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: meme
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/meme
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Latest release: over 3 years ago
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Papers Mentioning meme 31
10.15252/embj.2020106388
Unraveling the features of somatic transposition in the <i>Drosophila</i> intestineCited by: 25
Author(s): Katarzyna Siudeja, Marius van den Beek, Nick Riddiford, Benjamin Boumard, Annabelle Wurmser, Marine Stefanutti, Sonia Lameiras, Allison J. Bardin
Software Mentions: 12
Published: over 3 years ago
10.7717/peerj.8965
CFSP: a collaborative frequent sequence pattern discovery algorithm for nucleic acid sequence classificationCited by: 2
Author(s): Huan Peng
Software Mentions: 9
Published: over 4 years ago
10.1093/database/baz046
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing dataCited by: 621
Author(s): Oscar Franzén, Li‐Ming Gan, Johan Björkegren
Software Mentions: 8
Published: almost 6 years ago
10.1186/s13072-019-0305-6
CGGBP1 regulates CTCF occupancy at repeatsCited by: 12
Author(s): Divyesh Patel, Manthan Patel, Subhamoy Datta, Uma Singh
Software Mentions: 8
Published: about 5 years ago
10.1038/s41598-019-40949-0
Extensive conservation of the proneuropeptide and peptide prohormone complement in mollusksCited by: 17
Author(s): André Luiz de Oliveira, Andrew Calcino, Andreas Wanninger
Software Mentions: 8
Published: over 5 years ago
10.7554/eLife.31977
Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility lociCited by: 101
Author(s): Matthias Thurner, Martijn van de Bunt, Jason Torres, Anubha Mahajan, Vibe Nylander, Amanda J. Bennett, Kyle J. Gaulton, Amy Barrett, Carla Burrows, Christopher G. Bell, Robert Lowe, Stephan Beck, Vardhman K. Rakyan, Anna L. Gloyn, Mark I. McCarthy
Software Mentions: 7
Published: almost 7 years ago
10.1186/s13059-018-1589-8
Enhancers in the Peril lincRNA locus regulate distant but not local genesCited by: 20
Author(s): Abigail F. Groff, A. Rasim Barutcu, Jordan P. Lewandowski, John L. Rinn
Software Mentions: 6
Published: almost 6 years ago
10.1371/journal.pcbi.1006373
Designing and running an advanced Bioinformatics and genome analyses course in TunisiaCited by: 6
Author(s): Fatma Z. Guerfali, Dhafer Laouini, Abdellatif Boudabous, Fredj Tekaia
Software Mentions: 5
Published: almost 6 years ago
10.1186/s13059-015-0863-2
IL-4 orchestrates STAT6-mediated DNA demethylation leading to dendritic cell differentiationCited by: 89
Author(s): Roser Vento‐Tormo, Carlos Company, Javier Rodríguez-Ubreva, Lorenzo de la Rica, José Urquiza, Biola M. Javierre, Radhakrishnan Sabarinathan, Ana Luque, Manel Esteller, Josep M. Aran, Damiana Álvarez-Errico, Esteban Ballestar
Software Mentions: 5
Published: almost 9 years ago
10.1111/tpj.14769
The Arabidopsis transcription factor AINTEGUMENTA orchestrates patterning genes and auxin signaling in the establishment of floral growth and formCited by: 33
Author(s): Beth A. Krizek, Ivory C. Blakley, Yen‐Yi Ho, Nowlan H. Freese, Ann E. Loraine
Software Mentions: 5
Published: over 4 years ago
10.1111/imb.12513
Integrative transcriptomic and genomic analysis of odorant binding proteins and chemosensory proteins in aphidsCited by: 45
Author(s): Q. Wang, Jing‐Jiang Zhou, J.-T. Liu, Huang Guixiu, Weina Xu, Qiaoqin Zhang, J.-L. Chen, Fengquan Liu, X.-C. Li, Siyi Gu
Software Mentions: 5
Published: about 6 years ago
10.3390/plants10061154
Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in RiceCited by: 9
Author(s): Hongjia Zhang, Seong-Ho Jang, San Mar Lar, Ah-Rim Lee, Fangyuan Cao, Jeonghwan Seo, Soon-Wook Kwon
Software Mentions: 4
Published: over 3 years ago
10.1186/s12864-016-2840-x
Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phaseCited by: 20
Author(s): Margarita Andreevskaya, Per Johansson, Elina Jääskeläinen, Tanja Rämö, Jarmo Ritari, Lars Paulín, Johanna Björkroth, Petri Auvinen
Software Mentions: 4
Published: over 8 years ago
10.1002/2211-5463.12275
In silico analysis of heme oxygenase structural homologues identifies group‐specific conservationsCited by: 1
Author(s): J. Logan Irvin, Alexander J. Ropelewski, John Perozich
Software Mentions: 4
Published: about 7 years ago
10.1186/1471-2164-6-169
The EH1 motif in metazoan transcription factorsCited by: 67
Author(s): Richard R. Copley
Software Mentions: 4
Published: almost 19 years ago
10.1371/journal.pcbi.1004478
Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial GenomeCited by: 37
Author(s): Marco Galardini, Matteo Brilli, Giulia Spini, Matteo Rossi, Bianca Roncaglia, Aïda Bani, Chiancianesi Manuela, Marco Moretto, Kristof Engelen, Giovanni Bacci, Francesco Pini, Emanuele G. Biondi, Marco Bazzicalupo, Alessio Mengoni
Software Mentions: 4
Published: about 9 years ago
10.1186/1471-2105-8-337
Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifsCited by: 124
Author(s): Mamoon Rashid, Sudipto Saha, Gajendra P. S. Raghava
Software Mentions: 4
Published: about 17 years ago
10.1371/journal.pone.0214723
Identification of factors associated with duplicate rate in ChIP-seq dataCited by: 6
Author(s): Shulan Tian, Shu‐Lin Peng, Michael Kalmbach, Krutika S. Gaonkar, Aditya Bhagwate, Wei Ding, Jeanette E. Eckel‐Passow, Huihuang Yan, Susan L. Slager
Software Mentions: 3
Published: over 5 years ago
10.1186/s12862-015-0319-z
The plant Polycomb repressive complex 1 (PRC1) existed in the ancestor of seed plants and has a complex duplication historyCited by: 28
Author(s): Lidija Berke, Berend Snel
Software Mentions: 3
Published: over 9 years ago
10.1186/1471-2148-7-78
Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolutionCited by: 279
Author(s): Christian Rausch, Ilka Hoof, Tilmann Weber, Wolfgang Wohlleben, Daniel H. Huson
Software Mentions: 3
Published: almost 18 years ago
10.1186/s12864-016-2585-6
Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plantsCited by: 70
Author(s): Marijke J. van Baren, Charles Bachy, Emily Nahas Reistetter, Samuel O. Purvine, Jane Grimwood, Sebastian Sudek, Hang Yu, Camille Poirier, Thomas J. Deerinck, Alan Kuo, Igor V. Grigoriev, Chee-Hong Wong, Richard Smith, Stephen Callister, Chia Lin Wei, Jeremy Schmutz, Alexandra Z. Worden
Software Mentions: 3
Published: over 8 years ago
10.1186/s12870-021-03093-4
Identification and validation of a novel locus, Qpm-3BL, for adult plant resistance to powdery mildew in wheat using multilocus GWASCited by: 11
Author(s): Xijun Du, Weina Xu, Chaojun Peng, Chunxin Li, Yu Zhang, Lin Hu
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pcbi.1007578
Accurate prediction of kinase-substrate networks using knowledge graphsCited by: 19
Author(s): Vít Nováček, Gavin McGauran, David Matallanas, Alfonso Blanco, Piero Conca, Emir Muñoz, Luca Costabello, Kamalesh Kanakaraj, Zeeshan Nawaz, Brian Walsh, Sameh K. Mohamed, Pierre-Yves Vandenbussche, Colm J. Ryan, Walter Kölch, Dirk Fey
Software Mentions: 3
Published: almost 4 years ago
10.1002/2211-5463.12685
Genome‐wide analysis of the callose enzyme families of fertile and sterile flower buds of the Chinese cabbage (<i>Brassica rapa</i> L. ssp. <i>pekinensis</i>)Cited by: 5
Author(s): Yanan Pu, Lingyun Hou, Yinlong Guo, Ikram Ullah, Yongping Yang, Yanling Yue
Software Mentions: 3
Published: over 5 years ago
10.1534/g3.117.300301
Whole-Genome Sequence Accuracy Is Improved by Replication in a Population of Mutagenized SorghumCited by: 26
Author(s): Charles Addo‐Quaye, Mitch Tuinstra, Nicola Carraro, Clifford F. Weil, Brian P. Dilkes
Software Mentions: 3
Published: over 6 years ago
10.3390/genes8090202
Auxin Response Factor Genes Repertoire in Mulberry: Identification, and Structural, Functional and Evolutionary AnalysesCited by: 16
Author(s): Vinay Kumar Baranwal, Nisha Negi, Paramjit Khurana
Software Mentions: 2
Published: about 7 years ago
10.3389/fmicb.2019.02520
Beyond a Ribosomal RNA Methyltransferase, the Wider Role of MraW in DNA Methylation, Motility and Colonization in Escherichia coli O157:H7Cited by: 8
Author(s): Xuefang Xu, Heng Zhang, Ying Huang, Yuan Zhang, Changde Wu, Pengya Gao, Zhaogang Teng, Xu Luo, Xiao-Fang Peng, Xiaoyuan Wang, Dai Wang, Ji Pu, Hongqing Zhao, Xuancheng Lu, Shuangshuang Lu, Changyun Ye, Yuhui Dong, Ruiting Lan, Jianguo Xu
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.ppat.1002788
Control of Virulence by Small RNAs in Streptococcus pneumoniaeCited by: 136
Author(s): Beth Mann, Tim van Opijnen, Jianmin Wang, Caroline Obert, Yongdong Wang, Caroline Robert, Daniel McGoldrick, Granger Ridout, Andrew Camilli, Elaine Tuomanen, Jason W. Rosch
Software Mentions: 2
Published: over 12 years ago
10.1186/s12934-017-0651-7
Nutrient starvation leading to triglyceride accumulation activates the Entner Doudoroff pathway in Rhodococcus jostii RHA1Cited by: 13
Author(s): Antonio Juárez, Juan A. Villa, Val F. Lanza, Beatriz Lázaro, Fernando de la Cruz, Héctor M. Alvarez, Gabriel Moncalián
Software Mentions: 2
Published: over 7 years ago
10.1186/1471-2164-7-176
Similarities and differences of polyadenylation signals in human and flyCited by: 49
Author(s): Dorota Retelska, Christian Iseli, Philipp Bücher, C. Victor Jongeneel, Félix Naef
Software Mentions: 2
Published: over 18 years ago
10.3390/ijms221910478
Comparative and Systematic Omics Revealed Low Cd Accumulation of Potato StMTP9 in Yeast: Suggesting a New Mechanism for Heavy Metal DetoxificationCited by: 3
Author(s): Dandan Li, Guandi He, Weijun Tian, Muhammad Saleem, Yun Huang, Lulu Meng, Danxia Wu, Tengbing He
Software Mentions: 2
Published: about 3 years ago