10.3389/fcimb.2020.625576

Phylogeography of Human and Animal Coxiella burnetii Strains: Genetic Fingerprinting of Q Fever in Belgium
Cited by: 12
Author(s): Sara Tomaiuolo, Samira Boarbi, Tiziano Fancello, Patrick P. Michel, Damien Desqueper, Fabien Grégoire, Jozefien Callens, David Frétin, Bert Devriendt, Eric Cox, Marcella Mori
Software Mentions: 2
Published: over 5 years ago

10.3389/fcimb.2021.673966

In Vivo and In Vitro Genome-Wide Profiling of RNA Secondary Structures Reveals Key Regulatory Features in Plasmodium falciparum
Cited by: 4
Author(s): Yanwei Qi, Yuhong Zhang, Guixing Zheng, Bingxia Chen, Mengxin Zhang, Jian Li, Tao Peng, Jun Huang, Xinhua Wang
Software Mentions: 2
Published: over 5 years ago

10.3389/fcimb.2021.555072

Microbiota Detection Patterns Correlate With Presence and Severity of Barrett’s Esophagus
Cited by: 4
Author(s): Ikenna Okereke, Aaron L. Miller, Daniel C. Jupiter, Catherine Hamilton, Gabriel Reep, Timothy Krill, Clark R. Andersen, Richard B. Pyles
Software Mentions: 2
Published: over 5 years ago

10.3389/fcimb.2019.00123

Genomic and Epidemiological Evidence of a Dominant Panton-Valentine Leucocidin-Positive Methicillin Resistant Staphylococcus aureus Lineage in Sri Lanka and Presence Among Isolates From the United Kingdom and Australia
Cited by: 8
Author(s): Sharla M. McTavish, Sarah J Snow, Ellie C Cook, Bruno Pichon, Sarah Coleman, Geoffrey W. Coombs, Stanley Pang, César A. Arias, Lorena Díaz, Emma Boldock, Sue Davies, M. Udukala, Angela Kearns, Sisira Siribaddana, Thushan I. de Silva
Software Mentions: 2
Published: over 7 years ago

10.3389/fncel.2017.00003

Deep Sequencing of the Human Retinae Reveals the Expression of Odorant Receptors
Cited by: 17
Author(s): Nikolina Jovancevic, Kirsten A. Wunderlich, Claudia Haering, Caroline Flegel, Désirée Maßberg, Markus Weinrich, Lea Weber, Lars Tebbe, Anselm Kampik, Günter Gisselmann, Uwe Wolfrum, Hanns Hatt, Lian Gelis
Software Mentions: 2
Published: over 9 years ago

10.3389/fncel.2017.00348

Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
Cited by: 7
Author(s): Nikolay Aseyev, Aliya Vinarskaya, Matvey Roshchin, Tatiana Korshunova, Aleksey Malyshev, Alena B. Zuzina, Victor N. Ierusalimsky, M. S. Lemak, И. С. Захаров, Novikov Ia, P. M. Kolosov, Е. А. Чеснокова, С. А. Волкова, Artem S. Kasianov, Л. А. Урошлев, Yekaterina Popova, Richard D. Boyle, P. M. Balaban
Software Mentions: 2
Published: almost 9 years ago

10.3389/fendo.2018.00611

Tissue-Based Mapping of the Fathead Minnow (Pimephales promelas) Transcriptome and Proteome
Cited by: 5
Author(s): Candice M. Lavelle, L. Cody Smith, Joseph H. Bisesi, Fahong Yu, Cecilia Silva-Sanchez, David Moraga-Amador, A. Buerger, Natàlia García-Reyero, Tara Sabo‐Attwood, Nancy D. Denslow
Software Mentions: 2
Published: almost 8 years ago

10.3389/fpls.2016.01184

Genome-Wide Analysis of MicroRNA Responses to the Phytohormone Abscisic Acid in Populus euphratica
Cited by: 27
Author(s): Hui Duan, Xiaoxuan Lu, Conglong Lian, Yi An, Xinli Xia, Weilun Yin
Software Mentions: 2
Published: about 10 years ago

10.3389/fendo.2019.00739

Circulating miRNA Expression Profiling in Primary Aldosteronism
Cited by: 20
Author(s): Ábel Decmann, G Nyírő, Ottó Darvasi, Péter István Turai, Irina Bancos, Ravinder Kaur, Raffaele Pezzani, Maurizio Iacobone, Ivana Kraljević, Darko Kaštelan, Mirko Parasiliti-Caprino, Mauro Maccario, Nina Nirschl, Daniel A. Heinrich, Martín Reincke, Attila Patócs, Péter Igaz
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.29938

Msn2/4 regulate expression of glycolytic enzymes and control transition from quiescence to growth
Cited by: 47
Author(s): Zheng Kuang, Sudarshan Pinglay, Hongkai Ji, Jef D. Boeke
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pgen.1004211

An Epigenetic Signature in Peripheral Blood Associated with the Haplotype on 17q21.31, a Risk Factor for Neurodegenerative Tauopathy
Cited by: 65
Author(s): Yun Li, Jason Chen, Renee L. Sears, Fuying Gao, Eric Klein, Anna Karydas, Michael D. Geschwind, Howard J. Rosen, Adam L. Boxer, Weilong Guo, Matteo Pellegrini, Steve Horvath, Bruce L. Miller, Daniel H. Geschwind, Giovanni Coppola
Software Mentions: 2
Published: over 12 years ago

10.3389/fgene.2019.00531

RNA-Seq Revealed Novel Non-proliferative Retinopathy Specific Circulating MiRNAs in T2DM Patients
Cited by: 24
Author(s): Zimeng Li, Ying Dong, Chang He, Xingchen Pan, Dianyuan Liu, Jianli Yang, Liankun Sun, Peng Chen, Qing Wang
Software Mentions: 2
Published: over 7 years ago

10.3389/fgene.2019.00296

Mining Magnaporthe oryzae sRNAs With Potential Transboundary Regulation of Rice Genes Associated With Growth and Defense Through Expression Profile Analysis of the Pathogen-Infected Rice
Cited by: 7
Author(s): Hao Zhang, Sifei Liu, Haowu Chang, Mengping Zhan, Qing‐Ming Qin, Borui Zhang, Zhi Li, Yuanning Liu
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2021.683481

Bacteriomic Analyses of Asian Citrus Psyllid and Citrus Samples Infected With “Candidatus Liberibacter asiaticus” in Southern California and Huanglongbing Management Implications
Cited by: 4
Author(s): Jiaquan Huang, Zhigang Dai, Zheng Zhang, Priscila A da Silvia, Lucita Kumagai, Qijun Xiang, Jianchi Chen, Xiaoling Deng
Software Mentions: 2
Published: over 5 years ago

10.1016/j.gdata.2015.11.013

In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data
Cited by: 5
Author(s): Suyash Agarwal, N. S. Nagpure, Prachi Srivastava, Basdeo Kushwaha, Ravindra Kumar, Manmohan Pandey, Shreya Srivastava
Software Mentions: 2
Published: over 10 years ago

10.3389/fgene.2021.634635

Research on the Mechanism of Soybean Resistance to Phytophthora Infection Using Machine Learning Methods
Cited by: 5
Author(s): Junxia Chi, Shizeng Song, Hao Zhang, Yuanning Liu, Hengyi Zhao, Liyan Dong
Software Mentions: 2
Published: over 5 years ago

10.3389/fnut.2018.00081

Abundantly Present miRNAs in Milk-Derived Extracellular Vesicles Are Conserved Between Mammals
Cited by: 98
Author(s): Martijn J. C. van Herwijnen, Tom A.P. Driedonks, L. Basten Snoek, Aart Kroon, Marije Kleinjan, R. Jorritsma, Corné M. J. Pieterse, Esther N. M. Nolte‐‘t Hoen, Marca H. M. Wauben
Software Mentions: 2
Published: about 8 years ago

10.3389/fgene.2021.660366

UMIc: A Preprocessing Method for UMI Deduplication and Reads Correction
Cited by: 4
Author(s): Maria Tsagiopoulou, Μαρία Μανιού, Nikolaos Pechlivanis, Anastasis Togkousidis, Michaela Kotrová, Tobias Hutzenlaub, Ilias Kappas, Anastasia Chatzidimitriou, Fotis Psomopoulos
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.18270

MYC activation and BCL2L11 silencing by a tumour virus through the large-scale reconfiguration of enhancer-promoter hubs
Cited by: 74
Author(s): C. David Wood, Hildegonda Veenstra, Sarika Khasnis, Andrea Gunnell, Helen Webb, Claire Shannon-Lowe, Simon Andrews, Cameron S. Osborne, Michelle J. West
Software Mentions: 2
Published: about 10 years ago

10.1186/gb-2010-11-10-r104

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
Cited by: 141
Author(s): Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stéphane Terry, David Z. Chen, Joel Rozowsky, Ashutosh Tewari, Naoki Kitabayashi, Benjamin Moss, Mark S. Chee, Francesca Demichelis, Mark A. Rubin, Mark Gerstein
Software Mentions: 2
Published: about 16 years ago

10.7554/eLife.06722

Quality control of transcription start site selection by nonsense-mediated-mRNA decay
Cited by: 105
Author(s): Christophe Malabat, Frank Feuerbach, Laurence Ma, Cosmin Saveanu, Alain Jacquier
Software Mentions: 2
Published: over 11 years ago

10.15252/embj.2020107455

<i>HASTY</i> , the <i>Arabidopsis EXPORTIN5</i> ortholog, regulates cell‐to‐cell and vascular microRNA movement
Cited by: 27
Author(s): Florian Brioudes, Florence Jay, Alexis Sarazin, Thomas Grentzinger, Emanuel A. Devers, Olivier Voinnet
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2020.00375

Identifying Candida albicans Gene Networks Involved in Pathogenicity
Cited by: 4
Author(s): Graham H. Thomas, Judith M. Bain, Susan Budge, Alistair J. P. Brown, Ryan M. Ames
Software Mentions: 2
Published: over 6 years ago

10.3389/fpls.2016.01055

Phytochrome and Ethylene Signaling Integration in Arabidopsis Occurs via the Transcriptional Regulation of Genes Co-targeted by PIFs and EIN3
Cited by: 22
Author(s): Jinkil Jeong, Keunhwa Kim, Mi Eon Kim, Hye Gi Kim, Gwi Suk Heo, Ohkmae Kim Park, Youn‐Il Park, Giltsu Choi, Eunkyoo Oh
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.09571

Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development
Cited by: 95
Author(s): J. Ż̷ylicz, Sabine Dietmann, Ufuk Günesdogan, Jim Hackett, Delphine Cougot, Caroline Lee, M. Azim Surani
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pbio.1002316

Bromodomain Proteins Contribute to Maintenance of Bloodstream Form Stage Identity in the African Trypanosome
Cited by: 53
Author(s): Danae Schulz, Monica R. Mugnier, Eda Margaret Paulsen, Hee Sook Kim, Chun Wa Chung, David F. Tough, Inmaculada Rioja, Rab K. Prinjha, F. Nina Papavasiliou, Erik Debler
Software Mentions: 2
Published: almost 11 years ago

10.3389/fmicb.2017.00126

Exo-miRExplorer: A Comprehensive Resource for Exploring and Comparatively Analyzing Exogenous MicroRNAs
Cited by: 5
Author(s): Ling‐Ling Zheng, Kai-Wen Deng, An-Cheng Deng, Jie Wu, Jianhua Yang, Zhao‐Rong Lun, Liang‐Hu Qu
Software Mentions: 2
Published: over 9 years ago

10.1093/database/bax074

Echinobase: an expanding resource for echinoderm genomic information
Cited by: 60
Author(s): Parul Kudtarkar, R. Andrew Cameron
Software Mentions: 2
Published: almost 10 years ago

10.3389/fgene.2021.602528

Transcriptome and Comparative Chloroplast Genome Analysis of Vincetoxicum versicolor: Insights Into Molecular Evolution and Phylogenetic Implication
Cited by: 10
Author(s): Xiaolei Yu, Wenxiu Wang, Hongxia Yang, Xiaoying Zhang, Dan Wang, Xiaoxuan Tian
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2019.01183

Transcriptome Analysis Identifies Candidate Genes and Pathways Associated With Feed Efficiency in Hu Sheep
Cited by: 25
Author(s): Deyin Zhang, Xiaoxue Zhang, Fadi Li, Chong Li, Yongfu La, Futao Mo, Guoze Li, Yukun Zhang, Xiaolong Li, Qizhi Song, Yuan Zhao, Weimin Wang
Software Mentions: 2
Published: almost 7 years ago

10.15252/embj.201592532

Sororin actively maintains sister chromatid cohesion
Cited by: 84
Author(s): René Ladurner, Emanuel Kreidl, Miroslav P Ivanov, Heinz Ekker, Maria Helena Idarraga-Amado, Georg A. Busslinger, Gordana Wutz, David A. Cisneros, Jan‐Michael Peters
Software Mentions: 2
Published: over 10 years ago

10.7554/eLife.52212

MS-275, a class 1 histone deacetylase inhibitor augments glucagon-like peptide-1 receptor agonism to improve glycemic control and reduce obesity in diet-induced obese mice
Cited by: 9
Author(s): Shilpak Dilip Bele, Shravan Babu Girada, Arnab Ray, Abhishek Gupta, Srinivas Oruganti, Phanithi Prakash Babu, Rahul Sr Rayalla, Shashi Vardhan Kalivendi, Ahamed Ibrahim, Vishwajeet Puri, Venkateswar Adalla, Madhumohan R. Katika, Richard D. DiMarchi, Prasenjit Mitra
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2019.00957

Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes
Cited by: 7
Author(s): Jiarong Guo, John F. Quensen, Yanni Sun, Qiong Wang, C. Titus Brown, James R. Cole, James M. Tiedje
Software Mentions: 2
Published: about 7 years ago

10.3389/fgene.2021.695178

Changthangi Pashmina Goat Genome: Sequencing, Assembly, and Annotation
Cited by: 0
Author(s): Basharat Ahmad Bhat, Nazir Ahmad Ganai, Ashutosh Singh, Rakeeb Ahmad Mir, Syed Mudasir Ahmad, Sajad Majeed Zargar, Firdose Ahmad Malik
Software Mentions: 2
Published: over 5 years ago

10.15252/embj.201695323

<scp>GT</scp> ‐rich promoters can drive <scp>RNA</scp> pol <scp>II</scp> transcription and deposition of H2A.Z in African trypanosomes
Cited by: 65
Author(s): Carolin Wedel, Konrad U. Förstner, Ramona Derr, T. Nicolai Siegel
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.21615

TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24− cancer cells
Cited by: 33
Author(s): Debjani Pal, Anja Pertot, Nitin H. Shirole, Zhan Yao, Naishitha Anaparthy, Tyler Garvin, Hilary Cox, Kenneth Chang, Fred Rollins, Jude Kendall, Leyla Edwards, Vijay A Singh, Gary C. Stone, Michael C. Schatz, James Hicks, Gregory J. Hannon, Raffaella Sordella
Software Mentions: 2
Published: almost 10 years ago

10.1038/emboj.2013.177

Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor
Cited by: 192
Author(s): Graziano Martello, Paul Bertone, Austin Smith
Software Mentions: 2
Published: about 13 years ago

10.3389/fgene.2019.00105

Using Pan RNA-Seq Analysis to Reveal the Ubiquitous Existence of 5′ and 3′ End Small RNAs
Cited by: 14
Author(s): Xiao Xu, Haishuo Ji, Xiufeng Jin, Zhi Cheng, Xuemei Yao, Yanqiang Liu, Qiang Zhao, Tao Zhang, Jishou Ruan, Wenjun Bu, Ze Chen, Shan Gao
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1004090

Defining NELF-E RNA Binding in HIV-1 and Promoter-Proximal Pause Regions
Cited by: 55
Author(s): John M. Pagano, Ho Young Kwak, Colin T. Waters, Rebekka O. Sprouse, Brian S. White, Abdullah Ozer, Kylan Szeto, David Shalloway, Harold G. Craighead, John T. Lis
Software Mentions: 2
Published: almost 13 years ago

10.7554/eLife.17548

Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage
Cited by: 208
Author(s): Caroline Townsend Stork, M Bocek, Madzia P Crossley, Julie Sollier, Lionel A. Sanz, Frédéric Chédin, Tomek Swigut, Karlene A. Cimprich
Software Mentions: 2
Published: about 10 years ago

10.3390/diagnostics10090701

Sepsis Diagnostics: Intensive Care Scoring Systems Superior to MicroRNA Biomarker Testing
Cited by: 1
Author(s): Fabian Link, Knut Krohn, Anna-Maria Burgdorff, Annett Christel, Julia Schümann
Software Mentions: 2
Published: about 6 years ago

10.1186/gb-2014-15-1-r2

Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs
Cited by: 111
Author(s): Matthew B Friedersdorf, Jack D. Keene
Software Mentions: 2
Published: almost 13 years ago

10.1242/dev.136051

microRNA deep sequencing in two adult stem cell populations identifies miR-501 as novel regulator of myosin heavy chain during muscle regeneration
Cited by: 15
Author(s): Amir Mizbani, Edlira Luca, Elisabeth J. Rushing, Jan Krützfeldt
Software Mentions: 2
Published: almost 11 years ago

10.1186/gb-2013-14-1-r2

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
Cited by: 176
Author(s): Todd J. Treangen, Sergey Koren, Daniel Sommer, Bo Liu, Irina Astrovskaya, Brian D. Ondov, Aaron E. Darling, Adam M. Phillippy, Mihai Pop
Software Mentions: 2
Published: almost 14 years ago

10.1186/gb-2013-14-11-r129

Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture
Cited by: 77
Author(s): Stefan Grob, Marc W. Schmid, Nathan W. Luedtke, Thomas Wicker, Ueli Grossniklaus
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pgen.1008291

Monitoring the interplay between transposable element families and DNA methylation in maize
Cited by: 49
Author(s): Jaclyn M. Noshay, Sarah N. Anderson, Peng Zhou, Lexiang Ji, William A. Ricci, Zefu Lu, Michelle C. Stitzer, Peter A. Crisp, Candice N. Hirsch, Xiaoyu Zhang, Robert J. Schmitz, Nathan M. Springer
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pgen.1006783

Global analysis of double-strand break processing reveals in vivo properties of the helicase-nuclease complex AddAB
Cited by: 14
Author(s): Anjana Badrinarayanan, Tung B. K. Le, Jan-Hendrik Spille, Ibrahima Cissé, Michael T. Laub
Software Mentions: 2
Published: over 9 years ago

10.3389/fpls.2018.01160

Global Transcriptome Analyses Reveal Differentially Expressed Genes of Six Organs and Putative Genes Involved in (Iso)flavonoid Biosynthesis in Belamcanda chinensis
Cited by: 8
Author(s): Mei Tian, Xiang Zhang, Zhu Yu, Xie GuangHui, Min-Jian Qin
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pbio.3000636

Millipede genomes reveal unique adaptations during myriapod evolution
Cited by: 15
Author(s): Zhe Qu, Wenyan Nong, Wai Lok So, Tom Barton-Owen, Yiqian Li, Thomas Leung, Chade Li, Tobias Baril, Hon Kit Wong, Thomas Swale, Ting‐Fung Chan, Alexander Hayward, Sai-Ming Ngai, Jerome H.L. Hui
Software Mentions: 2
Published: about 6 years ago

10.1186/gb-2013-14-8-r92

A global profiling of uncapped mRNAs under cold stress reveals specific decay patterns and endonucleolytic cleavages in Brachypodium distachyon
Cited by: 22
Author(s): Jingyu Zhang, Zhiwei Mao, Kang Chong
Software Mentions: 2
Published: almost 14 years ago

10.3389/fmicb.2020.01716

Differential Regulation of miRNA Profiles of Human Cells Experimentally Infected by Leishmania donovani Isolated From Indian Visceral Leishmaniasis and Post-Kala-Azar Dermal Leishmaniasis
Cited by: 7
Author(s): Ashish Kumar, Saravanan Vijaykumar, Manas Ranjan Dikhit, Kumar Abhishek, Rimi Mukherjee, Abhik Sen, Pradeep Das, Sushmita Das
Software Mentions: 2
Published: about 6 years ago

10.3389/fpls.2017.00093

Understanding Host-Pathogen Interactions with Expression Profiling of NILs Carrying Rice-Blast Resistance Pi9 Gene
Cited by: 44
Author(s): Priyanka Jain, Pankaj Kumar Singh, Ritu Kapoor, Apurva Khanna, Amolkumar U. Solanke, S. Gopala Krishnan, Ashok Kumar Singh, Vinay Sharma, Tilak Raj Sharma
Software Mentions: 2
Published: over 9 years ago

10.1186/s13059-014-0576-y

Rapid reprogramming of epigenetic and transcriptional profiles in mammalian culture systems
Cited by: 132
Author(s): Colm E. Nestor, Raffaele Ottaviano, Diana Reinhardt, Hazel A Cruickshanks, Heidi K. Mjoseng, Rhoanne C. McPherson, Antonio Lentini, John P. Thomson, Donncha S. Dunican, Sari Pennings, Stephen M. Anderton, Mikael Benson, Richard R. Meehan
Software Mentions: 2
Published: over 11 years ago

10.3390/nu13020614

Acute Effects of Cheddar Cheese Consumption on Circulating Amino Acids and Human Skeletal Muscle
Cited by: 8
Author(s): Naomi M.M.P. de Hart, Ziad Mahmassani, Paul T. Reidy, Joshua Kelley, Alison McKenzie, Jonathan J Petrocelli, M.J. Bridge, Lisa Baird, Eric D. Bastian, Loren S. Ward, Michael Howard, Micah J. Drummond
Software Mentions: 2
Published: over 5 years ago

10.1016/j.ajhg.2017.01.011

Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice
Cited by: 61
Author(s): Gaëlle Carrat, Ming Hu, Marie‐Sophie Nguyen‐Tu, Pauline Chabosseau, Kyle J. Gaulton, Martijn van de Bunt, Afshan Siddiq, Mario Falchi, Matthias Thurner, Mickaël Canouil, François Pattou, Isabelle Leclerc, Timothy J. Pullen, Matthew Cane, Priyanka Prabhala, William W. Greenwald, Anke Schulte, Piero Marchetti, Mark Ibberson, Patrick E. MacDonald, Jocelyn E. Manning Fox, Anna L. Gloyn, Philippe Froguel, Michele Solimena, Mark I. McCarthy, Guy A. Rutter
Software Mentions: 2
Published: over 9 years ago

10.1111/age.12992

Identification and characterization of miRNAs during early pregnancy in domestic sheep
Cited by: 6
Author(s): Kisun Pokharel, Jaana Peippo, Menghua Li, Juha Kantanen
Software Mentions: 2
Published: about 6 years ago

10.1186/s12859-017-1601-4

QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing
Cited by: 34
Author(s): Shanrong Zhao, William Gordon, Sarah Du, Chi Zhang, Wen He, Li Xi, Sachin Mathur, Michael Agostino, Theresa Paradis, David von Schack, Michael S. Vincent, Baohong Zhang
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-12-S14-S2

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
Cited by: 417
Author(s): Qiongyi Zhao, Yi Wang, Yawei Kong, Da Luo, Xuan Li, Pei Hao
Software Mentions: 2
Published: almost 15 years ago

10.1186/s12859-017-1873-8

riboviz: analysis and visualization of ribosome profiling datasets
Cited by: 35
Author(s): Oana Carja, Tongji Xing, Eric Wallace, Joshua B. Plotkin, Premal Shah
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12859-017-1548-5

Manananggal - a novel viewer for alternative splicing events
Cited by: 7
Author(s): Matthias Barann, Ralf Zimmer, Fabian Birzele
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-11-514

Data structures and compression algorithms for high-throughput sequencing technologies
Cited by: 45
Author(s): Kenneth Daily, Paul Rigor, Scott Christley, Xiaohui Xie, Pierre Baldi
Software Mentions: 2
Published: about 16 years ago

10.1186/s12859-015-0704-z

EMSAR: estimation of transcript abundance from RNA-seq data by mappability-based segmentation and reclustering
Cited by: 18
Author(s): Mi Kyung Lee, Chae Hwa Seo, B. Alver, Sanghyuk Lee, Peter J. Park
Software Mentions: 2
Published: about 11 years ago

10.1186/s12859-018-2570-y

Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)
Cited by: 38
Author(s): Dmitry A. Kuzmin, Sergey Feranchuk, Vadim V. Sharov, Alexander N. Cybin, Stepan V. Makolov, Yuliya A. Putintseva, Н. В. Орешкова, Konstantin V. Krutovsky
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-021-04004-y

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis
Cited by: 7
Author(s): Carlo Ferravante, Domenico Memoli, Domenico Palumbo, Paolo Ciaramella, Antonio Di Loria, Ylenia D’Agostino, Giovanni Nassa, Francesca Rizzo, Roberta Tarallo, Alessandro Weisz, Giorgio Giurato
Software Mentions: 2
Published: over 5 years ago

10.1186/s12915-020-00926-w

miR-31-5p regulates cold acclimation of the wood-boring beetle Monochamus alternatus via ascaroside signaling
Cited by: 26
Author(s): Bin Zhang, Lilin Zhao, Jing Ning, Jacob D. Wickham, Huanfang Tian, Xiaoming Zhang, Meiling Yang, Xiangming Wang, Sun Jian
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-213X-14-15

Integrated proteomic and transcriptomic analysis of the Aedes aegyptieggshell
Cited by: 58
Author(s): Osvaldo Marinotti, Tuan Ngo, Bianca Burini Kojin, Shao‐Pei Chou, Brian D. Nguyen, Jennifer Juhn, Rebeca Carballar-Lejarazú, Pedro N. Marinotti, Xiaofang Jiang, Marika F. Walter, Zhijian Tu, Paul D. Gershon, Anthony A. James
Software Mentions: 2
Published: over 12 years ago

10.1186/s12861-015-0089-2

MiR-21 is required for efficient kidney regeneration in fish
Cited by: 27
Author(s): Beate Hoppe, Stefan Pietsch, Martin Franke, Sven Engel, Marco Groth, Matthias Platzer, Christoph Englert
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12862-016-0844-4

Genetic mechanisms of bone digestion and nutrient absorption in the bone-eating worm Osedax japonicus inferred from transcriptome and gene expression analyses
Cited by: 19
Author(s): Norio Miyamoto, Masa‐aki Yoshida, Hisao Koga, Yoshihiro Fujiwara
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-016-3271-4

Identification and characterization of microRNAs in Humulus lupulus using high-throughput sequencing and their response to Citrus bark cracking viroid (CBCVd) infection
Cited by: 25
Author(s): Ajay Kumar Mishra, G Duraisamy, J. Matoušek, Sebastjan Radišek, Branka Javornik, Jernej Jakše
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-020-07318-y

Unbiased RNA-Seq-driven identification and validation of reference genes for quantitative RT-PCR analyses of pooled cancer exosomes
Cited by: 17
Author(s): Yanjun Dai, Yumeng Cao, Jens Köhler, Aiping Lu, Shaohua Xu, Haiyun Wang
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-015-1442-3

Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes
Cited by: 20
Author(s): Chen Jiao, Min Gao, Xiping Wang, Zhangjun Fei
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-14-415

Global transcriptome profiles of Camellia sinensis during cold acclimation
Cited by: 239
Author(s): Xinchao Wang, Qiongyi Zhao, Chun-Lei Ma, Zong Hong Zhang, Hongli Cao, Yawei Kong, Chuan Yue, Xinyuan Hao, Liang Chen, Jianqiang Ma, Jiye Jin, Xuan Li, Yajun Yang
Software Mentions: 2
Published: over 13 years ago

10.1186/s12864-015-2011-5

The Perchlorate Reduction Genomic Island: Mechanisms and Pathways of Evolution by Horizontal Gene Transfer
Cited by: 30
Author(s): Ryan A. Melnyk, John D. Coates
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2164-15-98

A genomic perspective to assessing quality of mass-reared SIT flies used in Mediterranean fruit fly (Ceratitis capitata) eradication in California
Cited by: 31
Author(s): Bernarda Calla, Brian E. Hall, Shaobin Hou, Scott M. Geib
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-020-06906-2

Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element
Cited by: 16
Author(s): Ze Chen, Yibo Xuan, Guangcai Liang, Xiaolong Yang, Zhou Yu, Stephen C. Barker, Samuel Kelava, Wenjun Bu, Jingze Liu, Shan Gao
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-15-1115

Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo
Cited by: 47
Author(s): Kenji Nakahigashi, Yuki Takai, Yuh Shiwa, Masahiko Wada, Masayuki Honma, Hideki Yoshikawa, Masaru Tomita, Akio Kanai, Hirotada Mori
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2164-13-578

Identification of essential genes of the periodontal pathogen Porphyromonas gingivalis
Cited by: 120
Author(s): Brian Klein, Elizabeth L Tenorio, David W. Lazinski, Andrew Camilli, Marilyn J. Duncan, Linden T. Hu
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2164-14-255

A zebrafish high throughput screening system used for Staphylococcus epidermidis infection marker discovery
Cited by: 60
Author(s): Wouter J. Veneman, Oliver W. Stockhammer, Leonie de Boer, Sebastian A. J. Zaat, Annemarie H. Meijer, Herman P. Spaink
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12864-017-3556-2

Response of microRNAs to cold treatment in the young spikes of common wheat
Cited by: 60
Author(s): Guang Song, Rongzhi Zhang, Shujuan Zhang, Yulian Li, Jie Gao, Xiao Han, Mingli Chen, Jiao Wang, Wei Li, Genying Li
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-017-4090-y

De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly
Cited by: 19
Author(s): Monika Frazier, Martin Helmkampf, M. Renee Bellinger, Scott M. Geib, Misaki Takabayashi
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-017-3505-0

Improved annotation with de novo transcriptome assembly in four social amoeba species
Cited by: 6
Author(s): Reema Singh, Hajara M. Lawal, Christina Schilde, Gernot Glöckner, Geoffrey J. Barton, Pauline Schaap, Christian Callebaut
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-14-298

5′ tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction
Cited by: 195
Author(s): Joseph M. Dhahbi, Stephen R. Spindler, Hani Atamna, Amy Yamakawa, Dario Boffelli, Patricia L. Mote, David I. K. Martin
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2164-14-273

Six novel Y chromosome genes in Anophelesmosquitoes discovered by independently sequencing males and females
Cited by: 105
Author(s): Andrew Brantley Hall, Yumin Qi, Vladimir A. Timoshevskiy, Maria V. Sharakhova, Igor V. Sharakhov, Zhijian Tu
Software Mentions: 2
Published: over 13 years ago

10.1186/s12864-015-1456-x

Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data
Cited by: 48
Author(s): Richard Orton, Caroline F. Wright, Marco J. Morelli, David J. King, David Paton, Donald P. King, Daniel T. Haydon
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-14-704

Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals
Cited by: 92
Author(s): Sebastian Baumgarten, Till Bayer, Manuel Aranda, Yi Jin Liew, Adrian R. Carr, Gos Micklem, Christian R. Voolstra
Software Mentions: 2
Published: about 13 years ago

10.1186/s12864-020-6730-x

Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus)
Cited by: 18
Author(s): Xiaoli Huang, Yanxin Jiang, Wanting Zhang, Yingyin Cheng, Yaping Wang, Xiaocui Ma, You Duan, L. Xia, Yaxin Chen, Nan Wu, Minjun Shi, Xiao-Qin Xia
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-015-1577-2

Neural transcriptome reveals molecular mechanisms for temporal control of vocalization across multiple timescales
Cited by: 29
Author(s): Ni Feng, Daniel J. Fergus, Andrew H. Bass
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-017-3570-4

Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation
Cited by: 41
Author(s): Jiaming Chen, Xiaoqiang Yang, Xiaomao Huang, Shi-Hua Duan, Chengnian Long, Jiakuan Chen, Jun Rong
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-015-2147-3

Combined metabolome and transcriptome profiling provides new insights into diterpene biosynthesis in S. pomifera glandular trichomes
Cited by: 38
Author(s): Fotini A. Trikka, Alexandros K. Nikolaidis, Codruţa Ignea, Aphrodite Tsaballa, Leto‐Aikaterini Tziveleka, Efstathia Iοannou, Vassilios Roussis, Eleni A. Stea, Dragana Božić, Anagnostis Argiriou, Angelos K. Kanellis, Sotirios C. Kampranis, Antonios M. Makris
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-015-1965-7

Deep sequencing shows microRNA involvement in bovine mammary gland adaptation to diets supplemented with linseed oil or safflower oil
Cited by: 56
Author(s): Ran Li, Frédéric Beaudoin, Adolf A. Ammah, Nathalie Bissonnette, C. Benchaar, Xin Zhao, Chuzhao Lei, Eveline M. Ibeagha‐Awemu
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-017-3549-1

Effect of light and prey availability on gene expression of the mixotrophic chrysophyte, Ochromonas sp.
Cited by: 25
Author(s): Alle A. Y. Lie, Zhenfeng Liu, Ramón Terrado, Avery O. Tatters, Karla B. Heidelberg, David A. Caron
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-019-5521-8

Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development
Cited by: 16
Author(s): Kathleen D. DeBoer, Su Melser, Jana Sperschneider, Lars G. Kamphuis, Gagan Garg, Lingling Gao, Karen M. Frick, Karam B. Singh
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-018-4932-2

RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes
Cited by: 36
Author(s): Likai Wang, Yanpeng Xi, Sibum Sung, Hong Qiao
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-015-1253-6

Transcriptome analysis of northern elephant seal (Mirounga angustirostris) muscle tissue provides a novel molecular resource and physiological insights
Cited by: 27
Author(s): Jane Khudyakov, Likit Preeyanon, Cory D. Champagne, Rudy M. Ortiz, Daniel E. Crocker
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-016-2514-8

Small RNA and PARE sequencing in flower bud reveal the involvement of sRNAs in endodormancy release of Japanese pear (Pyrus pyrifolia 'Kosui')
Cited by: 21
Author(s): Songling Bai, Takanori Saito, Akiko Ito, Phạm Anh Tuấn, Ying Xu, Yuanwen Teng, Takaya Moriguchi
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-16-S13-S6

Comparison of American mink embryonic stem and induced pluripotent stem cell transcriptomes
Cited by: 24
Author(s): А. Г. Мензоров, N. M. Matveeva, Marios Nektarios Markakis, Veniamin Fishman, K. Christensen, А. А. Хабарова, Inna E. Pristyazhnyuk, Elena A. Kizilova, Susanna Cirera, Razvan Anistoroaei, O. L. Serov
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-015-1492-6

Histone modifications induced by MDV infection at early cytolytic and latency phases
Cited by: 13
Author(s): Apratim Mitra, Juan Luo, Yanghua He, Yue Gu, Huanmin Zhang, Keji Zhao, Kairong Cui, Jiuzhou Song
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-018-4533-0

Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes
Cited by: 56
Author(s): Yuanxin Xi, Jiejun Shi, Wenqian Li, Kaori Tanaka, Kendra L. Allton, Dana Richardson, Jing Li, Hector L. Franco, Anusha Nagari, Venkat S. Malladi, Luis Della Coletta, Melissa S. Simper, Khandan Keyomarsi, Jianjun Shen, Mark T. Bedford, Xiaobing Shi, Michelle C. Barton, W. Lee Kraus, Wei Li, Sharon Y.R. Dent
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-015-1251-8

Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum
Cited by: 33
Author(s): Bin-Bin Xie, Dan Li, Wenhao Shi, Qi‐Long Qin, Xiaowei Wang, Jin-Cheng Rong, Caiyun Sun, Feng Huang, Xiying Zhang, Xiaowei Dong, Xiu-Lan Chen, Biao Zhou, Yuzhong Zhang, Xiao‐Yan Song
Software Mentions: 2
Published: over 11 years ago

10.1186/s12864-018-4463-x

The aquatic animals’ transcriptome resource for comparative functional analysis
Cited by: 4
Author(s): Chih‐Hung Chou, Hsi‐Yuan Huang, Wei‐Chih Huang, Sheng Da Hsu, Chung-Der Hsiao, Chia-Yu Liu, Yu-Hung Chen, Yuchen Liu, Wei Huang, Meng-Lin Lee, Yi‐Chang Chen, Hsien-Da Huang
Software Mentions: 2
Published: over 8 years ago