Ecosyste.ms: Papers

10.1371/journal.pone.0257047

Off-chip prefetching based on Hidden Markov Model for non-volatile memory architectures
Cited by: 0
Author(s): Adrián Lamela, Óscar G. Ossorio, Guillermo Vinuesa, Benjamín Sahelices
Software Mentions: 10
Published: about 3 years ago

10.1038/srep30794

Genome-wide Identification and Structural, Functional and Evolutionary Analysis of WRKY Components of Mulberry
Cited by: 33
Author(s): Vinay Kumar Baranwal, Nisha Negi, Paramjit Khurana
Software Mentions: 7
Published: over 8 years ago

10.1186/s13100-019-0156-5

Subtype classification and functional annotation of L1Md retrotransposon promoters
Cited by: 15
Author(s): Meng Zhou, Andrew D. Smith
Software Mentions: 6
Published: over 5 years ago

10.1186/s13068-018-1036-9

Genome-resolved metagenomics of sugarcane vinasse bacteria
Cited by: 16
Author(s): Noriko A. Cassman, Késia Silva Lourenço, Janaína Braga do Carmo, Heitor Cantarella, Eiko E. Kuramae
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pgen.1009038

Selection and hybridization shaped the rapid spread of African honey bee ancestry in the Americas
Cited by: 40
Author(s): Erin Calfee, Marcelo Nicolás Agra, Marí­a Alejandra Palacio, Santiago R. Ramírez, Graham Coop
Software Mentions: 6
Published: about 4 years ago

10.1128/mSystems.00385-21

Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil
Cited by: 22
Author(s): Yunha Hwang, Janina Rahlff, Dirk Schulze‐Makuch, Michael Schloter, Alexander J. Probst
Software Mentions: 6
Published: over 3 years ago

10.3389/fpls.2018.00018

Genome-Wide Identification of Cyclic Nucleotide-Gated Ion Channel Gene Family in Wheat and Functional Analyses of TaCNGC14 and TaCNGC16
Cited by: 37
Author(s): Jia Guo, Md. Ashraful Islam, Haocheng Lin, Changan Ji, Yinghui Duan, Peng Liu, Qingdong Zeng, Brad Day, Zhensheng Kang, Jun Guo
Software Mentions: 5
Published: almost 7 years ago

10.1093/g3journal/jkab074

MultiPhATE2: code for functional annotation and comparison of phage genomes
Cited by: 11
Author(s): Carol L. Ecale Zhou, Jeffrey A. Kimbrel, Robert A. Edwards, Katelyn McNair, Brian Souza, Stephanie Malfatti
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2164-15-946

Conservation analysis of the CydX protein yields insights into small protein identification and evolution
Cited by: 35
Author(s): Rondine J. Allen, Evan P. Brenner, Caitlin E. VanOrsdel, Jessica J. Hobson, David J. Hearn, Matthew R. Hemm
Software Mentions: 5
Published: almost 10 years ago

10.1534/g3.119.400617

Population Selection and Sequencing of<i>Caenorhabditis elegans</i>Wild Isolates Identifies a Region on Chromosome III Affecting Starvation Resistance
Cited by: 21
Author(s): Amy K. Webster, Anthony Hung, Brad T. Moore, Ryan Guzman, James M. Jordan, Rebecca E. W. Kaplan, Jonathan D. Hibshman, Robyn E. Tanny, Daniel E. Cook, Erik C. Andersen, L. Ryan Baugh
Software Mentions: 4
Published: about 5 years ago

10.1016/j.envsoft.2018.02.011

Modelling background air pollution exposure in urban environments: Implications for epidemiological research
Cited by: 27
Author(s): Álvaro Gómez-Losada, José C.M. Pires, Rafael Pino‐Mejías
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-020-07100-0

Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus
Cited by: 16
Author(s): Marina Athanasouli, Hanh Witte, Christian Weiler, Tobias Loschko, Gabi Eberhardt, Ralf J. Sommer, Christian Rödelsperger
Software Mentions: 4
Published: about 4 years ago

10.1186/gb-2008-9-1-r7

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Cited by: 2,092
Author(s): Brian J. Haas, Steven L. Salzberg, Wei Zhu, Mihaela Pertea, Jonathan Allen, Joshua Orvis, Owen White, C. Robin Buell, Jennifer Wortman
Software Mentions: 4
Published: almost 17 years ago

10.1038/s41598-019-40659-7

Genome-wide Analysis of bZIP Transcription Factors in wheat and Functional Characterization of a TabZIP under Abiotic Stress
Cited by: 70
Author(s): Pragya Agarwal, Vinay Kumar Baranwal, Paramjit Khurana
Software Mentions: 3
Published: over 5 years ago

10.1155/2015/813047

<i>In Silico</i>Identification of Highly Conserved Epitopes of Influenza A H1N1, H2N2, H3N2, and H5N1 with Diagnostic and Vaccination Potential
Cited by: 17
Author(s): José Esteban Muñoz-Medina, Carlos Javier Sánchez-Vallejo, Alfonso Méndez‐Tenorio, Irma Eloísa Monroy-Muñoz, Javier Ángeles-Martínez, Andrea Santos Coy-Arechavaleta, Clara Esperanza Santacruz-Tinoco, Joaquín González-Ibarra, Yu-Mei Anguiano-Hernández, César González-Bonilla, Eva Ramón-Gallegos, José Alberto Díaz-Quiñonez
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-021-07828-3

The CaCA superfamily genes in Saccharum: comparative analysis and their functional implications in response to biotic and abiotic stress
Cited by: 9
Author(s): Weihua Su, Chang Zhang, Dongjiao Wang, Yongjuan Ren, Tingting Sun, Jingfang Feng, Yachun Su, Liping Xu, Mutian Shi, Youxiong Que
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-021-07689-w

Genome-wide analysis of R2R3-MYB transcription factors family in the autopolyploid Saccharum spontaneum: an exploration of dominance expression and stress response
Cited by: 13
Author(s): Yuan Yuan, Xiping Yang, Mengfan Feng, Hongyan Ding, Muhammad Tahir Khan, Jisen Zhang, Muqing Zhang
Software Mentions: 2
Published: about 3 years ago

10.1186/s12864-019-6389-3

Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses
Cited by: 13
Author(s): Qi Yang, Xiaocui Niu, Xiao-Li Tian, Xiujuan Zhang, Jingyu Cong, Ruigang Wang, Guosheng Zhang, G. Li
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-018-4680-3

Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity
Cited by: 48
Author(s): Paula Moolhuijzen, Pao Theen See, James K. Hane, Gongjun Shi, Zhaohui Liu, Richard P. Oliver, Caroline S. Moffat
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-018-5214-8

Comparative genomics of downy mildews reveals potential adaptations to biotrophy
Cited by: 42
Author(s): Kyle Fletcher, Steven J. Klosterman, Lida Derevnina, Frank N. Martin, Lien Bertier, S. T. Koike, Sebastian Reyes-Chin-Wo, Beiquan Mou, Richard W. Michelmore
Software Mentions: 2
Published: almost 6 years ago

10.3390/v13050928

Phage Biocontrol of Pseudomonas aeruginosa in Water
Cited by: 10
Author(s): Ari Kauppinen, Sallamaari Siponen, Tarja Pitkänen, Karin Holmfeldt, Anna Pursiainen, Eila Torvinen, Ilkka T. Miettinen
Software Mentions: 2
Published: over 3 years ago

10.3390/plants8080275

Genome-Wide Identification, Expression Pattern Analysis and Evolution of the Ces/Csl Gene Superfamily in Pineapple (Ananas comosus)
Cited by: 7
Author(s): Shijiang Cao, Han Cheng, Jiashuo Zhang, Mohammad Aslam, Mei Yan, Anqi Hu, Lili Lin, Simon Peter Ojolo, Hui Zhao, S. V. G. N. Priyadarshani, Yu Yu, Gaoshao Cao, Yuan Qin
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1003272

Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica
Cited by: 161
Author(s): Rays H. Y. Jiang, Irene de Bruijn, Brian J. Haas, Rodrigo Belmonte, Lars Löbach, James Christie, Guido Van den Ackerveken, Arnaud Bottin, Vincent Bulone, Sara M. Díaz-Moreno, Bernard Dumas, Fan Lin, Elodie Gaulin, F. Govers, Laura J. Grenville‐Briggs, Neil R. Horner, Joshua Z. Levin, Marco Mammella, H.J.G. Meijer, Paul F. Morris, Chad Nusbaum, Stan Oome, Andrew J. Phillips, David van Rooyen, Elzbieta Rzeszutek, Márcia Saraiva, Chris J. Secombes, Michael Seidl, Berend Snel, Joost H. M. Stassen, Sean M. Sykes, Sucheta Tripathy, Herbert van den Berg, Julio Vega-Arreguín, Stephan Wawra, Sarah Young, Qiandong Zeng, Javier Diéguez‐Uribeondo, Carsten Russ, Brett M. Tyler, Pieter van West
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0194487

The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites
Cited by: 24
Author(s): Goro Tanifuji, Shun Takabayashi, Keitaro Kume, Mizue Takagi, Takuro Nakayama, Ryoma Kamikawa, Yuji Inagaki, Takeji Hashimoto
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0189738

The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees
Cited by: 21
Author(s): Paul Schmid‐Hempel, Markus Aebi, Seth M. Barribeau, Toshihiko Kitajima, Louis du Plessis, Regula Schmid‐Hempel, Stefan Zoller
Software Mentions: 2
Published: almost 7 years ago

10.12688/f1000research.18776.2

RVDB-prot, a reference viral protein database and its HMM profiles
Cited by: 37
Author(s): Thomas Bigot, Sarah Temmam, Philippe Pérot, Marc Éloit
Software Mentions: 2
Published: about 4 years ago

10.3389/fmicb.2015.00440

The genomes of closely related Pantoea ananatis maize seed endophytes having different effects on the host plant differ in secretion system genes and mobile genetic elements
Cited by: 61
Author(s): Raheleh Sheibani-Tezerji, Muhammad Naveed, Marc-André Jehl, Angela Sessitsch, Thomas Rattei, Birgit Mitter
Software Mentions: 2
Published: over 9 years ago

10.3389/fnins.2018.00603

Task-Evoked Dynamic Network Analysis Through Hidden Markov Modeling
Cited by: 117
Author(s): Andrew Quinn, Diego Vidaurre, Romesh Abeysuriya, Robert Becker, Anna C. Nobre, Mark W. Woolrich
Software Mentions: 2
Published: about 6 years ago

10.1093/gbe/evv079

Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees
Cited by: 48
Author(s): Daniel Tamarit, Kirsten Ellegaard, Johan Wikander, Tobias Olofsson, Alejandra Vásquez, Siv G. E. Andersson
Software Mentions: 2
Published: over 9 years ago

10.1128/JB.00639-19

Nisin J, a Novel Natural Nisin Variant, Is Produced by Staphylococcus capitis Sourced from the Human Skin Microbiota
Cited by: 44
Author(s): Julie N O'Sullivan, Paula M. O’Connor, Mary C. Rea, Órla O’Sullivan, Calum J. Walsh, Brian Healy, Harsh Mathur, Des Field, Colin Hill, R. Paul Ross
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41396-020-00750-8

Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils
Cited by: 18
Author(s): Andrew T. Giguere, Stephanie A. Eichorst, Dimitri V. Meier, Craig W. Herbold, Andreas Richter, Chris Greening, Dagmar Woebken
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.54532

Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases
Cited by: 47
Author(s): Rahil Taujale, Aarya Venkat, Liang-Chin Huang, Zhongliang Zhou, Wayland Yeung, Khaled Rasheed, Sheng Li, Arthur S. Edison, Kelley W. Moremen, Natarajan Kannan
Software Mentions: 2
Published: over 4 years ago

10.3390/microorganisms8040554

Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation
Cited by: 10
Author(s): Luz Breton‐Deval, Ayixón Sánchez-Reyes, Alejandro Sánchez-Flores, Katy Juárez, Ilse Salinas-Peralta, Patricia Mussali-Galante
Software Mentions: 1
Published: over 4 years ago

10.3390/toxins9080234

Venomics of Remipede Crustaceans Reveals Novel Peptide Diversity and Illuminates the Venom’s Biological Role
Cited by: 27
Author(s): Björn M. von Reumont, Eivind A.B. Undheim, Robin-Tobias Jauss, Ronald A. Jenner
Software Mentions: 1
Published: over 7 years ago

10.21315/tlsr2018.29.1.3

Genome Organization of Escherichia Phage YD-2008.s: A New Entry to Siphoviridae Family
Cited by: 2
Author(s): Dharmela Sellvam, Nyok-Sean Lau, Yahya Mat Arip
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-016-2556-y

Rapid genomic changes in Drosophila melanogaster adapting to desiccation stress in an experimental evolution system
Cited by: 39
Author(s): Lin Kang, Dau Dayal Aggarwal, Eugenia Rashkovetsky, Abraham B. Korol, Pawel Michalak
Software Mentions: 1
Published: over 8 years ago

10.3389/fphys.2020.594845

Genome Mining and Expression Analysis of Carboxylesterase and Glutathione S-Transferase Genes Involved in Insecticide Resistance in Eggplant Shoot and Fruit Borer, Leucinodes orbonalis (Lepidoptera: Crambidae)
Cited by: 7
Author(s): B Kariyanna, A. Prabhuraj, R. Asokan, Aditi Agrawal, R. Gandhi Gracy, Poonam Jyoti, T. Venkatesan, M. Bheemanna, Basavaraj Kalmath, J. R. Diwan, Y. Pampanna, M. Mohan
Software Mentions: 1
Published: almost 4 years ago

10.3389/fpls.2018.00161

Different Modes of Gene Duplication Show Divergent Evolutionary Patterns and Contribute Differently to the Expansion of Gene Families Involved in Important Fruit Traits in Pear (Pyrus bretschneideri)
Cited by: 68
Author(s): Xin Qiao, Hong Yin, Leiting Li, Runze Wang, Juyou Wu, Shaoling Zhang
Software Mentions: 1
Published: over 6 years ago

10.1128/MRA.00779-20

Complete Genome Sequence of<i>Sulfitobacter</i>Phage ϕGT1, Isolated from a Tidal Flat
Cited by: 2
Author(s): Chung Yeon Hwang, Yirang Cho, Gwang Il Jang, Byung C. Cho, Stephen C. Hardies
Software Mentions: 1
Published: about 4 years ago

10.1186/1475-2859-10-30

Characterization of a cryptic plasmid pSM429 and its application for heterologous expression in psychrophilic Pseudoalteromonas
Cited by: 16
Author(s): Dian‐Li Zhao, Zichao Yu, Ping‐Yi Li, Zhaoyu Wu, Xiu-Lan Chen, Mei Shi, Yong Yu, Bo Chen, Biao Zhou, Yuzhong Zhang
Software Mentions: 1
Published: over 13 years ago

10.1242/bio.036137

Evolution and multiple origins of zona pellucida genes in vertebrates
Cited by: 12
Author(s): Jia‐Xun Feng, Huanfang Tian, Qiaomu Hu, Yan Meng, Hang Xiao
Software Mentions: 1
Published: almost 6 years ago

10.1186/1756-0500-7-388

ClonorESTdb: a comprehensive database for Clonorchis sinensis EST sequences
Cited by: 13
Author(s): Dae‐Won Kim, Won Gi Yoo, Sang‐Hyun Lee, Myoung-Ro Lee, Yu-Jung Kim, Shin‐Hyeong Cho, Won-Ja Lee, Jung‐Won Ju
Software Mentions: 1
Published: over 10 years ago

10.1186/s12951-015-0137-x

A nanomolecular approach to decrease adhesion of biofouling-producing bacteria to graphene-coated material
Cited by: 48
Author(s): Carolina Parra, Fernando Dorta, Edra Jiménez, Ricardo Henríquez, Cristián Ramírez, Rodrigo Rojas, Patricio Villalobos
Software Mentions: 1
Published: almost 9 years ago

10.3390/ijerph18147385

Can Administrative Health Data Improve the Gold Standard? Evidence from a Model of the Progression of Myocardial Infarction
Cited by: 0
Author(s): Son Nghiem, Jonathan Williams, Clifford Afoakwah, Quan Huynh, Shu‐Kay Ng, Joshua Byrnes
Software Mentions: 1
Published: over 3 years ago

10.1186/s12866-019-1400-3

Ruminal metagenomic analyses of goat data reveals potential functional microbiota by supplementation with essential oil-cobalt complexes
Cited by: 20
Author(s): Zhaomin Lei, Ke Zhang, Chao Li, Ting Jiao, Jianping Wu, Yubing Wei, Kechuan Tian, Chong Li, Defu Tang, Delmer Davis, D. P. Casper, Hui Jiang, Xiaolong Wang, Jianfu Wang
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1004109

DAF-16/FoxO Directly Regulates an Atypical AMP-Activated Protein Kinase Gamma Isoform to Mediate the Effects of Insulin/IGF-1 Signaling on Aging in Caenorhabditis elegans
Cited by: 51
Author(s): Jennifer M. A. Tullet, Caroline Araiz, Matthew J. Sanders, Catherine Au, Alexandre Benedetto, Irene Papatheodorou, Emily Clark, Kathrin Schmeißer, Daniel C. Jones, Eugene F. Schuster, Janet M. Thornton, David Gems
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0088947

Genomic Survey, Gene Expression Analysis and Structural Modeling Suggest Diverse Roles of DNA Methyltransferases in Legumes
Cited by: 42
Author(s): Rohini Garg, Romika Kumari, Sneha Tiwari, Shweta Goyal
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0194335

Molecular evolution and functional divergence of eukaryotic translation initiation factor 2-alpha kinases
Cited by: 11
Author(s): K. Hari Krishna, Mithilesh Kumar
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0010909

MixHMM: Inferring Copy Number Variation and Allelic Imbalance Using SNP Arrays and Tumor Samples Mixed with Stromal Cells
Cited by: 31
Author(s): Zongzhi Liu, Ao Li, Vincent P. Schulz, Min Chen, David Tuck
Software Mentions: 1
Published: over 14 years ago

10.1186/s12864-019-5679-0

Genomic analyses of aminoacyl tRNA synthetases from human-infecting helminths
Cited by: 1
Author(s): Preeti Goel, Suhel Parvez, Amit Sharma
Software Mentions: 1
Published: over 5 years ago

10.3390/v10100577

Biodiversity of Streptococcus thermophilus Phages in Global Dairy Fermentations
Cited by: 27
Author(s): Katherine Lavelle, Inés Martínez, Horst Neve, Gabriele Andrea Lugli, Charles M. A. P. Franz, Marco Ventura, Fabio Dal Bello, Douwe van Sinderen, Jennifer Mahony
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-021-96711-y

HES and Mox genes are expressed during early mesoderm formation in a mollusk with putative ancestral features
Cited by: 0
Author(s): Attila Placido Sachslehner, Elisabeth Zieger, Andrew Calcino, Andreas Wanninger
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pone.0018509

An Integrated Approach for Finding Overlooked Genes in Shigella
Cited by: 8
Author(s): Junping Peng, Jian Yang, Qi Jin
Software Mentions: 1
Published: over 13 years ago

10.1093/database/baz094

ApicoTFdb: the comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factors
Cited by: 2
Author(s): Rahila Sardar, Abhinav Kaushik, Rajan Kumar Pandey, Asif Mohmmed, Shakir Ali, Dinesh Gupta
Software Mentions: 1
Published: almost 6 years ago