmetz
Software Mentions: 3
Published: over 9 years ago

10.1186/s13321-021-00529-9

MAYGEN: an open-source chemical structure generator for constitutional isomers based on the orderly generation principle
Cited by: 6
Author(s): Mehmet Aziz Yirik, Maria Sorokina, Christoph Steinbeck
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-016-3237-6

Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe
Cited by: 64
Author(s): Yuriko Harigaya, Roy Parker
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-017-3749-8

The link between adjacent codon pairs and mRNA stability
Cited by: 29
Author(s): Yuriko Harigaya, Roy Parker
Software Mentions: 3
Published: over 7 years ago

10.1186/2041-1480-5-5

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
Cited by: 47
Author(s): Toshiaki Katayama, Mark D. Wilkinson, Kiyoko F. Aoki‐Kinoshita, Seiichiro Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Ono Hiromasa, Hidemasa Bono, Simon Kocbek, Jan Aerts, Yukie Akune, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Joachim Baran, Jerven Bolleman, Raoul Jean Pierre Bonnal, Pier Luigi Buttigieg, Matthew P. Campbell, Yi An Chen, Hirokazu Chiba, Peter J. A. Cock, K. Bretonnel Cohen, Alexandru Constantin, Geraint Duck, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Naohisa Goto, Robert Hoehndorf, Yoshinobu Igarashi, Hidetoshi Itaya, Maori Ito, Wataru Iwasaki, Matúš Kalaš, Takeo Katoda, Taejoon Kim, Anna Kokubu, Yusuke Komiyama, Masaaki Kotera, Camille Laibe, Hilmar Lapp, Thomas Lütteke, M. Scott Marshall, Mori Takaaki, Hiroshi Mori, Mizuki Morita, Katsuhiko Murakami, Mitsuteru Nakao, Hisashi Narimatsu, Hiroyo Nishide, Yosuke Nishimura, Johan Nyström-Persson, Soichi Ogishima, Yasunobu Okamura, Shujiro Okuda, Kazuki Oshita, Nicolle H. Packer, Pjotr Prins, René Ranzinger, Philippe Rocca-Serra, Susanna Assunta Sansone, Hiromichi Sawaki, Sung Ho Shin, Andrea Splendiani, Francesco Strozzi, Shu Tadaka, Filip V. Toukach, Ikuo Uchiyama, Masahito Umezaki, Rutger A. Vos, Patricia L. Whetzel, Issaku Yamada, Chisato Yamasaki, Riu Yamashita, William S. York, Christian M. Zmasek, Shoko Kawamoto, Toshihisa Takagi
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pcbi.1007046

A new method for inferring timetrees from temporally sampled molecular sequences
Cited 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: almost 5 years ago

10.1093/emph/eoaa005

An African origin for Mycobacterium bovis
Cited by: 35
Author(s): Chloé Loiseau, Fabrizio Menardo, Abraham Aseffa, Elena Hailu, Balako Gumi, Gobena Ameni, Stefan Berg, Leen Rigouts, Suelee Robbe‐Austerman, Jakob Zinsstag, Sébastien Gagneux, Daniela Brites
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.ppat.1009786

Cuban history of CRF19 recombinant subtype of HIV-1
Cited by: 4
Author(s): Anna Zhukova, Jakub Voznica, Miraine Dávila Felipe, Thu‐Hien To, Lissette Pérez, Yenisleidys Martínez, Yanet Pintos, M. L. Rodríguez Méndez, Olivier Gascuel, Vivian Kourí
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pcbi.1008504

Chemical graph generators
Cited by: 4
Author(s): Mehmet Aziz Yirik, Christoph Steinbeck
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.ppat.1008357

Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak
Cited by: 18
Author(s): Maxime Godfroid, Tal Dagan, Matthias Merker, Thomas A. Kohl, Roland Diel, Florian P. Maurer, Stefan Niemann, Anne Kupczok
Software Mentions: 3
Published: about 4 years ago

10.1038/s41598-017-03820-8

Tracing the epidemic history of HIV-1 CRF01_AE clusters using near-complete genome sequences
Cited by: 31
Author(s): Xingguang Li, Haizhou Liu, Lu Liu, Yi Feng, Marcia L. Kalish, Simon Y. W. Ho, Yiming Shao
Software Mentions: 2
Published: over 7 years ago

10.1186/s12862-018-1210-5

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods
Cited by: 16
Author(s): Sebastián Duchêne, David A. Duchêne, Jemma L. Geoghegan, Zoe A. Dyson, Jane Hawkey, Kathryn E. Holt
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2017.00097

Simultaneous Methylation-Level Assessment of Hundreds of CpG Sites by Targeted Bisulfite PCR Sequencing (TBPseq)
Cited by: 6
Author(s): Kyuheum Jeon, Byungkuk Min, Jung Sun Park, Yong‐Kook Kang
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-018-4993-2

Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development
Cited by: 38
Author(s): Xianwen Meng, Peijing Zhang, Qi Chen, Jingjing Wang, Ming Chen
Software Mentions: 2
Published: about 6 years ago

10.1038/s42003-018-0025-7

Triplicate parallel life cycle divergence despite gene flow in periodical cicadas
Cited by: 9
Author(s): Tomochika Fujisawa, Tsunemaro Koyama, Satoshi Kakishima, John R. Cooley, Chris Simon, Jin Yoshimura, Teiji Sota
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2020.601839

Identification of New Helicobacter pylori Subpopulations in Native Americans and Mestizos From Peru
Cited by: 6
Author(s): Andrés Julián Gutiérrez-Escobar, Billie Velapatiño, Víctor Borda, Charles S. Rabkin, Eduardo Tarazona‐Santos, Lilia Cabrera, Jaime Cok, Catherine C. Hooper, M Helena Jahuira Arias, Phabiola Herrera, Mehwish Noureen, Difei Wang, Judith Romero–Gallo, Bao Tran, Richard M. Peek, Douglas E. Berg, Robert H. Gilman, M. Constanza Camargo
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41426-017-0009-6

Origin and dispersal of Hepatitis E virus
Cited by: 43
Author(s): Diego Forni, Rachele Cagliani, Mario Clerici, Manuela Sironi
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2020.00468

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria
Cited by: 1,516
Author(s): Anton Hördt, Marina García López, Jan P. Meier‐Kolthoff, Marcel Schleuning, Lisa-Maria Weinhold, Brian J. Tindall, Sabine Gronow, Nikos C. Kyrpides, Tanja Woyke, Markus Göker
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.35082

Changes in global and thalamic brain connectivity in LSD-induced altered states of consciousness are attributable to the 5-HT2A receptor
Cited by: 218
Author(s): Katrin H. Preller, Joshua B. Burt, Jie Lisa Ji, Charles Schleifer, Brendan Adkinson, Philipp Stämpfli, Erich Seifritz, Grega Repovš, John H. Krystal, John D. Murray, Franz X. Vollenweider, Alan Antičević
Software Mentions: 1
Published: about 6 years ago

10.1186/s12879-018-3247-x

Molecular characterization of invasive meningococcal isolates in Burkina Faso as the relative importance of serogroups X and W increases, 2008–2012
Cited by: 8
Author(s): Adam C. Retchless, Malika Congo-Ouédraogo, Dinanibè Kambiré, Jeni Vuong, Alex Chen, Fang Hu, Absétou Ky Ba, Abdoul–Salam Ouédraogo, Soumeya Hema‐Ouangraoua, Jaymin C. Patel, Renan Ernest Traoré, Lassana Sangaré, Xin Wang
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2458-6-152

Correlates of condom use in a sample of MSM in Ecuador
Cited by: 25
Author(s): Juan Pablo Gutiérrez, Diana Molina-Yépez, Ken Morrison, Fiona Samuels, Stefano Bertozzi
Software Mentions: 1
Published: over 18 years ago

10.3390/md16070236

Computational Methodologies in the Exploration of Marine Natural Product Leads
Cited by: 66
Author(s): Florbela Pereira, João Aires-de-Sousa
Software Mentions: 1
Published: over 6 years ago

10.1128/MCB.00806-15

Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution
Cited by: 30
Author(s): Guiyuan Han, Vinesh Vinayachandran, Alain R. Bataille, Bong Soo Park, Ka Yim Chan-Salis, Cheryl A. Keller, Maria Long, Shaun Mahony, Ross C. Hardison, B. Franklin Pugh
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13567-019-0692-5

Assessing biases in phylodynamic inferences in the presence of super-spreaders
Cited by: 3
Author(s): Arata Hidano, M. Carolyn Gates
Software Mentions: 1
Published: about 5 years ago

10.3390/v11080720

Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage
Cited by: 11
Author(s): Anne Kupczok, Tal Dagan
Software Mentions: 1
Published: over 5 years ago

10.3390/v13040644

The Phylogeography of Potato Virus X Shows the Fingerprints of Its Human Vector
Cited by: 9
Author(s): Segundo Fuentes, Adrian J. Gibbs, Mohammad Reza Hajizadeh, Antonio Martín Pérez, Ian Adams, C. E. Fribourg, Jan Kreuze, Adrian Fox, Neil Boonham, R. A. C. Jones
Software Mentions: 1
Published: over 3 years ago

10.3390/v13091790

Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes
Cited by: 14
Author(s): Xuhua Xia
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pone.0203994

Bio-inspired visual self-localization in real world scenarios using Slow Feature Analysis
Cited by: 9
Author(s): Benjamin Metka, Mathias Franzius, Ute Bauer-Wersing
Software Mentions: 1
Published: about 6 years ago

10.1080/22221751.2021.1943538

Genomic evolution and virulence association of <i>Clostridioides difficile</i> sequence type 37 (ribotype 017) in China
Cited by: 9
Author(s): Xingxing Xu, Yuo Luo, Huan Chen, Xiaojun Song, Qiao Bian, Xianjun Wang, Qian Liang, Jianhong Zhao, Chunhui Li, Guangzhong Song, Jun Yang, Lin Sun, Jianmin Jiang, Huanying Wang, Bo Zhu, Guangyong Ye, Liang Chen, Yi‐Wei Tang, Dazhi Jin
Software Mentions: 1
Published: almost 4 years ago

10.12688/f1000research.28318.2

Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim
Cited by: 17
Author(s): Fabrizio Menardo, Liliana K. Rutaihwa, Michaela Zwyer, Sònia Borrell, Iñaki Comas, Emilyn Costa Conceição, Mireia Coscollá, Helen Cox, Moses Joloba, Horng-Yunn Dou, Julia Feldmann, Lukas Fenner, Janet Fyfe, Qian Gao, Darı́o Garcı́a de Viedma, Alberto L. García‐Basteiro, Sebastian M. Gygli, Jerry Hella, Hellen Hiza, Levan Jugheli, Lujeko Kamwela, Midori Kato‐Maeda, Qingyun Liu, Serej D. Ley, Chloé Loiseau, Surakameth Mahasirimongkol, Bijaya Malla, Prasit Palittapongarnpim, Niaina Rakotosamimanana, Voahangy Rasolofo, Miriam Reinhard, Klaus Reither, Mohamed Sasamalo, Rafael Silva Duarte, Christophe Sola, Philip Noël Suffys, Karla Valéria Batista Lima, Dorothy Yeboah-Manu, Christian Beisel, Daniela Brites, Sébastien Gagneux
Software Mentions: 1
Published: over 3 years ago

10.3389/fonc.2020.01697

Diagnostic and Prognostic Values of Serum EpCAM, TGM2, and HE4 Levels in Endometrial Cancer
Cited by: 7
Author(s): Ting Lan, Chunyan Mu, Zhongcheng Wang, Yue Wang, Ying Liu, Yueqin Mai, Shibao Li, Hao Xu, Bing Gu, Lan Luo, Ping Ma
Software Mentions: 1
Published: about 4 years ago

10.1186/s40694-016-0028-4

The beauty and the morbid: fungi as source of inspiration in contemporary art
Cited by: 12
Author(s): Corrado Nai, Vera Meyer
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.ppat.1008067

The molecular clock of Mycobacterium tuberculosis
Cited by: 102
Author(s): Fabrizio Menardo, Sebastián Duchêne, Daniela Brites, Sébastien Gagneux
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-019-47616-4

Direct test of the FLRW metric from strongly lensed gravitational wave observations
Cited by: 54
Author(s): Shuo Cao, Jing-Zhao Qi, Zhoujian Cao, Marek Biesiada, Li Jin, Yu Pan, Zong-Hong Zhu
Software Mentions: 1
Published: about 5 years ago

10.3390/s16070948

A Novel Line Space Voting Method for Vanishing-Point Detection of General Road Images
Cited by: 19
Author(s): Ziyan Wu, Wei Fu, Xue Ren, Wen Wang
Software Mentions: 1
Published: over 8 years ago

10.3390/s19020408

Infrared-Inertial Navigation for Commercial Aircraft Precision Landing in Low Visibility and GPS-Denied Environments
Cited by: 16
Author(s): Lei Zhang, Zhengjun Zhai, Lang He, Pengcheng Wen, Wensheng Niu
Software Mentions: 1
Published: almost 6 years ago

10.1093/sysbio/syv068

Fast Dating Using Least-Squares Criteria and Algorithms
Cited by: 305
Author(s): Thu Hien To, Matthieu Jung, Samantha Lycett, Olivier Gascuel
Software Mentions: 1
Published: about 9 years ago

10.1093/infdis/jiy044

Molecular Epidemiology of HIV-1 Subtype B Reveals Heterogeneous Transmission Risk: Implications for Intervention and Control
Cited by: 26
Author(s): Erik Volz, Stéphane Le Vu, Oliver Ratmann, Anna Tostevin, David Dunn, Chloe Orkin, Siobhan O’Shea, Valérie Delpech, Alison E Brown, Noël Gill, Christophe Fraser
Software Mentions: 1
Published: over 6 years ago

10.1186/s12862-018-1192-3

A comparison of methods for estimating substitution rates from ancient DNA sequence data
Cited by: 22
Author(s): K. Jun Tong, David A. Duchêne, Sebastián Duchêne, Jemma L. Geoghegan, Simon Y. W. Ho
Software Mentions: 1
Published: over 6 years ago

Projects: cran: LSD

Papers Mentioning LSD 55