Ecosyste.ms: Papers

10.18632/oncotarget.24720

2’-Hydroxyflavanone effectively targets RLIP76-mediated drug transport and regulates critical signaling networks in breast cancer
Cited by: 19
Author(s): Lokesh Dalasanur Nagaprashantha, Jyotsana Singhal, Hongzhi Li, Charles Warden, Xueli Liu, David Horne, Yogesh C. Awasthi, Ravi Salgia, Sharad S. Singhal
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms22157951

Protein Arginine Methyltransferase 1 Is Essential for the Meiosis of Male Germ Cells
Cited by: 3
Author(s): Sahar Waseem, Sudeep Kumar, Kanghoon Lee, Byoung-Ha Yoon, Mirang Kim, Hail Kim, Keesook Lee
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-14-912

The nucleosome regulates the usage of polyadenylation sites in the human genome
Cited by: 17
Author(s): Huan Huang, Jiao Chen, Hongde Liu, Xiao Sun
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-017-03874-8

Analysis of Müller glia specific genes and their histone modification using Hes1-promoter driven EGFP expressing mouse
Cited by: 19
Author(s): Kazuko Ueno, Toshiro Iwagawa, Genki Ochiai, Hideto Koso, Hiromitsu Nakauchi, Masao Nagasaki, Yutaka Suzuki, Sumiko Watanabe
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22157946

Suppressing Pyroptosis Augments Post-Transplant Survival of Stem Cells and Cardiac Function Following Ischemic Injury
Cited by: 1
Author(s): Chang Youn Lee, Seahyoung Lee, Seongtae Jeong, Jiyun Lee, Ho Seong Seo, Sunhye Shin, Jun‐Hee Park, Bomi Song, Il-Kwon Kim, Jin Ho Choi, Sang Woo Kim, Gyoonhee Han, Soyeon Lim
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-017-03976-3

Comparative transcriptomic and proteomic analyses provide insights into the key genes involved in high-altitude adaptation in the Tibetan pig
Cited by: 34
Author(s): Bo Zhang, Yangzom Chamba, Peng Shang, Zhixiu Wang, Jun Ma, Liyuang Wang
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-03980-7

HIF-1-mediated suppression of mitochondria electron transport chain function confers resistance to lidocaine-induced cell death
Cited by: 43
Author(s): Akihisa Okamoto, Chisato Sumi, Hiromasa Tanaka, Munenori Kusunoki, Teppei Iwai, Kenichiro Nishi, Yoshiyuki Matsuo, Hiroshi Harada, Keizo Takenaga, Hidemasa Bono, Kiichi Hirota
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-019-3306-3

SpliceFinder: ab initio prediction of splice sites using convolutional neural network
Cited by: 34
Author(s): Ruohan WANG, Zishuai Wang, Jianping Wang, Shuai Cheng Li
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-019-6277-x

Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR
Cited by: 2
Author(s): Gemma B. Danks, Heloisa Galbiati, Martina Raasholm, Yamila N. Torres Cleuren, Eivind Valen, Pavla Navrátilová, Eric M. Thompson
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms22179574

Culturomics Approach to Identify Diabetic Foot Infection Bacteria
Cited by: 8
Author(s): Michał Złoch, Ewelina Maślak, Wojciech Kupczyk, Marek Jackowski, Paweł Pomastowski, Bogusław Buszewski
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-017-05279-z

Genome-wide analysis of long noncoding RNA profiling in PRRSV-infected PAM cells by RNA sequencing
Cited by: 21
Author(s): Jing Zhang, Pu Sun, Lu Gan, Weijie Bai, Zhijia Wang, Dong Liu, Yimei Cao, Yuanfang Fu, Pinghua Li, Xingwen Bai, Xueqing Ma, Huang Bao, Yingli Chen, Zaixin Liu, Zengjun Lu
Software Mentions: 1
Published: over 7 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

10.1186/1471-2105-12-S5-S2

Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length
Cited by: 3
Author(s): Shaoke Lou, Jing‐Woei Li, Hao Qin, Aldrin Kay-Yuen Yim, Leung-Yau Lo, Bing Ni, Kwong‐Sak Leung, Stephen Kwok‐Wing Tsui, Ting‐Fung Chan
Software Mentions: 1
Published: over 13 years ago

10.1038/s41598-017-05702-5

Global transcriptome analysis identifies differentially expressed genes related to lipid metabolism in Wagyu and Holstein cattle
Cited by: 55
Author(s): Wanlong Huang, Yuntao Guo, Weihua Du, Xiuxiu Zhang, Li Ai, Xiangyang Miao
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-016-1384-z

The role of nucleotide composition in premature termination codon recognition
Cited by: 3
Author(s): Fouad Zahdeh, Liran Carmel
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-017-04303-6

Genome-wide Identification and Characterization of Natural Antisense Transcripts by Strand-specific RNA Sequencing in Ganoderma lucidum
Cited by: 16
Author(s): Junjie Shao, Haimei Chen, Dan Yang, Mei Jiang, Hui Zhang, Bin Wu, Jianqin Li, Lichai Yuan, Chang Liu
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms221810106

Efficient Neutrophil Activation Requires Two Simultaneous Activating Stimuli
Cited by: 21
Author(s): Sanne Mol, Florianne Hafkamp, Laura Varela, Neena Simkhada, Esther W. M. Taanman-Kueter, Sander W. Tas, Marca H. M. Wauben, Tom Groot Kormelink, Esther C. de Jong
Software Mentions: 1
Published: about 3 years ago

10.1098/rsob.170119

The requirement of Mettl3-promoted <i>MyoD</i> mRNA maintenance in proliferative myoblasts for skeletal muscle differentiation
Cited by: 66
Author(s): Kensuke Kudou, Tetsuro Komatsu, Jumpei Nogami, Kazuhira Maehara, Akihito Harada, Hiroshi Saeki, Eiji Oki, Yoshihiko Maehara, Yasuyuki Ohkawa
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-017-06516-1

Novel risk genes for systemic lupus erythematosus predicted by random forest classification
Cited by: 42
Author(s): Jonas Carlsson Almlöf, Andrei Alexsson, Juliana Imgenberg‐Kreuz, Lina Sylwan, Christofer Bäcklin, Dag Leonard, Gunnel Nordmark, Karolina Tandre, Maija‐Leena Eloranta, Leonid Padyukov, Christine Bengtsson, Andreas Jönsen, Solbritt Rantapää-Dahlqvist, Christopher Sjöwall, Anders Bengtsson, Iva Gunnarsson, Elisabet Svenungsson, Lars Rönnblom, Johanna K. Sandling, Ann‐Christine Syvänen
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2105-13-S6-S9

A context-based approach to identify the most likely mapping for RNA-seq experiments
Cited by: 16
Author(s): Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel
Software Mentions: 1
Published: over 12 years ago

10.3390/ijms221810036

Quinolone Resistance of Actinobacillus pleuropneumoniae Revealed through Genome and Transcriptome Analyses
Cited by: 4
Author(s): Xiaoping Ma, Bowen Zheng, Jiafan Wang, Gen Li, Sanjie Cao, Yiping Wen, Xiaobo Huang, Zhuang Zuo, Zhijun Zhong, Yu Gu
Software Mentions: 1
Published: about 3 years ago

10.1186/s12864-018-4895-3

Expression profile analysis reveals that Aspergillus fumigatus but not Aspergillus niger makes type II epithelial lung cells less immunological alert
Cited by: 9
Author(s): Natalia Escobar, Iván Valdés, E. M. Keizer, Soledad R. Ordoñez, Robin A. Ohm, Han A. B. Wösten, Hans de Cock
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-06988-1

Identification of an operon involved in fluoride resistance in Enterobacter cloacae FRM
Cited by: 11
Author(s): Xiaoqing Liu, Jian Tian, Lihui Liu, Tao Zhu, Xiaoxia Yu, Xiaoyu Chu, Bin Yao, Ningfeng Wu, Yanting Fan
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.25456

Loss-of-function mutations in Zn-finger DNA-binding domain of <i>HNF4A</i> cause aberrant transcriptional regulation in liver cancer
Cited by: 16
Author(s): Hiroaki Taniguchi, Akihiro Fujimoto, Hidetoshi Kono, Mayuko Furuta, Masashi Fujita, Hidewaki Nakagawa
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-07070-6

GFusion: an Effective Algorithm to Identify Fusion Genes from Cancer RNA-Seq Data
Cited by: 9
Author(s): Jian Zhao, Qi Chen, Jing Wu, Ping Han, Xiaofeng Song
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms221910288

Identification of Estrogen Signaling in a Prioritization Study of Intraocular Pressure-Associated Genes
Cited by: 4
Author(s): Hannah Youngblood, E.J. Parker, Jingwen Cai, Kristin Perkumas, Hongfang Yu, Jason Sun, Sylvia B. Smith, Kathryn E. Bollinger, Janey L. Wiggs, Louis R. Pasquale, Michael A. Hauser, W. Daniel Stamer, Yutao Liu
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-017-08348-5

STAT3-induced long noncoding RNAs in multiple myeloma cells display different properties in cancer
Cited by: 25
Author(s): Stefanie Petrou Binder, Nadine Hösler, Diana Riedel, Ivonne Zipfel, Tilo Buschmann, Christoph Kämpf, Kristin Reiche, Renate Burger, Martin Gramatzki, Jörg Hackermüller, Peter F. Stadler, Friedemann Horn
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-016-1251-y

BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori
Cited by: 32
Author(s): Qi Zhou, Bindan Zhang, Qiuhan Yu, Ze Zhang
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-34277-y

Deep sequencing and miRNA profiles in alcohol-induced neuroinflammation and the TLR4 response in mice cerebral cortex
Cited by: 35
Author(s): Juan R. Ureña‐Peralta, Silvia Alfonso-Loeches, C. M. Cuesta-Diaz, Francisco García‐García, Consuelo Guerri
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-34315-9

The Beta-adrenergic agonist, Ractopamine, increases skeletal muscle expression of Asparagine Synthetase as part of an integrated stress response gene program
Cited by: 11
Author(s): David M. Brown, Kevin J. Ryan, Zoe Daniel, Molebeledi Horatius Dambe Mareko, Richard Talbot, Joanna Moreton, Tom Giles, Richard D. Emes, Charlie Hodgman, Tim Parr, John M. Brameld
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-015-1728-5

Transcriptome sequencing of microglial cells stimulated with TLR3 and TLR4 ligands
Cited by: 48
Author(s): Amitabh Das, Jin Choul Chai, Sun Hwa Kim, Young Seek Lee, Kyoung Sun Park, Kyoung Hwa Jung, Young Gyu Chai
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-34320-y

Exogenous Pi supplementation improved the salt tolerance of maize (Zea mays L.) by promoting Na+ exclusion
Cited by: 19
Author(s): Yong Sun, Chunhua Mu, Haixue Zheng, Shouping Lu, Hua Zhang, Xuecai Zhang, Xia Liu
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2164-14-739

Probing functional polymorphisms in the dengue vector, Aedes aegypti
Cited by: 12
Author(s): Mariangela Bonizzoni, Monica Britton, Osvaldo Marinotti, William A. Dunn, Joseph Fass, Anthony A. James
Software Mentions: 1
Published: about 11 years ago

10.1038/s41598-018-34318-6

Drought-induced susceptibility for Cenangium ferruginosum leads to progression of Cenangium-dieback disease in Pinus koraiensis
Cited by: 13
Author(s): Minji Ryu, Ratnesh Chandra Mishra, Junhyun Jeon, Sun Keun Lee, Hyeun‐Jong Bae
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2164-14-21

RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum
Cited by: 76
Author(s): Chunzhao Zhao, C. Waalwijk, P.J.G.M. de Wit, Dingzhong Tang, Théo van der Lee
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12864-018-5034-x

TraRECo: a greedy approach based de novo transcriptome assembler with read error correction using consensus matrix
Cited by: 2
Author(s): Seokho Yoon, Daeseung Kim, Keunsoo Kang, Woong June Park
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-018-35202-z

Expression profiling of lncRNAs and mRNAs reveals regulation of muscle growth in the Pacific abalone, Haliotis discus hannai
Cited by: 8
Author(s): Jianfang Huang, Xuan Luo, Liting Zeng, Zekun Huang, Meng Huang, You Wang, Caihuan Ke
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms221910892

Salt Stress Promotes Abscisic Acid Accumulation to Affect Cell Proliferation and Expansion of Primary Roots in Rice
Cited by: 22
Author(s): Yingying Huang, Jiahao Zhou, Yuxiang Li, Ruidang Quan, Juan Wang, Rongfeng Huang, Hua Qin
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-018-36304-4

Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene
Cited by: 33
Author(s): Jonathan M. Cocker, Jonathan Wright, Jinhong Li, David Swarbreck, Sarah Dyer, Mario Cáccamo, Philip M. Gilmartin
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-15-780

Conservation and functional influence of alternative splicing in wood formation of Populus and Eucalyptus
Cited by: 33
Author(s): Peng Xu, Yawei Kong, Dongli Song, Cheng Huang, Xuan Li, Laigeng Li
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-018-36484-z

Thermopriming reprograms metabolic homeostasis to confer heat tolerance
Cited by: 58
Author(s): Natalia Serrano, Lexiang Yu, Ahmed Bahieldin, Magdy M. Mahfouz
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-018-36693-6

Mitochondrial and chloroplast genomes provide insights into the evolutionary origins of quinoa (Chenopodium quinoa Willd.)
Cited by: 25
Author(s): Peter J. Maughan, Lindsay Chaney, Damien J. Lightfoot, Brian J. Cox, Mark Tester, Eric N. Jellen, David E. Jarvis
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-018-36607-6

Smooth Muscle Transcriptome Browser: offering genome-wide references and expression profiles of transcripts expressed in intestinal SMC, ICC, and PDGFRα+ cells
Cited by: 15
Author(s): Adrienne Breland, Se Eun Ha, Brian G. Jorgensen, Byungchang Jin, Treg A. Gardner, Kenton M. Sanders, Seungil Ro
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-015-1329-3

Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. oryzae provides novel insights into the broad-spectrum hypersensitive response
Cited by: 23
Author(s): Fan Zhang, Liying Huang, Fan Zhang, Jauhar Ali, Casiana Vera Cruz, Dalong Zhuo, Zhenglin Du, Zhikang Li, Yongli Zhou
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-017-3507-y

Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae
Cited by: 58
Author(s): Jin Lirong, Guanglin Li, Dawei Yu, Wei Huang, Chao Cheng, Shengjie Liao, Qinghua Wu, Yi Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-37124-2

RgsD negatively controls development, toxigenesis, stress response, and virulence in Aspergillus fumigatus
Cited by: 15
Author(s): Young Kim, Minwoo Lee, Sang-Cheol Jun, Youngjoon Choi, Jae‐Hyuk Yu, Kwang‐Soo Shin
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms221910849

Transcriptome-Wide Analysis Reveals a Role for Extracellular Matrix and Integrin Receptor Genes in Otic Neurosensory Differentiation from Human iPSCs
Cited by: 9
Author(s): Lejo Johnson Chacko, Hanae Lahlou, Claudia Steinacher, Saïd Assou, Yassine Messat, József Dudás, Albert S.B. Edge, Berta Crespo, Moira Crosier, Consolato Sergi, Anneliese Schrott‐Fischer, Azel Zine
Software Mentions: 1
Published: about 3 years ago

10.1186/s12864-017-4172-x

Chromatin states responsible for the regulation of differentially expressed genes under 60Co~γ ray radiation in rice
Cited by: 11
Author(s): Xiucai Pan, Yuan Fang, Xueming Yang, Dongyang Zheng, Lifen Chen, Lei Wang, Jin Xiao, Xiue Wang, Kai Wang, Zhukuan Cheng, Hengxiu Yu, Wenli Zhang
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2164-15-715

Genome-wide transcriptome analysis shows extensive alternative RNA splicing in the zoonotic parasite Schistosoma japonicum
Cited by: 15
Author(s): Xiangshu Piao, Nan Hou, Pengfei Cai, Shuai Liu, Chuang Wu, Qijun Chen
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-018-4821-8

Evolutionary divergence of 3’ UTRs in cichlid fishes
Cited by: 19
Author(s): Xiong Peng, C. Darrin Hulsey, Axel Meyer, Paolo Franchini
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-38398-2

Transcriptional responses of wheat roots inoculated with Arthrobacter nitroguajacolicus to salt stress
Cited by: 71
Author(s): Maryam Safdarian, Hossein Askari, Vahid Shariati J, Ghorbanali Nematzadeh
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms221910765

Tauroursodeoxycholic Acid Decreases Keloid Formation by Reducing Endoplasmic Reticulum Stress as Implicated in the Pathogenesis of Keloid
Cited by: 6
Author(s): Sun Je Kim, Seong Eun Lee, Shinae Yi, Sangmi Jun, Yoon-Sun Yi, Harsha Nagar, Cuk-Seong Kim, Chungmin Shin, Min‐Kyung Yeo, Yea Eun Kang, Hye Ran Yang
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-018-37697-y

Comparative transcriptome analysis reveals differentially expressed genes related to the tissue-specific accumulation of anthocyanins in pericarp and aleurone layer for maize
Cited by: 24
Author(s): Tingchun Li, Wei Zhang, Huaying Yang, Qing Dong, Jie Ren, Honghong Fan, Xin Zhang, Yingbing Zhou
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2105-13-S6-S11

Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data
Cited by: 48
Author(s): Boyko Kakaradov, Hui Xiong, Leo J. Lee, Nebojša Jojić, Brendan J. Frey
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-14-193

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq
Cited by: 28
Author(s): Cheng‐Lin Liu, Jinwen Ma, Chung‐Che Chang, Xiaobo Zhou
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-019-39928-2

Transcriptome analysis of a rice cultivar reveals the differentially expressed genes in response to wild and mutant strains of Xanthomonas oryzae pv. oryzae
Cited by: 18
Author(s): Chunlian Wang, Rezwan Tariq, Zhiyuan Ji, Zheng Wei, Kaili Zheng, Rukmini Mishra, Kun Zhao
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-40091-x

Amelogenic transcriptome profiling in ameloblast-like cells derived from adult gingival epithelial cells
Cited by: 7
Author(s): Sun-Yi Hyun, Seyoung Mun, Kyung-Jung Kang, Jong-Chan Lim, Shinyoung Kim, Kyudong Han, Young-Joo Jang
Software Mentions: 1
Published: over 5 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: about 4 years ago

10.1186/s12864-021-07723-x

Genetic analysis of three maize husk traits by QTL mapping in a maize-teosinte population
Cited by: 4
Author(s): Xiaolei Zhang, Lu Ming, Aiai Xia, Tao Xu, Zhenhai Cui, Ruiying Zhang, Wenguo Liu, Yan He
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-12-587

Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum
Cited by: 301
Author(s): María José López-Barragán, Jacob E. Lemieux, Mariam Quiñones, Kim C. Williamson, Alvaro Molina-Cruz, Kairong Cui, Carolina Barillas‐Mury, Keji Zhao, Xin-zhuan Su
Software Mentions: 1
Published: almost 13 years ago

10.1186/s40478-021-01243-1

Defining tumor-associated vascular heterogeneity in pediatric high-grade and diffuse midline gliomas
Cited by: 14
Author(s): Xiao‐Hong Wei, Michaël H. Meel, Marjolein Breur, Marianna Bugiani, Esther Hulleman, Timothy N. Phoenix
Software Mentions: 1
Published: about 3 years ago

10.1186/s12864-020-07337-9

Comparative transcriptome analysis uncovers roles of hydrogen sulfide for alleviating cadmium toxicity in Tetrahymena thermophila
Cited by: 9
Author(s): Hongrui Lv, Jing Xu, Bo Tao, Wei Wang
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-019-41675-3

Detection of novel fusion-transcripts by RNA-Seq in T-cell lymphoblastic lymphoma
Cited by: 27
Author(s): Pilar López-Nieva, Pablo Fernández-Navarro, Osvaldo Graña‐Castro, Eduardo Andrés-León, Javíer Santos, María Villa‐Morales, María Ángeles Cobos-Fernández, Laura González-Sánchez, Marcos Malumbres, María Salazar, José Fernández‐Piqueras
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-41748-3

Global Gene Networks in 3D4/31 Porcine Alveolar Macrophages Treated with Antigenic Epitopes of Actinobacillus pleuropneumoniae ApxIA, IIA, and IVA
Cited by: 5
Author(s): Suji Kim, Myung Whan Oh, Woo Bin Park, Han Sang Yoo
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-41703-2

RNA-seq reveals the involvement of key genes for aerobic adaptation in rice
Cited by: 23
Author(s): Amol S. Phule, Kalyani M. Barbadikar, Sheshu Madhav Maganti, P. Seguttuvel, D. Subrahmanyam, M.B.B. Prasad Babu, Polumetla Ananda Kumar
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-41796-9

Transcriptional response of grapevine to infection with the fungal pathogen Lasiodiplodia theobromae
Cited by: 11
Author(s): Wei Zhang, Jiye Yan, Xinghong Li, Qikai Xing, K. W. Thilini Chethana, Wensheng Zhao
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-41778-x

Environmental interactions are regulated by temperature in Burkholderia seminalis TC3.4.2R3
Cited by: 3
Author(s): Priscila Jane Romano de Oliveira Gonçalves, Carmen C. Denman, Almir José Ferreira, Sarina Tsui, Marcelo Brocchi, Brendan W. Wren, Welington Luiz Araújo
Software Mentions: 1
Published: over 5 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

10.1186/1471-2164-11-663

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads
Cited by: 198
Author(s): Jeffrey A. Martin, Vincent M. Bruno, Zhide Fang, Xiangru Meng, Matthew J. Blow, Tao Zhang, Gavin Sherlock, M Snyder, Wang Zhong
Software Mentions: 1
Published: almost 14 years ago

10.1038/s41598-019-42393-6

Comparative RNA sequencing reveals that HPV16 E6 abrogates the effect of E6*I on ROS metabolism
Cited by: 15
Author(s): Philippe Paget-Bailly, Koceila Meznad, Diane Bruyère, Jérôme Perrard, Michaël Herfs, Alain C. Jung, Christiane Mougin, Jean‐Luc Prétet, Aurélie Baguet
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-015-1922-5

Exploration of alternative splicing events in ten different grapevine cultivars
Cited by: 21
Author(s): Emilio Potenza, Marco Racchi, Lieven Sterck, E. Coller, Elisa Asquini, Silvio C. E. Tosatto, Riccardo Velasco, Yves Van de Peer, Alessandro Cestaro
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-019-5430-x

Comparative transcriptomic analysis unveils interactions between the regulatory CarS protein and light response in Fusarium
Cited by: 14
Author(s): Macarena Ruger-Herreros, Obdulia Parra-Rivero, Javier Pardo-Medina, Francisco J. Romero–Campero, M. Carmen Limón, Javier Ávalos
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-019-42179-w

Maternal DCAF13 Regulates Chromatin Tightness to Contribute to Embryonic Development
Cited by: 11
Author(s): Yang Liu, Long‐Wen Zhao, Jingling Shen, Heng‐Yu Fan, Yan Jin
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-016-2510-z

A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica
Cited by: 12
Author(s): Vishal Singh Somvanshi, Shachi Gahoi, Prakash Banakar, Prasoon Kumar Thakur, Mukesh Kumar, Manisha R. Sajnani, Priyatama Pandey, Uma Rao
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-019-43259-7

The implication of plastid transcriptome analysis in petaloid monocotyledons: A case study of Lilium lancifolium (Liliaceae, Liliales)
Cited by: 3
Author(s): Hoang Dang Khoa, Joohwan Kim
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-43578-9

Differences in the molecular signatures of mucosal-associated invariant T cells and conventional T cells
Cited by: 25
Author(s): Daeui Park, Hong Gi Kim, Miok Kim, Tamina Park, Hyung‐Ho Ha, Dong Hoon Lee, Kang-Seo Park, Seong Jun Park, Hae Ja Lim, Chang Hoon Lee
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-15-1071

Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi
Cited by: 20
Author(s): Raúl Castanera, Gúmer Pérez, Leticia Rodríguez López, Rubén Sancho, Francisco Santoyo, Manuel Alfaro, Toni Gabaldón, Antonio G. Pisabarro, José A. Oguiza, Lucı́a Ramı́rez
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2164-12-516

The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach
Cited by: 36
Author(s): Jun Odawara, Akihito Harada, Tomohiko Yoshimi, Kazuhira Maehara, Taro Tachibana, Seiji Okada, Koichi Akashi, Yasuyuki Ohkawa
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0094604

Acupuncture Promotes Angiogenesis after Myocardial Ischemia through H3K9 Acetylation Regulation at VEGF Gene
Cited by: 62
Author(s): Shu-ping Fu, Su-Yun He, Bin Xu, Chenyao Hu, Lu Shen, Weixing Shen, Yan Huang, Hao Hong, Qian Li, Ning Wang, Xuan-Liang Liu, Fanrong Liang, Bing-Mei Zhu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0129598

Transcriptomic Analysis Reveals Possible Influences of ABA on Secondary Metabolism of Pigments, Flavonoids and Antioxidants in Tomato Fruit during Ripening
Cited by: 74
Author(s): Wangshu Mou, Dongdong Li, Zisheng Luo, Linchun Mao, Tiejin Ying
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0172491

Activation of odorant receptor in colorectal cancer cells leads to inhibition of cell proliferation and apoptosis
Cited by: 49
Author(s): Lea Weber, Klaudia Al-Refae, Juliane Ebbert, Peter Jägers, Janine Altmüller, Christian Becker, Stephan A. Hahn, Günter Gisselmann, Hanns Hatt
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0147273

A Genome-Wide mRNA Expression Profile in Caenorhabditis elegans under Prolonged Exposure to 1750MHz Radiofrequency Fields
Cited by: 7
Author(s): Yan Gao, Yiming Lu, Jianming Yi, Zhihui Li, Dawen Gao, Zhoulong Yu, Tongning Wu, Chenggang Zhang
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

10.1371/journal.pone.0052506

Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species
Cited by: 138
Author(s): Elsa Góngora-Castillo, Kevin L. Childs, Greg Fedewa, John Hamilton, David K. Liscombe, Maria Magallanes‐Lundback, Kranthi K. Mandadi, Ezekiel Nims, Weerawat Runguphan, Brieanne Vaillancourt, Marina Varbanova-Herde, Dean DellaPenna, Thomas D. McKnight, Sarah E. O’Connor, C. Robin Buell
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41598-019-43979-w

Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq
Cited by: 19
Author(s): Naresh V.R. Mutha, Waleed K. Mohammed, Natalio Krasnogor, Geok Yuan Annie Tan, Wei Yee Wee, Yongming Li, Siew Woh Choo, Nicholas S. Jakubovics
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0092720

A Designed Experiments Approach to Optimization of Automated Data Acquisition during Characterization of Bacteria with MALDI-TOF Mass Spectrometry
Cited by: 22
Author(s): Lin Zhang, Connie M. Borror, Todd R. Sandrin
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0170652

Identification of a Putative Quantitative Trait Gene for Resistance to Obesity in Mice Using Transcriptome Analysis and Causal Inference Tests
Cited by: 5
Author(s): Akira Ishikawa
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0066511

Genome-Wide Survey of Cold Stress Regulated Alternative Splicing in Arabidopsis thaliana with Tiling Microarray
Cited by: 60
Author(s): Noam Leviatan, Noam Alkan, Dena Leshkowitz, Robert Fluhr
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0187424

Beyond the polymerase-γ theory: Production of ROS as a mode of NRTI-induced mitochondrial toxicity
Cited by: 23
Author(s): Reuben L. Smith, Josephine M.E. Tan, Martijs J. Jonker, Aldo Jongejan, Thomas Buissink, Steve Veldhuijzen, Antoine H. C. van Kampen, Stanley Brul, Hans van der Spek
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0124877

RNA-Seq Analysis of the Host Response to Staphylococcus aureus Skin and Soft Tissue Infection in a Mouse Model
Cited by: 20
Author(s): Rebecca A. Brady, Vincent M. Bruno, Drusilla L Burns
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-018-5239-z

Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra
Cited by: 27
Author(s): Odile Rogier, Aurélien Chateigner, Souhila Amanzougarene, Marie-Claude Lesage-Descauses, Sandrine Balzergue, Véronique Brunaud, José Caïus, Ludivine Soubigou‐Taconnat, Véronique Jorge, Vincent Segura
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0076572

RNA-Seq Reveals Differential Gene Expression in Staphylococcus aureus with Single-Nucleotide Resolution
Cited by: 16
Author(s): Joseph Osmundson, Scott Dewell, Seth A. Darst
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0211773

Comparative transcriptome analysis of mammary epithelial cells at different stages of lactation reveals wide differences in gene expression and pathways regulating milk synthesis between Jersey and Kashmiri cattle
Cited by: 35
Author(s): Sajad Ahmad Bhat, Syed Mudasir Ahmad, Eveline M. Ibeagha‐Awemu, Basharat Ahmad Bhat, Muneer Ahmad Dar, Peerzada Tajamul Mumtaz, Riaz Ahmad Shah, Nazir Ahmad Ganai
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0127883

Whole Transcriptome of the Venom Gland from Urodacus yaschenkoi Scorpion
Cited by: 55
Author(s): Karen Luna-Ramírez, Verónica Quintero-Hernández, Víctor Rivelino Juárez-González, Lourival D. Possani
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-15-1026

Comparative transcriptome sequencing of tolerant rice introgression line and its parents in response to drought stress
Cited by: 100
Author(s): Liying Huang, Fan Zhang, Wensheng Wang, Yongli Zhou, Binying Fu, Zhikang Li
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0149702

Comparative Transcriptomic Analysis of Primary Duck Hepatocytes Provides Insight into Differential Susceptibility to DHBV Infection
Cited by: 5
Author(s): Yan Liang, Su Qu, Gang Liu, Lei Liu, Yao Yu, Guohui Ding, Yanfeng Zhao, Yixue Li, Youhua Xie, Junqi Zhang, Di Qu
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0097814

Characterization of Natural Antisense Transcript, Sclerotia Development and Secondary Metabolism by Strand-Specific RNA Sequencing of Aspergillus flavus
Cited by: 14
Author(s): Xuecheng Wu, Bin Zhou, Chang Yin, Yong Guo, Ying Lin, Li Pan, Bin Wang
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0180478

PLATINUM SENSITIVE 2 LIKE impacts growth, root morphology, seed set, and stress responses
Cited by: 12
Author(s): Amr R.A. Kataya, Maria T. Creighton, Toga Pangihotan Napitupulu, Christine Sætre, Behzad Shiroud Heidari, Peter Ruoff, Cathrine Lillo
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0149373

Effect of Dietary Restriction and Subsequent Re-Alimentation on the Transcriptional Profile of Bovine Skeletal Muscle
Cited by: 27
Author(s): Kate Keogh, David A. Kenny, Paul Cormican, Matthew S. McCabe, A. K. Kelly, Sinéad M. Waters
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0068907

Changes in the Transcriptome of the Human Endometrial Ishikawa Cancer Cell Line Induced by Estrogen, Progesterone, Tamoxifen, and Mifepristone (RU486) as Detected by RNA-Sequencing
Cited by: 40
Author(s): Karin Tamm-Rosenstein, Jaak Simm, Marina Suhorutshenko, Andres Salumets, Madis Metsis
Software Mentions: 1
Published: over 11 years ago