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: LSD
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/LSD
Lots of Superior Depictions
6 versions
Latest release: over 4 years ago
2 dependent packages
512 downloads last month
Papers Mentioning LSD 55
10.1128/mBio.01105-19
Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian SubcontinentCited 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 variationCited 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 TransPhyloCited 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 ArabidopsisCited 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 disabilityCited 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 phylogeniesCited 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 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
10.1038/s41598-018-22725-8
Erosion of natural darkness in the geographic ranges of cactiCited 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 EvolutionCited 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 reservoirCited 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 analysisCited 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 tuberculosisCited 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 BacteriaCited 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 PhylogeniesCited 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 RegionsCited 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 variabilityCited 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 principleCited 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 pombeCited by: 64
Author(s): Yuriko Harigaya, Roy Parker
Software Mentions: 3
Published: about 8 years ago
10.1186/s12864-017-3749-8
The link between adjacent codon pairs and mRNA stabilityCited 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 domainsCited 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 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: almost 5 years ago
10.1093/emph/eoaa005
An African origin for Mycobacterium bovisCited 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-1Cited 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: over 3 years ago
10.1371/journal.pcbi.1008504
Chemical graph generatorsCited 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 outbreakCited 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 sequencesCited 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 methodsCited 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 developmentCited by: 38
Author(s): Xianwen Meng, Peijing Zhang, Qi Chen, Jingjing Wang, Ming Chen
Software Mentions: 2
Published: over 6 years ago
10.1038/s42003-018-0025-7
Triplicate parallel life cycle divergence despite gene flow in periodical cicadasCited 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 PeruCited 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 virusCited by: 43
Author(s): Diego Forni, Rachele Cagliani, Mario Clerici, Manuela Sironi
Software Mentions: 2
Published: almost 7 years ago
10.3389/fmicb.2020.00468
Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of AlphaproteobacteriaCited 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 receptorCited 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, 2008–2012Cited 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 EcuadorCited 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 LeadsCited 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 ResolutionCited 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-spreadersCited 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 LineageCited 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 VectorCited 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 GenomesCited 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 AnalysisCited 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 ChinaCited 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 RimCited 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 CancerCited 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 artCited 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 tuberculosisCited 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 observationsCited by: 54
Author(s): Shuo Cao, Jing-Zhao Qi, Zhoujian Cao, Marek Biesiada, Li Jin, Yu Pan, Zong-Hong Zhu
Software Mentions: 1
Published: over 5 years ago
10.3390/s16070948
A Novel Line Space Voting Method for Vanishing-Point Detection of General Road ImagesCited 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 EnvironmentsCited 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 AlgorithmsCited 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 ControlCited 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 dataCited 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