bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.18632/aging.203157

Immune infiltration-related N6-methyladenosine RNA methylation regulators influence the malignancy and prognosis of endometrial cancer
Cited by: 19
Author(s): Jian Ma, Di Yang, Xiaolong Ma
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-018-19837-6

Persistent activation of interlinked type 2 airway epithelial gene networks in sputum-derived cells from aeroallergen-sensitized symptomatic asthmatics
Cited by: 15
Author(s): Anya C. Jones, Niamh M. Troy, Elisha White, Elysia M. Hollams, Alexander M. Gout, Kak-Ming Ling, Anthony Kicic, Stephen M. Stick, Peter D. Sly, Patrick G. Holt, Graham L. Hall, Anthony Bosco
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-19954-2

Different milk diets have substantial effects on the jejunal mucosal immune system of pre-weaning calves, as demonstrated by whole transcriptome sequencing
Cited by: 18
Author(s): H.M. Hammon, D. Frieten, C. Gerbert, Christian Koch, G. Dusel, Rosemarie Weikard, Christa Kühn
Software Mentions: 1
Published: over 8 years ago

10.1186/s12935-021-01820-3

miR-129-5p inhibits clear cell renal cell carcinoma cell proliferation, migration and invasion by targeting SPN
Cited by: 6
Author(s): Bin Gao, Limin Wang, Na Zhang, Miaomiao Han, Yubo Zhang, Huancai Liu, Dawei Sun, Xiaolong Xiao, Yifei Liu
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.63502

Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection
Cited by: 88
Author(s): Anastasia A. Minervina, Ekaterina A. Komech, Aleksei Titov, Meriem Bensouda Koraichi, Elisa Rosati, Ilgar Z. Mamedov, André Franke, Grigory A. Efimov, Dmitriy M. Chudakov, Thierry Mora, Aleksandra M. Walczak, Yuri B Lebedev, Mikhail V. Pogorelyy
Software Mentions: 1
Published: over 5 years ago

10.1186/s12935-021-02001-y

CircRNA NALCN acts as an miR-493-3p sponge to regulate PTEN expression and inhibit glioma progression
Cited by: 10
Author(s): Yi Liu, Simin Chen, Gang Peng, Yixiang Liao, Xue‐Gong Fan, Zuping Zhang, Chenfu Shen
Software Mentions: 1
Published: about 5 years ago

10.1186/s12935-021-02075-8

Elevated exosome-derived miRNAs predict osimertinib resistance in non-small cell lung cancer
Cited by: 24
Author(s): Xinying Li, Cen Chen, Zimu Wang, Jiaxin Liu, Wei Sun, Kaikai Shen, Lv Y, Suhua Zhu, Ping Zhan, Tangfeng Lv, Yong Song
Software Mentions: 1
Published: about 5 years ago

10.18632/aging.101904

The acute transcriptional response to resistance exercise: impact of age and contraction mode
Cited by: 14
Author(s): Colleen S. Deane, Ryan M. Ames, Bethan E. Phillips, Michael N. Weedon, Craig R. G. Willis, Catherine Boereboom, Haitham Abdulla, Syed S I Bukhari, Jonathan N. Lund, John P. Williams, Daniel J. Wilkinson, Kenneth Smith, Iain J. Gallagher, Fawzi Kadi, Nathaniel J. Szewczyk, Philip J. Atherton, Timothy Etheridge
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-21525-4

Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations
Cited by: 35
Author(s): Brooke R. Druliner, Panwen Wang, Taejeong Bae, Saurabh Baheti, Seth W. Slettedahl, Douglas W. Mahoney, Nikolaos Vasmatzis, Hang Xu, Min‐Soo Kim, Matthew A. Bockol, Daniel R. O’Brien, Diane E. Grill, Nathaniel D. Warner, Miguel Munoz-Gomez, Kimberlee Kossick, Ruth A. Johnson, Mohamad Mouchli, Donna Felmlee-Devine, Jill Washechek-Aletto, Thomas C. Smyrk, Ann L. Oberg, Junwen Wang, Nicholas Chia, Alexej Abyzov, David A. Ahlquist, Lisa A. Boardman
Software Mentions: 1
Published: over 8 years ago

10.1186/s12935-021-01808-z

LINC00958 promotes the proliferation of TSCC via miR-211-5p/CENPK axis and activating the JAK/STAT3 signaling pathway
Cited by: 19
Author(s): Bo Jia, Junfeng Dao, Jae-Sook Han, Zhijie Huang, Xiang Sun, Xianghuai Zheng, Shijian Xiang, Zhou Hui-xi, Shuguang Liu
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-15-116

ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs
Cited by: 36
Author(s): Mark A. van de Wiel, Maarten Neerincx, Tineke E. Buffart, Daoud Sie, Henk M.W. Verheul
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2105-14-110

Differential expression analysis for paired RNA-seq data
Cited by: 18
Author(s): Lisa Chung, John Ferguson, Wei Zheng, Feng Qian, Vincent M. Bruno, Ruth R. Montgomery, Hongyu Zhao
Software Mentions: 1
Published: over 13 years ago

10.1038/s41598-018-21371-4

Characterization of gene regulation and protein interaction networks for Matrin 3 encoding mutations linked to amyotrophic lateral sclerosis and myopathy
Cited by: 28
Author(s): María Carolina Gallego Iradi, Judy C. Triplett, James Thomas, Rachel Davila, Anthony M Crown, Hilda Brown, Jada Lewis, Maurice S. Swanson, Guilian Xu, Edgardo Rodríguez-Lebrón, David R. Borchelt
Software Mentions: 1
Published: over 8 years ago

10.1186/s12935-021-01839-6

Comprehensive analysis of the transcriptome‐wide m6A methylome in invasive malignant pleomorphic adenoma
Cited by: 16
Author(s): Zhaolong Han, Biao Yang, Qin Wang, Yuhua Hu, Yuqiong Wu, Zhen Tian
Software Mentions: 1
Published: over 5 years ago

10.1186/s12935-020-01295-8

Construction of a metastasis-associated ceRNA network reveals a prognostic signature in lung cancer
Cited by: 22
Author(s): Qing Cao, Zewen Dong, Shuzhen Liu, Guoyan An, Bianbian Yan, Lei Lei
Software Mentions: 1
Published: over 6 years ago

10.1186/s12974-020-01964-5

Oligodendrocyte-specific Argonaute profiling identifies microRNAs associated with experimental autoimmune encephalomyelitis
Cited by: 8
Author(s): Qin Ma, Atsuko Matsunaga, Brenda Ho, Jorge R. Oksenberg, Alessandro Didonna
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13058-018-1059-y

Metastatic breast cancer cells overexpress and secrete miR-218 to regulate type I collagen deposition by osteoblasts
Cited by: 53
Author(s): Xuxiang Liu, Minghui Cao, Melanie R. Palomares, Xiwei Wu, Arthur Li, Yan Wei, Miranda Fong, Wing-Chung Chan, Shizhen Emily Wang
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-23714-7

Vitamin C promotes apoptosis in breast cancer cells by increasing TRAIL expression
Cited by: 61
Author(s): David W. Sant, Sushmita Mustafi, Christopher B. Gustafson, Joshua Chen, Joyce M. Slingerland, Gaofeng Wang
Software Mentions: 1
Published: over 8 years ago

10.1186/s13058-018-0963-5

Dependence receptor UNC5A restricts luminal to basal breast cancer plasticity and metastasis
Cited by: 14
Author(s): Maria B. Padua, Poornima Bhat‐Nakshatri, Manjushree Anjanappa, Mayuri Prasad, Yangyang Hao, Xi Rao, Sheng Liu, Jun Wan, Yunlong Liu, Kyle McElyea, Max Jacobsen, George E. Sandusky, Sandra K. Althouse, Susan M. Perkins, Harikrishna Nakshatri
Software Mentions: 1
Published: over 8 years ago

10.3390/brainsci11070913

Characterization of Early Life Stress-Affected Gut Microbiota
Cited by: 12
Author(s): Noriyoshi Usui, Hideo Matsuzaki, Shoichi Shimada
Software Mentions: 1
Published: about 5 years ago

10.18632/aging.101269

The effects of graded levels of calorie restriction: XI. Evaluation of the main hypotheses underpinning the life extension effects of CR using the hepatic transcriptome
Cited by: 28
Author(s): Davina Derous, Sharon E. Mitchell, Lu Wang, Cara L Green, Yingchun Wang, Luonan Chen, Jing–Dong Jackie Han, Daniel E. L. Promislow, David Lusseau, Alex Douglas, John R. Speakman
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-018-24284-4

Measurement of metabolite variations and analysis of related gene expression in Chinese liquorice (Glycyrrhiza uralensis) plants under UV-B irradiation
Cited by: 33
Author(s): Xiao Zhang, Xiaoli Ding, Yaxi Ji, Shouchuang Wang, Yingying Chen, Jie Luo, Yingbai Shen, Peng Li
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2105-15-S17-S2

Identification of genes and pathways involved in kidney renal clear cell carcinoma
Cited by: 45
Author(s): William Yang, Kenji Yoshigoe, Xiang Qin, Jun S. Liu, Jack Yang, Andrzej Niemierko, Youping Deng, Yunlong Liu, A. Keith Dunker, Zhongxue Chen, Liangjiang Wang, Dong Xu, Hamid R. Arabnia, Weida Tong, Mary Qu Yang
Software Mentions: 1
Published: almost 12 years ago

10.3390/brainsci9070155

Regional Analysis of the Brain Transcriptome in Mice Bred for High and Low Methamphetamine Consumption
Cited by: 16
Author(s): Robert Hitzemann, Ovidiu D. Iancu, Cheryl Reed, Harue Baba, Denesa R. Lockwood, Tamara J. Phillips
Software Mentions: 1
Published: about 7 years ago

10.1093/brain/awab123

Aromatic <scp>l</scp>-amino acid decarboxylase deficiency: a patient-derived neuronal model for precision therapies
Cited by: 14
Author(s): Giada Rossignoli, Karolin Krämer, Eleonora Lugarà, Haya Alrashidi, Simon Pope, Carmen De La Fuente Barrigon, Katy Barwick, Giovanni Bisello, Joanne Ng, John R. Counsell, Gabriele Lignani, Simon Heales, Mariarita Bertoldi, Serena Barral, Manju A. Kurian
Software Mentions: 1
Published: over 5 years ago

10.1038/s41416-018-0321-5

Exploring the transcriptome of hormone-naive multifocal prostate cancer and matched lymph node metastases
Cited by: 7
Author(s): Linnéa Schmidt, Mia Møller, Christa Haldrup, Siri H. Strand, Søren Vang, Jakob Hedegaard, Søren Høyer, Michael Borre, Torben F. Ørntoft, Karina D. Sørensen
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-11-564

Empirical bayes analysis of sequencing-based transcriptional profiling without replicates
Cited by: 45
Author(s): Zhijin Wu, Bethany D. Jenkins, Tatiana A. Rynearson, Sonya T. Dyhrman, Mak A. Saito, Melissa L. Mercier, LeAnn P. Whitney
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12974-019-1527-z

Transcriptome profiling of brain myeloid cells revealed activation of Itgal, Trem1, and Spp1 in western diet-induced obesity
Cited by: 31
Author(s): Hongtian Yang, Leah C. Graham, Alaina M. Reagan, Weronika Grabowska, William H. Schott, Gareth R. Howell
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-020-64288-7

Transcriptome profile analysis of two Vicia faba cultivars with contrasting salinity tolerance during seed germination
Cited by: 19
Author(s): Fangwen Yang, Hongwei Chen, Changyan Liu, Li Li, Liangjun Liu, Xuesong Han, Zhengjie Wan, Aihua Sha
Software Mentions: 1
Published: over 6 years ago

10.1038/s41416-018-0263-y

Targeting peroxiredoxin 1 impairs growth of breast cancer cells and potently sensitises these cells to prooxidant agents
Cited by: 45
Author(s): Małgorzata Bajor, Agata O Zych, Agnieszka Graczyk-Jarzynka, Angelika Muchowicz, Małgorzata Firczuk, Lech Trzeciak, Paweł Gaj, Antoni Domagała, Marta Siernicka, Agnieszka Zagożdżon, Paweł Siedlecki, Monika Kniotek, Patrick C. O’Leary, Jakub Goła̧b, Radosław Zagożdżon
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41416-021-01441-7

Essential role of the histone lysine demethylase KDM4A in the biology of malignant pleural mesothelioma (MPM)
Cited by: 4
Author(s): Moshe Lapidot, Abigail Case, Ellen Weisberg, Chengcheng Meng, Sarah R. Walker, Swati Garg, Wei Ni, Klaus Podar, Yin P. Hung, Ruben D. Carrasco, Aine Knott, Prafulla C. Gokhale, Sunil Sharma, Alex Pozhitkov, Prakash Kulkarni, David A. Frank, Ravi Salgia, James D. Griffin, Srinivas Vinod Saladi, Raphael Bueno, Martin Sattler
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-64022-3

Transcriptome profiling reveals insertional mutagenesis suppressed the expression of candidate pathogenicity genes in honeybee fungal pathogen, Ascosphaera apis
Cited by: 3
Author(s): Awraris Getachew, Tessema Aynalem Abejew, Jiangli Wu, Jin Xu, Yu Hou, Jian Tan, Peng-Jie Wu, Yan Tu, Weipeng Kang, Zheng Wang, Shufa Xu
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-64890-9

Transcriptomic evidence that insulin signalling pathway regulates the ageing of subterranean termite castes
Cited by: 13
Author(s): Haroon, Xiaoming Ma, Yuxin Li, Hongxin Zhang, Qing Liu, Xiaoqing Su, Lianxi Xing
Software Mentions: 1
Published: over 6 years ago

10.1038/s41413-018-0037-4

Characterization of a novel murine Sost ERT2 Cre model targeting osteocytes
Cited by: 19
Author(s): Daniel Maurel, Tsutomu Matsumoto, Julian Vallejo, Mark Johnson, Sarah L. Dallas, Yukiko Kitase, Marco Brotto, Michael Wacker, Marie A. Harris, S. E. Harris, Lynda F. Bonewald
Software Mentions: 1
Published: over 7 years ago

10.18632/aging.101947

The small non-coding RNA profile of mouse oocytes is modified during aging
Cited by: 9
Author(s): Bettina P. Mihalas, Nicole J. Camlin, Miguel J Xavier, Alexandra E. Peters, Janet E. Holt, Jessie M. Sutherland, Eileen A. McLaughlin, Andrew L. Eamens, Brett Nixon
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-021-04201-9

Fusion of single-cell transcriptome and DNA-binding data, for genomic network inference in cortical development
Cited by: 0
Author(s): Thomas E. Bartlett
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-65536-6

Opposite Roles of the JMJD1A Interaction Partners MDFI and MDFIC in Colorectal Cancer
Cited by: 16
Author(s): Shushan Yuan, Yongming Li, Sangphil Oh, Bin Zhang, Willard M. Freeman, Sook Shin, Ralf Janknecht
Software Mentions: 1
Published: over 6 years ago

10.1186/s13068-015-0245-8

Uniconazole-induced starch accumulation in the bioenergy crop duckweed (Landoltia punctata) II: transcriptome alterations of pathways involved in carbohydrate metabolism and endogenous hormone crosstalk
Cited by: 46
Author(s): Yang Liu, Yang Fang, Mengjun Huang, Yanling Jin, Jiaolong Sun, Tao Xiang, Guohua Zhang, Kai He, Yun Zhao, Hai Zhao
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-020-66469-w

Transcriptomic study in women with trisomy 21 identifies a possible role of the GTPases of the immunity-associated proteins (GIMAP) in the protection of breast cancer
Cited by: 13
Author(s): André Mégarbané, David Piquemal, Anne-Sophie Rebillat, Samantha Stora, Fabien Pierrat, Roman Bruno, Florian Noguier, Clotilde Mircher, Aimé Ravel, Marie Vilaire-Meunier, Sophie Durand, Gérard Lefranc
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-66500-0

Transcriptome analyses suggest that changes in fungal endophyte lifestyle could be involved in grapevine bud necrosis
Cited by: 13
Author(s): Thales Henrique Cherubino Ribeiro, Christiane Noronha Fernandes-Brum, C. R. de Souza, Frédérico Alcântara Novelli Dias, Osmar de Almeida-Junior, Murilo de Albuquerque Regina, Kellen Kauanne Pimenta de Oliveira, Gabriel Lasmar dos Reis, Larissa Maia de Oliveira, Fernanda de Paula Fernandes, Laurent Torregrosa, Jorge Teodoro de Souza, Antônio Chalfun-Júnior
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-66675-6

Transcriptome profiling of the flowering transition in saffron (Crocus sativus L.)
Cited by: 23
Author(s): Jing Hu, Yuping Liu, Xiaohui Tang, Huajing Rao, Chaoxiang Ren, Chen Jiang, Qinghua Wu, Yi Jiang, Fuchang Geng, Jin Pei
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-66021-w

Functional shell matrix proteins tentatively identified by asymmetric snail shell morphology
Cited by: 11
Author(s): Akito Ishikawa, Keisuke Shimizu, Yukinobu Isowa, Takeshi Takeuchi, Rongjun Zhao, Keiji Kito, Manabu Fujie, Noriyuki Satoh, Kazuhiko Endo
Software Mentions: 1
Published: about 6 years ago

10.1186/s13068-019-1377-z

Enhancing co-translational folding of heterologous protein by deleting non-essential ribosomal proteins in Pichia pastoris
Cited by: 7
Author(s): Xihao Liao, Jing Zhao, Shuli Liang, Jingjie Jin, Li Cheng, Ruiming Xiao, Lu Li, Meijin Guo, Gong Zhang, Ying Lin
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-64257-0

Core Binding Factors are essential for ovulation, luteinization, and female fertility in mice
Cited by: 10
Author(s): Somang Lee-Thacker, Hayce Jeon, Yohan Choi, Ichiro Taniuchi, Takeshi Takarada, Yukio Yoneda, Che Myong Ko, Misung Jo
Software Mentions: 1
Published: about 6 years ago

10.1186/s13068-015-0203-5

Genome-wide transcriptional analysis suggests hydrogenase- and nitrogenase-mediated hydrogen production in Clostridium butyricum CWBI 1009
Cited by: 34
Author(s): Magdalena Całusińska, Christopher Hamilton, Pieter Monsieurs, Grégory Mathy, Natalie Leys, Fabrice Franck, Bernard Joris, Philippe Thonart, Serge Hiligsmann, Annick Wilmotte
Software Mentions: 1
Published: over 11 years ago

10.1042/BSR20203973

Identification of KIF4A and its effect on the progression of lung adenocarcinoma based on the bioinformatics analysis
Cited by: 9
Author(s): Yexun Song, Wen-Fang Tang, Hui Li
Software Mentions: 1
Published: over 5 years ago

10.1042/BSR20191731

A susceptibility biomarker identification strategy based on significantly differentially expressed ceRNA triplets for ischemic cardiomyopathy
Cited by: 3
Author(s): Yongxin Zou, Yahui Wang, Zherou Rong, Benliang Wei, Yang Liu, Zhaona Song, Wenshuai Li, Erqiang Hu, Gui Deng, Yuehan He, Jun-Jie Liu, Lina Chen, Wan Li
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21249719

The Genome-Wide Impact of Nipblb Loss-of-Function on Zebrafish Gene Expression
Cited by: 1
Author(s): M. Spreafico, Eleonora Mangano, Mara Mazzola, Clarissa Consolandi, Roberta Bordoni, Cristina Battaglia, Silvio Bicciato, Anna Marozzi, Anna Pistocchi
Software Mentions: 1
Published: over 5 years ago

10.1042/BSR20191845

miR-96-5p enhances cell proliferation and invasion via targeted regulation of ZDHHC5 in gastric cancer
Cited by: 8
Author(s): Baolong Wang, Xianrong Liu, Xiangtao Meng
Software Mentions: 1
Published: over 6 years ago

10.1042/BSR20181173

MicroRNA-550a is associated with muscle system conferring poorer survival for esophageal cancer
Cited by: 2
Author(s): Housong Hong, Taisheng Liu, Haipeng Wu, Jinye Zhang, Xiaoshun Shi, Xiaobing Le, Allen M. Chen, Hong-ying Mo, Qianqian Huang, Zhou Hong-bin, Xin Rao
Software Mentions: 1
Published: over 7 years ago

10.1042/BSR20203481

Mitochondria-related core genes and TF-miRNA-hub mrDEGs network in breast cancer
Cited by: 13
Author(s): Lirong Yan, Ang Wang, Zhi Lv, Yuan Yuan, Qinying Xu
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-67476-7

Co-expression based cancer staging and application
Cited by: 7
Author(s): Xiangchun Yu, Sha Cao, Yi Zhou, Zhezhou Yu, Ying Xu
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-67635-w

Genomics and transcriptomics analysis reveals the mechanism of isobutanol tolerance of a laboratory evolved Lactococcus lactis strain
Cited by: 7
Author(s): Jaya Gupta, Sagar Thapa, Madhulika Verma, Ritu Som, Kakali Mukherjee
Software Mentions: 1
Published: about 6 years ago

10.1042/BSR20192706

Analysis of CASP12 diagnostic and prognostic values in cervical cancer based on TCGA database
Cited by: 3
Author(s): Feng Guo, Beilei Zhang, Caizhi Chen, Wen Zou
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-020-66387-x

Combined PLT and NE to predict the prognosis of patients with locally advanced cervical cancer
Cited by: 5
Author(s): Han Wang, Wen-Ming Chen, Yong-Heng Zhou, Jianping Shi, Yongzhen Huang, Wenjie Wang
Software Mentions: 1
Published: about 6 years ago

10.1042/BSR20181640

FAM83D is associated with gender, AJCC stage, overall survival and disease-free survival in hepatocellular carcinoma
Cited by: 9
Author(s): Xuling Liu, Hong Gao, Jie Zhang, Dongying Xue
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22010364

Multi-Omics Characterization of Inflammatory Bowel Disease-Induced Hyperplasia/Dysplasia in the Rag2−/−/Il10−/− Mouse Model
Cited by: 7
Author(s): Qiyuan Han, Thomas J. Y. Kono, Charles G. Knutson, N. Parry, Charles E. Seiler, James G. Fox, Steven R. Tannenbaum, Natalia Tretyakova
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-68339-x

Transcriptional and in silico analyses of MIF cytokine and TLR signalling interplay in the LPS inflammatory response of Ciona robusta
Cited by: 9
Author(s): Vincenzo Arizza, Angela Bonura, Laura La Paglia, Alfonso Urso, Annalisa Pinsino, Aiti Vizzini
Software Mentions: 1
Published: about 6 years ago

10.1042/BSR20204297

Genome-wide identification and characterization of perirenal adipose tissue microRNAs in rabbits fed a high-fat diet
Cited by: 2
Author(s): Jie Wang, Jiahao Shao, Yanhong Li, Mauricio A. Elzo, Xianbo Jia, Songjia Lai
Software Mentions: 1
Published: over 5 years ago

10.1186/s12859-019-3144-3

ProtRank: bypassing the imputation of missing values in differential expression analysis of proteomic data
Cited by: 7
Author(s): Matúš Medo, Daniel M. Aebersold, Michaela Medová
Software Mentions: 1
Published: almost 7 years ago

10.1042/BSR20210051

GCH1-regulated miRNAs are potential targets for microglial activation in neuropathic pain
Cited by: 9
Author(s): Shu Fang Jia, Guowu Chen, Yanhu Liang, Xiao Liang, Chun Meng
Software Mentions: 1
Published: about 5 years ago

10.1042/BSR20203804

Integrated analysis of ceRNA network and tumor-infiltrating immune cells in esophageal cancer
Cited by: 5
Author(s): Yuhua Chen, Hao Zhou, Zhendong Wang, Zhanghao Huang, Jinjie Wang, Miaosen Zheng, Xuejun Ni, Lei Liu
Software Mentions: 1
Published: over 5 years ago

10.1042/BSR20194432

Development of a novel prognostic signature for predicting the overall survival of bladder cancer patients
Cited by: 3
Author(s): Huamei Tang, Lijuan Kan, Tong Ou, Dayang Chen, Xiaowei Dou, Wei Wu, Xiang Ji, Mengmeng Wang, Zhi‐Hong Zong, Hongmei Mo, Xiuming Zhang, Dan Xiong
Software Mentions: 1
Published: over 6 years ago

10.3390/biom11060771

Transcriptional Cascade in the Regulation of Flowering in the Bamboo Orchid Arundina graminifolia
Cited by: 10
Author(s): Sagheer Ahmad, Chuqiao Lu, Jieqiu Wu, Yonglu Wei, Jie Gao, Jianpeng Jin, Chuanyuan Zheng, Genfa Zhu, Fengming Yang
Software Mentions: 1
Published: over 5 years ago

10.3390/biom11020203

Unravelling the Role of LncRNA WT1-AS/miR-206/NAMPT Axis as Prognostic Biomarkers in Lung Adenocarcinoma
Cited by: 18
Author(s): Wen Li, Yu Liu, Zi Jin Li, Yi Shi, Jing Deng, Jie Bai, Liang Ma, Xiao Zeng, Shan Shan Feng, Jia Ren, Feijun Luo, Duo Yan Rong, Xiaoqi Chen, Hua Yin, Chen Zhu, Da Fu
Software Mentions: 1
Published: over 5 years ago

10.18632/aging.102407

A cluster of long non-coding RNAs exhibit diagnostic and prognostic values in renal cell carcinoma
Cited by: 27
Author(s): Gong Chen, Di Liu, Huageng Liang, Hongmei Yang, Ke Chen, Xiaoping Zhang
Software Mentions: 1
Published: almost 7 years ago

10.3390/biom10091220

MDA-MB-231 Breast Cancer Cells Resistant to Pleurocidin-Family Lytic Peptides Are Chemosensitive and Exhibit Reduced Tumor-Forming Capacity
Cited by: 6
Author(s): Ashley L. Hilchie, Erin E. Gill, Melanie R. Power Coombs, Reza Falsafi, Robert E. W. Hancock, David W. Hoskin
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-69434-9

Comparative transcriptome analysis of Sclerotinia sclerotiorum revealed its response mechanisms to the biological control agent, Bacillus amyloliquefaciens
Cited by: 18
Author(s): Xiaoxiang Yang, Lei Zhang, Yunjia Xiang, Lei Du, Xiaoqin Huang, Yong Liu
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-67760-6

A cluster of metabolism-related genes predict prognosis and progression of clear cell renal cell carcinoma
Cited by: 21
Author(s): Mei Liu, Qiufeng Pan, Ruihai Xiao, Yi Yu, Wenbao Lu, Longwang Wang
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-68637-4

Cellular, mitochondrial and molecular alterations associate with early left ventricular diastolic dysfunction in a porcine model of diabetic metabolic derangement
Cited by: 14
Author(s): Ilkka Heinonen, Oana Sorop, Bas M. van Dalen, Rob C I Wüst, Jens van de Wouw, Vincent J. de Beer, Yanti Octavia, Richard van Duin, Youri Hoogstrate, Lau Blonden, Milla Alkio, Katja Anttila, Andrew Stubbs, Jolanda van der Velden, Daphne Merkus, Dirk J. Duncker
Software Mentions: 1
Published: about 6 years ago

10.18632/aging.202628

Genetic predisposition and bioinformatics analysis of ATP-sensitive potassium channels polymorphisms with the risks of elevated apolipoprotein B serum levels and its related arteriosclerosis cardiovascular disease
Cited by: 4
Author(s): Cheng Liu, Tianwang Guan, Yanxian Lai, Junfang Zhan, Yan Shen
Software Mentions: 1
Published: over 5 years ago

10.3390/biom10040613

3D Cell Culture-Based Global miRNA Expression Analysis Reveals miR-142-5p as a Theranostic Biomarker of Rectal Cancer Following Neoadjuvant Long-Course Treatment
Cited by: 7
Author(s): Linas Kunigenas, Vaidotas Stankevičius, Audrius Dulskas, Elzbieta Budginaite, Gediminas Alzbutas, Eugenijus Stratilatovas, Nils Cordes, Kęstutis Sužiedėlis
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-70484-2

Construct a circRNA/miRNA/mRNA regulatory network to explore potential pathogenesis and therapy options of clear cell renal cell carcinoma
Cited by: 50
Author(s): Shengjie Bai, Yinying Wu, Yanli Yan, Shuai Shao, Jiangzhou Zhang, Jiaxin Liu, Baojun Hui, Rui Li, Hailin Ma, Xiaozhi Zhang, Juan Ren
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms22020783

MBNL2 Regulates DNA Damage Response via Stabilizing p21
Cited by: 11
Author(s): Jun Cai, Ningchao Wang, Guanglan Lin, Haowei Zhang, Weidong Xie, Yaou Zhang, Ning Xu
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22031237

LncRNA H19-Derived miR-675-5p Accelerates the Invasion of Extravillous Trophoblast Cells by Inhibiting GATA2 and Subsequently Activating Matrix Metalloproteinases
Cited by: 9
Author(s): Manabu Ogoyama, Akihide Ohkuchi, Dongqing Zhao, Shigeki Matsubara, Toshihiro Tajima
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-70932-z

Elucidation of resistance signaling and identification of powdery mildew resistant mapping loci (ClaPMR2) during watermelon-Podosphaera xanthii interaction using RNA-Seq and whole-genome resequencing approach
Cited by: 6
Author(s): Mihir Mandal, Haktan Suren, Chandrasekar S. Kousik
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-71050-6

RNA-Seq analysis of differentially expressed genes of Staphylococcus epidermidis isolated from postoperative endophthalmitis and the healthy conjunctiva
Cited by: 3
Author(s): Qing Liu, Nan Chen, Huabo Chen, Yusen Huang
Software Mentions: 1
Published: about 6 years ago

10.3390/biomedicines9030280

Role of RGMc as a Neogenin Ligand in Follicular Development in the Ovary
Cited by: 0
Author(s): Yu Jin Kim, Young Joon Park, Yeo Reum Park, Young Sang Kim, Hye Ran Lee, Sang Jin Lee, Myung‐Joo Kim, KyuBum Kwack, Jung Jae Ko, Jae Ho Lee
Software Mentions: 1
Published: over 5 years ago

10.3390/biomedicines9040388

Pharmacological Inhibition of WIP1 Sensitizes Acute Myeloid Leukemia Cells to the MDM2 Inhibitor Nutlin-3a
Cited by: 6
Author(s): Maria Chiara Fontana, Jacopo Nanni, Andrea Ghelli Luserna di Rorà, Elisabetta Petracci, Antonella Padella, Martina Ghetti, Anna Ferrari, Giovanni Marconi, Simona Soverini, Ilaria Iacobucci, Cristina Papayannidis, Antonio Curti, Ernesta Audisio, Maria Benedetta Giannini, Michela Rondoni, Francesco Lanza, Michèle Cavo, Giovanni Martinelli, Giorgia Simonetti
Software Mentions: 1
Published: over 5 years ago

10.1186/s12859-017-1745-2

TnseqDiff: identification of conditionally essential genes in transposon sequencing studies
Cited by: 35
Author(s): Lili Zhao, Mark T. Anderson, Weisheng Wu, Harry L. T. Mobley, Michael A. Bachman
Software Mentions: 1
Published: about 9 years ago

10.1155/2017/4352450

The miRNA Expression Profile in Acute Myocardial Infarct Using Sheep Model with Left Ventricular Assist Device Unloading
Cited by: 4
Author(s): Xiaoqian Yan, Yu Gan, Haibo Chen, Guang-Mao Liu, Shengshou Hu, Jianye Zhou
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-020-72117-0

A central role for the transcriptional regulator VtlR in small RNA-mediated gene regulation in Agrobacterium tumefaciens
Cited by: 9
Author(s): James A. Budnick, Lauren M. Sheehan, Miranda. J. Ginder, Kevin C. Failor, Julia. M. Perkowski, John. F. Pinto, Kirsten A. Kohl, Lin Kang, Pawel Michalak, Li Luo, Jason E. Heindl, Clayton C. Caswell
Software Mentions: 1
Published: almost 6 years ago

10.1155/2020/7871918

De novo Transcriptome Reveals Gene Changes in the Development of the Endosperm Chalazal Haustorium in Taxillus chinensis (DC.) Danser
Cited by: 8
Author(s): Shugen Wei, Lingyun Wan, Lili He, Ying Wei, Hairong Long, Xiaowen Ji, Jine Fu, Limei Pan
Software Mentions: 1
Published: over 6 years ago

10.1155/2020/4830847

The ceRNA Network Has Potential Prognostic Value in Clear Cell Renal Cell Carcinoma: A Study Based on TCGA Database
Cited by: 3
Author(s): Haosheng Liu, Zhaowen Zhu, Jianxiong Fang, Tianqi Liu, Zhenhui Zhang, Chao Zhao, Xiao‐Yong Pu, Jiumin Liu
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-72448-y

Proteasomal degradation of polycomb-group protein CBX6 confers MMP-2 expression essential for mesothelioma invasion
Cited by: 6
Author(s): Katsuya Sakai, Takumi Nishiuchi, Shoichiro Tange, Yoshinori Suzuki, Seiji Yano, Minoru Terashima, Takeshi Suzuki, Kunio Matsumoto
Software Mentions: 1
Published: almost 6 years ago

10.1155/2020/9502560

The YTH Domain Family of N6-Methyladenosine “Readers” in the Diagnosis and Prognosis of Colonic Adenocarcinoma
Cited by: 17
Author(s): Dian Xu, Jun Shao, Huan Song, Jianming Wang
Software Mentions: 1
Published: over 6 years ago

10.1155/2021/5597135

A New Lectin from Auricularia auricula Inhibited the Proliferation of Lung Cancer Cells and Improved Pulmonary Flora
Cited by: 2
Author(s): Zhendong Liu, Liang Li, Bei Xue, Dandan Zhao, Yanlong Zhang, Xiufeng Yan
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-74049-1

De novo transcriptome analysis of the critically endangered alpine Himalayan herb Nardostachys jatamansi reveals the biosynthesis pathway genes of tissue-specific secondary metabolites
Cited by: 8
Author(s): Nisha Dhiman, Anil Kumar, Dinesh Kumar, Amita Bhattacharya
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms22041960

Pharmacogenomic Profile and Adverse Drug Reactions in a Prospective Therapeutic Cohort of Chagas Disease Patients Treated with Benznidazole
Cited by: 1
Author(s): Lucas Augusto Moysés Franco, Carlos Henrique Valente Moreira, Lewis Buss, Léa Campos de Oliveira, Roberta Cristina Ruedas Martins, Erika R. Manuli, José Ângelo Lauletta Lindoso, Michael P. Busch, Alexandre C. Pereira, Éster Cerdeira Sabino
Software Mentions: 1
Published: over 5 years ago

10.1155/2021/8875971

High FAM189B Expression and Its Prognostic Value in Patients with Gastric Cancer
Cited by: 3
Author(s): Changliang Wu, Quan-Xiao Tan, Dan Liŭ, Jun-E Jiang, Ting Lu, Zu-Mei Huang, Yingjie Su
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-74789-0

Metabolomic and transcriptomic analyses reveal the regulation of pigmentation in the purple variety of Dendrobium officinale
Cited by: 23
Author(s): Xinqiao Zhan, Jufeng Qi, Bin Zhou, Bizeng Mao
Software Mentions: 1
Published: almost 6 years ago

10.1155/2017/2503847

Fish Oil Feeding Modulates the Expression of Hepatic MicroRNAs in a Western-Style Diet-Induced Nonalcoholic Fatty Liver Disease Rat Model
Cited by: 11
Author(s): Hualin Wang, Yang Shao, Fahu Yuan, Na Li, Hongyu Zhang, Chaodong Wu, Zhiguo Liu
Software Mentions: 1
Published: over 9 years ago

10.1155/2020/7340312

Pediococcus acidilactici P25 Protected Caenorhabditis elegans against Enterotoxigenic Escherichia coli K88 Infection and Transcriptomic Analysis of Its Potential Mechanisms
Cited by: 9
Author(s): Keqin Tan, Dun Deng, Xianyong Ma, Yiyan Cui, Zhonghuan Tian
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-14-357

Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data
Cited by: 29
Author(s): Chung I. Li, Pei Fang Su, Yu Shyr
Software Mentions: 1
Published: almost 13 years ago

10.1038/s41598-020-73164-3

Assessing the prognostic value of stemness-related genes in breast cancer patients
Cited by: 5
Author(s): Wenjie Wang, Han Wang, Meng-Sen Wang, Yongzhen Huang, Yuan Ma, Jie Qi, Jianping Shi, Wei Li
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-75537-0

Enhanced FGFR3 activity in postmitotic principal neurons during brain development results in cortical dysplasia and axonal tract abnormality
Cited by: 5
Author(s): Jui-Yen Huang, Bruna Baumgarten Krebs, Marisha Lynn Miskus, May Lin Russell, Eamonn Patrick Duffy, Jason Michael Graf, Hui-Chen Lu
Software Mentions: 1
Published: almost 6 years ago

10.1155/2020/9426204

Effects of Cardiac Sympathetic Neurodegeneration and PPARγ Activation on Rhesus Macaque Whole Blood miRNA and mRNA Expression Profiles
Cited by: 1
Author(s): Jeanette M. Metzger, Mary S. Lopez, Jenna Kropp Schmidt, Megan E. Murphy, Raghu Vemuganti, Marina E. Emborg
Software Mentions: 1
Published: over 6 years ago

10.1155/2019/6763596

Cross-platform Data Analysis Reveals a Generic Gene Expression Signature for Microsatellite Instability in Colorectal Cancer
Cited by: 8
Author(s): Anna Pačínková, Vlad Popovici
Software Mentions: 1
Published: over 7 years ago

10.1155/2020/3801748

Four Autophagy-Related lncRNAs Predict the Prognosis of HCC through Coexpression and ceRNA Mechanism
Cited by: 23
Author(s): Hao Wu, Tiantian Liu, Jianni Qi, Chengyong Qin, Qing Zhu
Software Mentions: 1
Published: almost 6 years ago

10.1155/2019/7505260

RNA-Sequencing and Bioinformatics Analysis of Long Noncoding RNAs and mRNAs in the Prefrontal Cortex of Mice Following Repeated Social Defeat Stress
Cited by: 4
Author(s): Xian Wang, Shaolei Ma, Mao Mao, Caijuan Li, Xiaofeng Shen, Shunqing Xu, Jianjun Yang
Software Mentions: 1
Published: over 7 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

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Papers Mentioning edgeR 6,568