Ecosyste.ms: Papers

10.1186/s13073-016-0285-0

Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins
Cited by: 55
Author(s): Chan Zhou, Samuel R. York, Jennifer Y. Chen, Joshua V. Pondick, Daniel L. Motola, Raymond T. Chung, Alan C. Mullen
Software Mentions: 11
Published: over 8 years ago

10.3390/ijms21124217

Transcriptome, Spliceosome and Editome Expression Patterns of the Porcine Endometrium in Response to a Single Subclinical Dose of Salmonella Enteritidis Lipopolysaccharide
Cited by: 6
Author(s): Łukasz Paukszto, Anita Mikołajczyk, J Jastrzebski, Marta Majewska, Kamil Dobrzyń, Marta Kieżun, Tadeusz Kamiński
Software Mentions: 11
Published: over 4 years ago

10.1002/advs.201901850

<i>Mesostigma viride</i> Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta
Cited by: 29
Author(s): Zhe Liang, Yuke Geng, Changmian Ji, Hongwu Du, Chui Eng Wong, Qian Zhang, Ye Zhang, Pingxian Zhang, Adeel Riaz, Sadaruddin Chachar, Yike Ding, Jing Wen, Yun-Wen Wu, Mingcheng Wang, Hongkun Zheng, Yanmin Wu, Viktor Demko, Lisha Shen, Han Xiao, Pengpeng Zhang, Xiaofeng Gu, Hao Yu
Software Mentions: 10
Published: about 5 years ago

10.3390/cancers12051122

The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate Cancer
Cited by: 11
Author(s): M. Friedrich, Karolin Wiedemann, Kristin Reiche, Sven-Holger Puppel, Gabriele Pfeifer, Ivonne Zipfel, Stefanie Petrou Binder, Ulrike Köhl, G Müller, Kurt Engeland, Achim Aigner, S. Füssel, M. Fröhner, Claudia Peitzsch, Anna Dubrovska, Michael Rade, Sabina Christ, S Schreiber, Jörg Hackermüller, Jörg Lehmann, Marieta Toma, Michael H. Muders, Ulrich Sommer, Gustavo Baretton, Manfred P. Wirth, Friedemann Horn
Software Mentions: 9
Published: over 4 years ago

10.18632/oncotarget.12122

Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis
Cited by: 37
Author(s): Jing Hu, Jiu Hua Xu, Lin Pang, Hongying Zhao, Feng Li, Yulan Deng, Ling Liu, Yujia Lan, Xinxin Zhang, Tingting Zhao, Chaohan Xu, Xu Chun, Yun Xiao, Xia Li
Software Mentions: 8
Published: about 8 years ago

10.1111/pbi.12958

The developmental dynamics of the <i>Populus</i> stem transcriptome
Cited by: 92
Author(s): Qing Chao, Zili Gao, Dong Zhang, Biligen-Gaowa Zhao, Fengqin Dong, Chunxiang Fu, Lijun Liu, Bai-Chen Wang
Software Mentions: 8
Published: over 6 years ago

10.1186/s12864-020-07123-7

Illuminating the dark side of the human transcriptome with long read transcript sequencing
Cited by: 76
Author(s): Richard Kuo, Yuanyuan Cheng, Runxuan Zhang, John W. Brown, Jacqueline Smith, Alan Archibald, David W. Burt
Software Mentions: 8
Published: about 4 years ago

10.18632/oncotarget.10834

Dysregulated long intergenic non-coding RNA modules contribute to heart failure
Cited by: 15
Author(s): Lin Pang, Jing Hu, Guanxiong Zhang, Xiang Li, Xinxin Zhang, Fulong Yu, Yujia Lan, Jiu Hua Xu, Bo Pang, Dong Han, Yun Xiao, Xia Li
Software Mentions: 8
Published: over 8 years ago

10.1097/j.pain.0000000000001416

Comprehensive analysis of long noncoding RNA expression in dorsal root ganglion reveals cell-type specificity and dysregulation after nerve injury
Cited by: 41
Author(s): Georgios Baskozos, J. D. K. Dawes, Jean-Sébastien Austin, Ana Antunes-Martins, Lucy A. McDermott, Alex Clark, Teodora Trendafilova, Jon Lees, Stephen B. McMahon, Jeffrey S. Mogil, Christine Orengo, David L.H. Bennett
Software Mentions: 7
Published: about 6 years ago

10.3389/fgene.2019.00309

Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions
Cited by: 26
Author(s): Simon A. Hardwick, Samuel D. Bassett, Dominik C. Kaczorowski, James Blackburn, Kirston Barton, Nenad Bartoniček, Shaun Carswell, Hagen Tilgner, Clement T. Loy, Glenda M. Halliday, Tim R. Mercer, Martin A. Smith, John S. Mattick
Software Mentions: 7
Published: over 5 years ago

10.3389/fcell.2020.593007

Exploring Additional Valuable Information From Single-Cell RNA-Seq Data
Cited by: 12
Author(s): Yunjin Li, Qiyue Xu, Duojiao Wu, Geng Chen
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13073-020-00788-5

Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation
Cited by: 10
Author(s): Shi Yang Liu, Nathan Harmston, Trudy Lee Glaser, Yunka Wong, Zheng Zhong, Babita Madan, David M. Virshup, Enrico Petretto
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0071745

Impact of Library Preparation on Downstream Analysis and Interpretation of RNA-Seq Data: Comparison between Illumina PolyA and NuGEN Ovation Protocol
Cited by: 20
Author(s): Zhifu Sun, Yan W. Asmann, Asha Nair, Yuji Zhang, Liguo Wang, Krishna R. Kalari, Aditya Bhagwate, Tiffany R. Baker, Jennifer M. Carr, Jean Pierre A. Kocher, Edith A. Perez, E. Aubrey Thompson
Software Mentions: 6
Published: over 11 years ago

10.1186/s12859-017-1594-z

Identification of long non-coding transcripts with feature selection: a comparative study
Cited by: 20
Author(s): Giovanna Maria Ventola, Teresa Maria Rosaria Noviello, Salvatore D’Aniello, Antonietta Spagnuolo, Michele Ceccarelli, Luigi Cerulo
Software Mentions: 6
Published: over 7 years ago

10.1155/2016/9185496

Lncident: A Tool for Rapid Identification of Long Noncoding RNAs Utilizing Sequence Intrinsic Composition and Open Reading Frame Information
Cited by: 12
Author(s): Siyu Han, Yanchun Liang, Ying Liu, Wei Du
Software Mentions: 6
Published: almost 9 years ago

10.7717/peerj.8548

Comprehensive analysis of long non-coding RNAs and mRNAs in skeletal muscle of diabetic Goto-Kakizaki rats during the early stage of type 2 diabetes
Cited by: 1
Author(s): Wenlu Zhang, Yunmeng Bai, Zixi Chen, Xingsong Li, Shuang Fu, Lizhen Huang, Shudai Lin, Hongli Du
Software Mentions: 6
Published: almost 5 years ago

10.3390/biomedicines9091120

Neural Precursor Cells Expanded Inside the 3D Micro-Scaffold Nichoid Present Different Non-Coding RNAs Profiles and Transcript Isoforms Expression: Possible Epigenetic Modulation by 3D Growth
Cited by: 3
Author(s): Letizia Messa, Bianca Barzaghini, Federica Rey, Cecilia Pandini, Gian Vincenzo Zuccotti, Cristina Cereda, Stephana Carelli, Manuela Teresa Raimondi
Software Mentions: 6
Published: about 3 years ago

10.3389/fgene.2020.565006

Similarities and Differences of Photosynthesis Establishment Related mRNAs and Novel lncRNAs in Early Seedlings (Coleoptile/Cotyledon vs. True Leaf) of Rice and Arabidopsis.
Cited by: 7
Author(s): Yafei Shi, Jian Chen, Xin Hou
Software Mentions: 6
Published: almost 5 years ago

10.1016/j.csbj.2019.04.012

Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts
Cited by: 23
Author(s): Isaac A. Babarinde, Yuhao Li, Andrew P. Hutchins
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0108010

LncRBase: An Enriched Resource for lncRNA Information
Cited by: 58
Author(s): Sohini Chakraborty, Aritra Deb, Ranjan Kumar Maji, Sudipto Saha, Zhumur Ghosh
Software Mentions: 6
Published: about 10 years ago

10.1186/s12864-017-3568-y

Conserved expression of transposon-derived non-coding transcripts in primate stem cells
Cited by: 41
Author(s): LeeAnn Ramsay, Maria C. Marchetto, Maxime Caron, Shu-Huang Chen, Stephan Busche, Tony Kwan, Tomi Pastinen, Fred H. Gage, Guillaume Bourque
Software Mentions: 6
Published: over 7 years ago

10.3390/genes11121500

Global Profiling of lncRNAs Expression Responsive to Allopolyploidization in Cucumis
Cited by: 7
Author(s): Panqiao Wang, Xiaqing Yu, Zhanguo Zhu, Yufei Zhai, Qinzheng Zhao, Meng Yang, Ji Li, Qunfeng Lou, Jinfeng Chen
Software Mentions: 6
Published: almost 4 years ago

10.1155/2018/8354350

Systematic Analysis of RNA Regulatory Network in Rat Brain after Ischemic Stroke
Cited by: 11
Author(s): Liu Juan, Kunshan Zhang, Bin Hu, Siguang Li, Qing Li, Yuan Luo, Yang Wang, Zhifeng Deng
Software Mentions: 6
Published: almost 7 years ago

10.3390/cells10040921

Sex-Biased lncRNA Signature in Fetal Growth Restriction (FGR)
Cited by: 2
Author(s): Aleksandra Lipka, J Jastrzebski, Łukasz Paukszto, Karol G Makowczenko, Elżbieta Łopieńska–Biernat, Marek Gowkielewicz, Ewa Lepiarczyk, Marta Wiszpolska, Mariusz Majewski, Marta Majewska
Software Mentions: 6
Published: over 3 years ago

10.1016/j.cub.2018.09.026

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis
Cited by: 35
Author(s): Ignacio E. Schor, Giovanni Bussotti, Matilda Maleš, Mattia Forneris, Rebecca R. Viales, Anton J. Enright, Eileen E. M. Furlong
Software Mentions: 6
Published: about 6 years ago

10.1093/dnares/dsz015

Uncovering the mouse olfactory long non-coding transcriptome with a novel machine-learning model
Cited by: 8
Author(s): Antônio Pedro Camargo, Thiago S. Nakahara, Luiz E R Firmino, Paulo H.M. Netto, João Batista Plácido do Nascimento, Elisa Donnard, Pedro A. F. Galante, Marcelo Falsarella Carazzolle, Bettina Malnic, Fábio Papes
Software Mentions: 6
Published: over 5 years ago

10.15252/embr.202051289

LncRNA <i>Ctcflos</i> orchestrates transcription and alternative splicing in thermogenic adipogenesis
Cited by: 16
Author(s): Andrea Bast‐Habersbrunner, Christoph Kiefer, Peter Weber, Tobias Fromme, Anna Schießl, Petra Schwalie, Bart Deplancke, Yongguo Li, Martin Klingenspor
Software Mentions: 6
Published: over 3 years ago

10.1038/srep32753

HIPSTR and thousands of lncRNAs are heterogeneously expressed in human embryos, primordial germ cells and stable cell lines
Cited by: 35
Author(s): Dinar Yunusov, Letícia Anderson, Luis DaSilva, Joanna Wysocka, Toshihiko Ezashi, R. M. Roberts, Sérgio Verjovski-Almeida
Software Mentions: 6
Published: about 8 years ago

10.3389/fcell.2021.633747

Transcriptome Analysis Reveals Differentially Expressed Genes and Long Non-coding RNAs Associated With Fecundity in Sheep Hypothalamus With Different FecB Genotypes
Cited by: 10
Author(s): Si Chen, Xiaofei Guo, Xiaoyun He, Ran Di, Xiaosheng Zhang, Jinlong Zhang, Xiangyu Wang
Software Mentions: 6
Published: over 3 years ago

10.1155/2017/6218353

Circular RNAs: Biogenesis, Function, and a Role as Possible Cancer Biomarkers
Cited by: 105
Author(s): Luka Bolha, Metka Ravnik‐Glavač, Damjan Glavač
Software Mentions: 5
Published: almost 8 years ago

10.1186/s12920-019-0596-2

Transcriptome analysis identified a novel 3-LncRNA regulatory network of transthyretin attenuating glucose induced hRECs dysfunction in diabetic retinopathy
Cited by: 14
Author(s): Jun Shao, Yunbin Zhang, Guangming Fan, Yu Xin, Yong Yao
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-017-17460-5

Integrated DNA methylome and transcriptome analysis reveals the ethylene-induced flowering pathway genes in pineapple
Cited by: 22
Author(s): Jiabin Wang, Zhiying Li, Ming Lei, Yuhua Fu, Jiaju Zhao, Meng-Fei Ao, Li Xu
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-017-14595-3

UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq
Cited by: 27
Author(s): Zhifu Sun, Asha Nair, Xianfeng Chen, Naresh Prodduturi, Junwen Wang, Jean Pierre A. Kocher
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-017-11807-8

Genomic and transcriptomic analysis of the toluene degrading black yeast Cladophialophora immunda
Cited by: 36
Author(s): Barbara Blasi, Hakim Tafer, Christina Kustor, Caroline Poyntner, Ksenija Lopandić, Katja Sterflinger
Software Mentions: 5
Published: about 7 years ago

10.1093/bib/bbz018

CAFU: a Galaxy framework for exploring unmapped RNA-Seq data
Cited by: 11
Author(s): Siyuan Chen, Chengzhi Ren, Jingjing Zhai, Jinxin Yu, Xuyang Zhao, Zelong Li, Ting Zhang, Wenlong Ma, Zhaoxue Han, Chuang Ma
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-017-14451-4

Expression and regulation of long noncoding RNAs during the osteogenic differentiation of periodontal ligament stem cells in the inflammatory microenvironment
Cited by: 13
Author(s): Qingbin Zhang, Li Chen, Shiman Cui, Yan Li, Qi Zhao, Weimin Cao, Shixiang Lai, Sanjun Yin, Zhixiang Zuo
Software Mentions: 5
Published: about 7 years ago

10.1186/s13059-014-0429-8

Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer
Cited by: 177
Author(s): Nicole M. White, Christopher R. Cabanski, Jessica Silva-Fisher, Ha X. Dang, Ramaswamy Govindan, Christopher A. Maher
Software Mentions: 5
Published: over 10 years ago

10.1186/s12985-017-0882-6

ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells
Cited by: 49
Author(s): Benxia Hu, Yongxia Huo, Liping Yang, Guijun Chen, Min‐Hua Luo, Jing Yang, Jumin Zhou
Software Mentions: 5
Published: about 7 years ago

10.3390/pathogens10091196

Nanopore Assay Reveals Cell-Type-Dependent Gene Expression of Vesicular Stomatitis Indiana Virus and Differential Host Cell Response
Cited by: 2
Author(s): Balázs Kakuk, A. Kiss, Gábor Torma, Zsolt Csabai, István Prazsák, Máté Mizik, Klára Megyeri, Dóra Tombácz, Zsolt Boldogkői
Software Mentions: 5
Published: about 3 years ago

10.1093/gigascience/giaa143

High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant <i>Monomorium pharaonis</i>
Cited by: 7
Author(s): Qionghua Gao, Zijun Xiong, Rasmus Stenbak Larsen, Long Zhang, Jie Zhao, Guo Ding, Ruoping Zhao, Chengyuan Liu, Ran Hao, Guojie Zhang
Software Mentions: 5
Published: almost 4 years ago

10.1093/gigascience/giy086

Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye
Cited by: 17
Author(s): Jang il Sohn, Kyoungwoo Nam, Hyosun Hong, Jun Mo Kim, Dajeong Lim, Kyung Tai Lee, Yoon Jung, Chang Yeon Cho, Namshin Kim, Han Ha Chai, Jin Wu Nam
Software Mentions: 5
Published: over 6 years ago

10.1074/mcp.RA118.000832

Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets
Cited by: 17
Author(s): Zhe Ren, Da Qi, Nina Pugh, Kai Li, Bo Wen, Ruo Zhou, Shaohang Xu, Siqi Liu, Andrew R. Jones
Software Mentions: 5
Published: almost 6 years ago

10.15252/msb.156172

Comprehensive assembly of novel transcripts from unmapped human RNA‐Seq data and their association with cancer
Cited by: 17
Author(s): Majid Kazemian, Min Ren, Jian-Xin Lin, Wei Liao, Rosanne Spolski, Warren J. Leonard
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0204234

Large scale changes in the transcriptome of Eisenia fetida during regeneration
Cited by: 28
Author(s): Aksheev Bhambri, Neeraj Dhaunta, Surendra Singh Patel, Mitali Hardikar, Abhishek Bhatt, Nagesh Srikakulam, Shruti Shridhar, Shamsudheen Karuthedath Vellarikkal, Rajesh Pandey, Rijith Jayarajan, Ankit Verma, Vikram Kumar, Pradeep Gautam, Yukti Khanna, Jameel Ahmed Khan, Bastian Fromm, Kevin J. Peterson, Vinod Scaria, Sridhar Sivasubbu, Beena Pillai
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0245487

Genetic mechanisms associated with floral initiation and the repressive effect of fruit on flowering in apple (Malus x domestica Borkh)
Cited by: 5
Author(s): Chris Gottschalk, Songwen Zhang, Phil Schwallier, Sean M. Rogers, Martin J. Bukovac, Steve van Nocker
Software Mentions: 5
Published: almost 4 years ago

10.3389/fgene.2019.01126

Characterization of Full-Length Transcriptome Sequences and Splice Variants of Lateolabrax maculatus by Single-Molecule Long-Read Sequencing and Their Involvement in Salinity Regulation
Cited by: 29
Author(s): Yuan Tian, Haishen Wen, Xin Qi, Xiaoyan Zhang, Shikai Liu, Bingyu Li, Yalong Sun, Jifang Li, Feng He, Wenzhao Yang, Yun Li
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-017-3817-0

lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets
Cited by: 22
Author(s): Yixiao Gong, Hsin‐Chun Huang, Yu Liang, Thomas Trimarchi, Iannis Aifantis, Aristotelis Tsirigos
Software Mentions: 5
Published: over 7 years ago

10.3389/fcimb.2016.00136

The Transcriptome of Exophiala dermatitidis during Ex-vivo Skin Model Infection
Cited by: 22
Author(s): Caroline Poyntner, Barbara Blasi, Elsa Arcalís, Ursula Mirastschijski, Katja Sterflinger, Hakim Tafer
Software Mentions: 5
Published: about 8 years ago

10.1186/s12859-018-2013-9

TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association
Cited by: 8
Author(s): Seo Won Choi, Jin Wu Nam
Software Mentions: 5
Published: almost 7 years ago

10.3389/fgene.2021.625019

Novel Non-coding RNA Analysis in Multiple Myeloma Identified Through High-Throughput Sequencing
Cited by: 5
Author(s): Minqiu Lu, Yin Wu, Wen Gao, Ying Tian, Guorong Wang, Aijun Liu, Wen-Ming Chen
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms22020787

Full-Length Transcriptome Analysis of Four Different Tissues of Cephalotaxus oliveri
Cited by: 13
Author(s): Ziqing He, Yingjuan Su, Ting Wang
Software Mentions: 5
Published: almost 4 years ago

10.3389/fnins.2016.00071

BBBomics-Human Blood Brain Barrier Transcriptomics Hub
Cited by: 28
Author(s): Krishna R. Kalari, Kevin J. Thompson, Asha Nair, Xiaojia Tang, Matthew A. Bockol, Navya Jhawar, Suresh Kumar Swaminathan, Val J. Lowe, Karunya K. Kandimalla
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.15657

An integrative transcriptomic atlas of organogenesis in human embryos
Cited by: 55
Author(s): Dave T. Gerrard, Andrew Berry, Rachel Jennings, Karen Piper Hanley, Nicoletta Bobola, Neil A. Hanley
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-018-19984-w

Comparative transcriptome analysis reveals molecular response to salinity stress of salt-tolerant and sensitive genotypes of indica rice at seedling stage
Cited by: 51
Author(s): Jun Wang, Zhu Jun, Yadong Zhang, Fangjun Fan, Wenqi Li, Fangquan Wang, Zhong WeiGong, Cailin Wang, Jie Yang
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12864-020-06784-8

The nuclear and mitochondrial genomes of Frieseomelitta varia – a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste
Cited by: 13
Author(s): Flávia Cristina de Paula Freitas, A. P. Lourenço, Francis Morais Franco Nunes, Alexandre Rossi Paschoal, Fabiano Carlos Pinto de Abreu, Fábio O. Barbin, Luana Bataglia, Carlos Antônio Mendes Cardoso-Júnior, Mário Sérgio Cervoni, Saura R. Silva, Fernanda Dalarmi, Marco Antônio Del Lama, Thiago S. Depintor, Kátia Maria Ferreira, Paula Salles Gória, Michael C. Jaskot, Denyse Cavalcante Lago, Danielle Luna˗Lucena, Lívia Maria Rosatto Moda, Leonardo Penteado Nascimento, Matheus Pedrino, Franciene Rabiço Oliveira, Fernanda C. Sanches, Douglas Elias Santos, Carolina G. Santos, Joseana Vieira, Angel Roberto Barchuk, Klaus Hartfelder, Zilá Luz Paulino Simões, M. M. G. Bitondi, Daniel Guariz Pinheiro
Software Mentions: 5
Published: over 4 years ago

10.1038/s41420-020-0263-6

Temporal transcriptome analysis of neuronal commitment reveals the preeminent role of the divergent lncRNA biotype and a critical candidate gene during differentiation
Cited by: 3
Author(s): Bharat Prajapati, Mahar Fatima, Mena Fatma, Priya Maddhesiya, Himali Arora, Teesta Naskar, Subhashree Devasenapathy, Pankaj Seth, Subrata Sinha
Software Mentions: 5
Published: over 4 years ago

10.1186/s12870-020-02702-y

Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development
Cited by: 3
Author(s): Xiaobo Zhao, Chunjuan Li, Hao Zhang, Yan Cheng, Quanxi Sun, Juan Wang, Cuiling Yuan, Shiguang Shan
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-019-6432-4

Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis
Cited by: 2
Author(s): Amita Kashyap, Adelaide Rhodes, Brent Kronmiller, Josie Berger, Ashley Champagne, Edward W. Davis, Mitchell V. Finnegan, Matthew Geniza, David A. Hendrix, Christiane V. Löhr, Vanessa M. Petro, Thomas J. Sharpton, Jackson Wells, Clinton W. Epps, Pankaj Jaiswal, Brett M. Tyler, Stephen A. Ramsey
Software Mentions: 5
Published: almost 5 years ago

10.1038/sdata.2015.51

De novo transcriptome profiling of highly purified human lymphocytes primary cells
Cited by: 34
Author(s): Raoul Jean Pierre Bonnal, Valeria Ranzani, Alberto Arrigoni, Serena Maria Curti, Ilaria Panzeri, Paola Gruarin, Sergio Abrignani, Grazisa Rossetti, Massimiliano Pagani
Software Mentions: 5
Published: about 9 years ago

10.1186/s12864-021-07615-0

Identification of the conserved long non-coding RNAs in myogenesis
Cited by: 0
Author(s): Anupam Bhattacharya, Simang Champramary, Tanya Tripathi, Debajit Thakur, Ilya Ioshikhes, Satyendra Kumar Singh, Soumyadeep Nandi
Software Mentions: 4
Published: over 3 years ago

10.1186/s12870-019-2087-1

Whole-transcriptome RNA sequencing reveals the global molecular responses and ceRNA regulatory network of mRNAs, lncRNAs, miRNAs and circRNAs in response to copper toxicity in Ziyang Xiangcheng (Citrus junos Sieb. Ex Tanaka)
Cited by: 34
Author(s): Xing-Zheng Fu, Xiaoyong Zhang, Jie-Ya Qiu, Xue Zhou, Meng Yuan, Yuan He, Chun ChangPin, Li Cao, Lili Li, Peng LiangZhi
Software Mentions: 4
Published: about 5 years ago

10.1186/s12870-020-02637-4

Revealing the full-length transcriptome of caucasian clover rhizome development
Cited by: 13
Author(s): Xiujie Yin, Kun Yi, Yihang Zhao, Yue Hu, Li Xu, Taotao He, Jiaxue Liu, Guowen Cui
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-018-4946-9

Full-length transcriptome sequences and the identification of putative genes for flavonoid biosynthesis in safflower
Cited by: 61
Author(s): Chen Jiang, Xiaohui Tang, Chaoxiang Ren, Bin Wei, Yingliang Wu, Qinghua Wu, Jin Pei
Software Mentions: 4
Published: over 6 years ago

10.1016/j.csbj.2020.11.030

The computational approaches of lncRNA identification based on coding potential: Status quo and challenges
Cited by: 22
Author(s): Jing Li, Xuan Zhang, Changning Liu
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-020-77520-1

Time-course profiling of bovine alphaherpesvirus 1.1 transcriptome using multiplatform sequencing
Cited by: 8
Author(s): Norbert Moldován, Gábor Torma, Gábor Gulyás, Ákos Hornyák, Zoltán Zádori, Victoria A Jefferson, Zsolt Csabai, Miklós Boldogkői, Dóra Tombácz, Florencia Meyer, Zsolt Boldogköi
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-020-80635-0

Differentially expressed lncRNAs in liver tissues of TX mice with hepatolenticular degeneration
Cited by: 5
Author(s): Juan Zhang, Ying Ma, Denghui Xie, Bao Yuan-cheng, Weiren Yang, Han Wang, Huaizhou Jiang, Hui Han, Ting Dong
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12865-020-00344-1

Identification of differentially expressed circulating exosomal lncRNAs in IgA nephropathy patients
Cited by: 17
Author(s): Na Guo, Qin Zhou, Xiang Huang, Jia-Kuo Yu, Qianqian Han, Baoting Nong, Yuanyan Xiong, Peifeng Liang, Jiajia Li, Min Feng, Jun Lv, Qiongqiong Yang
Software Mentions: 4
Published: over 4 years ago

10.1007/s00239-020-09939-z

A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila
Cited by: 51
Author(s): Brennen Heames, Julia Schmitz, Erich Bornberg‐Bauer
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-017-17996-6

Identification of long non-coding RNAs in the immature and mature rat anterior pituitary
Cited by: 19
Author(s): Dong-Xu Han, Xiaolong Sun, Yao Fu, Changjiang Wang, Jianbo Li, Hao Jiang, Yan Gao, Chengzhen Chen, Bao Yuan, Jiabao Zhang
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-017-15822-7

Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease
Cited by: 23
Author(s): Chao Ren, Feng Liu, Zhangyi Ouyang, Gaole An, Chenghui Zhao, Jun Shuai, Shuhong Cai, Xiaochen Bo, Wenjie Shu
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-018-37872-1

Long non-coding RNA repertoire and open chromatin regions constitute midbrain dopaminergic neuron - specific molecular signatures
Cited by: 10
Author(s): Joshua M. Gendron, Claire Sauty-Colace, Nicolas Beaume, Hugues Cartonnet, Justine Guégan, Damien Ulveling, Corinne Pardanaud-Glavieux, Ivan Moszer, Hélène Cheval, Philippe Ravassard
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-019-5895-7

Comparative physiology and transcriptome analysis allows for identification of lncRNAs imparting tolerance to drought stress in autotetraploid cassava
Cited by: 21
Author(s): Xiao Liang, Xianwen Shang, Sheng Cao, Xuewen Xie, Wendan Zeng, Lingyun Lu, Songbi Chen, Huabing Yan
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-2776-1

Long non-coding RNAs are major contributors to transcriptome changes in sunflower meiocytes with different recombination rates
Cited by: 28
Author(s): Nathalia Flórez-Zapata, M. Humberto Reyes-Valdés, Octavio Martínez
Software Mentions: 4
Published: over 8 years ago

10.1038/srep34838

lncScore: alignment-free identification of long noncoding RNA from assembled novel transcripts
Cited by: 39
Author(s): Jian Zhao, Xiaofeng Song, Kai Wang
Software Mentions: 4
Published: about 8 years ago

10.1038/s41422-020-00458-6

Mutual dependency between lncRNA LETN and protein NPM1 in controlling the nucleolar structure and functions sustaining cell proliferation
Cited by: 25
Author(s): Xianteng Wang, Xiaolin Hu, Wanlu Song, Hui Xu, Zhao Xiao, Rongxia Huang, Qing-Ran Bai, Fan Zhang, Yongzhen Chen, Yu Liu, Jau–Shiung Fang, Xin Li, Qin Shen, Haitao Zhao, Xuerui Yang
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-017-00823-3

Systematic identification and characterization of cardiac long intergenic noncoding RNAs in zebrafish
Cited by: 11
Author(s): Lei Wang, Xiao Ma, Xiaolei Xu, Yuji Zhang
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-71905-y

Whole transcriptome approach to evaluate the effect of aluminium hydroxide in ovine encephalon
Cited by: 9
Author(s): Endika Varela-Martínez, Martin Bilbao‐Arribas, Naiara Abendaño, Javier Asín, Marta Pérez, Damián F. de Andrés, Lluís Luján, Begoña M. Jugo
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.25607

lncRNA requirements for mouse acute myeloid leukemia and normal differentiation
Cited by: 47
Author(s): M. Joaquina Delás, Leah R. Sabin, Egor Dolzhenko, Simon Knott, Ester Munera Maravilla, Benjamin T. Jackson, Sophia A Wild, Tatjana Kovačević, Eva Maria Stork, Meng Zhou, Nicolas Erard, Emily Lee, David R. Kelley, Mareike Roth, Inês Barbosa, Johannes Zuber, John L. Rinn, Andrew D. Smith, Gregory J. Hannon
Software Mentions: 4
Published: about 7 years ago

10.1186/s40104-019-0340-y

Flutamide-induced alterations in transcriptional profiling of neonatal porcine ovaries
Cited by: 14
Author(s): Katarzyna Knapczyk-Stwora, Anna Nynca, Renata E. Ciereszko, Łukasz Paukszto, J Jastrzebski, Elzbieta Czaja, Patrycja Witek, Marek Koziorowski, Maria Słomczyńska
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-15-636

In depth annotation of the Anopheles gambiae mosquito midgut transcriptome
Cited by: 30
Author(s): Alejandro Padrón, Alvaro Molina-Cruz, Mariam Quiñones, José M. C. Ribeiro, Urvashi N. Ramphul, Janneth Rodrigues, Kui Shen, Ashley Haile, José L. Ramirez, Carolina Barillas‐Mury
Software Mentions: 4
Published: over 10 years ago

10.1186/s40104-021-00626-7

NORHA, a novel follicular atresia-related lncRNA, promotes porcine granulosa cell apoptosis via the miR-183-96-182 cluster and FoxO1 axis
Cited by: 16
Author(s): Yao Wang, Zengxiang Pan, Xiaohong Du, Jinbi Zhang, Honglin Liu, Qifa Li
Software Mentions: 4
Published: about 3 years ago

10.1186/s13059-016-0932-1

Single-cell analysis of long non-coding RNAs in the developing human neocortex
Cited by: 291
Author(s): Siyuan John Liu, Tomasz J. Nowakowski, Alex A. Pollen, Jan H. Lui, Max A. Horlbeck, Frank J. Attenello, Daniel He, Jonathan S. Weissman, Arnold R. Kriegstein, Aaron A. Diaz, Daniel A. Lim
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-017-3691-9

Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human
Cited by: 106
Author(s): Richard Kuo, Elizabeth Tseng, Lél Eöry, Ian R. Paton, Alan Archibald, David W. Burt
Software Mentions: 4
Published: over 7 years ago

10.1111/jcmm.16133

Identification of Smad3‐related transcriptomes in type‐2 diabetic nephropathy by whole transcriptome RNA sequencing
Cited by: 3
Author(s): Qin Zhou, Hong-Hong Guo, Chaolun Yu, Xiao‐Ru Huang, Lijun Liang, Puhua Zhang, Jia-Kuo Yu, Jizhou Zhang, Ting‐Fung Chan, Rong Ma, Hui‐Yao Lan
Software Mentions: 4
Published: almost 4 years ago

10.3390/genes11090981

PreLnc: An Accurate Tool for Predicting lncRNAs Based on Multiple Features
Cited by: 6
Author(s): Lei Cao, Yupeng Wang, Changwei Bi, Qiaolin Ye, Tongming Yin, Ning Ye
Software Mentions: 4
Published: over 4 years ago

10.1186/s12943-019-1115-y

LINC02273 drives breast cancer metastasis by epigenetically increasing AGR2 transcription
Cited by: 118
Author(s): Bingqiu Xiu, Yayun Chi, Lei Liu, Weiru Chi, Qi Zhang, Jiajian Chen, Rong Guo, Jingjing Si, Lun Li, Jian Xue, Zhi‐Ming Shao, Zhao-Hui Wu, Shenglin Huang, Jiong Wu
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12944-018-0915-1

Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue
Cited by: 19
Author(s): Guoze Wang, Kun Du, Shiyan Hu, Shiyi Chen, Xianbo Jia, Mingcheng Cai, Yu Shi, Jie Wang, Songjia Lai
Software Mentions: 4
Published: almost 6 years ago

10.3390/life10110300

Regulatory Potential of Long Non-Coding RNAs (lncRNAs) in Boar Spermatozoa with Good and Poor Freezability
Cited by: 3
Author(s): Leyland Fraser, Łukasz Paukszto, Anna Mańkowska, Paweł Brym, Przemysław Gilun, J Jastrzebski, Chandra Shekhar Pareek, Dibyendu Kumar, Mariusz Pierzchała
Software Mentions: 4
Published: about 4 years ago

10.1534/g3.114.016238

A Survey of Imprinted Gene Expression in Mouse Trophoblast Stem Cells
Cited by: 27
Author(s): J. Mauro Calabrese, Joshua Starmer, Megan D. Schertzer, Della Yee, Terry Magnuson
Software Mentions: 4
Published: over 9 years ago

10.3390/antiox9050402

Long Non-Coding RNA and mRNA Profiling in Early-Stage Bovine Embryos Treated with Glutathione
Cited by: 1
Author(s): Qihao Guo, Linlin Cui, Weijun Sun, Li Feng, Hao Huang, Xueming Zhao, Huabin Zhu, Weihua Du
Software Mentions: 4
Published: over 4 years ago

10.3389/fpls.2021.635784

Transcriptomic Analysis of Changes in Gene Expression During Flowering Induction in Sugarcane Under Controlled Photoperiodic Conditions
Cited by: 13
Author(s): João Ricardo Vieira Manechini, Paulo Henrique da Silva Santos, Elisson Romanel, Michael dos Santos Brito, Maximiliano Salles Scarpari, Stephen D. Jackson, Luciana Rossini Pinto, Renato Vicentini
Software Mentions: 4
Published: over 3 years ago

10.3390/genes10090672

PredLnc-GFStack: A Global Sequence Feature Based on a Stacked Ensemble Learning Method for Predicting lncRNAs from Transcripts
Cited by: 20
Author(s): Shuai Liu, Xiaohan Zhao, Guangyan Zhang, Weiyang Li, Feng Liu, Shichao Liu, Wen Zhang
Software Mentions: 4
Published: about 5 years ago

10.3390/genes12060896

Comparative Transcriptome Analysis Reveals Sex-Based Differences during the Development of the Adult Parasitic Wasp Cotesia vestalis (Hymenoptera: Braconidae)
Cited by: 2
Author(s): Yuenan Zhou, Pei‐Ling Yang, Shuang Xie, Min Shi, Jianhua Huang, Zhizhi Wang, Xue-Xin Chen
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-019-6163-6

PacBio single-molecule long-read sequencing shed new light on the complexity of the Carex breviculmis transcriptome
Cited by: 20
Author(s): Ke Teng, Wan Teng, Haifeng Wen, Yuesen Yue, Weier Guo, Juying Wu, Xing Fan
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-019-5832-9

A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis
Cited by: 23
Author(s): Lijun Wang, Xiaoling Jiang, Lei Wang, Wei Wang, Chunling Fu, Xin Yan, Xinxin Geng
Software Mentions: 4
Published: over 5 years ago

10.1155/2018/1264697

Identification of 170 New Long Noncoding RNAs in<i> Schistosoma mansoni</i>
Cited by: 17
Author(s): Victor Fernandes de Oliveira, Lauro A. G. Moares, Ester Alves Mota, Liana K. Jannotti-Passos, Paulo Marcos Zech Coelho, Ana Carolina Alves de Mattos, Flávia Fernanda Búbula Couto, Brian E. Caffrey, Annalisa Marsico, Renata Guerra‐Sá
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2020.603454

Identifying Candidate Genes Involved in the Regulation of Early Growth Using Full-Length Transcriptome and RNA-Seq Analyses of Frontal and Parietal Bones and Vertebral Bones in Bighead Carp (Hypophthalmichthys nobilis)
Cited by: 6
Author(s): Weiwei Luo, Ying Zhou, Junru Wang, Xin Yu, Jingou Tong
Software Mentions: 4
Published: almost 4 years ago

10.12688/f1000research.52350.2

RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction
Cited by: 6
Author(s): Thaís Ramos, Nilbson R. O. Galindo, Raúl Arias‐Carrasco, Cecília F. da Silva, Vinícius Maracaja-Coutinho, Thaís Gaudêncio do Rêgo
Software Mentions: 4
Published: over 3 years ago

10.3389/fcell.2020.00369

Coding and Non-coding RNAs: Molecular Basis of Forest-Insect Outbreaks
Cited by: 9
Author(s): Sufang Zhang, Sifan Shen, Zhihui Yang, Xiangbo Kong, Fu Liu, Zhen Zhang
Software Mentions: 4
Published: over 4 years ago

10.1093/database/baab047

OUP accepted manuscript
Cited by: 1
Author(s): Song Gu, Guangjie Zhang, Si Qin, Jiawen Dai, Zhen Song, Yingshuang Wang
Software Mentions: 4
Published: almost 4 years ago