pypi: TopHat | Projects | Ecosyste.ms: Papers

10.7554/eLife.02046

Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency
Cited by: 171
Author(s): Yul W. Yang, Ryan A. Flynn, Yong Chen, Kun Qu, Biao Wan, Kevin C. Wang, Ming Lei, Howard Y. Chang
Software Mentions: 1
Published: about 11 years ago

10.1186/s12931-019-1146-3

Defining a role for lung function associated gene GSTCD in cell homeostasis
Cited by: 5
Author(s): Amanda Henry, Kelly Probert, Ceri E. Stewart, Dhruma Thakker, Sangita Bhaker, Sheyda Azimi, Ian P. Hall, Ian Sayers
Software Mentions: 1
Published: over 5 years ago

10.1186/s12977-014-0067-y

NUCKS1, a novel Tat coactivator, plays a crucial role in HIV-1 replication by increasing Tat-mediated viral transcription on the HIV-1 LTR promoter
Cited by: 17
Author(s): Hye-Young Kim, Byeong‐Sun Choi, Sung Soon Kim, Tae-Young Roh, Jihwan Park, Choon Sik Yoon
Software Mentions: 1
Published: over 10 years ago

10.1186/s12977-015-0161-9

Human endogenous retroviruses sustain complex and cooperative regulation of gene-containing loci and unannotated megabase-sized regions
Cited by: 15
Author(s): Martin Sokol, Karen Margrethe Jessen, Finn Skou Pedersen
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-15-988

Map of open and closed chromatin domains in Drosophila genome
Cited by: 19
Author(s): Béatrice Milon, Yan Sun, Weizhong Chang, Todd Creasy, Anup Mahurkar, Amol C. Shetty, Dmitry I. Nurminsky, Maria Nurminskaya
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-14-803

A whole transcriptomal linkage analysis of gene co-regulation in insecticide resistant house flies, Musca domestica
Cited by: 41
Author(s): Ming Li, William Reid, Lee Zhang, J. G. Scott, Xiwu Gao, Michael Kristensen, Nannan Liu
Software Mentions: 1
Published: over 11 years ago

10.7554/eLife.59459

Reciprocal interaction between mesenchymal stem cells and transit amplifying cells regulates tissue homeostasis
Cited by: 12
Author(s): Junjun Jing, Jifan Feng, Jinyuan Li, Hu Zhao, Thach-Vu Ho, Jinzhi He, Yuan Yuan, Tingwei Guo, Jiahui Du, Mark M. Urata, Paul T. Sharpe, Yang Chai
Software Mentions: 1
Published: about 4 years ago

10.1186/s12284-018-0243-0

Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa
Cited by: 16
Author(s): Weiwen Kong, Li Ding, Jia Cheng, Bin Wang
Software Mentions: 1
Published: over 6 years ago

10.1186/s12284-018-0251-0

Constitutive expression of REL1 confers the rice response to drought stress and abscisic acid
Cited by: 17
Author(s): Jiayan Liang, Shujun Guo, Bo Sun, Qing Liu, Xiong-Hui Chen, Haifeng Peng, Zemin Zhang, Qingjun Xie
Software Mentions: 1
Published: over 6 years ago

10.1186/s12284-019-0273-2

Dissecting molecular mechanisms underlying salt tolerance in rice: a comparative transcriptional profiling of the contrasting genotypes
Cited by: 34
Author(s): Raheleh Mirdar Mansuri, Zahra‐Sadat Shobbar, Nadali Babaeian Jelodar, Mohammad Reza Ghaffari, Ghorbanali Nematzadeh, Saeedeh Asari
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12885-015-1844-2

SUMOylation of sPRDM16 promotes the progression of acute myeloid leukemia
Cited by: 10
Author(s): Shengfu Dong, Jieping Chen
Software Mentions: 1
Published: over 9 years ago

10.1186/s12284-019-0324-8

Mutations in the microRNA172 binding site of SUPERNUMERARY BRACT (SNB) suppress internode elongation in rice
Cited by: 9
Author(s): Hyeonso Ji, Chang‐deok Han, Gang-Seob Lee, Ki‐Hong Jung, Do-Yu Kang, Jun Seok Oh, Hyoja Oh, Kyeong-Seong Cheon, Song Lim Kim, Inchan Choi, Jeongho Baek, Kyung-Hwan Kim
Software Mentions: 1
Published: over 5 years ago

10.1186/s12284-020-00401-8

Transcriptome Sequencing and iTRAQ of Different Rice Cultivars Provide Insight into Molecular Mechanisms of Cold-Tolerance Response in Japonica Rice
Cited by: 15
Author(s): Yan Jia, Hualong Liu, Zhaojun Qu, Jin Wang, Xinpeng Wang, Zhuoqian Wang, Liang Yang, Dong Zhang, Detang Zou, Hongwei Zhao
Software Mentions: 1
Published: over 4 years ago

10.1186/s12885-017-3945-6

Assessment of piRNA biogenesis and function in testicular germ cell tumors and their precursor germ cell neoplasia in situ
Cited by: 16
Author(s): Ildar Gainetdinov, Yulia V. Skvortsova, Sofia A. Kondratieva, Alexey V. Klimov, Alexey Tryakin, Tatyana Azhikina
Software Mentions: 1
Published: about 7 years ago

10.1186/s12284-021-00454-3

Decreased Vascular Bundle 1 affects mitochondrial and plant development in rice
Cited by: 5
Author(s): Lisha Zhang, Ping Feng, Yao Deng, Wuzhong Yin, Yingchun Wan, Ting Lei, Guanghua He, Nan Wang
Software Mentions: 1
Published: about 4 years ago

10.1186/s12284-021-00473-0

The Rice GLYCINE-RICH PROTEIN 3 Confers Drought Tolerance by Regulating mRNA Stability of ROS Scavenging-Related Genes
Cited by: 17
Author(s): Jae Sung Shim, Suhyun Park, Dong-Keun Lee, Youn Shic Kim, Soo-Chul Park, Mark Christian Felipe R. Redillas, Jun Sung Seo, Ju-Kon Kim
Software Mentions: 1
Published: almost 4 years ago

10.1186/1471-2164-15-806

Dual transcriptional profiling of mice and Toxoplasma gondii during acute and chronic infection
Cited by: 168
Author(s): Kelly J. Pittman, Matthew T. Aliota, Laura J. Knoll
Software Mentions: 1
Published: over 10 years ago

10.1177/2472555217717473

Identifying Inhibitors of Inflammation: A Novel High-Throughput MALDI-TOF Screening Assay for Salt-Inducible Kinases (SIKs)
Cited by: 45
Author(s): Rachel E. Heap, Anthony G. Hope, Lesley-Anne Pearson, Kathleen M. S. E. Reyskens, Stuart P. McElroy, C. James Hastie, David W. Porter, J. Simon C. Arthur, David W. Gray, Matthias Trost
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.21835

Genome-wide analysis of circular RNAs in prenatal and postnatal muscle of sheep
Cited by: 30
Author(s): Cunyuan Li, Xiaoyue Li, Yang Yao, Qiman Ma, Wei Ni, Xiangyu Zhang, Yang Cao, Wureli Hazi, Dawei Wang, Renzhe Quan, Xiaoxu Hou, Zhijin Liu, Qianqian Zhan, Li Liu, Mengdan Zhang, Shuting Yu, Shengwei Hu
Software Mentions: 1
Published: over 7 years ago

10.1186/s12885-018-4409-3

Comprehensive gene expression analysis of canine invasive urothelial bladder carcinoma by RNA-Seq
Cited by: 49
Author(s): Shingo Maeda, Hirotaka Tomiyasu, Masamichi Tsuboi, Akiko Inoue, Genki Ishihara, Takao Uchikai, James Chambers, Kazuyuki Uchida, Tomohiro Yonezawa, Naoaki Matsuki
Software Mentions: 1
Published: almost 7 years ago

10.1126/sciadv.aba1070

The genetic architecture of a host shift: An adaptive walk protected an aphid and its endosymbiont from plant chemical defenses
Cited by: 36
Author(s): Kumar Saurabh Singh, Bartlomiej J. Troczka, Ana Duarte, Vasileia Balabanidou, Nasser Trissi, Leonela Carabajal Paladino, Petr Nguyen, Christoph Zimmer, Kyriaki Maria Papapostolou, Emma Randall, Bettina Lueke, František Marec, Emanuele Mazzoni, Martin S. Williamson, Alex Hayward, Ralf Nauen, John Vontas, Chris Bass
Software Mentions: 1
Published: almost 5 years ago

10.18632/oncotarget.13554

Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq
Cited by: 12
Author(s): Yihao Yang, Ya Zhang, Xin Qu, Junfeng Xia, Dongqi Li, Xiaojuan Li, Yu Wang, Zewei He, Li Su, Yonghong Zhou, Lin Xie, Zuozhang Yang
Software Mentions: 1
Published: about 8 years ago

10.1126/sciadv.abb4565

Viral cGAMP nuclease reveals the essential role of DNA sensing in protection against acute lethal virus infection
Cited by: 22
Author(s): Bruno Hernáez, Graciela Alonso, Iliana Georgana, Misbah El-Jesr, Rocı́o Martı́n, Kathy H.Y. Shair, Cornelius Fischer, Sascha Sauer, Carlos Maluquer de Motes, Antonio Alcamı́
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-018-4691-0

Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris
Cited by: 17
Author(s): Tatsuhiro Nomaguchi, Yoshiaki Maeda, Tomoko Yoshino, Toru Asahi, Leïla Tirichine, Chris Bowler
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2164-15-674

BAC and RNA sequencing reveal the brown planthopper resistance gene BPH15 in a recombination cold spot that mediates a unique defense mechanism
Cited by: 61
Author(s): Wentang Lv, Ba Du, Xinxin Shangguan, Yan Zhao, Yufang Pan, Lili Zhu, Yuqing He, Guangming He
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-015-1460-1

Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii
Cited by: 60
Author(s): A. Paola Zuluaga, Montserrat Solé, Haibin Lu, Elsa Góngora-Castillo, Brieanne Vaillancourt, Núria S. Coll, C. Robin Buell, Marc Valls
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-14-53

Small RNA pyrosequencing in the protozoan parasite Entamoeba histolytica reveals strain-specific small RNAs that target virulence genes
Cited by: 26
Author(s): Hanbang Zhang, Gretchen Ehrenkaufer, Neil Hall, Upinder Singh
Software Mentions: 1
Published: about 12 years ago

10.1038/sdata.2014.17

Genome-wide functional genomic and transcriptomic analyses for genes regulating sensitivity to vorinostat
Cited by: 14
Author(s): Katrina J. Falkenberg, Cathryn M. Gould, Ricky W. Johnstone, Kaylene J. Simpson
Software Mentions: 1
Published: over 10 years ago

10.1038/sdata.2014.13

Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats
Cited by: 22
Author(s): Ying Yu, Chen Zhao, Zhenqiang Su, Charles Wang, James C. Fuscoe, Weida Tong, Leming Shi
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-015-1344-4

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts
Cited by: 131
Author(s): Alison C. Testa, James K. Hane, Simon R. Ellwood, Richard P. Oliver
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-13-489

Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cows
Cited by: 24
Author(s): Cathriona Foley, Aspinas Chapwanya, Christopher J. Creevey, Fernando Narciandi, Derek W. Morris, Elaine Kenny, Paul Cormican, John J. Callanan, Cliona O’Farrelly, Kieran G. Meade
Software Mentions: 1
Published: over 12 years ago

10.1186/s12885-019-5337-6

Encapsulated miR-200c and Nkx2.1 in a nuclear/mitochondria transcriptional regulatory network of non-metastatic and metastatic lung cancer cells
Cited by: 4
Author(s): Olga D’Almeida, Omar Mothar, Esther A. Bondzie, Yolande Lieumo, Laure Tagne, Sumeet Gupta, Thomas L. Volkert, Stuart S. Levine, Jean-Bosco Tagne
Software Mentions: 1
Published: about 6 years ago

10.1186/s12885-019-5360-7

Hypoxia-induced cancer stemness acquisition is associated with CXCR4 activation by its aberrant promoter demethylation
Cited by: 25
Author(s): Nahyeon Kang, Su Yeon Choi, Tae Young Kim, Chang Dong Yeo, Chan Kwon Park, Young Kyoon Kim, Taejung Kim, Seong Beom Lee, Sug Hyung Lee, Jong Y. Park, Mi Sun Park, Hyeon Woo Yim, Seung Joon Kim
Software Mentions: 1
Published: about 6 years ago

10.1038/sdata.2017.45

A high-throughput molecular data resource for cutaneous neurofibromas
Cited by: 22
Author(s): Sara J.C. Gosline, Hubert Weinberg, Pamela Knight, Thomas Yu, Xindi Guo, Nripesh Prasad, Angela L. Jones, Shristi Shrestha, Braden Boone, Shawn Levy, Salvatore La Rosa, Annette Bakker
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-15-S12-S3

Application of quantitative trait locus mapping and transcriptomics to studies of the senescence-accelerated phenotype in rats
Cited by: 8
Author(s): Elena E. Korbolina, Nikita I. Ershov, L. O. Bryzgalov, N. G. Kolosova
Software Mentions: 1
Published: about 10 years ago

10.1038/sdata.2017.105

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes
Cited by: 51
Author(s): Ono Hiromasa, Osamu Ogasawara, Kosaku Okubo, Hidemasa Bono
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-016-2837-5

The genome-wide role of HSF-1 in the regulation of gene expression in Caenorhabditis elegans
Cited by: 119
Author(s): Jessica Brunquell, Stephanie A. Morris, Yin Lu, Feng Cheng, Sandy D. Westerheide
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-016-2780-5

Transcriptome analysis of maize resistance to Fusarium graminearum
Cited by: 37
Author(s): Yongjie Liu, Yikun Guo, Changjian Ma, Dongfeng Zhang, Chao Wang, Qin Yang
Software Mentions: 1
Published: over 8 years ago

10.18632/aging.104120

Histone methyltransferase SETD2 inhibits tumor growth via suppressing CXCL1-mediated activation of cell cycle in lung adenocarcinoma
Cited by: 13
Author(s): You Zhou, Xiao Zheng, Bin Xu, Hepu Deng, Lüjun Chen, Jingting Jiang
Software Mentions: 1
Published: over 4 years ago

10.1038/sdata.2018.283

Transcriptome and protein interaction profiling in cancer cells with mutations in histone H3.3
Cited by: 3
Author(s): Jinyeong Lim, Joo Hyun Park, Annika Baude, Jörg Fellenberg, Jozef Zustin, Florian Haller, Irene Krücken, Hyun Guy Kang, Christoph Plass, Anders M. Lindroth
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2164-14-824

The chromatin modification by SUMO-2/3 but not SUMO-1 prevents the epigenetic activation of key immune-related genes during Kaposi’s sarcoma associated herpesvirus reactivation
Cited by: 29
Author(s): Pei Ching Chang, Chia Yang Cheng, Mel Campbell, Yi Cheng Yang, Hung Wei Hsu, Ting Chang, Chia Han Chu, Yi Wei Lee, Chiu Lien Hung, Shi Mei Lai, Clifford G. Tepper, Wen Ping Hsieh, Hsei Wei Wang, Chuan Yi Tang, Wen-Ching Wang, Hsing Jien Kung
Software Mentions: 1
Published: about 12 years ago

10.1038/sdata.2019.9

The sequence and de novo assembly of Oxygymnocypris stewartii genome
Cited by: 30
Author(s): Haiping Liu, Shijun Xiao, Nan Wu, Di Wang, Yanchao Liu, Chaowei Zhou, Qiyong Liu, Ruibin Yang, Wenkai Jiang, Qiqi Liang, Wangjiu, Chi Zhang, Junhua Gong, Xiaohui Yuan, Zhenbo Mou
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2164-14-379

Alternative splicing tends to avoid partial removals of protein-protein interaction sites
Cited by: 4
Author(s): Alessio Colantoni, Valerio Bianchi, Pier Federico Gherardini, Gianpaolo Scalia Tomba, Gabriele Ausiello, Manuela Helmer-Citterich, Fabrizio Ferrè
Software Mentions: 1
Published: over 11 years ago

10.1038/s41597-019-0110-x

A draft genome for Spatholobus suberectus
Cited by: 20
Author(s): Shuangshuang Qin, Lingqing Wu, Kunhua Wei, Ying Liang, Zhijun Song, Xiaolei Zhou, Shuo Wang, Mingjie Li, Qinghua Wu, Kaijian Zhang, Yuanyuan Hui, Shuying Wang, Miao Jin, Zhongyi Zhang
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.14049

Combination treatment of prostate cancer with FGF receptor and AKT kinase inhibitors
Cited by: 20
Author(s): Shi Feng, Li‐Xiong Shao, Patricia Castro, Ilsa M. Coleman, Peter S. Nelson, Paul D. Smith, Barry R. Davies, Michael Ittmann
Software Mentions: 1
Published: about 8 years ago

10.1038/s41597-019-0139-x

Chromosome assembly of Collichthys lucidus, a fish of Sciaenidae with a multiple sex chromosome system
Cited by: 24
Author(s): Mingyi Cai, Yu Zeng, Shijun Xiao, Wanbo Li, Zhaofang Han, Fang Han, Junzhu Xiao, Fujiang Liu, Zhiyong Wang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41597-019-0149-8

Whole-exome and whole-transcriptome sequencing of canine mammary gland tumors
Cited by: 22
Author(s): Ka Kyung Kim, Byung-Joon Seung, Dohyun Kim, Hee Myung Park, Sejoon Lee, Doo Won Song, Gun-Ho Lee, Jae‐Ho Cheong, Hojung Nam, Jung-Hyang Sur, Sang Woo Kim
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-016-3232-y

Gene expression profile of intramuscular muscle in Nellore cattle with extreme values of fatty acid
Cited by: 44
Author(s): Mariana Piatto Berton, Larissa Fernanda Simielli Fonseca, Daniela F. J. Gimenez, Bruno Lapo Utembergue, Aline Silva Mello Cesar, Luiz Lehmann Coutinho, M. V. F. Lemos, Carolyn Aboujaoude, Angélica Simone Cravo Pereira, Rafael M. de O. Silva, Nedenia Bonvino Stafuzza, Fabieli Loise Braga Feitosa, Hermenegildo Lucas Justino Chiaia, Bianca Ferreira Olivieri, Elisa Peripolli, Rafael Lara Tonussi, Daniel M. Gordo, Rafael Espigolan, Adrielle Matias Ferrinho, Lenise Freitas Mueller, Lúcia Galvão de Albuquerque, Henrique Nunes de Oliveira, S. K. Duckett, Fernando Baldi
Software Mentions: 1
Published: about 8 years ago

10.1186/s12885-015-1708-9

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens
Cited by: 17
Author(s): Wei Liao, Gwen Jordaan, Phillipp Nham, Ryan T. Phan, Matteo Pelegrini, Sanjai Sharma
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-016-3122-3

Multi-omics analysis reveals regulators of the response to PDGF-BB treatment in pulmonary artery smooth muscle cells
Cited by: 22
Author(s): Jidong Chen, Xiaolei Cui, Zhengjiang Qian, Yanjiao Li, Kang Kang, Junle Qu, L i Li, Deming Gou
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-14-41

De novotranscriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity
Cited by: 98
Author(s): Luca Venturini, Alberto Ferrarini, Sara Zenoni, Giovanni Battista Tornielli, Marianna Fasoli, Silvia Dal Santo, Andrea Minio, Genny Buson, Paola Tononi, Elisa Zago, Gianpiero Zamperin, Diana Bellin, Mario Pezzotti, Massimo Delledonne
Software Mentions: 1
Published: about 12 years ago

10.1186/s12864-015-1464-x

Global liver gene expression differences in Nelore steers with divergent residual feed intake phenotypes
Cited by: 102
Author(s): P. C. Tizioto, Luiz Lehmann Coutinho, Jared E. Decker, Robert D. Schnabel, Kamila de Oliveira da Rosa, P. S. N. Oliveira, Marcela Maria de Souza, Gerson Barreto Mourão, R. R. Túllio, Amália Saturnino Chaves, Dante Pazzanese Duarte Lanna, Adhemar Zerlotini-Neto, Maurício de Alvarenga Mudadu, Jeremy F. Taylor, Luciana Correia de Almeida Regitano
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-018-5391-5

Identification of putative fecundity-related gustatory receptor genes in the brown planthopper Nilaparvata lugens
Cited by: 13
Author(s): Kui Dong Kang, Yang Pan, Lie Chen, Rui Pang, Lujun Yu, Wenwu Zhou, Zhiliang Zhu, Wenqing Zhang
Software Mentions: 1
Published: about 6 years ago

10.1038/s41597-021-00947-2

Eight soybean reference genome resources from varying latitudes and agronomic traits
Cited by: 9
Author(s): Jeffrey Shih-Chieh Chu, Bo Peng, Kun Tang, Xiao Su Yi, Huangkai Zhou, Huan Wang, Guang Li, Jiantian Leng, Nansheng Chen, Xianzhong Feng
Software Mentions: 1
Published: over 3 years ago

10.1186/s12885-015-1259-0

Role of the splicing factor SRSF4 in cisplatin-induced modifications of pre-mRNA splicing and apoptosis
Cited by: 35
Author(s): Maude Gabriel, Yves Delforge, Adeline Deward, Yvette Habraken, Benoît Hennuy, Jacques Piette, Roscoe Klinck, Benoît Chabot, Alain Colige, Charles Lambert
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep08199

The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio)
Cited by: 56
Author(s): Jiong-Tang Li, Guangyuan Hou, Xue Kong, Chunyan Li, Jianming Zeng, Hengde Li, Gao Xiao, Xiaomin Li, Xin Sun
Software Mentions: 1
Published: about 10 years ago

10.1038/srep08567

Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae
Cited by: 92
Author(s): Junhyun Jeon, Jaeyoung Choi, Gir-Won Lee, Sook‐Young Park, Aram Huh, Ralph A. Dean, Yong-Hwan Lee
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep08790

Genome-wide DNA methylome analysis reveals epigenetically dysregulated non-coding RNAs in human breast cancer
Cited by: 55
Author(s): Yongsheng Li, Yunpeng Zhang, Shengli Li, Jianping Lu, Juan Chen, Yuan Wang, Yixue Li, Juan Xu, Xia Li
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-14-794

The Drosophila early ovarian transcriptome provides insight to the molecular causes of recombination rate variation across genomes
Cited by: 19
Author(s): Andrew B. Adrian, Josep M. Comeron
Software Mentions: 1
Published: about 12 years ago

10.1038/srep09170

ANGPTL2 increases bone metastasis of breast cancer cells through enhancing CXCR4 signaling
Cited by: 43
Author(s): Tetsuro Masuda, Motoyoshi Endo, Yutaka Yamamoto, Haruki Odagiri, Tsuyoshi Kadomatsu, Takayuki Nakamura, Hironori Tanoue, Hitoshi Ichikawa, Masaki Yugami, Keishi Miyata, Jun Morinaga, Haruki Horiguchi, Ikuyo Motokawa, Kazutoyo Terada, M. Morioka, Ichiro Manabe, Hirotaka Iwase, Hiroshi Mizuta, Yuichi Oike
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep10294

MicroRNA-23b Promotes Avian Leukosis Virus Subgroup J (ALV-J) Replication by Targeting IRF1
Cited by: 54
Author(s): Zhenhui Li, Biao Chen, Mei Feng, Hongjia Ouyang, Ming Zheng, Qiao Ye, Qinghua Nie, Xiquan Zhang
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep10205

The pluripotency factor NANOG promotes the formation of squamous cell carcinomas
Cited by: 33
Author(s): Adelaida R. Palla, Daniela Piazzolla, Noelia Alcázar, Marta Cañamero, Osvaldo Graña, Gonzalo Goméz-López, Orlando Domı́nguez, Marta Dueñas, Jesús M. Paramio, Manuel Serrano
Software Mentions: 1
Published: almost 10 years ago

10.18632/oncotarget.21460

Identification of <i>SPOP</i> related metabolic pathways in prostate cancer
Cited by: 12
Author(s): Min Yan, Huan Qi, Jia Li, Guozhu Ye, Yaping Shao, Tongming Li, Jing Liu, Hulin Piao, Guowang Xu
Software Mentions: 1
Published: over 7 years ago

10.1038/srep10651

Cellular microRNA miR-26a suppresses replication of porcine reproductive and respiratory syndrome virus by activating innate antiviral immunity
Cited by: 42
Author(s): Xiaojuan Jia, Yuhai Bi, Jing Li, Qing Xie, Hanchun Yang, Wenjun Liu
Software Mentions: 1
Published: over 9 years ago

10.1038/srep09737

Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress
Cited by: 58
Author(s): Antonis Giannakakis, Jingxian Zhang, Piroon Jenjaroenpun, Srikanth Nama, Norliyana Zainolabidin, Mei Yee Aau, Aliaksandr A. Yarmishyn, Candida Vaz, Anna V. Ivshina, Oleg V. Grinchuk, Mathijs Voorhoeve, Leah A. Vardy, Prabha Sampath, Vladimir A. Kuznetsov, Igor V. Kurochkin, Ernesto Guccione
Software Mentions: 1
Published: over 9 years ago

10.18632/aging.101082

Aging is associated with an expansion of CD49fhi mammary stem cells that show a decline in function and increased transformation potential
Cited by: 12
Author(s): Qian Dong, Hui Gao, Yuanshuo Shi, Fuchuang Zhang, Xiang Gu, Anqi Wu, Danhan Wang, Yuanhong Chen, Abhik Bandyopadhyay, I‐Tien Yeh, Benjamin J. Daniel, Yidong Chen, Yi Zou, Vivienne I. Rebel, Christi A. Walter, Jianxin Lü, Changjiang Huang, LuZhe Sun
Software Mentions: 1
Published: over 8 years ago

10.1038/srep11207

Non-coding RNAs derived from an alternatively spliced REST transcript (REST-003) regulate breast cancer invasiveness
Cited by: 10
Author(s): Nan Sook Lee, Oleg V. Evgrafov, Tade Souaiaia, Adrineh Bonyad, Jennifer Herstein, Joo Yeun Lee, Jihong Kim, Yan Ning, Marcos Sixto, Andrew C. Weitz, Heinz‐Josef Lenz, Kai Wang, James A. Knowles, Michael F. Press, Paul M. Salvaterra, K. Kirk Shung, Robert H. Chow
Software Mentions: 1
Published: over 9 years ago

10.7554/eLife.03528

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq
Cited by: 260
Author(s): Julie L. Aspden, Ying Chen Eyre-Walker, Roger Phillips, Unum Amin, Muhammad Ali Mumtaz, Michèle Brocard, Juan-Pablo Couso
Software Mentions: 1
Published: over 10 years ago

10.1038/srep12335

Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples
Cited by: 54
Author(s): Stefan Graw, Richard Meier, Kay Minn, Clark Bloomer, Andrew K. Godwin, Brooke L. Fridley, Anda Vlad, Peter Beyerlein, Jeremy Chien
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-018-4529-9

Effects of a wide range of dietary forage-to-concentrate ratios on nutrient utilization and hepatic transcriptional profiles in limit-fed Holstein heifers
Cited by: 16
Author(s): Haitao Shi, Jun Zhang, Shengli Li, Shoukun Ji, Zhijun Cao, Hongtao Zhang, Yajing Wang
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-015-1760-5

Identification and transcriptomic profiling of genes involved in increasing sugar content during salt stress in sweet sorghum leaves
Cited by: 113
Author(s): Na Sui, Zhen Yang, Mingli Liu, Baoshan Wang
Software Mentions: 1
Published: over 9 years ago

10.1038/srep12922

The human papillomavirus (HPV) E7 protein antagonises an Imiquimod-induced inflammatory pathway in primary human keratinocytes
Cited by: 29
Author(s): Kathryn H. Richards, Christopher W. Wasson, Oliver Watherston, Rosella Doble, G. Eric Blair, Miriam Wittmann, Andrew Macdonald
Software Mentions: 1
Published: over 9 years ago

10.1038/srep13074

Integrated analysis of miRNA/mRNA network in placenta identifies key factors associated with labor onset of Large White and Qingping sows
Cited by: 12
Author(s): Huanan Li, Bin Wu, Junnan Geng, Jiawei Zhou, Rong Zheng, Jin Choul Chai, Fenge Li, Jian Peng, Siwen Jiang
Software Mentions: 1
Published: over 9 years ago

10.1038/srep13059

Transcriptomic Analysis of the Regulation of Rhizome Formation in Temperate and Tropical Lotus (Nelumbo nucifera)
Cited by: 89
Author(s): Mei Yang, Liming Zhu, Cheng Pan, Liming Xu, Yanling Liu, Weidong Ke, Pingfang Yang
Software Mentions: 1
Published: over 9 years ago

10.1038/srep13208

SRSF1 and hnRNP H antagonistically regulate splicing of COLQ exon 16 in a congenital myasthenic syndrome
Cited by: 31
Author(s): Mohammad Alinoor Rahman, Yoshiteru Azuma, Farhana Nasrin, Jun Takeda, Mohammad Nazim, Khalid Ahsan, Akio Matsubara, Andrew G. Engel, Kinji Ohno
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-12-448

A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing
Cited by: 86
Author(s): Congying Chen, Huashui Ai, Jun Ren, Wanbo Li, Pinghua Li, Ruimin Qiao, Jing Ouyang, Ming Yang, Junwu Ma, Lusheng Huang
Software Mentions: 1
Published: over 13 years ago

10.1038/srep13750

Whole genome and transcriptome sequencing of matched primary and peritoneal metastatic gastric carcinoma
Cited by: 65
Author(s): Jie Zhang, Jiawen Huang, Yixuan Chen, Fei Yuan, H. Zhang, Feng Yan, M. J. Wang, G. Wang, Mingwan Su, Guankun Lu, Yi Huang, Hong Jie Dai, Jun Ji, J. N. Zhang, Yannan Jiang, S. J. Chen, Zhenggang Zhu, Yingyan Yu
Software Mentions: 1
Published: over 9 years ago

10.1038/srep13885

In vivo Monitoring of Transcriptional Dynamics After Lower-Limb Muscle Injury Enables Quantitative Classification of Healing
Cited by: 22
Author(s): Carlos A. Aguilar, Anna Shcherbina, Darrell O. Ricke, Ramona Pop, Christopher T. Carrigan, Casey A. Gifford, Maria L. Urso, Melissa A. Kottke, Alexander Meissner
Software Mentions: 1
Published: over 9 years ago

10.7554/eLife.03913

Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid
Cited by: 11
Author(s): Jia Wang, Wen Yao, Dan Zhu, Weibo Xie, Qifa Zhang
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-14-201

Xylem transcription profiles indicate potential metabolic responses for economically relevant characteristics of Eucalyptusspecies
Cited by: 29
Author(s): Marcela Salazar, Leandro Costa do Nascimento, Eduardo Leal Oliveira Camargo, Danieli Cristina Gonçalves, Jorge Lepikson Neto, Wesley Leoricy Marques, Paulo José Pereira Lima Teixeira, Piotr A. Mieczkowski, Jorge Maurı́cio Costa Mondego, Marcelo Falsarella Carazzolle, Ana Carolina Deckmann, Gonçalo Amarante Guimarães Pereira
Software Mentions: 1
Published: almost 12 years ago

10.1038/srep15184

The conservation and signatures of lincRNAs in Marek’s disease of chicken
Cited by: 41
Author(s): Yanghua He, Yi Ding, Fei Zhan, Huanmin Zhang, Bo Han, Gangqing Hu, Keji Zhao, Ning Yang, Ying Yu, Mao Li, Jiuzhou Song
Software Mentions: 1
Published: over 9 years ago

10.1038/srep16132

Integrated analysis of microRNA and mRNA expression profiles in abdominal adipose tissues in chickens
Cited by: 54
Author(s): Huang Hu, R. R. Liu, Guiping Zhao, Q.H. Li, Maiqing Zheng, J. J. Zhang, S. F. Li, Ling Zhong, Jian Kang Wen
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-019-6197-9

Transcriptome profiling analysis of sex-based differentially expressed mRNAs and lncRNAs in the brains of mature zebrafish (Danio rerio)
Cited by: 16
Author(s): Wenliang Yuan, Shouwen Jiang, Dan Sun, Zhichao Wu, Wei Cai, Chaoxu Dai, Linhua Jiang, Syd S. Peng
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-017-3841-0

Genome-wide comparative transcriptome analysis of CMS-D2 and its maintainer and restorer lines in upland cotton
Cited by: 35
Author(s): Jianyong Wu, Meng Zhang, Bingbing Zhang, Xuexian Zhang, Liping Guo, Ting Qi, Hailin Wang, Jinfa Zhang, Chaozhu Xing
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.08413

Generation of an expandable intermediate mesoderm restricted progenitor cell line from human pluripotent stem cells
Cited by: 25
Author(s): Nathan Kumar, James Richter, Josh Cutts, Kevin T. Bush, Cleber A. Trujillo, Sanjay K. Nigám, Terry Gaasterland, David A. Brafman, Karl Willert
Software Mentions: 1
Published: over 9 years ago

10.18632/aging.101032

The progeroid gene BubR1 regulates axon myelination and motor function
Cited by: 22
Author(s): Chan Il Choi, Ki Hyun Yoo, S. M. Qasim Hussaini, Byeong Tak Jeon, John Welby, Haiyun Gan, Isobel A. Scarisbrick, Zhiguo Zhang, Darren J. Baker, Jan M. van Deursen, Moses Rodriguez, Mi Hyeon Jang
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-015-1594-1

Genomic landscape of rat strain and substrain variation
Cited by: 84
Author(s): Roel Hermsen, Joep de Ligt, Wim Spee, Francis Blokzijl, Sebastian Schäfer, Eleonora Adami, Sander Boymans, Stephen C. Flink, Ruben van Boxtel, Robin H. van der Weide, Tim Aitman, Norbert Hübner, Marieke Simonis, Boris Tabakoff, Victor Guryev, Edwin Cuppen
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-015-2313-7

What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual
Cited by: 27
Author(s): Lynsey K. Whitacre, P. C. Tizioto, JaeWoo Kim, Tad S. Sonstegard, Steven G. Schroeder, L. J. Alexander, Juan F. Medrano, Robert D. Schnabel, Jeremy F. Taylor, Jared E. Decker
Software Mentions: 1
Published: about 9 years ago

10.7554/eLife.40392

Wnt11 directs nephron progenitor polarity and motile behavior ultimately determining nephron endowment
Cited by: 42
Author(s): Lori L. O’Brien, Alexander N. Combes, Kieran M. Short, Nils O. Lindström, Peter H. Whitney, Luise A. Cullen‐McEwen, Adler Ju, Ahmed Abdelhalim, Odyssé Michos, John F. Bertram, Ian Smyth, Melissa H. Little, Andrew P. McMahon
Software Mentions: 1
Published: about 6 years ago

10.1038/srep17383

RBFOX3/NeuN is Required for Hippocampal Circuit Balance and Function
Cited by: 50
Author(s): Hanying Wang, Pei-Fen Hsieh, De-Fong Huang, Pey-Shyuan Chin, Chih-Hsuan Chou, Chun-Che Tung, Shin-Yuan Chen, Li-Jen Lee, Susan Shur‐Fen Gau, Hsiang‐Po Huang
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2407-14-842

Dexrazoxane may prevent doxorubicin-induced DNA damage via depleting both Topoisomerase II isoforms
Cited by: 118
Author(s): Shiwei Deng, Tao Yan, Cathleen Jendrny, Andrea Nemecek, Mladen Vincetic, Ute Gödtel-Armbrust, Leszek Wojnowski
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-017-4077-8

Comparative transcriptome analysis of cotton fiber development of Upland cotton (Gossypium hirsutum) and Chromosome Segment Substitution Lines from G. hirsutum × G. barbadense
Cited by: 45
Author(s): Pengtao Li, Mi Wang, Quánwěi Lú, Qún Gě, Mamun Ur Rashid, Àiyīng Liú, Jǔwǔ Gōng, Hǎihóng Shāng, Wànkuí Gǒng, Jùnwén Lǐ, Weiwu Song, Lixue Guo, Wei Su, Shaoqi Li, Xiaoping Guo, Yùzhēn Shí, Yǒulù Yuán
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.21553

Genome-wide gene expression analysis in the amphioxus, Branchiostoma belcheri after poly (I: C) challenge using strand-specific RNA-seq
Cited by: 3
Author(s): Qi-Lin Zhang, Zhengqing Xie, Mingzhu Liang, Bang Luo, Xiuqiang Wang, Jun-Yuan Chen
Software Mentions: 1
Published: over 7 years ago

10.1038/srep19007

Comparative transcriptomic analysis uncovers the complex genetic network for resistance to Sclerotinia sclerotiorum in Brassica napus
Cited by: 113
Author(s): Jian Wu, Qing Zhao, Qingyong Yang, Han Liu, Qingyuan Li, Xinqi Yi, Yan Cheng, Liang Guo, Chuchuan Fan, Yongming Zhou
Software Mentions: 1
Published: about 9 years ago

10.1038/srep19349

Comparative transcriptome analysis highlights the crucial roles of photosynthetic system in drought stress adaptation in upland rice
Cited by: 53
Author(s): Zhengfeng Zhang, Yuanyuan Li, Benze Xiao
Software Mentions: 1
Published: about 9 years ago

10.1038/srep20270

Transcriptional comparison of human induced and primary midbrain dopaminergic neurons
Cited by: 39
Author(s): Ninuo Xia, Pengbo Zhang, Fang Fang, Zhengyuan Wang, Megan Rothstein, Benjamin Angulo, Rosaria Chiang, James Taylor, Renee A. Reijo Pera
Software Mentions: 1
Published: about 9 years ago

10.1038/srep20376

Negative regulation of initial steps in skeletal myogenesis by mTOR and other kinases
Cited by: 5
Author(s): Raphael A. Wilson, Jing Liu, Lin Xu, James Annis, Sara Helmig, Gregory L. Moore, Casey Timmerman, Carla Grandori, Yanbin Zheng, Stephen X. Skapek
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2164-12-628

Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis
Cited by: 67
Author(s): Alessandro Guida, Claudia Lindstädt, Sarah Maguire, Chen Ding, Desmond G. Higgins, Nicola Corton, Matthew Berriman, Geraldine Butler
Software Mentions: 1
Published: about 13 years ago

10.1038/srep20715

Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network
Cited by: 58
Author(s): Xiwen Xu, Xionghui Zhou, Ruiru Wang, Wenlei Peng, Yue An, Lingling Chen
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-016-2716-0

Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance
Cited by: 39
Author(s): Yadong Huang, Lin Li, Kevin P. Smith, Gary J. Muehlbauer
Software Mentions: 1
Published: almost 9 years ago

Projects: pypi: TopHat

Papers Mentioning TopHat 5,017