bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s12885-017-3251-3

Transcriptional changes induced by bevacizumab combination therapy in responding and non-responding recurrent glioblastoma patients
Cited by: 16
Author(s): Thomas Urup, Line Mærsk Staunstrup, Signe Regner Michaelsen, Kristoffer Vitting-Seerup, Marc Bennedbæk, Anders Toft, Lars Rønn Olsen, Lars Jønson, Shohreh Issazadeh‐Navikas, Helle Broholm, Petra Hamerlik, Hans Skovgaard Poulsen, Ulrik Lassen
Software Mentions: 1
Published: over 9 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: almost 9 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: almost 9 years ago

10.3390/molecules22081292

Apigenin Impacts the Growth of the Gut Microbiota and Alters the Gene Expression of Enterococcus
Cited by: 28
Author(s): Minqian Wang, Jenni Firrman, Liqing Zhang, Gustavo Arango-Argoty, Peggy M. Tomasula, LinShu Liu, Weidong Xiao, Kit L. Yam
Software Mentions: 1
Published: about 9 years ago

10.18632/oncotarget.10216

Desmoglein 2 promotes vasculogenic mimicry in melanoma and is associated with poor clinical outcome
Cited by: 36
Author(s): Lih Y. Tan, Chris Mintoff, M. Zahied Johan, Brenton Ebert, Clare G. Fedele, You Fang Zhang, Pacman Szeto, Karen E. Sheppard, Grant A. McArthur, Erwin Foster‐Smith, Andrew Ruszkiewicz, Michael P. Brown, Claudine S. Bonder, Mark Shackleton, Lisa M. Ebert
Software Mentions: 1
Published: over 10 years ago

10.3390/molecules23123276

Effect of Aspergillus flavus Fungal Elicitor on the Production of Terpenoid Indole Alkaloids in Catharanthus roseus Cambial Meristematic Cells
Cited by: 18
Author(s): Chuxin Liang, Chang Chen, Pengfei Zhou, Lv Xu, Jianhua Zhu, Jincai Liang, Jiachen Zi, Rongmin Yu
Software Mentions: 1
Published: almost 8 years ago

10.3390/molecules26051210

Divergent and Overlapping Roles for Selected Phytochemicals in the Regulation of Pathological Cardiac Hypertrophy
Cited by: 8
Author(s): Levi Evans, Yiqui Shen, Abigail Bender, Leah Burnett, Musheng Li, Justine S. Habibian, Tong Zhou, Bradley S. Ferguson
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.10333

Dual tumor suppressing and promoting function of Notch1 signaling in human prostate cancer
Cited by: 24
Author(s): Karine Lefort, Paola Ostano, Maurizia Mello-Grand, Valérie Calpini, Maria Scatolini, Antonella Farsetti, G. Paolo Dotto, Giovanna Chiorino
Software Mentions: 1
Published: over 10 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

10.3390/molecules22020324

Transcriptomic Analysis of Leaf in Tree Peony Reveals Differentially Expressed Pigments Genes
Cited by: 29
Author(s): Jianrang Luo, Qianqian Shi, Lixin Niu, Yanlong Zhang
Software Mentions: 1
Published: over 9 years ago

10.1186/s12967-018-1739-5

NovelmiRNA-25 inhibits AMPD2 in peripheral blood mononuclear cells of patients with systemic lupus erythematosus and represents a promising novel biomarker
Cited by: 26
Author(s): Gangqiang Guo, Huijing Wang, Xinyu Shi, Lele Ye, Kai Wu, Kuan‐Yu Lin, Sisi Ye, Baoqing Li, Huidi Zhang, Qiaoai Lin, Shuang Ye, Xiangyang Xue, Chaosheng Chen
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12915-017-0354-x

MicroRNA miR-29 controls a compensatory response to limit neuronal iron accumulation during adult life and aging
Cited by: 70
Author(s): Roberto Ripa, Adam Antebi, Marco Terrigno, Luca Pandolfini, Aurora Savino, Valeria Arcucci, Marco Groth, Eva Terzibasi Tozzini, Mario Baumgart, Alessandro Cellerino
Software Mentions: 1
Published: over 9 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/s12943-021-01384-w

Identification of lymphocyte cell-specific protein-tyrosine kinase (LCK) as a driver for invasion and migration of oral cancer by tumor heterogeneity exploitation
Cited by: 15
Author(s): Jonas Weiße, Julia Rosemann, Lisa Müller, Matthias Kappler, Alexander W. Eckert, Markus Glaß, Danny Misiak, Stefan Hüttelmaier, Wolfgang G. Ballhausen, Meçhthild Hatzfeld, Monika Haemmerle, Tony Gutschner
Software Mentions: 1
Published: over 5 years ago

10.1186/s12943-018-0820-2

The lncRNA MACC1-AS1 promotes gastric cancer cell metabolic plasticity via AMPK/Lin28 mediated mRNA stability of MACC1
Cited by: 167
Author(s): Yang Zhao, Yajing Liu, Lin Li, Qiong Huang, Wanming He, Shuyi Zhang, Shilin Dong, Zhaowei Wen, Jinjun Rao, Wangjun Liao, Min Shi
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.10729

Ago-RIP-Seq identifies Polycomb repressive complex I member CBX7 as a major target of miR-375 in prostate cancer progression
Cited by: 32
Author(s): Julia M. A. Pickl, Diana Tichy, Vladimir Kuryshev, Yanis Tolstov, Michael Falkenstein, Julia Schüler, Daniel Reidenbach, Agnes Hotz‐Wagenblatt, Glen Kristiansen, Wilfried Roth, Boris Hadaschik, Markus Hohenfellner, Stefan Duensing, Doreen Heckmann, Holger Sültmann
Software Mentions: 1
Published: over 10 years ago

10.1186/s12943-019-1056-5

A novel tumor suppressor protein encoded by circular AKT3 RNA inhibits glioblastoma tumorigenicity by competing with active phosphoinositide-dependent Kinase-1
Cited by: 193
Author(s): Xin Xia, Xixi Li, Fanying Li, Xujia Wu, Maolei Zhang, Huangkai Zhou, Nunu Huang, Xuesong Yang, Feizhe Xiao, Dawei Liu, Lixuan Yang, Nu Zhang
Software Mentions: 1
Published: about 7 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/s12943-019-1004-4

RNA N6-methyladenosine demethylase FTO promotes breast tumor progression through inhibiting BNIP3
Cited by: 363
Author(s): Yi Niu, Ziyou Lin, Arabella Wan, Honglei Chen, Heng Liang, Lei Sun, Yuan Wang, Xi Li, Xiaofeng Xiong, Bo Wei, Xiaobin Wu, Gang Wan
Software Mentions: 1
Published: over 7 years ago

10.1186/s13041-020-00589-2

Transcriptomic analysis of long noncoding RNAs and mRNAs expression profiles in the spinal cord of bone cancer pain rats
Cited by: 4
Author(s): Xinran Hou, Yingqi Weng, Qulian Guo, Zhuofeng Ding, Jian Wang, Jiajia Dai, Anqi Wei, Zongbin Song
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-019-3247-x

A protocol to evaluate RNA sequencing normalization methods
Cited by: 64
Author(s): Zachary B. Abrams, Travis Johnson, Kun Huang, Philip R. O. Payne, Kevin R. Coombes
Software Mentions: 1
Published: almost 7 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/s12859-016-0926-8

Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack
Cited by: 2
Author(s): Renée X. de Menezes, Leila Mohammadi, Jelle J. Goeman, Judith M. Boer
Software Mentions: 1
Published: over 10 years ago

10.26508/lsa.202000651

The transcriptional landscape analysis of basal cell carcinomas reveals novel signalling pathways and actionable targets
Cited by: 10
Author(s): Ivan V. Litvinov, Pingxing Xie, Scott R. Gunn, Denis Sasseville, Philippe Lefrançois
Software Mentions: 1
Published: over 5 years ago

10.26508/lsa.202000688

IL-36 signaling in keratinocytes controls early IL-23 production in psoriasis-like dermatitis
Cited by: 33
Author(s): Jack Goldstein, Esen Yonca Bassoy, Assunta Caruso, Jennifer Palomo, Emiliana Rodriguez, Sylvain Lemeille, Cem Gabay
Software Mentions: 1
Published: over 6 years ago

10.26508/lsa.201800036

Serine catabolism is essential to maintain mitochondrial respiration in mammalian cells
Cited by: 53
Author(s): Stéphanie Lucas, Guohua Chen, Siddhesh Aras, Jian Wang
Software Mentions: 1
Published: over 8 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

10.18632/oncotarget.10239

Prognostic significance of PLIN1 expression in human breast cancer
Cited by: 33
Author(s): Cefan Zhou, Ming Wang, Li Zhou, Yi Zhang, Weiyong Liu, Wenying Qin, Rong He, Lu Yang, Yefu Wang, Xing-Zhen Chen, Jingfeng Tang
Software Mentions: 1
Published: over 10 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

10.26508/lsa.202000985

The AXL-PYK2-PKCα axis as a nexus of stemness circuits in TNBC
Cited by: 5
Author(s): Lohit Khera, Yaron Vinik, Flavio Maina, Sima Lev
Software Mentions: 1
Published: over 5 years ago

10.1186/2049-3002-1-11

Respiratory complex I is essential to induce a Warburg profile in mitochondria-defective tumor cells
Cited by: 74
Author(s): Claudia Calabrese, Luisa Iommarini, Ivana Kurelac, Maria Antonietta Calvaruso, Mariantonietta Capristo, Pier‐Luigi Lollini, Patrizia Nanni, Christian Bergamini, Giordano Nicoletti, Carla De Giovanni, Anna Ghelli, Valentina Giorgio, Mariano Francesco Caratozzolo, Flaviana Marzano, Caterina Manzari, Christine M. Betts, Valerio Carelli, Claudio Ceccarelli, Marcella Attimonelli, Giovanni Romeo, Romana Fato, Michela Rugolo, Apollonia Tullo, Giuseppe Gasparre, Anna Maria Porcelli
Software Mentions: 1
Published: over 13 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

10.1186/s40170-021-00270-9

Targeting MYC-enhanced glycolysis for the treatment of small cell lung cancer
Cited by: 19
Author(s): Kasey R. Cargill, C. Allison Stewart, Elizabeth M. Park, Kavya Ramkumar, Robert J. Cardnell, Qi Wang, Lixia Diao, Ли Шен, You-Hong Fan, Wai Kin Chan, Philip L. Lorenzi, Trudy G. Oliver, Lauren A. Byers
Software Mentions: 1
Published: about 5 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

10.18632/oncotarget.12841

Serum exosomal miR-4772-3p is a predictor of tumor recurrence in stage II and III colon cancer
Cited by: 89
Author(s): Chang Liu, Cathy Eng, Jianjun Shen, Yue Lu, Yoko Takata, Amir Mehdizadeh, George J. Chang, Miguel A. Rodrı́guez-Bigas, Yanan Li, Ping Chang, Yiming Mao, Manal M. Hassan, Fangyu Wang, Donghui Li
Software Mentions: 1
Published: about 10 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

10.1002/cam4.2099

Identification of competitive endogenous RNAs network in breast cancer
Cited by: 13
Author(s): Xiaojin Wang, Jiahui Wan, Zhanxiang Xu, Jiangbo Shu, Lin Ji, Yutian Liu, Shuwen Zhai, Rongjun Cui
Software Mentions: 1
Published: over 7 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: over 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: over 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: over 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: over 6 years ago

10.1002/cam4.432

<scp>HER2</scp> as a target in invasive urothelial carcinoma
Cited by: 35
Author(s): Joaquim Bellmunt, Lillian Werner, Aristotle Bamias, André P. Fay, Rachel S. Park, Markus Riester, Shamini Selvarajah, Justine A. Barletta, David M. Berman, Silvia de Muga, Marta Salido, Enrique Gallardo, Federico Rojo, Elizabeth A. Guancial, Richard Bambury, Stephanie A. Mullane, Toni K. Choueiri, Massimo Loda, Edward C. Stack, Jonathan E. Rosenberg
Software Mentions: 1
Published: over 11 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: over 6 years ago

10.1002/cam4.2089

SIRT3 elicited an anti‐Warburg effect through HIF1α/PDK1/PDHA1 to inhibit cholangiocarcinoma tumorigenesis
Cited by: 37
Author(s): Lei Xu, Li Yang, Lixing Zhou, Robert Dorfman, Li Liu, Rui Cai, Chenfei Jiang, Dehua Tang, Yuming Wang, Xiaoping Zou, Lei Wang, Mingming Zhang
Software Mentions: 1
Published: over 7 years ago

10.1002/cam4.2097

Circulating PD‐1 (+) cells may participate in immune evasion in peripheral T‐cell lymphoma and chidamide enhance antitumor activity of PD‐1 (+) cells
Cited by: 10
Author(s): Wei Zhang, Haorui Shen, Yan Zhang, Wei Wang, Shaoxuan Hu, Dongmei Zou, Daobin Zhou
Software Mentions: 1
Published: over 7 years ago

10.1002/cam4.3963

Pivotal factors associated with the immunosuppressive tumor microenvironment and melanoma metastasis
Cited by: 21
Author(s): Chuan Zhang, Dan Dang, Lele Cong, Hongyan Sun, Xianling Cong
Software Mentions: 1
Published: over 5 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

10.1002/cam4.719

Transcriptome profiling reveals novel gene expression signatures and regulating transcription factors of <scp>TGF</scp> β ‐induced epithelial‐to‐mesenchymal transition
Cited by: 32
Author(s): Liutao Du, Shota Yamamoto, Brian L. Burnette, Danshang Huang, Kun Gao, Neema Jamshidi, Michael Kuo
Software Mentions: 1
Published: over 10 years ago

10.1002/cam4.2071

Candidate genes involved in metastasis of colon cancer identified by integrated analysis
Cited by: 24
Author(s): Yiming Zhou, Yiwen Zang, Yi Yang, Jianbin Xiang, Zongyou Chen
Software Mentions: 1
Published: over 7 years ago

10.1002/cam4.3406

Seven immune‐related genes prognostic power and correlation with tumor‐infiltrating immune cells in hepatocellular carcinoma
Cited by: 22
Author(s): Tiantian Liu, Hao Wu, Jianni Qi, Chengyong Qin, Qing Zhu
Software Mentions: 1
Published: about 6 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: over 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: over 6 years ago

10.1002/cam4.4167

A robust signature of immune‐related long non‐coding RNA to predict the prognosis of bladder cancer
Cited by: 10
Author(s): Cong Lai, Zhenyu Wu, Zhuohang Li, Hao Yu, Kuiqing Li, Zhuang Tang, Cheng Liu, Kecheng Xu
Software Mentions: 1
Published: about 5 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: over 6 years ago

10.1186/s12935-020-01221-y

A long non-coding RNA LINC00461-dependent mechanism underlying breast cancer invasion and migration via the miR-144-3p/KPNA2 axis
Cited by: 12
Author(s): Qiang Zhang, Xiaoyan Jin, Wei Shi, Xin Chen, Wenyang Pang, Xiang Yu, Linjun Yang
Software Mentions: 1
Published: over 6 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

10.1038/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: over 6 years ago

10.1186/s12935-019-0901-3

In silico analysis excavates potential biomarkers by constructing miRNA-mRNA networks between non-cirrhotic HCC and cirrhotic HCC
Cited by: 16
Author(s): Bo Ding, Weiyang Lou, Jingxing Liu, LI Ruo-han, Jing Chen, Weimin Fan
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: over 5 years ago

10.1186/s12935-018-0704-y

Silencing TRIP13 inhibits cell growth and metastasis of hepatocellular carcinoma by activating of TGF-β1/smad3
Cited by: 31
Author(s): Jianning Yao, Xuexiu Zhang, Yingbo Zhang, Dan Zhao, Bing Gao, Haining Zhou, Shilin Gao, Lianfeng Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12935-020-01483-6

MiR-145-5p suppresses the proliferation, migration and invasion of gastric cancer epithelial cells via the ANGPT2/NOD_LIKE_RECEPTOR axis
Cited by: 28
Author(s): Kai Zhou, Bingbing Song, Ming Q. Wei, Jubo Fang, Yufen Xu
Software Mentions: 1
Published: about 6 years ago

10.1186/s12935-020-01388-4

Identification of prognostic factors for intrahepatic cholangiocarcinoma using long non-coding RNAs-associated ceRNA network
Cited by: 7
Author(s): Zhen Kang, Lixin Guo, Zhuo Zhu, Rongfeng Qu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12935-021-01819-w

LINC00221 silencing prevents the progression of hepatocellular carcinoma through let-7a-5p-targeted inhibition of MMP11
Cited by: 7
Author(s): Lin Yang, Hailong Si, Meng Ma, Fang Yu, Yongchao Jiang, Jintao Wang, Cheng Zhang, Haijuan Xiao
Software Mentions: 1
Published: over 5 years ago

10.1186/s12935-021-01814-1

Identification of four genes and biological characteristics of esophageal squamous cell carcinoma by integrated bioinformatics analysis
Cited by: 13
Author(s): Yexun Song, Wang Xy, Fengjun Wang, Xiaowei Peng, Peiyu Li, Shaojun Liu, Decai Zhang
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.13857

Induction of hypoxia and necrosis in multicellular tumor spheroids is associated with resistance to chemotherapy treatment
Cited by: 143
Author(s): Silvio Däster, Nunzia Amatruda, Diego Calabrese, Robert Ivánek, Eleonora Turrini, Raoul A. Droeser, Paul Zajac, Carmela Fimognari, Giulio C. Spagnoli, Giovanna Iezzi, Valentina Mele, Manuele Giuseppe Muraro
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12935-019-1074-9

Identifying a ten-microRNA signature as a superior prognosis biomarker in colon adenocarcinoma
Cited by: 15
Author(s): Rong Ma, Yimeng Zhao, Miao He, Hongfeng Zhao, Yifan Zhang, Shubo Zhou, Mengcong Gao, Di Di, Jue Wang, Jian Ding, Minjie Wei
Software Mentions: 1
Published: almost 7 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: over 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/oncotarget.13936

A childhood acute lymphoblastic leukemia-specific lncRNA implicated in prednisolone resistance, cell proliferation, and migration
Cited by: 33
Author(s): Manon Ouimet, Simon Drouin, Mathieu Lajoie, Maxime Caron, Pascal St-Onge, Romain Gioia, Chantal Richer, Daniel Sinnett
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12935-019-1040-6

Silencing expression of PHF14 in glioblastoma promotes apoptosis, mitigates proliferation and invasiveness via Wnt signal pathway
Cited by: 9
Author(s): Shuai Wu, Chen Luo, Fengjiao Li, Nazia Hameed, Qiu-yan Jin, Jie Zhang
Software Mentions: 1
Published: almost 7 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

10.18632/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

10.1186/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

10.1038/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

10.1186/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

10.1186/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: over 5 years ago

10.18632/oncotarget.11938

Ex vivo miRNome analysis in Ptch1+/− cerebellum granule cells reveals a subset of miRNAs involved in radiation-induced medulloblastoma
Cited by: 12
Author(s): Barbara Tanno, Gabriele Babini, Simona Leonardi, Paola Giardullo, Ilaria De Stefano, Emanuela Pasquali, A. Ottolenghi, Michael J. Atkinson, Anna Saran, Mariateresa Mancuso
Software Mentions: 1
Published: about 10 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

10.1038/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: about 6 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/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

10.1038/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: about 6 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/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: about 8 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: about 6 years ago

10.1186/s40478-020-01099-x

Microglial gene signature reveals loss of homeostatic microglia associated with neurodegeneration of Alzheimer’s disease
Cited by: 116
Author(s): Akira Sobue, Okiru Komine, Yuichiro Hara, Fumito Endo, Hideaki Mizoguchi, Seiji Watanabe, Shigeo Murayama, Takashi Saito, Takaomi C. Saido, Naruhiko Sahara, Makoto Higuchi, Tomoo Ogi, Koji Yamanaka
Software Mentions: 1
Published: almost 6 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

10.1038/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: about 6 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: over 5 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: over 7 years ago

10.1186/s12967-018-1637-x

Molecular network-based identification of competing endogenous RNAs and mRNA signatures that predict survival in prostate cancer
Cited by: 36
Author(s): Ning Xu, Yupeng Wu, Hubin Yin, Xue-Yi Xue, Xin Gou
Software Mentions: 1
Published: about 8 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: about 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

10.1093/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

10.1155/2021/9917060

Increased EHHADH Expression Predicting Poor Survival of Osteosarcoma by Integrating Weighted Gene Coexpression Network Analysis and Experimental Validation
Cited by: 1
Author(s): Juncheng Cui, Guoliang Yi, Jinxin Li, Yangtao Li, Dongyang Qian
Software Mentions: 1
Published: over 5 years ago

10.1155/2018/7538204

An Efficient Feature Selection Strategy Based on Multiple Support Vector Machine Technology with Gene Expression Data
Cited by: 25
Author(s): Ying Zhang, Qingchun Deng, Wenbin Liang, Xuan Zou
Software Mentions: 1
Published: about 8 years ago

10.1155/2021/5585884

Identification of MicroRNAs in Taxillus chinensis (DC.) Danser Seeds under Cold Stress
Cited by: 5
Author(s): Jine Fu, Lingyun Wan, Lina Song, Lili He, Ni Jiang, Hairong Long, Juan Huo, Xiaowen Ji, Ying Wei, Shugen Wei, Limei Pan
Software Mentions: 1
Published: over 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568