Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: TopHat

https://packages.ecosyste.ms/registries/pypi.org/packages/TopHat

TopHat Platform
3 versions
Latest release: about 12 years ago
9 downloads last month

Papers Mentioning TopHat 5,017

10.1371/journal.pcbi.1003314
Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data
Cited by: 75
Author(s): Ridvan Eksi, Hong Dong Li, Rajasree Menon, Yuchen Wen, Gilbert S. Omenn, Matthias Kretzler, Yuanfang Guan
Software Mentions: 1
Published: about 11 years ago
10.1038/s41598-018-33204-5
Transcriptomic analysis reveals a controlling mechanism for NLRP3 and IL-17A in dextran sulfate sodium (DSS)-induced colitis
Cited by: 15
Author(s): Ting-Yun Lin, Shu‐Yi Yin, Pei-Wen Hsiao, Ning‐Sun Yang, I-Jen Wang
Software Mentions: 1
Published: about 6 years ago
10.1038/s41598-018-33407-w
Effects of dietary protein restriction followed by realimentation on growth performance and liver transcriptome alterations of lamb
Cited by: 12
Author(s): Kai Cui, B. Wang, Ma T, B. W., Naifeng Zhang, Yan Tu, Qiyu Diao
Software Mentions: 1
Published: about 6 years ago
10.1186/s12974-018-1071-2
Chi3l3: a potential key orchestrator of eosinophil recruitment in meningitis induced by Angiostrongylus cantonensis
Cited by: 16
Author(s): Shuo Wan, Xiaoqiang Sun, Fengshi Wu, Zilong Yu, Lifu Wang, Dan-Dan Lin, Zhengyu Li, Zhongdao Wu
Software Mentions: 1
Published: almost 7 years ago
10.1371/journal.pbio.1000590
Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq
Cited by: 193
Author(s): Susan E. Lott, Jacqueline E. Villalta, Gary P. Schroth, Shujun Luo, Leath A. Tonkin, Michael B. Eisen
Software Mentions: 1
Published: almost 14 years ago
10.1186/s12974-015-0260-5
RNA sequencing reveals distinct mechanisms underlying BET inhibitor JQ1-mediated modulation of the LPS-induced activation of BV-2 microglial cells
Cited by: 36
Author(s): Kyoung Hwa Jung, Amitabh Das, Jin Choul Chai, Sun Hwa Kim, Nishi Morya, Kyoung Sun Park, Young Seek Lee, Young Gyu Chai
Software Mentions: 1
Published: over 9 years ago
10.1371/journal.pbio.3000630
Cell-autonomous light sensitivity via Opsin3 regulates fuel utilization in brown adipocytes
Cited by: 33
Author(s): Mari Sato, Taichi Tsuji, Kunyan Yang, Xiaozhi Ren, Jonathan M. Dreyfuss, Tian Lian Huang, Chih-Hao Wang, Farnaz Shamsi, Luiz O. Leiria, Matthew D. Lynes, King Wai Yau, Yu–Hua Tseng
Software Mentions: 1
Published: almost 5 years ago
10.1038/s41598-018-33891-0
Identification of Differentially Expressed Non-coding RNA in Porcine Alveolar Macrophages from Tongcheng and Large White Pigs Responded to PRRSV
Cited by: 19
Author(s): Yueran Zhen, Fengqing Wang, Wan Liang, Jianjian Liu, Guangzhen Gao, Yan Wang, Xuewen Xu, Qiuju Su, Qingde Zhang, Bang Liu
Software Mentions: 1
Published: about 6 years ago
10.1038/s41598-020-71002-0
Global identification of a marine diatom long noncoding natural antisense transcripts (NATs) and their response to phosphate fluctuations
Cited by: 13
Author(s): Maria Helena Cruz de Carvalho, Chris Bowler
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pbio.3000294
Hidden genomic evolution in a morphospecies—The landscape of rapidly evolving genes in Tetrahymena
Cited by: 23
Author(s): Jie Xiong, Wentao Yang, Kai Chen, Chuanqi Jiang, Yang Ma, Xiaocui Chai, Guangwu Yan, Guangying Wang, Dan Yuan, Yifan Liu, Shelby L. Bidwell, Nikhat Zafar, Michalis Hadjithomas, Vivek Krishnakumar, Robert S. Coyne, Eduardo Orias, Wei Miao
Software Mentions: 1
Published: over 5 years ago
10.1038/s41598-020-71968-x
Identification of effector candidate genes of Rhizoctonia solani AG-1 IA expressed during infection in Brachypodium distachyon
Cited by: 4
Author(s): Sobhy S. H. Abdelsalam, Yusuke Kouzai, Megumi Watanabe, Komaki Inoue, Hidenori Matsui, Mikihiro Yamamoto, Yuki Ichinose, Kazuhiro Toyoda, Seiji Tsuge, Keiichi Mochida, Yoshiteru Noutoshi
Software Mentions: 1
Published: about 4 years ago
10.1038/s41598-020-71701-8
Humic acid enhances heat stress tolerance via transcriptional activation of Heat-Shock Proteins in Arabidopsis
Cited by: 28
Author(s): Joon‐Yung Cha, Sang-Ho Kang, Imdad Ali, Sang Cheol Lee, Myung Geun Ji, Song Yi Jeong, Gyeong-Im Shin, Min Gab Kim, Jong-Rok Jeon, Woe‐Yeon Kim
Software Mentions: 1
Published: about 4 years ago
10.1186/s12974-014-0173-8
Molecular profile of cochlear immunity in the resident cells of the organ of Corti
Cited by: 53
Author(s): Qunfeng Cai, R. Robert Vethanayagam, Sheng‐Yung Yang, Jonathan Bard, Jennifer Jamison, David Cartwright, Yan Dong, Bo Hu
Software Mentions: 1
Published: about 10 years ago
10.1186/s12974-018-1240-3
Long noncoding RNA MALAT1 in exosomes drives regenerative function and modulates inflammation-linked networks following traumatic brain injury
Cited by: 124
Author(s): Niketa A. Patel, Lauren D. Moss, Jea-Young Lee, Naoki Tajiri, Sandra Acosta, Charles E. Hudson, Sajan Parag, Denise R. Cooper, Cesario V. Borlongan, Paula C. Bickford
Software Mentions: 1
Published: over 6 years ago
10.1038/s41598-020-73713-w
Rosettes integrity protects Plasmodium vivax of being phagocytized
Cited by: 13
Author(s): Letusa Albrecht, Stefanie Costa Pinto Lopes, Ana Beatriz Iung Enembreck da Silva, Vanessa Carneiro Barbosa, Rodrigo Pm de Almeida, André Machado Siqueira, Juliana Almeida Leite, Najara Bittencourt, Hellen Geremias dos Santos, Catarina Bourgard, Luiz Fernando Cardoso Garcia, Ana Carolina Andrade Vitor Kayano, Irene S. Soares, Bruce Russell, Laurent Rénia, Marcus Lacerda, Fabio T. M. Costa
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pbio.1001518
Selecting One of Several Mating Types through Gene Segment Joining and Deletion in Tetrahymena thermophila
Cited by: 78
Author(s): Marcella D. Cervantes, Eileen P. Hamilton, Jie Xiong, Michael J. Lawson, Dan Yuan, Michalis Hadjithomas, Wei Miao, Eduardo Orias
Software Mentions: 1
Published: over 11 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: over 9 years ago
10.1371/journal.pbio.3000782
Phase separation of Arabidopsis EMB1579 controls transcription, mRNA splicing, and development
Cited by: 28
Author(s): Shujun Zhang, Zhankun Li, Naizhi Chen, Yao Huang, Shanjin Huang
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pbio.2006522
H3K36 trimethylation mediated by SETD2 regulates the fate of bone marrow mesenchymal stem cells
Cited by: 65
Author(s): Lijun Wang, Ningning Niu, Li Li, Rui Shao, Huiling Ouyang, Weiguo Zou
Software Mentions: 1
Published: about 6 years ago
10.1371/journal.pbio.1000625
The Reality of Pervasive Transcription
Cited by: 379
Author(s): Michael B. Clark, Paulo Amaral, Felix Schlesinger, Marcel E. Dinger, Ryan J. Taft, John L. Rinn, Chris P. Ponting, Peter F. Stadler, Kevin V. Morris, Antonin Morillon, Joel Rozowsky, Mark Gerstein, Claes Wahlestedt, Yoshihide Hayashizaki, Piero Carninci, T Gingeras, John S. Mattick
Software Mentions: 1
Published: over 13 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: about 12 years ago
10.1038/s41598-020-76076-4
Vimentin protects differentiating stem cells from stress
Cited by: 31
Author(s): Sundararaghavan Pattabiraman, Gajendra Kumar Azad, Triana Amen, Shlomi Brielle, Jung Eun Park, Siu Kwan Sze, Eran Meshorer, Daniel Kaganovich
Software Mentions: 1
Published: about 4 years ago
10.1038/s41598-020-74852-w
Identification and dereplication of endophytic Colletotrichum strains by MALDI TOF mass spectrometry and molecular networking
Cited by: 9
Author(s): Morgane Barthélémy, Vincent Guérineau, Grégory Genta‐Jouve, Mélanie Roy, Jérôme Chave, Régis Guillot, Léonie Pellissier, Jean‐Luc Wolfender, Didier Stien, Véronique Éparvier, David Touboul
Software Mentions: 1
Published: about 4 years ago
10.1038/s41598-020-76519-y
Gene duplication, rather than epigenetic changes, drives FGF4 overexpression in KIT/PDGFRA/SDH/RAS-P WT GIST
Cited by: 8
Author(s): Milena Urbini, Annalisa Astolfi, Valentina Indio, Margherita Nannini, Angela Schipani, Maria Giulia Bacalini, Sabrina Angelini, Gloria Ravegnini, Giovanni Calice, Massimo Del Gaudio, Paola Secchiero, Paola Ulivi, Elisa Gruppioni, Maria Abbondanza Pantaleo
Software Mentions: 1
Published: about 4 years ago
10.1038/s41598-020-77604-y
Effects of dietary n-3-PUFA supplementation, post-insemination plane of nutrition and pregnancy status on the endometrial transcriptome of beef heifers
Cited by: 4
Author(s): Carla Surlis, Paul Cormican, Sinéad M. Waters, Patrick Lonergan, Kate Keogh, David Noel Doyle, David A. Kenny
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pbio.1001806
Phosphoinositide Metabolism Links cGMP-Dependent Protein Kinase G to Essential Ca2+ Signals at Key Decision Points in the Life Cycle of Malaria Parasites
Cited by: 180
Author(s): Mathieu Brochet, Mark O. Collins, Terry Smith, Eloise Thompson, Sarah Sebastian, Katrin Volkmann, Frank Schwach, Lia Chappell, Ana Gomes, Matthew Berriman, Julian C. Rayner, David A. Baker, Jyoti S. Choudhary, Oliver Billker
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pbio.3000418
Activation of the intrinsic fibroinflammatory program in adult pancreatic acinar cells triggered by Hippo signaling disruption
Cited by: 26
Author(s): Jun Li, Ming Gao, Michael Nipper, Janice Jianhong Deng, Francis E. Sharkey, Randy L. Johnson, Howard C. Crawford, Yidong Chen, Pei Wang
Software Mentions: 1
Published: about 5 years ago
10.1007/s13365-017-0596-y
Peromyscus leucopus mouse brain transcriptome response to Powassan virus infection
Cited by: 9
Author(s): Luwanika Mlera, Kimberly Meade-White, Eric Dahlstrom, Rachel Baur, Kishore Kanakabandi, Kimmo Virtaneva, Stephen F. Porcella, Marshall E. Bloom
Software Mentions: 1
Published: about 7 years ago
10.1371/journal.pbio.1001647
Analysis of the RelA:CBP/p300 Interaction Reveals Its Involvement in NF-κB-Driven Transcription
Cited by: 113
Author(s): Sulakshana Mukherjee, Marcelo Behar, Harry Birnbaum, Alexander Hoffmann, Peter E. Wright, Gourisankar Ghosh
Software Mentions: 1
Published: about 11 years ago
10.1038/s41598-020-79197-y
Effects of activation of the LINE-1 antisense promoter on the growth of cultured cells
Cited by: 3
Author(s): Takeshi Honda, Yuki Nishikawa, Kensuke Nishimura, Da Teng, Kazuhiro Takemoto, Keiji Ueda
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pbio.3000452
A hormone receptor pathway cell-autonomously delays neuron morphological aging by suppressing endocytosis
Cited by: 10
Author(s): Charlotte Richardson, Callista Yee, Kang Shen
Software Mentions: 1
Published: about 5 years ago
10.1371/journal.pbio.2004049
Reporters to mark and eliminate basal or luminal epithelial cells in culture and in vivo
Cited by: 16
Author(s): O. Sonzogni, Jennifer Haynes, Laurie A. Seifried, Yahia M. Kamel, Kai Huang, Michael D. BeGora, Faith Au Yeung, Céline Robert-Tissot, Yujing J. Heng, Xin Yuan, Gerbug M. Wulf, Ken J. Kron, Elvin Wagenblast, Mathieu Lupien, Thomas Kislinger, Gregory J. Hannon, Senthil K. Muthuswamy
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pbio.2006966
Environment-induced same-sex mating in the yeast Candida albicans through the Hsf1–Hsp90 pathway
Cited by: 17
Author(s): Guijian Guan, Tao Li, Huizhen Yue, Weihong Liang, Jiao Gong, Bing Jian, Qiushi Zheng, Amanda O. Veri, Shuru Fan, Nicole Robbins, Leah E. Cowen, Guanghua Huang
Software Mentions: 1
Published: over 5 years ago
10.1080/20002297.2019.1643205
<i>Staphylococcus aureus</i> induces COX-2-dependent proliferation and malignant transformation in oral keratinocytes
Cited by: 16
Author(s): Yuxia Wang, Shiyu Liu, Bolei Li, Yaling Jiang, Xinxuan Zhou, Jing Chen, Mingyun Li, Biao Ren, Xian Peng, Xuedong Zhou, Lei Cheng
Software Mentions: 1
Published: almost 6 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: almost 10 years ago
10.1371/journal.pbio.3000563
Mediator MED23 regulates inflammatory responses and liver fibrosis
Cited by: 7
Author(s): Zhichao Wang, Dan Cao, Chonghui Li, Lihua Min, Gang Wang
Software Mentions: 1
Published: almost 5 years ago
10.3390/plants9101298
Overexpression of OsC3H10, a CCCH-Zinc Finger, Improves Drought Tolerance in Rice by Regulating Stress-Related Genes
Cited by: 22
Author(s): So Yoon Seong, Jae Sung Shim, Seung Woon Bang, Ju-Kon Kim
Software Mentions: 1
Published: about 4 years ago
10.1038/s41598-021-83162-8
Comparative analysis of the transcriptomes of two rice subspecies during domestication
Cited by: 5
Author(s): Hongbo Pang, Qiang Chen, Yueying Li, Ze Wang, Longkun Wu, Qing Yang, Xiaoming Zheng
Software Mentions: 1
Published: almost 4 years ago
10.1038/s41598-021-83152-w
Using antisense oligonucleotides for the physiological modulation of the alternative splicing of NF1 exon 23a during PC12 neuronal differentiation
Cited by: 3
Author(s): Josep Biayna, Helena Mazuelas, Bernat Gel, Ernest Terribas, Gabrijela Dumbović, Inma Rosas, Juana Fernández‐Rodríguez, Ignacio Blanco, Elisabeth Castellanos, Meritxell Carrió, Conxi Lázaro, Eduard Serra
Software Mentions: 1
Published: almost 4 years ago
10.18632/oncotarget.17958
Identification of SRF-E2F1 fusion transcript in EWSR-negative myoepithelioma of the soft tissue
Cited by: 14
Author(s): Milena Urbini, Annalisa Astolfi, Valentina Indio, Giuseppe Tarantino, Salvatore Serravalle, Maristella Saponara, Margherita Nannini, Alessandro Gronchi, Marco Fiore, Roberta Maestro, Monica Brenca, Angelo Paolo Dei Tos, Gian Paolo Dagrada, Tiziana Negri, Silvana Pilotti, Paolo G. Casali, Guido Biasco, Andrea Pession, Silvia Stacchiotti, Maria Abbondanza Pantaleo
Software Mentions: 1
Published: over 7 years ago
10.1186/s13048-020-00664-1
Circular RNA hsa_circ_0078607 suppresses ovarian cancer progression by regulating miR-518a-5p/Fas signaling pathway
Cited by: 29
Author(s): Nan Zhang, Yue Jin, Qiubo Hu, Shanshan Cheng, Chao Wang, Zhiyou Yang, Yu Wang
Software Mentions: 1
Published: over 4 years ago
10.1038/s41598-021-84444-x
Adventitial delivery of nanoparticles encapsulated with 1α, 25-dihydroxyvitamin D3 attenuates restenosis in a murine angioplasty model
Cited by: 5
Author(s): Chuanqi Cai, Sreenivasulu Kilari, Chunrong Zhao, Avishek Singh, Michael L. Simeon, Avanish Misra, Yiqing Li, Edwin A. Takahashi, Rajiv Kumar, Sanjay Misra
Software Mentions: 1
Published: over 3 years ago
10.1186/s13048-016-0213-3
Genome-wide transcriptional regulation of estrogen receptor targets in fallopian tube cells and the role of selective estrogen receptor modulators
Cited by: 20
Author(s): Georgette Moyle-Heyrman, Matthew J. Schipma, Matthew Dean, David A. Davis, Joanna E. Burdette
Software Mentions: 1
Published: almost 9 years ago
10.1038/s41598-021-85245-y
Genome-wide transcriptome profiling uncovers differential miRNAs and lncRNAs in ovaries of Hu sheep at different developmental stages
Cited by: 13
Author(s): Samina Shabbir, Prerona Boruah, Lijuan Xie, Muhammad Fakhar‐e‐Alam Kulyar, Mohsin Nawaz, Salsabeel Yousuf, Tianyi Liu, Farhat Jabeen, Xiangyang Miao
Software Mentions: 1
Published: over 3 years ago
10.1186/1757-2215-7-17
Novel three-dimensional in vitro models of ovarian endometriosis
Cited by: 35
Author(s): Doerthe Brueggmann, Claire Templeman, Anna Starzinski‐Powitz, Nagesh Rao, Simon A. Gayther, Kate Lawrenson
Software Mentions: 1
Published: almost 11 years ago
10.18632/oncotarget.17417
Transcriptomic profiles of human foreskin fibroblast cells in response to orf virus
Cited by: 8
Author(s): Daxiang Chen, Mingjian Long, Bin Xiao, Yufeng Xiong, Huiqin Chen, Yu Chen, Zhenzhan Kuang, Ming Li, Yanni Wu, Daniel L. Rock, Daozhi Gong, Yong Wang, Hongqing He, Fang Liu, Shuhong Luo, Wenbo Hao
Software Mentions: 1
Published: over 7 years ago
10.3390/plants10050823
Transcriptional Changes of Cell Wall Organization Genes and Soluble Carbohydrate Alteration during Leaf Blade Development of Rice Seedlings
Cited by: 1
Author(s): Jae-Yeon Joo, Me-Sun Kim, Jwakyung Sung
Software Mentions: 1
Published: over 3 years ago
10.1038/s41598-021-87054-9
An EAV-HP insertion in the promoter region of SLCO1B3 has pleiotropic effects on chicken liver metabolism based on the transcriptome and proteome analysis
Cited by: 2
Author(s): Jianfei Chen, Guoying Hua, Deguo Han, Xinyue Zheng, Xianggui Dong, Shuxiang Wang, Junjiang Long, Zhangqian Zheng, Ailing Wang, Jiankui Wang, Xiaotong Wang, Xuemei Deng
Software Mentions: 1
Published: over 3 years ago
10.1038/s41598-021-88055-4
Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants
Cited by: 4
Author(s): Hangxia Jin, Xiaomin Yu, Qinghua Yang, Xujun Fu, Fengjie Yuan
Software Mentions: 1
Published: over 3 years ago
10.3390/plants9030344
Transcriptome Analysis Reveals Candidate Genes Related to Anthocyanin Biosynthesis in Different Carrot Genotypes and Tissues
Cited by: 19
Author(s): Meng Geng, Sabine K. Clausen, Søren K. Rasmussen
Software Mentions: 1
Published: over 4 years ago
10.1038/s41598-021-87784-w
Comparative transcriptome analysis of cells from different areas reveals ROS responsive mechanism at sclerotial initiation stage in Morchella importuna
Cited by: 6
Author(s): Qizheng Liu, Guangcun He, Jinkang Wei, Caihong Dong
Software Mentions: 1
Published: over 3 years ago
10.18632/oncotarget.6960
Use of HLA peptidomics and whole exome sequencing to identify human immunogenic neo-antigens
Cited by: 126
Author(s): Shelly Kalaora, Eilon Barnea, Efrat Merhavi-Shoham, Nouar Qutob, Jamie K. Teer, Nilly Shimony, Jacob Schachter, Steven A. Rosenberg, Michal J. Besser, Arie Admon, Yardena Samuels
Software Mentions: 1
Published: almost 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: over 8 years ago
10.3390/plants9091112
Transcriptomic Analysis of a Susceptible African Maize Line to Fusarium verticillioides Infection
Cited by: 9
Author(s): Humaira Lambarey, Naadirah Moola, Amy Veenstra, Shane L. Murray, Mohamed Suhail Rafudeen
Software Mentions: 1
Published: about 4 years ago
10.1038/s41598-021-91154-x
Transcriptomic landscape of early age onset of colorectal cancer identifies novel genes and pathways in Indian CRC patients
Cited by: 16
Author(s): Manish Pratap Singh, Suresh Rai, Nand Kumar Singh, Sameer Srivastava
Software Mentions: 1
Published: over 3 years ago
10.3390/plants8090302
Circular and Micro RNAs from Arabidopsis thaliana Flowers Are Simultaneously Isolated from AGO-IP Libraries
Cited by: 15
Author(s): Érika Frydrych Capelari, Guilherme Cordenonsi da Fonseca, Frank Guzmán, Rogério Margis
Software Mentions: 1
Published: about 5 years ago
10.1038/s41598-021-92282-0
Long-chain saturated fatty acids in breast milk are associated with the pathogenesis of atopic dermatitis via induction of inflammatory ILC3s
Cited by: 9
Author(s): Weng Sheng Kong, Naohiro Tsuyama, Hiroko Inoue, Yun Guo, Sho Mokuda, Asako Nobukiyo, Nobuhiro Nakatani, Fumiya Yamaide, Taiji Nakano, Yoichi Kohno, Kazutaka Ikeda, Yumiko Nakanishi, Hiroshi Ohno, Makoto Arita, Naoki Shimojo, Morio Kanno
Software Mentions: 1
Published: over 3 years ago
10.3390/plants9020204
Transcriptome and Phytochemical Analysis Reveals the Alteration of Plant Hormones, Characteristic Metabolites, and Related Gene Expression in Tea (Camellia sinensis L.) Leaves During Withering
Cited by: 16
Author(s): Ping Xu, Hui Su, Sheng Zhao, Rong Jin, Haiyan Cheng, Anan Xu, Wanyi Lai, Yin X, Yuefei Wang
Software Mentions: 1
Published: almost 5 years ago
10.18632/oncotarget.6724
<i>NTRK1</i> fusions for the therapeutic intervention of Korean patients with colon cancer
Cited by: 23
Author(s): Do Youn Park, Chan Choi, Eunah Shin, Jae Hyuk Lee, Chae Hwa Kwon, Hong Jae Jo, Hyeong Rok Kim, Hyunsung Kim, Nahmgun Oh, Ji Shin Lee, Ok Ku Park, Eok Park, Jonghoon Park, Jong Yeon Shin, Jong‐Il Kim, Jeong Sun Seo, Hee Dong Park, Joonghoon Park
Software Mentions: 1
Published: almost 9 years ago
10.3390/plants8040101
Transcriptomic Analysis of Orange Fruit Treated with Pomegranate Peel Extract (PGE)
Cited by: 19
Author(s): Imen Belgacem, Sonia Pangallo, Ahmed Abdelfattah, Flora V. Romeo, S. O. Cacciola, Maria Giulia Li Destri Nicosia, Gabriele Ballistreri, Leonardo Schena
Software Mentions: 1
Published: over 5 years ago
10.3390/plants9050596
Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat
Cited by: 10
Author(s): Behnam Derakhshani, Habtamu Ayalew, Kohei Mishina, Tsuyoshi Tanaka, Yoshihiro Kawahara, Hossein Jafary, Youko Oono
Software Mentions: 1
Published: over 4 years ago
10.1038/s41598-021-94529-2
BCG therapy is associated with long-term, durable induction of Treg signature genes by epigenetic modulation
Cited by: 9
Author(s): Ryan C Keefe, Hiroyuki Takahashi, Lý Thị Trần, Kacie J. Nelson, Nathan Ng, Willem M. Kühtreiber, Denise L. Faustman
Software Mentions: 1
Published: over 3 years ago
10.1007/s00497-019-00362-z
Comparative transcriptome analysis reveals new molecular pathways for cucumber genes related to sex determination
Cited by: 21
Author(s): Magdalena Pawełkowicz, Leszek P. Pryszcz, Agnieszka Skarzyńska, Rafał Wóycicki, Kacper Posyniak, Jacek Rymuszka, Zbigniew Przybecki, Wojciech Pląder
Software Mentions: 1
Published: almost 6 years ago
10.1007/s11105-018-1088-9
Genomic and Transcriptomic Analysis Identified Gene Clusters and Candidate Genes for Oil Content in Peanut (Arachis hypogaea L.)
Cited by: 16
Author(s): Xiaohua Wang, Ping Xu, Yin Liang, Yan Ren, Shuangling Li, Yùzhēn Shí, Thomas D. Alcock, Qing Xiong, Wei Qian, Xiaoyuan Chi, Manish K. Pandey, Rajeev K. Varshney, Ming Yüan
Software Mentions: 1
Published: over 6 years ago
10.1007/s11103-020-01005-y
Transcriptional and metabolite analysis reveal a shift in direct and indirect defences in response to spider-mite infestation in cucumber (Cucumis sativus)
Cited by: 18
Author(s): Jun He, Harro J. Bouwmeester, Marcel Dicke, Iris F. Kappers
Software Mentions: 1
Published: over 4 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
10.1111/tpj.14728
Disturbance of floral colour pattern by activation of an endogenous pararetrovirus, petunia vein clearing virus, in aged petunia plants
Cited by: 20
Author(s): Kazunori Kuriyama, Midori Tabara, Hiromitsu Moriyama, Akira Kanazawa, Hisashi Koiwa, Hideki Takahashi, Teruyuki Fukuhara
Software Mentions: 1
Published: over 4 years ago
10.1111/tpj.14976
BdWRKY38 is required for the incompatible interaction of <i>Brachypodium distachyon</i> with the necrotrophic fungus <i>Rhizoctonia solani</i>
Cited by: 15
Author(s): Yusuke Kouzai, Minami Shimizu, Komaki Inoue, Yukiko Uehara‐Yamaguchi, Kotaro Takahagi, Risa Nakayama, Takakazu Matsuura, Izumi C. Mori, Takashi Hirayama, Sobhy S. H. Abdelsalam, Yoshiteru Noutoshi, Keiichi Mochida
Software Mentions: 1
Published: about 4 years ago
10.1002/pld3.136
Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing
Cited by: 3
Author(s): Nowlan H. Freese, April R. Estrada, Ivory C. Blakley, Jinjie Duan, Ann E. Loraine
Software Mentions: 1
Published: over 5 years ago
10.1007/s00299-016-2065-0
Comparative transcriptome profiling of upland (VS16) and lowland (AP13) ecotypes of switchgrass
Cited by: 13
Author(s): Vasudevan Ayyappan, Malay C. Saha, Jyothi Thimmapuram, Venkateswara R. Sripathi, Ketaki P. Bhide, Elizabeth Fiedler, Rita K. Hayford, Venu Kalavacharla
Software Mentions: 1
Published: about 8 years ago
10.1038/s41598-021-97712-7
Toward enhanced catalytic activity of magnetic nanoparticles integrated into 3D reduced graphene oxide for heterogeneous Fenton organic dye degradation
Cited by: 10
Author(s): Fatemeh Sadegh, Nikolaos Politakos, Estíbaliz González de San Román, Oihane Sánz, Ali Reza Modarresi‐Alam, Radmila Tomovská
Software Mentions: 1
Published: about 3 years ago
10.1038/s41598-021-97787-2
Empagliflozin maintains capillarization and improves cardiac function in a murine model of left ventricular pressure overload
Cited by: 15
Author(s): Masaaki Nakao, Ippei Shimizu, Goro Katsuumi, Yohko Yoshida, Masayoshi Suda, Yuka Hayashi, Ryutaro Ikegami, Yu‐Chun Hsiao, Shujiro Okuda, Tomoyoshi Soga, Tohru Minamino
Software Mentions: 1
Published: about 3 years ago
10.18632/oncotarget.7203
Non-coding RNA LINC00857 is predictive of poor patient survival and promotes tumor progression via cell cycle regulation in lung cancer
Cited by: 46
Author(s): Lihui Wang, Yanli He, Weijun Liu, S. J. Bai, Lei Xiao, Jie Zhang, Saravana M. Dhanasekaran, Zhuwen Wang, Shanker Kalyana-Sundaram, O. Alejandro Balbin, Sudhanshu Shukla, Yi Lü, Jules Lin, Rishindra M. Reddy, Philip W. Carrott, William R. Lynch, Andrew C. Chang, Arul M. Chinnaiyan, David G. Beer, Jian Zhang, Guoan Chen
Software Mentions: 1
Published: almost 9 years ago
10.1038/s41598-021-98544-1
Prognostic association of starvation-induced gene expression in head and neck cancer
Cited by: 3
Author(s): Mareomi Hamada, Hiroaki Inaba, Kyoko Nishiyama, Sho Yoshida, Yoshiaki Yura, Michiyo Matsumoto‐Nakano, Narikazu Uzawa
Software Mentions: 1
Published: about 3 years ago
10.1038/s41598-021-99157-4
Interferon-inducible protein, IFIX, has tumor-suppressive effects in oral squamous cell carcinoma
Cited by: 3
Author(s): Shan Wang, Fang Li, Haojun Fan
Software Mentions: 1
Published: about 3 years ago
10.1093/pcp/pcu188
Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation
Cited by: 54
Author(s): Hajime Ohyanagi, Tomoyuki Takano, Shin Terashima, Mariko Kobayashi, Maasa Kanno, Kanehisa Morimoto, Hiromi Kitano, Yohei Sasaki, Misa Saito, Satomi Asano, Soichi Ozaki, Toru Kudo, Koji Yokoyama, Koichiro Aya, Keita Suwabe, Go Suzuki, Koh Aoki, Yasutaka Kubo, Masao Watanabe, Makoto Matsuoka, Kentarô Yano
Software Mentions: 1
Published: almost 10 years ago
10.1155/2014/594579
Transcriptome Sequencing in a Tibetan Barley Landrace with High Resistance to Powdery Mildew
Cited by: 26
Author(s): Xingquan Zeng, Xiaomei Luo, Yulin Wang, Qijun Xu, Lijun Bai, Hongjun Yuan, Nyima Tashi
Software Mentions: 1
Published: almost 11 years ago
10.1038/s41392-018-0030-9
TdIF1: a putative oncogene in NSCLC tumor progression
Cited by: 11
Author(s): Yujuan Zhang, Zhigang Wang, Yanqing Huang, Muying Ying, Yifan Wang, Juan Xiong, Qi Liu, Fan Cao, Rakesh Kumar Joshi, Yanling Liu, Derong Xu, Meng Zhang, Keng Yuan, Nan Zhou, James Koropatnick, Wei‐Ping Min
Software Mentions: 1
Published: about 6 years ago
10.1038/s41392-020-00273-w
Rab22a-NeoF1: a promising target for osteosarcoma patients with lung metastasis
Cited by: 5
Author(s): Kai Xie, Xinyi Zhang, Yongguang Tao
Software Mentions: 1
Published: about 4 years ago
10.1038/s41392-021-00713-1
AHR mediates the aflatoxin B1 toxicity associated with hepatocellular carcinoma
Cited by: 32
Author(s): Qing Zhu, Yarui Ma, Junbo Liang, Zhewen Wei, Mo Li, Ying Zhang, Mei Liu, Huan He, Chunfeng Qu, Jianqiang Cai, Xiaobing Wang, Yi‐Xin Zeng, Yuchen Jiao
Software Mentions: 1
Published: over 3 years ago
10.1186/1758-907X-3-9
Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection
Cited by: 121
Author(s): Zhao Zhang, William E. Theurkauf, Zhiping Weng, Phillip D. Zamore
Software Mentions: 1
Published: almost 12 years ago
10.1186/s13395-017-0122-1
Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro
Cited by: 44
Author(s): Malina D. Doynova, James F. Markworth, David Cameron‐Smith, Mark H. Vickers, Justin M. O’Sullivan
Software Mentions: 1
Published: over 7 years ago
10.1186/s13395-018-0156-z
The complexity of titin splicing pattern in human adult skeletal muscles
Cited by: 48
Author(s): Marco Savarese, Per Harald Jonson, Sanna Huovinen, Lars Paulín, Petri Auvinen, Bjarne Udd, Peter Hackman
Software Mentions: 1
Published: over 6 years ago
10.1111/pbi.13234
Transcriptional landscape of pathogen‐responsive lnc <scp>RNA</scp> s in rice unveils the role of <scp>ALEX</scp> 1 in jasmonate pathway and disease resistance
Cited by: 76
Author(s): Yang Yu, Yufan Zhou, Yan-Zhao Feng, He Huang, Jianping Lian, Yuwei Yang, Meng-Qi Lei, Yuchan Zhang, Yue‐Qin Chen
Software Mentions: 1
Published: about 5 years ago
10.1111/pbi.13000
Gene regulatory networks for lignin biosynthesis in switchgrass <i>(Panicum virgatum</i>)
Cited by: 53
Author(s): Xiaolan Rao, Xin Chen, Hui Shen, Qin Ma, Guifen Li, Yuhong Tang, María J. Peña, William S. York, Taylor P. Frazier, Scott C. Lenaghan, Xirong Xiao, Fang Chen, Richard A. Dixon
Software Mentions: 1
Published: about 6 years ago
10.18632/oncotarget.7281
MALAT1 long ncRNA promotes gastric cancer metastasis by suppressing <i>PCDH10</i>
Cited by: 89
Author(s): Ying Qi, Hong Ooi, Jun Wu, Jian Chen, Xiaoli Zhang, Sheng Tan, Qing Yu, Yuanyuan Li, Yani Kang, Hua Li, Zirui Ray Xiong, Tao Zhu, Bingya Liu, Zongshu Shao, Xiaodong Zhao
Software Mentions: 1
Published: almost 9 years ago
10.1016/j.stemcr.2013.09.005
Analysis of SOX2-Expressing Cell Populations Derived from Human Pluripotent Stem Cells
Cited by: 30
Author(s): David A. Brafman, Noel Moya, Stephanie Allen-Soltero, Thomas Fellner, Megan Robinson, Zoë L. McMillen, Terry Gaasterland, Karl Willert
Software Mentions: 1
Published: about 11 years ago
10.1016/j.stemcr.2018.01.002
Comparison of Non-human Primate versus Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes for Treatment of Myocardial Infarction
Cited by: 43
Author(s): Xin Zhao, Haodong Chen, Dan Xiao, Huaxiao Yang, Ilanit Itzhaki, Xulei Qin, Tony Chour, Aitor Aguirre, Kim A. Lehmann, Young-Kyun Kim, Praveen Shukla, Alexandra Holmström, Joe Z. Zhang, Yan Zhuge, B Ndoye, Mingtao Zhao, Evgenios Neofytou, Wolfram‐Hubertus Zimmermann, Mohit Jain, Joseph C. Wu
Software Mentions: 1
Published: almost 7 years ago
10.1111/pbi.12795
Comparative transcriptome combined with morpho-physiological analyses revealed key factors for differential cadmium accumulation in two contrasting sweet sorghum genotypes
Cited by: 92
Author(s): Juanjuan Feng, Wenbao Jia, Sulian Lv, Hexigeduleng Bao, Fangfang Miao, Xuan Zhang, Jinhui Wang, Jihong Li, Dongsheng Li, Zhu C, Shizhong Li, Yinxin Li
Software Mentions: 1
Published: over 7 years ago
10.1016/j.stemcr.2017.09.012
Oocyte-Specific Homeobox 1, Obox1, Facilitates Reprogramming by Promoting Mesenchymal-to-Epithelial Transition and Mitigating Cell Hyperproliferation
Cited by: 13
Author(s): Lijun Wu, You Wu, Bing Peng, Zhenzhen Hou, Yu Dong, Kang Chen, Mingyue Guo, Han Li, Xia Chen, Xiaochen Kou, Yanhong Zhao, Yan Bi, Yixuan Wang, Hong Wang, Rongrong Le, Lan Kang, Shaorong Gao
Software Mentions: 1
Published: about 7 years ago
10.1016/j.stemcr.2018.02.014
A Critical Role of TET1/2 Proteins in Cell-Cycle Progression of Trophoblast Stem Cells
Cited by: 35
Author(s): Stephanie Chrysanthou, Claire E. Senner, Laura Woods, Elena Fineberg, Hanneke Okkenhaug, Sarah Burge, Vicente Pérez-García, Myriam Hemberger
Software Mentions: 1
Published: over 6 years ago
10.15252/embr.201846821
The lysine‐specific methyltransferase <scp>KMT</scp> 2C/ <scp>MLL</scp> 3 regulates <scp>DNA</scp> repair components in cancer
Cited by: 84
Author(s): Θεόδωρος Ράμπιας, Dimitris Karagiannis, Margaritis Avgeris, Alexander Polyzos, Antonis Kokkalis, Zoi Kanaki, Evgenia Kousidou, Maria Tzetis, Emmanouil Kanavakis, Konstantinos Stravodimos, Kalliopi N. Manola, Gabriel E. Pantelias, Andreas Scorilas, Apostolos Klinakis
Software Mentions: 1
Published: almost 6 years ago
10.1111/pbi.12586
Phosphorus remobilization from rice flag leaves during grain filling: an RNA-seq study
Cited by: 52
Author(s): Kwanho Jeong, Abdul Baten, Daniel Le Waters, Omar Pantoja, Cécile Julia, Matthias Wissuwa, Sigrid Heuer, Tobias Kretzschmar, Terry J. Rose
Software Mentions: 1
Published: over 8 years ago
10.1002/emmm.201303573
Defective minor spliceosome <scp>mRNA</scp> processing results in isolated familial growth hormone deficiency
Cited by: 86
Author(s): Jesús Argente, Raquel Flores, Armand Gutiérrez-Arumí, Bhupendra Verma, Gabriel Ángel Martos‐Moreno, Ivon Cuscò, Ali Oghabian, Julie A. Chowen, Mikko J. Frilander, Luis A. Pérez‐Jurado
Software Mentions: 1
Published: almost 11 years ago
10.1016/j.stemcr.2020.08.003
A p53-Dependent Checkpoint Induced upon DNA Damage Alters Cell Fate during hiPSC Differentiation
Cited by: 4
Author(s): Cara Bernadette Eldridge, Finian J. Allen, Alastair Crisp, Rodrigo A. Grandy, Ludovic Vallier, Julian E. Sale
Software Mentions: 1
Published: about 4 years ago
10.15252/emmm.201910697
Role of bulge epidermal stem cells and <scp>TSLP</scp> signaling in psoriasis
Cited by: 15
Author(s): Nuria Gago-López, Liliana F. Mellor, Diego Megı́as, Guillermo Martín-Serrano, Ander Izeta, Francisco Jiménez, Erwin F. Wagner
Software Mentions: 1
Published: about 5 years ago
10.15252/emmm.201404218
<scp>MED</scp>13‐dependent signaling from the heart confers leanness by enhancing metabolism in adipose tissue and liver
Cited by: 74
Author(s): Kedryn K. Baskin, Chad E. Grueter, Christine M. Kusminski, William L. Holland, Angie L. Bookout, Santosh Satapati, Yuyao Kong, Shawn C. Burgess, Craig R. Malloy, Philipp E. Scherer, Christopher B. Newgard, Rhonda Bassel‐Duby, Eric N. Olson
Software Mentions: 1
Published: almost 10 years ago
10.1111/pbi.12985
The red bayberry genome and genetic basis of sex determination
Cited by: 49
Author(s): Hui Jia, Hui Jia, Qing Cai, Yan Wang, Haibo Zhao, Wei Yang, Guo Yun Wang, Y.H. Li, Dong Zhan, Yu Shen, Qingfeng Niu, Le Chang, Jie Qiu, Lan Zhao, Han Xie, Wan Fu, Jing Jin, Xiong Wei Li, Yun Jiao, Chao Zhou, Ting‐Yuan Tu, Chun Yan Chai, Jin Gao, Longjiang Fan, Eric van de Weg, Jun Yi Wang, Gongxun Zhong
Software Mentions: 1
Published: over 6 years ago
10.15252/emmm.202012627
<i>Nanog</i> maintains stemness of <i>Lkb1</i> ‐deficient lung adenocarcinoma and prevents gastric differentiation
Cited by: 3
Author(s): Xinyuan Tong, Yueqing Chen, Xinsheng Zhu, Yi Ye, Yun Xue, Rui Wang, Yijun Gao, Wenjing Zhang, Wei‐Qiang Gao, Lei Xiao, Haiquan Chen, Peng Zhang, Hongbin Ji
Software Mentions: 1
Published: almost 4 years ago
10.1111/pbi.12799
Development of <scp>iFOX</scp> ‐hunting as a functional genomic tool and demonstration of its use to identify early senescence‐related genes in the polyploid <i>Brassica napus</i>
Cited by: 13
Author(s): Juan Ling, Renjie Li, Chinedu Charles Nwafor, Junluo Cheng, Maoteng Li, Nansheng Chen, Jian Wu, Lu Gan, Qingyong Yang, Chao Liu, Ming Chen, Yongming Zhou, Edgar B. Cahoon, Chunyu Zhang
Software Mentions: 1
Published: over 7 years ago