pypi: infernal | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1008866

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli
Cited by: 119
Author(s): Marie Touchon, Perrin Amandine, Jorge Moura de Sousa, Belinda Vangchhia, Samantha Burn, Claire O’Brien, Erick Denamur, David M. Gordon, Eduardo P. C. Rocha
Software Mentions: 16
Published: over 4 years ago

10.3389/fgene.2020.489357

Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results
Cited by: 13
Author(s): Alejandro Abdala Asbun, Marc Besseling, Sergio Balzano, Judith van Bleijswijk, Harry J. Witte, Laura Villanueva, Julia C. Engelmann
Software Mentions: 11
Published: about 4 years ago

10.1111/1755-0998.12443

The de novo genome assembly and annotation of a female domestic dromedary of North African origin
Cited by: 56
Author(s): Robert R. Fitak, Elmira Mohandesan, Jukka Corander, Pamela A. Burger
Software Mentions: 9
Published: over 9 years ago

10.1186/s13059-020-01998-1

Wheat chromatin architecture is organized in genome territories and transcription factories
Cited by: 89
Author(s): Lorenzo Concia, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Azahara Martin-Ramirez, Ying Huang, Magali Perez, Séverine Domenichini, Natalia Y. Rodriguez Granados, Soon-Kap Kim, Thomas Blein, Susan Duncan, Clement Pichot, Deborah Manza‐Mianza, Caroline Juéry, Etienne Paux, Graham Moore, Heribert Hirt, Catherine Bergounioux, Martín Crespi, Magdy M. Mahfouz, Abdelhafid Bendahmane, Chang Liu, Anthony Hall, Cécile Raynaud, David Latrasse, Moussa Benhamed
Software Mentions: 8
Published: over 4 years ago

10.1186/1471-2105-10-325

Riboswitch Detection Using Profile Hidden Markov Models
Cited by: 33
Author(s): Payal Singh, Pradipta Bandyopadhyay, Sudha Bhattacharya, Annangarachari Krishnamachari, Supratim Sengupta
Software Mentions: 7
Published: about 15 years ago

10.3389/fpls.2014.00708

plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants
Cited by: 19
Author(s): Deblina Patra, Mario Fasold, David Langenberger, Gerhard Steger, Ivo Große, Peter F. Stadler
Software Mentions: 7
Published: about 10 years ago

10.1093/gbe/evu133

Settling Down: The Genome of Serratia symbiotica from the Aphid Cinara tujafilina Zooms in on the Process of Accommodation to a Cooperative Intracellular Life
Cited by: 77
Author(s): Alejandro Manzano-Marı́n, Amparo Latorre
Software Mentions: 6
Published: over 10 years ago

10.1186/s12864-021-07636-9

Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation
Cited by: 8
Author(s): Werner Pieter Veldsman, Ke Yan, Jerome H.L. Hui, Ting‐Fung Chan, Juán Antonio Baeza, Jing Qin, Ka Hou Chu
Software Mentions: 6
Published: over 3 years ago

10.3389/fgene.2021.693541

The Evolutionary Patterns of Genome Size in Ensifera (Insecta: Orthoptera)
Cited by: 15
Author(s): Hao Yuan, Yuan Huang, Ying Mao, Nan Zhang, Yimeng Nie, Xue Zhang, Yafu Zhou, Shao-Li Mao
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2017.00147

An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences
Cited by: 2
Author(s): Josef Pánek, Martin Modrák, Marek Schwarz
Software Mentions: 5
Published: about 7 years ago

10.7717/peerj.8356

Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii
Cited by: 14
Author(s): Darrin T. Schultz, Jordan M. Eizenga, Russell Corbett-Detig, Warren R. Francis, Lynne M. Christianson, Steven H. D. Haddock
Software Mentions: 5
Published: almost 5 years ago

10.1186/1471-2105-9-219

ConStruct: Improved construction of RNA consensus structures
Cited by: 36
Author(s): Andreas Wilm, Kornelia Linnenbrink, Gerhard Steger
Software Mentions: 5
Published: over 16 years ago

10.3389/fmicb.2020.01826

Complete Genome Sequencing and Transcriptome Analysis of Nitrogen Metabolism of Succinivibrio dextrinosolvens Strain Z6 Isolated From Dairy Cow Rumen
Cited by: 19
Author(s): Samson Hailemariam, Shengguo Zhao, Jiaqi Wang
Software Mentions: 4
Published: over 4 years ago

10.1038/sdata.2018.305

The sequence and de novo assembly of hog deer genome
Cited by: 7
Author(s): Wei Wang, Yan Huang, Shiyi Chen, Zhenzhen Li, Jun Yi, Lili Niu, Jia-Po Deng, Weigang Chen, Yunfeng Pu, Xianbo Jia, Yu Qu, Ang Chen, Yan Zhong, Xiaoxi Yu, Shuai Pang, Wanlong Huang, Yue Han, Guangjian Liu, Jianqiu Yu
Software Mentions: 4
Published: almost 6 years ago

10.1093/gigascience/giz096

To assemble or not to resemble—A validated Comparative Metatranscriptomics Workflow (CoMW)
Cited by: 24
Author(s): Muhammad Zohaib Anwar, Anders Lanzén, Toke Bang‐Andreasen, Carsten Suhr Jacobsen
Software Mentions: 4
Published: over 5 years ago

10.6026/97320630013249

Identification of long non-coding RNA in rice lines resistant to Rice blast pathogen Maganaporthe oryzae
Cited by: 33
Author(s): Priyanka Jain, Vinay Sharma, Himanshu Dubey, Pankaj Kumar Singh, Ritu Kapoor, Mandeeep Kumari, Jaya Singh, Deepak Pawar, Deepak Singh Bisht, Amolkumar U. Solanke, Tapan Kumar Mondal, Tilak Raj Sharma
Software Mentions: 4
Published: over 7 years ago

10.1111/1751-7915.12190

The <scp>R</scp>sm regulon of plant growth‐promoting <scp>P</scp>seudomonas fluorescens <scp>SS</scp>101: role of small <scp>RNA</scp>s in regulation of lipopeptide biosynthesis
Cited by: 17
Author(s): Song Cui, Menno van der Voort, Judith E. van de Mortel, Karl A. Hassan, Liam D. H. Elbourne, Ian T. Paulsen, Joyce E. Loper, Jos M. Raaijmakers
Software Mentions: 4
Published: about 10 years ago

10.1111/1751-7915.12308

Functionally redundant but dissimilar microbial communities within biogas reactors treating maize silage in co‐fermentation with sugar beet silage
Cited by: 29
Author(s): Susanne Langer, Sharif Ahmed, Daniel Einfalt, Frank R. Bengelsdorf, Marian Kazda
Software Mentions: 4
Published: over 9 years ago

10.1186/1752-0509-7-S4-S13

Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems
Cited by: 9
Author(s): Lei Shang, David P. Gardner, Wei Xu, Jamie J. Cannone, Daniel P. Miranker, Stuart Ozer, Robin R. Gutell
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2164-13-459

Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae
Cited by: 52
Author(s): Agnieszka Podolska, Christian Anthon, Mads Bak, Niels Tommerup, Kerstin Skovgaard, Peter M. H. Heegaard, Jan Gorodkin, Susanna Cirera, Merete Fredholm
Software Mentions: 3
Published: over 12 years ago

10.1016/j.ijpara.2020.06.002

Extracellular vesicles from Heligmosomoides bakeri and Trichuris muris contain distinct microRNA families and small RNAs that could underpin different functions in the host
Cited by: 15
Author(s): Ruby White, Sujai Kumar, Wang Ngai Chow, E. Graeme Robertson, Kelly S. Hayes, Richard K. Grencis, María A. Duque-Correa, Amy H. Buck
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2019.03070

Genome-Based Comparison of All Species of the Genus Moorella, and Status of the Species Moorella thermoacetica and Moorella thermoautotrophica
Cited by: 12
Author(s): Stephanie Maria Anna Redl, Anja Poehlein, Carola Esser, Frank R. Bengelsdorf, Troy Jensen, Christian Bille Jendresen, Brian J. Tindall, Rolf Daniel, Peter Dürre, Alex Toftgaard Nielsen
Software Mentions: 3
Published: almost 5 years ago

10.1186/1748-7188-6-26

ViennaRNA Package 2.0
Cited by: 3,394
Author(s): Ronny Lorenz, Stephan H. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker
Software Mentions: 3
Published: about 13 years ago

10.3389/fmicb.2020.00482

Comparative Metatranscriptomics of Periodontitis Supports a Common Polymicrobial Shift in Metabolic Function and Identifies Novel Putative Disease-Associated ncRNAs
Cited by: 15
Author(s): Nikhil Ram-Mohan, Michelle M. Meyer
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0116230

Evaluation of Simultaneous Nutrient and COD Removal with Polyhydroxybutyrate (PHB) Accumulation Using Mixed Microbial Consortia under Anoxic Condition and Their Bioinformatics Analysis
Cited by: 10
Author(s): Jyotsnarani Jena, Ravindra Kumar, Anshuman Dixit, Satish Kumar Pandey, Trupti Das
Software Mentions: 3
Published: almost 10 years ago

10.3390/ijms221910300

Mitochondrial Genomes, Phylogenetic Associations, and SNP Recovery for the Key Invasive Ponto-Caspian Amphipods in Europe
Cited by: 8
Author(s): Tomasz Mamos, Michał Grabowski, Tomasz Rewicz, Jamie Bojko, Dominik Strapagiel, Artur Burzyński
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-016-2486-8

Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors
Cited by: 94
Author(s): Angela H. Williams, Mamta Sharma, Louise F. Thatcher, Sarwar Azam, James K. Hane, Jana Sperschneider, Brendan N. Kidd, Jonathan P. Anderson, Raju Ghosh, Gagan Garg, Judith Lichtenzveig, H. Corby Kistler, Terrance Shea, Sarah Young, Sally Anne G Buck, Lars G. Kamphuis, Rachit K. Saxena, S. Pande, Jun Li, Rajeev K. Varshney, Karam B. Singh
Software Mentions: 2
Published: almost 9 years ago

10.3390/v11030298

Functional RNA Structures in the 3′UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses
Cited by: 43
Author(s): Roman Ochsenreiter, Ivo L. Hofacker, Michael T. Wolfinger
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pcbi.1005383

Computational identification of the selenocysteine tRNA (tRNASec) in genomes
Cited by: 43
Author(s): Didac Santesmasses, Marco Mariotti, Roderic Guigó
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0108639

Detection of Very Long Antisense Transcripts by Whole Transcriptome RNA-Seq Analysis of Listeria monocytogenes by Semiconductor Sequencing Technology
Cited by: 15
Author(s): Stefanie Wehner, Gopala Krishna Mannala, Xiaoxing Qing, Ramakanth Madhugiri, Trinad Chakraborty, Mobarak Abu Mraheil, Torsten Hain, Manja Marz
Software Mentions: 2
Published: about 10 years ago

10.3389/fmicb.2020.594838

Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea
Cited by: 10
Author(s): Thandi S. Schwarz, Sarah J. Berkemer, Stephan H. Bernhart, Matthias Weiß, Sébastien Ferreira-Cerca, Peter F. Stadler, Anita Marchfelder
Software Mentions: 2
Published: about 4 years ago

10.3390/genes9080372

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes
Cited by: 12
Author(s): Maria Waldl, Bernhard C. Thiel, Roman Ochsenreiter, Alexander Holzenleiter, João Victor de Araújo Oliveira, Maria Emília M. T. Walter, Michael T. Wolfinger, Peter F. Stadler
Software Mentions: 2
Published: over 6 years ago

10.1093/gbe/evaa271

A Chromosome-Level Genome Assembly of the Dark Sleeper Odontobutis potamophila
Cited by: 7
Author(s): Yongyi Jia, Jianbo Zheng, Shili Liu, Fēi Li, Meili Chi, Sun Cheng, Zhimi Gu
Software Mentions: 2
Published: almost 4 years ago

10.1080/15476286.2020.1723328

Identification of RNA 3´ ends and termination sites in Haloferax volcanii
Cited by: 13
Author(s): Sarah J. Berkemer, Lisa‐Katharina Maier, Fabian Amman, Stephan H. Bernhart, Julia Wörtz, Pascal Märkle, Friedhelm Pfeiffer, Peter F. Stadler, Anita Marchfelder
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-020-64398-2

The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenetic position of Lobotiformes and biological conservation
Cited by: 2
Author(s): Shuai Sun, Yue Wang, Wenhong Zeng, Xiao Du, Lei Li, Xiaoning Hong, Xiaoyun Huang, He Zhang, Mengqi Zhang, Guangyi Fan, Xin Liu, Shanshan Liu
Software Mentions: 2
Published: over 4 years ago

10.1038/s41396-020-0610-x

Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP)
Cited by: 78
Author(s): Kshitij Tandon, Chien‐Yu Lu, Pei‐Wen Chiang, Naohiro Wada, Shan‐Hua Yang, Ya‐Fan Chan, Ping-Yun Chen, Hung-Yu Chang, Yu-Jing Chiou, Ming-Shean Chou, Wen-Ming Chen, Sen‐Lin Tang
Software Mentions: 2
Published: almost 5 years ago

10.3390/v11050401

Conserved Secondary Structures in Viral mRNAs
Cited by: 22
Author(s): Michael Kiening, Roman Ochsenreiter, Hans-Jörg Hellinger, Thomas Rattei, Ivo L. Hofacker, Dmitrij Frishman
Software Mentions: 1
Published: over 5 years ago

10.1534/g3.119.400164

High Quality Draft Genome of Arogyapacha (Trichopus zeylanicus), an Important Medicinal Plant Endemic to Western Ghats of India
Cited by: 8
Author(s): Biju Vadakkemukadiyil Chellappan, Shidhi Pr, Sheethal Vijayan, Veena S Rajan, Anu Sasi, Achuthsankar S. Nair
Software Mentions: 1
Published: over 5 years ago

10.1534/g3.119.400694

Sequencing and Functional Annotation of the Whole Genome of Shiraia bambusicola
Cited by: 7
Author(s): Xiyi Ren, Yongxiang Liu, Yi Tan, Yonghui Huang, Liu Zuo-yi, Xuanli Jiang
Software Mentions: 1
Published: almost 5 years ago

10.1186/s40793-016-0182-6

Whole genome shotgun sequence of Bacillus amyloliquefaciens TF28, a biocontrol entophytic bacterium
Cited by: 6
Author(s): Shumei Zhang, Wei Jiang, Jing Li, Liqiang Meng, Xu Cao, Jihua Hu, Yushuai Liu, Jingyu Chen, Sha Chang-qing
Software Mentions: 1
Published: over 8 years ago

10.1080/21505594.2020.1836910

Aminoglycoside riboswitch control of the expression of integron associated aminoglycoside resistance adenyltransferases
Cited by: 7
Author(s): Jun Zhang, Getong Liu, Xuhui Zhang, Yao‐Wen Chang, Shasha Wang, Weizhi He, Wenxia Sun, Dongrong Chen, Alastair I. H. Murchie
Software Mentions: 1
Published: about 4 years ago

10.1099/mgen.0.000101

Absence of genome reduction in diverse, facultative endohyphal bacteria
Cited by: 28
Author(s): David A. Baltrus, Kevin Dougherty, Kayla R. Arendt, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishna Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T. B. K. Reddy, Chew Yee Ngan, Chris Daum, Nicole Shapiro, Victor Markowitz, Natalia Ivanova, Nikos C. Kyrpides, Tanja Woyke, A. Elizabeth Arnold
Software Mentions: 1
Published: almost 8 years ago

10.3390/ani11020397

Genomics Analysis of Bacillus megaterium 1259 as a Probiotic and Its Effects on Performance in Lactating Dairy Cows
Cited by: 6
Author(s): Bobo Deng, Lin Wang, Qianbo Ma, Yu TongShui, Dalin Liu, Yi Dai, Guisen Zhao
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-016-3301-2

Phylogenetic distribution of plant snoRNA families
Cited by: 15
Author(s): Deblina Patra Bhattacharya, Sebastian Canzler, Stephanie Kehr, Jana Hertel, Ivo Große, Peter F. Stadler
Software Mentions: 1
Published: about 8 years ago

10.1186/s13099-016-0134-0

Complete genome of Vibrio parahaemolyticus FORC014 isolated from the toothfish
Cited by: 7
Author(s): Sojin Ahn, Han Young Chung, Sooyeon Lim, Kwondo Kim, Su Yeon Kim, Eun Jung Na, Kelsey Caetano-Anollés, Ju-Hoon Lee, Sangryeol Ryu, Sang Ho Choi, Heebal Kim
Software Mentions: 1
Published: about 8 years ago

10.1038/s41396-019-0533-6

Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids’ di-symbiotic systems
Cited by: 68
Author(s): Alejandro Manzano-Marı́n, Armelle Coeur d’Acier, Anne‐Laure Clamens, Céline Orvain, Corinne Cruaud, Valérie Barbe, Emmanuelle Jousselin
Software Mentions: 1
Published: about 5 years ago

10.1186/1471-2164-10-14

RepPop: a database for repetitive elements in Populus trichocarpa
Cited by: 29
Author(s): Fengfeng Zhou, Ying Xu
Software Mentions: 1
Published: almost 16 years ago

10.1038/srep20367

Comparison of Particle-Associated Bacteria from a Drinking Water Treatment Plant and Distribution Reservoirs with Different Water Sources
Cited by: 27
Author(s): G. Liu, Fangqiong Ling, E. J. van der Mark, Xuedong Zhang, Aleksandra Knezev, J.Q.J.C. Verberk, W.G.J. van der Meer, Gertjan Medema, W. T. Liu, Judith Dijk
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0152400

Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana
Cited by: 25
Author(s): Mercedes Berlanga, Carlos Lloréns, Jaume Comas, Ricardo Guerrero
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pntd.0006151

In vitro studies of Rickettsia-host cell interactions: Confocal laser scanning microscopy of Rickettsia helvetica-infected eukaryotic cell lines
Cited by: 11
Author(s): Stephanie Speck, Tanja Kern, Karin Aistleitner, Meik Dilcher, Gerhard Dobler, Sandra Eßbauer
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-020-06818-1

Genome re-sequencing and reannotation of the Escherichia coli ER2566 strain and transcriptome sequencing under overexpression conditions
Cited by: 6
Author(s): Lizhi Zhou, Hai Yu, Kaihang Wang, Tingting Chen, Yue Ma, Yang Huang, Jiajia Li, Liqin Liu, Yuqian Li, Zhibo Kong, Qingbing Zheng, Yingbin Wang, Ying Gu, Ningshao Xia
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1004053

The Genome of Spironucleus salmonicida Highlights a Fish Pathogen Adapted to Fluctuating Environments
Cited by: 64
Author(s): Feifei Xu, Jon Jerlström-Hultqvist, Elin Einarsson, Ásgeir Ástvaldsson, Staffan G. Svärd, Jan O. Andersson
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pgen.1004496

Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina)
Cited by: 77
Author(s): Volker Schwartze, Sascha Winter, Ekaterina Shelest, Marina Marcet‐Houben, Fabian Horn, Stefanie Wehner, Jörg Linde, Vito Valiante, Michael Sammeth, Konstantin Riege, Minou Nowrousian, Kerstin Kaerger, Ilse D. Jacobsen, Manja Marz, Axel A. Brakhage, Toni Gabaldón, Sebastian Böcker, Kerstin Voigt
Software Mentions: 1
Published: over 10 years ago

10.3389/fmicb.2018.00086

Polymorphism in Mitochondrial Group I Introns among Cryptococcus neoformans and Cryptococcus gattii Genotypes and Its Association with Drug Susceptibility
Cited by: 12
Author(s): Felipe E. E. S. Gomes, Thales Domingos Arantes, José Alex Lourenço Fernandes, Lucas Batista Ferreira, Héctor Romero, Sandra de Moraes Gimenes Bosco, Maria Tereza Barreto de Oliveira, G. Del Negro, Raquel Cordeiro Theodoro
Software Mentions: 1
Published: almost 7 years ago

Projects: pypi: infernal

Papers Mentioning infernal 54