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

10.7554/eLife.56273
SynGAP isoforms differentially regulate synaptic plasticity and dendritic development
Cited by: 50
Author(s): Yasuhisa Araki, Ingie Hong, Timothy R Gamache, Shaowen Ju, Leonardo Collado‐Torres, Joo Heon Shin, Richard L. Huganir
Software Mentions: 1
Published: over 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
10.1186/s12864-018-4897-1
Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies
Cited by: 87
Author(s): Sang-Goo Shin, Jena Jeong, Jae Yun Lim, Tae-Wook Kim, June Hyun Park, Ju-Kon Kim, Chanseok Shin
Software Mentions: 1
Published: over 6 years ago
10.3390/microorganisms7100375
Active Fungal Communities in Asymptomatic Eucalyptus grandis Stems Differ between a Susceptible and Resistant Clone
Cited by: 5
Author(s): Mandy Messal, Bernard Slippers, Sanushka Naidoo, Oliver Bezuidt, Martin Kemler
Software Mentions: 1
Published: about 5 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
10.7554/eLife.46426
Antagonistic interaction between Ezh2 and Arid1a coordinates root patterning and development via Cdkn2a in mouse molars
Cited by: 13
Author(s): Junjun Jing, Jifan Feng, Jingyuan Li, Xia Han, Jinzhi He, Thach-Vu Ho, Jiahui Du, Xuedong Zhou, Mark M. Urata, Yang Chai
Software Mentions: 1
Published: over 5 years ago
10.1038/s41379-020-0630-0
IGF2BP1 is the first positive marker for anaplastic thyroid carcinoma diagnosis
Cited by: 24
Author(s): Jacob Haase, Danny Misiak, Marcus Bauer, Nikolaos Pazaitis, Juliane Braun, Rebecca Pötschke, Alexander Mensch, Jessica L. Bell, Henning Dralle, Udo Siebolts, Claudia Wickenhauser, Kerstin Lorenz, Stefan Hüttelmaier
Software Mentions: 1
Published: almost 4 years ago
10.1186/1471-2164-15-182
Transcriptomic analysis of differentially expressed genes in the Ras1CA-overexpressed and wildtype posterior silk glands
Cited by: 14
Author(s): Li Ma, Qian Ma, Xuan Li, Leilei Cheng, Kai Li, Sheng Li
Software Mentions: 1
Published: over 10 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: almost 9 years ago
10.1186/s12864-016-2961-2
High concentrations of atmospheric ammonia induce alterations of gene expression in the breast muscle of broilers (Gallus gallus) based on RNA-Seq
Cited by: 37
Author(s): Bao Yi, Liang Chen, Renna Sa, Ruqing Zhong, Huan Xing, Hongfu Zhang
Software Mentions: 1
Published: over 8 years ago
10.1186/1471-2164-16-S12-S3
Detection of differentially methylated regions from bisulfite-seq data by hidden Markov models incorporating genome-wide methylation level distributions
Cited by: 44
Author(s): Yutaka Saitô, Toutai Mituyama
Software Mentions: 1
Published: almost 9 years ago
10.18632/oncotarget.14973
LncSubpathway: a novel approach for identifying dysfunctional subpathways associated with risk lncRNAs by integrating lncRNA and mRNA expression profiles and pathway topologies
Cited by: 8
Author(s): Yanjun Xu, Feng Li, Tan Wu, Yingqi Xu, Haixiu Yang, Qun Dong, Meiyu Zheng, Desi Shang, Chunlong Zhang, Yunpeng Zhang, Xia Li
Software Mentions: 1
Published: almost 8 years ago
10.1186/s13229-017-0174-4
RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome
Cited by: 67
Author(s): Natasha L. Pacheco, Michael R. Heaven, Leanne M. Holt, David K. Crossman, Kristin J. Boggio, Scott A. Shaffer, Daniel Flint, Michelle L. Olsen
Software Mentions: 1
Published: about 7 years ago
10.3389/fgene.2019.00068
Genomic and Transcriptomic Analysis of Amoebic Gill Disease Resistance in Atlantic Salmon (Salmo salar L.)
Cited by: 33
Author(s): Solomon Antwi Boison, Bjarne Gjerde, Borghild Hillestad, Shokouh Makvandi‐Nejad, Hooman K. Moghadam
Software Mentions: 1
Published: over 5 years ago
10.1007/s12035-020-01899-1
A Comprehensive Transcriptome Analysis Identifies FXN and BDNF as Novel Targets of miRNAs in Friedreich’s Ataxia Patients
Cited by: 8
Author(s): Julia O. Misiorek, Anna M. Schreiber, Martyna Olga Urbanek-Trzeciak, Magdalena Jazurek-Ciesiołka, Lauren Hauser, David R. Lynch, Marek Napierala, Марек Напиерала
Software Mentions: 1
Published: over 4 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: almost 9 years ago
10.7554/eLife.29677
RNG105/caprin1, an RNA granule protein for dendritic mRNA localization, is essential for long-term memory formation
Cited by: 42
Author(s): Kei Ichi Nakayama, Rie Ohashi, Yo Shinoda, Maya Yamazaki, Manabu Abe, Akihiro Fujikawa, Shuji Shigenobu, Akira Futatsugi, Masaharu Noda, Katsuhiko Mikoshiba, Teiichi Furuichi, Kenji Sakimura, Nobuyuki Shiina
Software Mentions: 1
Published: about 7 years ago
10.3389/fgene.2019.00346
Identification of DNA-Methylated CpG Islands Associated With Gene Silencing in the Adult Body Tissues of the Ogye Chicken Using RNA-Seq and Reduced Representation Bisulfite Sequencing
Cited by: 30
Author(s): Won-Jun Lim, Kyoung Hyoun Kim, Jaeyoon Kim, Seongmun Jeong, Namshin Kim
Software Mentions: 1
Published: over 5 years ago
10.3389/fgene.2018.00574
Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development
Cited by: 49
Author(s): Xuelian Ma, Hansheng Zhao, Wenying Xu, Qi You, Hengyu Yan, Zhimin Gao, Zhen Su
Software Mentions: 1
Published: almost 6 years ago
10.3389/fgene.2019.00100
Transcriptome Analysis Reveals Common and Differential Response to Low Temperature Exposure Between Tolerant and Sensitive Blue Tilapia (Oreochromis aureus)
Cited by: 27
Author(s): Tali Nitzan, Fotini Kokou, Adi Doron‐Faigenboim, Tatiana Slosman, Jakob Biran, Itzhak Mizrahi, Tatyana Zak, Ayana Benet, Avner Cnaani
Software Mentions: 1
Published: over 5 years ago
10.3389/fgene.2020.00484
Genome-Wide Identification and Evolutionary Analysis of NBS-LRR Genes From Dioscorea rotundata
Cited by: 26
Author(s): Yanmei Zhang, Min Chen, Ling Sun, Yue Wang, Jianmei Yin, Jia Liu, Xiaoqin Sun, Yue‐Yu Hang
Software Mentions: 1
Published: over 4 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: almost 9 years ago
10.3389/fgene.2014.00041
Brain-expressed 3′UTR extensions strengthen miRNA cross-talk between ion channel/transporter encoding mRNAs
Cited by: 14
Author(s): Claudia C. Wehrspaun, Chris P. Ponting, Ana C. Marques
Software Mentions: 1
Published: almost 11 years ago
10.3389/fgene.2017.00145
Identification of Splicing Quantitative Trait Loci (sQTL) in Drosophila melanogaster with Developmental Lead (Pb2+) Exposure
Cited by: 11
Author(s): Qian Wen, Katherine Gurdziel, Roger Piqué-Regi, Douglas M. Ruden
Software Mentions: 1
Published: about 7 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: almost 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: almost 9 years ago
10.1155/2018/8091283
Discovery of a Novel Microtubule Targeting Agent as an Adjuvant for Cancer Immunotherapy
Cited by: 9
Author(s): Fumi Sato-Kaneko, Xiaodong Wang, Shiyin Yao, Tadashi Hosoya, Fitzgerald Lao, Karen Messer, Minya Pu, Nikunj M. Shukla, Howard B. Cottam, Michael D. Chan, Dennis A. Carson, Maripat Corr, Tomoko Hayashi
Software Mentions: 1
Published: about 6 years ago
10.3389/fgene.2018.00178
Gene-Expression Analysis Identifies IGFBP2 Dysregulation in Dental Pulp Cells From Human Cleidocranial Dysplasia
Cited by: 3
Author(s): Stephen L Greene, Olga A. Mamaeva, David K. Crossman, Changming Lu, Mary MacDougall
Software Mentions: 1
Published: over 6 years ago
10.3389/fgene.2019.00392
GhWRKY6 Acts as a Negative Regulator in Both Transgenic Arabidopsis and Cotton During Drought and Salt Stress
Cited by: 35
Author(s): Zhi Li, Lei Li, Kehai Zhou, Yihao Zhang, Xiao Han, Yanpeng Din, Xianping Ge, Wenqiang Qin, Peng Wang, Fuguang Li, Zhiying Ma, Zhaoen Yang
Software Mentions: 1
Published: over 5 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: almost 9 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
10.1038/srep20758
Histological and transcriptome analyses of testes from Duroc and Meishan boars
Cited by: 28
Author(s): Haisheng Ding, Yan Luo, Min Liu, Jiazhu Huang, Dequan Xu
Software Mentions: 1
Published: almost 9 years ago
10.1038/srep21623
Expansion and stress responses of AP2/EREBP superfamily in Brachypodium Distachyon
Cited by: 60
Author(s): Lihong Chen, Jiapeng Han, Xianwen Deng, Shenglong Tan, Lili Li, Lun Li, Jian Zhou, Hai Peng, Guangxiao Yang, Guangyuan He, Weixiong Zhang
Software Mentions: 1
Published: almost 9 years ago
10.7554/eLife.52859
Phrenic-specific transcriptional programs shape respiratory motor output
Cited by: 10
Author(s): Alicia N Vagnozzi, Kiran Garg, Carola Dewitz, Matthew T. Moore, Jared M. Cregg, Lucie Jeannotte, Niccolò Zampieri, Lynn T. Landmesser, Polyxeni Philippidou
Software Mentions: 1
Published: almost 5 years ago
10.1038/srep21600
Fire blight disease reactome: RNA-seq transcriptional profile of apple host plant defense responses to Erwinia amylovora pathogen infection
Cited by: 32
Author(s): Tim Kamber, Jan P. Buchmann, Joël F. Pothier, Theo H. M. Smits, Thomas Wicker, Brion Duffy
Software Mentions: 1
Published: almost 9 years ago
10.1038/srep21250
L-Lactate protects neurons against excitotoxicity: implication of an ATP-mediated signaling cascade
Cited by: 74
Author(s): Pascal Jourdain, Igor Allaman, K. Rothenfusser, Hubert Fiumelli, Pierre Marquet, Pierre J. Magistretti
Software Mentions: 1
Published: almost 9 years ago
10.3389/fgene.2012.00124
Single-neuron RNA-Seq: technical feasibility and reproducibility
Cited by: 52
Author(s): Shenfeng Qiu, Shujun Luo, Oleg V. Evgrafov, Robin Li, Gary P. Schroth, Pat Levitt, James A. Knowles, Kai Wang
Software Mentions: 1
Published: almost 13 years ago
10.14336/AD.2018.1220
The Neuronal Activation of Deep Cerebellar Nuclei Is Essential for Environmental Enrichment-Induced Post-Stroke Motor Recovery
Cited by: 12
Author(s): Qun Zhang, Junfa Wu, Qili Shi, Mingyue Li, Chuanjie Wang, Xin Wang, Wenyuan Wang, Yi Wu
Software Mentions: 1
Published: almost 6 years ago
10.3389/fgene.2018.00513
Estrogen-Dependent Upregulation of Adcyap1r1 Expression in Nucleus Accumbens Is Associated With Genetic Predisposition of Sex-Specific QTL for Alcohol Consumption on Rat Chromosome 4
Cited by: 13
Author(s): John P. Spence, Jill L. Reiter, Bin Qiu, Hao Gu, Dawn Garcia, Lingling Zhang, Tamara Graves, Kent E. Williams, Paula J. Bice, Yi Zou, Zhao Lai, Weidong Yong, Tiebing Liang
Software Mentions: 1
Published: almost 6 years ago
10.1186/s12864-018-4754-2
Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs during Cryptosporidium baileyi infection
Cited by: 22
Author(s): Guan-Jing Ren, Xian-Cheng Fan, Ting-Li Liu, Shasha Wang, Guanghui Zhao
Software Mentions: 1
Published: over 6 years ago
10.3389/fgene.2014.00445
Developmental regulation of ecdysone receptor (EcR) and EcR-controlled gene expression during pharate-adult development of honeybees (Apis mellifera)
Cited by: 44
Author(s): Tathyana Rachel Palo Mello, Aline Carolina Aleixo, Daniel Guariz Pinheiro, Francis Morais Franco Nunes, Márcia Maria Gentile Bitondi, Klaus Hartfelder, Angel Roberto Barchuk, Zilá Luz Paulino Simões
Software Mentions: 1
Published: almost 10 years ago
10.14336/AD.2018.1027
Metabolomics Coupled with Transcriptomics Approach Deciphering Age Relevance in Sepsis
Cited by: 15
Author(s): Ding‐Qiao Xu, Shanting Liao, Pei Li, Qian Zhang, Yan Lv, Xiaowei Fu, Ming‐Hua Yang, Junsong Wang, Ling‐Yi Kong
Software Mentions: 1
Published: almost 6 years ago
10.18632/oncotarget.15213
PD-L1 up-regulation in melanoma increases disease aggressiveness and is mediated through miR-17-5p
Cited by: 83
Author(s): Valentina Audrito, Sara Serra, Aureliano Stingi, Francesca Orso, Federica Gaudino, Cinzia Bologna, Francesco Neri, Giulia Garaffo, Romina Nassini, Gianna Baroni, Eliana Rulli, Daniela Massi, Salvatore Oliviero, Roberto Piva, Daniela Taverna, Mario Mandalà, Silvia Deaglio
Software Mentions: 1
Published: almost 8 years ago
10.3389/fgene.2020.593994
Draft Genome of the Edible Oriental Insect Protaetia brevitarsis seulensis
Cited by: 4
Author(s): Joon Ha Lee, Myunghee Jung, Younhee Shin, Sathiyamoorthy Subramaniyam, In-Woo Kim, Minchul Seo, Mi Ae Kim, Seong Hyun Kim, Jihye Hwang, Eun Hwa Choi, Ui Wook Hwang, Jae Sam Hwang
Software Mentions: 1
Published: almost 4 years ago
10.3389/fgene.2021.665065
AutoEncoder-Based Computational Framework for Tumor Microenvironment Decomposition and Biomarker Identification in Metastatic Melanoma
Cited by: 0
Author(s): Yanding Zhao, Yadong Dong, Yongqi Sun, Chao Cheng
Software Mentions: 1
Published: over 3 years ago
10.1186/s12864-015-2075-2
Transcriptome profiling reveals distinctive traits of retinol metabolism and neonatal parallels in the MRL/MpJ mouse
Cited by: 10
Author(s): Justyna Podolak-Popinigis, Bartosz Górnikiewicz, Anna Ronowicz, Paweł Sachadyn
Software Mentions: 1
Published: about 9 years ago
10.3389/fgene.2018.00037
RNA-Seq Reveals Extensive Transcriptional Response to Heat Stress in the Stony Coral Galaxea fascicularis
Cited by: 24
Author(s): Jing Hou, Tao Xu, Dingjia Su, Ying Wu, Li Cheng, Jun Wang, Zhi Zhou, Yan Wang
Software Mentions: 1
Published: almost 7 years ago
10.3389/fgene.2018.00614
Genome Assembly for a Yunnan-Guizhou Plateau “3E” Fish, Anabarilius grahami (Regan), and Its Evolutionary and Genetic Applications
Cited by: 11
Author(s): Weixing Jiang, Ying Qiu, Xiaofu Pan, Yuanwei Zhang, Xiaoai Wang, Yunyun Lv, Chao Bian, Jia Li, Xinxin You, Jieming Chen, Kuo-Pin Yang, Jing Yang, Chao Sun, Qian Liu, Lei Cheng, Jing Yang, Qiong Shi
Software Mentions: 1
Published: almost 6 years ago
10.1186/1471-2164-14-612
Transcriptomic characterization of cold acclimation in larval zebrafish
Cited by: 131
Author(s): Yong Long, Guangliang Song, Junjun Yan, Xiaozhen He, Qing Li, Zongbin Cui
Software Mentions: 1
Published: about 11 years ago
10.3389/fgene.2019.00457
Transcriptome Analysis of the Breast Muscle of Xichuan Black-Bone Chickens Under Tyrosine Supplementation Revealed the Mechanism of Tyrosine-Induced Melanin Deposition
Cited by: 16
Author(s): Donghua Li, Xinlei Wang, Yawei Fu, Chenxi Zhang, Yanfang Cao, Jie Wang, Yanhua Zhang, Yuanfang Li, Yi Chen, Zhuanjian Li, Wenting Li, Ruirui Jiang, Guirong Sun, Yadong Tian, Guoxi Li, Xiangtao Kang
Software Mentions: 1
Published: over 5 years ago
10.1186/s12864-016-2423-x
Transcriptome adaptation of the bovine mammary gland to diets rich in unsaturated fatty acids shows greater impact of linseed oil over safflower oil on gene expression and metabolic pathways
Cited by: 46
Author(s): Eveline M. Ibeagha‐Awemu, Ran Li, Adolf A. Ammah, Pier-Luc Dudemaine, Nathalie Bissonnette, C. Benchaar, Xin Zhao
Software Mentions: 1
Published: almost 9 years ago
10.1186/s12864-018-5085-z
Analysis of Drosophila melanogaster testis transcriptome
Cited by: 36
Author(s): Viktor Vedelek, László Bodai, Gábor Grézal, Beatrix Kovacs, Imre Boros, Barbara Laurinyecz, Rita Sinka
Software Mentions: 1
Published: about 6 years ago
10.3389/fgene.2019.00768
The Trends in Global Gene Expression in Mouse Embryonic Stem Cells During Spaceflight
Cited by: 5
Author(s): Lili An, Yanming Liu, Yingjun Fan, Ning He, Fanlei Ran, Hongzhu Qu, Yanqiu Wang, Xuetong Zhao, Hongzhi Wang, Yue Jiang, Xiangdong Fang, Haiying Hang
Software Mentions: 1
Published: about 5 years ago
10.1038/srep22241
New insights into virulence mechanisms of rice pathogen Acidovorax avenae subsp. avenae strain RS-1 following exposure to ß-lactam antibiotics
Cited by: 7
Author(s): Bin Li, Mengyu Ge, Yang Zhang, Li Wang, Muhammad Ibrahim, Yanli Wang, Guochang Sun, Gongyou Chen
Software Mentions: 1
Published: over 8 years ago
10.3389/fgene.2016.00110
Comparative Epigenomic Profiling of the DNA Methylome in Mouse and Zebrafish Uncovers High Interspecies Divergence
Cited by: 28
Author(s): Chi Zhang, Yujin Hoshida, Kirsten C. Sadler
Software Mentions: 1
Published: over 8 years ago
10.3389/fgene.2019.00410
Defective Expression of Mitochondrial, Vacuolar H+-ATPase and Histone Genes in a C. elegans Model of SMA
Cited by: 2
Author(s): Xiaotong Gao, Jing Xu, Hao Chen, Dingwu Xue, Wen-Ju Pan, Chuanman Zhou, C. Yongchao, Long Ma
Software Mentions: 1
Published: over 5 years ago
10.3389/fgene.2020.601689
Genomic Characterization of WRKY Transcription Factors Related to Andrographolide Biosynthesis in Andrographis paniculata
Cited by: 17
Author(s): Rongrong Zhang, Zhenzhen Chen, Libing Zhang, Wei Yao, Zhichao Xu, Baosheng Liao, Yaolei Mi, Han Gao, Chunhong Jiang, Lixin Duan, Aijia Ji
Software Mentions: 1
Published: almost 4 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
10.1186/s12859-017-1732-7
ISVASE: identification of sequence variant associated with splicing event using RNA-seq data
Cited by: 0
Author(s): Hasan Awad Aljohi, Wanfei Liu, Qiang Lin, Jun Yu, Songnian Hu
Software Mentions: 1
Published: over 7 years ago
10.7554/eLife.23242
TCF7L1 promotes skin tumorigenesis independently of β-catenin through induction of LCN2
Cited by: 19
Author(s): Amy T. Ku, Timothy M. Shaver, Ajay S Rao, Jeffrey Howard, Christine N. Rodriguez, Qi Miao, Gloria E. Garcia, Diep Le, Diane Yang, Malgorzata Borowiak, Daniel N. Cohen, Vida Chitsazzadeh, A. Hafeez Diwan, Kenneth Y. Tsai, Hoang Nguyen
Software Mentions: 1
Published: over 7 years ago
10.1186/s13229-015-0017-0
Integrated analysis of whole-exome sequencing and transcriptome profiling in males with autism spectrum disorders
Cited by: 97
Author(s): Marta Codina‐Solà, Benjamín Rodríguez-Santiago, Aïda Homs, Javier Santoyo, Maria Rigau, Gemma Aznar-Laín, Miguel del Campo, Blanca Gener, Elisabeth Gabau, M.P. Botella, Armand Gutiérrez-Arumí, Guillermo Antiñolo, Luis A. Pérez‐Jurado, Ivon Cuscò
Software Mentions: 1
Published: over 9 years ago
10.1186/s12864-016-2861-5
Combination analysis of genome-wide association and transcriptome sequencing of residual feed intake in quality chickens
Cited by: 44
Author(s): Zuowei Xu, Congliang Ji, Yan Zhang, Zhe Zhang, Qiang Nie, Jiguo Xu, Dexiang Zhang, Xiquan Zhang
Software Mentions: 1
Published: over 8 years ago
10.3389/fgene.2019.00197
Analyses of MicroRNA and mRNA Expression Profiles Reveal the Crucial Interaction Networks and Pathways for Regulation of Chicken Breast Muscle Development
Cited by: 28
Author(s): Yuanfang Li, Yi Chen, Wenjiao Jin, Shouyi Fu, Donghua Li, Yanhua Zhang, Guirong Sun, Ruirui Jiang, Ruili Han, Zhuanjian Li, Xiangtao Kang, Guoxi Li
Software Mentions: 1
Published: over 5 years ago
10.1155/2016/8329513
Functions of<i>thga1</i>Gene in<i>Trichoderma harzianum</i>Based on Transcriptome Analysis
Cited by: 5
Author(s): Qing Sun, Xiliang Jiang, Li Pang, Lirong Wang, Li Mei
Software Mentions: 1
Published: almost 9 years ago
10.1186/s12864-017-4367-1
Genome-wide analyses of direct target genes of four rice NAC-domain transcription factors involved in drought tolerance
Cited by: 52
Author(s): Phil Hyun Chung, Harin Jung, Yang Do Choi, Ju-Kon Kim
Software Mentions: 1
Published: almost 7 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
10.1186/s12864-017-4236-y
Temporally distinct transcriptional regulation of myocyte dedifferentiation and Myofiber growth during muscle regeneration
Cited by: 9
Author(s): Ke’ale W. Louie, Alfonso Saera-Vila, Phillip E. Kish, Justin A. Colacino, Alon Kahana
Software Mentions: 1
Published: about 7 years ago
10.3389/fgene.2014.00025
Alternative splicing during Arabidopsis flower development results in constitutive and stage-regulated isoforms
Cited by: 37
Author(s): Haifeng Wang, Chenjiang You, Fang Rong Chang, Yingxiang Wang, Lei Wang, Ji Qi
Software Mentions: 1
Published: almost 11 years ago
10.1038/srep23526
Microbial oil-degradation under mild hydrostatic pressure (10 MPa): which pathways are impacted in piezosensitive hydrocarbonoclastic bacteria?
Cited by: 40
Author(s): Alberto Scoma, Marta Barbato, Emma Hernandez-Sanabria, Francesca Mapelli, Daniele Daffonchio, Sara Borin, Nico Boon
Software Mentions: 1
Published: over 8 years ago
10.1186/1471-2164-13-300
Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression
Cited by: 246
Author(s): Xin Li, Jingde Zhu, Fengyi Hu, Song Ge, Mingzhi Ye, Hui Xiang, Guojie Zhang, Xiaoming Zheng, Hongyu Zhang, Shilai Zhang, Qiong Li, Ruibang Luo, Chang Yu, Jian Yu, Jiantong Sun, Xiaoyu Zou, Xiaofeng Cao, Xianfa Xie, Jun Wang, Wen Wang
Software Mentions: 1
Published: over 12 years ago
10.3389/fimmu.2020.01536
Essential Role for CD30-Transglutaminase 2 Axis in Memory Th1 and Th17 Cell Generation
Cited by: 3
Author(s): Akane Suzuki, Ryoji Yagi, Motoko Kimura, Chiaki Iwamura, Kenta Shinoda, Atsushi Onodera, Kiyoshi Hirahara, Damon J. Tumes, Ryo Koyama‐Nasu, Siiri E. Iismaa, Robert M. Graham, Shinichiro Motohashi, Toshinori Nakayama
Software Mentions: 1
Published: over 4 years ago
10.1186/s13229-018-0191-y
Significant transcriptional changes in 15q duplication but not Angelman syndrome deletion stem cell-derived neurons
Cited by: 18
Author(s): Nora Urraca, Kevin A. Hope, A. Kaitlyn Victor, T. Grant Belgard, Rawaha Memon, Salil Goorha, Colleen Valdez, Quynh Tran, Sílvia Sánchez, Juanma Ramírez, Martin Donaldson, Dave Bridges, Lawrence T. Reiter
Software Mentions: 1
Published: almost 7 years ago
10.3389/fimmu.2017.00628
IL-10 Dysregulation in Acute Mountain Sickness Revealed by Transcriptome Analysis
Cited by: 40
Author(s): Bao Liu, Jian Chen, Long Zhang, Yixing Gao, Jianhua Cui, Erlong Zhang, Gang Xu, Yan Liang, Yu Liang, Jian Wang, Yuqi Gao
Software Mentions: 1
Published: over 7 years ago
10.3389/fimmu.2021.601611
Correlation Between Immune Lymphoid Cells and Plasmacytoid Dendritic Cells in Human Colon Cancer
Cited by: 6
Author(s): Jing Wu, Hang Cheng, Helei Wang, Guoxia Zang, Lingli Qi, Xinping Lv, Chunyan Liu, Shan Zhu, Mingyou Zhang, Jiuwei Cui, Hideki Ueno, Yongjun Liu, Jian Suo, Jingtao Chen
Software Mentions: 1
Published: over 3 years ago
10.3389/fimmu.2021.669819
Analysis of LncRNA-mRNA Co-Expression Profiles in Patients With Polycystic Ovary Syndrome: A Pilot Study
Cited by: 4
Author(s): Xiuhong Sun, Yishan Liu, Xinyu Gao, Meng‐Xuan Du, Mengge Gao, Xingming Zhong, Xiangcai Wei
Software Mentions: 1
Published: over 3 years ago
10.3389/fimmu.2021.631410
MR1-Restricted MAIT Cells From The Human Lung Mucosal Surface Have Distinct Phenotypic, Functional, and Transcriptomic Features That Are Preserved in HIV Infection
Cited by: 9
Author(s): Sharon Khuzwayo, Maphe Mthembu, Erin W. Meermeier, Sanjay M. Prakadan, Samuel W. Kazer, Thierry Bassett, Kennedy Nyamande, Dilshaad Fakey Khan, Priya Maharaj, Mohammed Mitha, Moosa Suleman, Zoey Mhlane, Dirhona Ramjit, Farina Karim, Alex K. Shalek, David Lewinsohn, Thumbi Ndung’u, Emily Wong
Software Mentions: 1
Published: over 3 years ago
10.3389/fimmu.2018.01100
SHIP1 Deficiency in Inflammatory Bowel Disease Is Associated With Severe Crohn’s Disease and Peripheral T Cell Reduction
Cited by: 13
Author(s): Sandra Fernandes, Neetu Srivastava, Raki Sudan, Frank A. Middleton, Amandeep K. Shergill, James C. Ryan, William G. Kerr
Software Mentions: 1
Published: over 6 years ago
10.1038/srep09698
Nelfinavir and Nelfinavir Analogs Block Site-2 Protease Cleavage to Inhibit Castration-Resistant Prostate Cancer
Cited by: 48
Author(s): Min Guan, Leila Su, Yate-Ching Yuan, Haiqing Li, Warren Chow
Software Mentions: 1
Published: over 9 years ago
10.1038/srep24066
Ethylene positively regulates cold tolerance in grapevine by modulating the expression of ETHYLENE RESPONSE FACTOR 057
Cited by: 89
Author(s): Xiaoming Sun, Tingting Zhao, Shuheng Gan, Xiaobo Ren, Linchuan Fang, Sospeter Karanja Karungo, Yi Wang, Liang Chen, Shaohua Li, H. P. Xin
Software Mentions: 1
Published: over 8 years ago
10.1111/acel.12598
Genetic interplay between human longevity and metabolic pathways - a large-scale eQTL study
Cited by: 13
Author(s): Robert Häsler, Geetha Venkatesh, Qihua Tan, Friederike Flachsbart, Anupam Sinha, Philip Rosenstiel, Wolfgang Lieb, Stefan Schreiber, Kaare Christensen, Lene Christiansen, Almut Nebel
Software Mentions: 1
Published: over 7 years ago
10.1186/1471-2105-13-S12-A3
Regulation of cell proliferation and apoptosis by growth hormone during zebrafish auditory hair cell regeneration
Cited by: 1
Author(s): Gopinath Rajadinakaran, Huifang Sun, Claire A. Rinehart, Eric C. Rouchka, Michael E. Smith
Software Mentions: 1
Published: over 12 years ago
10.3389/fimmu.2019.00832
RNAseq Profiling of Leukocyte Populations in Zebrafish Larvae Reveals a cxcl11 Chemokine Gene as a Marker of Macrophage Polarization During Mycobacterial Infection
Cited by: 53
Author(s): Julien Rougeot, Vincenzo Torraca, Ania Zakrzewska, Zakia Kanwal, Hans J. Jansen, Frida Sommer, Herman P. Spaink, Annemarie H. Meijer
Software Mentions: 1
Published: over 5 years ago
10.1038/srep24604
Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana
Cited by: 21
Author(s): Ruimin Gao, Peng Liu, Yuhan Yong, Sek‐Man Wong
Software Mentions: 1
Published: over 8 years ago
10.3389/fimmu.2019.01622
Transcriptome Analysis of Immune Response of mIgM+ B Lymphocytes in Japanese Flounder (Paralichthys olivaceus) to Lactococcus lactis in vitro Revealed That IFN I-3 Could Enhance Their Phagocytosis
Cited by: 19
Author(s): Xiaoqian Tang, Shun Fa Yang, Xiuzhen Sheng, Jing Xing, Wenbin Zhan
Software Mentions: 1
Published: over 5 years ago
10.1038/srep24611
CD14 in the TLRs signaling pathway is associated with the resistance to E. coli F18 in Chinese domestic weaned piglets
Cited by: 20
Author(s): Zhengchang Wu, Ying Liu, Wende Dong, Guoqiang Zhu, Shenglong Wu, Wenbin Bao
Software Mentions: 1
Published: over 8 years ago
10.1093/molbev/msu315
Evolution of the Insect Desaturase Gene Family with an Emphasis on Social Hymenoptera
Cited by: 60
Author(s): Martin Helmkampf, Elizabeth Cash, Juergen Gadau
Software Mentions: 1
Published: almost 10 years ago
10.3389/fimmu.2018.01101
T Cell Receptor Alpha Chain Genes in the Teleost Ballan Wrasse (Labrus bergylta) Are Subjected to Somatic Hypermutation
Cited by: 15
Author(s): Sumaira Bilal, Kai Kristoffer Lie, Øystein Sæle, Ivar Hordvik
Software Mentions: 1
Published: over 6 years ago
10.1186/s12864-019-6143-x
A leucine-rich repeat-receptor-like kinase gene SbER2–1 from sorghum (Sorghum bicolor L.) confers drought tolerance in maize
Cited by: 20
Author(s): Hanshuai Li, Xiao Han, Xinxiang Liu, Miaoyi Zhou, Wen Ren, Bingbing Zhao, Chuanli Ju, Ya Liu, Jiuran Zhao
Software Mentions: 1
Published: about 5 years ago
10.1038/srep24894
Transcriptome analysis of interactions between silkworm and cytoplasmic polyhedrosis virus
Cited by: 25
Author(s): Liang Jiang, Zhengwen Peng, Youbing Guo, Tingcai Cheng, Huizhen Guo, Qiang Sun, Ching-Hua Huang, Ping Zhao, Qingyou Xia
Software Mentions: 1
Published: over 8 years ago
10.1155/2018/8134902
The Potential Protective Effect of Curcumin on Amyloid-<i>β</i>-42 Induced Cytotoxicity in HT-22 Cells
Cited by: 13
Author(s): Lu Zhang, Yu Fang, Xuan Chen, Yajun Lian, Zhaoshu Zeng, Chuanjie Wu, Hua Zhu, Hong‐Liang Xu
Software Mentions: 1
Published: almost 7 years ago
10.18632/aging.101029
An intestinal microRNA modulates the homeostatic adaptation to chronic oxidative stress in C. elegans
Cited by: 25
Author(s): Masaomi Kato, Mohammed A. Kashem, Chao Cheng
Software Mentions: 1
Published: about 8 years ago
10.1038/srep25536
Population transcriptomics uncovers the regulation of gene expression variation in adaptation to changing environment
Cited by: 31
Author(s): Qin Xu, Caiyun Zhu, Yangyang Fan, Zhihong Song, Shilai Xing, Wei Liu, Juan Yan, Tao Su
Software Mentions: 1
Published: over 8 years ago
10.1155/2015/196082
Assessing Computational Steps for CLIP-Seq Data Analysis
Cited by: 8
Author(s): Qi Liu, Xue Zhong, Blair B. Madison, Anil K. Rustgi, Yu Shyr
Software Mentions: 1
Published: almost 10 years ago
10.3389/fimmu.2020.529614
The Signature Amino Acid Residue Serine 31 of HIV-1C Tat Potentiates an Activated Phenotype in Endothelial Cells
Cited by: 1
Author(s): Malini Menon, Roli Budhwar, Rohit Nandan Shukla, Kiran Bankar, Madavan Vasudevan, Udaykumar Ranga
Software Mentions: 1
Published: about 4 years ago
10.1186/s12864-016-3409-4
Comparative transcriptome analysis reveals candidate genes for the biosynthesis of natural insecticide in Tanacetum cinerariifolium
Cited by: 10
Author(s): Sana Khan, Swati Upadhyay, Feroz Khan, Sudeep Tandon, Rakesh Shukla, Sumit Ghosh, Vikrant Gupta, Sayan Banerjee, Laiq ur Rahman
Software Mentions: 1
Published: almost 8 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
10.3389/fimmu.2018.00015
TRAIL-Mediated Suppression of T Cell Receptor Signaling Inhibits T Cell Activation and Inflammation in Experimental Autoimmune Encephalomyelitis
Cited by: 31
Author(s): I‐Tsu Chyuan, Hwei-Fang Tsai, Chien-Sheng Wu, Chi-Chang Sung, Ping‐I Hsu
Software Mentions: 1
Published: almost 7 years ago
10.3389/fimmu.2017.00959
RNA Sequencing of Murine Norovirus-Infected Cells Reveals Transcriptional Alteration of Genes Important to Viral Recognition and Antigen Presentation
Cited by: 17
Author(s): Daniel Enosi Tuipulotu, Natalie E. Netzler, Jennifer H Lun, Jason M. Mackenzie, Peter A. White
Software Mentions: 1
Published: over 7 years ago
10.1038/srep26093
The Essential Role of H19 Contributing to Cisplatin Resistance by Regulating Glutathione Metabolism in High-Grade Serous Ovarian Cancer
Cited by: 111
Author(s): Zhong Zheng, Hong Xu, Shasha Suo, Xin Xu, Maowei Ni, Linhui Gu, Wei Chen, Liangyan Wang, Ye Zhao, Bing Teng, Yuejin Hua
Software Mentions: 1
Published: over 8 years ago
10.3389/fimmu.2019.02972
JAK Inhibition Differentially Affects NK Cell and ILC1 Homeostasis
Cited by: 6
Author(s): Laura Vian, Mimi T. Le, Nathalia Gazaniga, Jacqueline Kieltyka, Christine Liu, Giuseppe Pietropaolo, Stefania Dell’Orso, Stephen R. Brooks, Yasuko Furumoto, Craig J. Thomas, John J. O’Shea, Giuseppe Sciumè, Massimo Gadina
Software Mentions: 1
Published: almost 5 years ago