Ecosyste.ms: Papers

10.15252/embj.2020106388

Unraveling the features of somatic transposition in the <i>Drosophila</i> intestine
Cited 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 classification
Cited 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 data
Cited 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 repeats
Cited 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 mollusks
Cited 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 loci
Cited 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: over 6 years ago

10.1186/s13059-018-1589-8

Enhancers in the Peril lincRNA locus regulate distant but not local genes
Cited 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 Tunisia
Cited 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 differentiation
Cited 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 form
Cited 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 aphids
Cited 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 Rice
Cited 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 phase
Cited 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 conservations
Cited 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 factors
Cited 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 Genome
Cited 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 motifs
Cited 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 data
Cited 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 history
Cited 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 evolution
Cited 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 plants
Cited 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 GWAS
Cited 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 graphs
Cited 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 Sorghum
Cited 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 Analyses
Cited 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:H7
Cited 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: almost 5 years ago

10.1371/journal.ppat.1002788

Control of Virulence by Small RNAs in Streptococcus pneumoniae
Cited 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 RHA1
Cited 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 fly
Cited 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 Detoxification
Cited 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