bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-59610-2

MiR-4435 is an UQCRB-related circulating miRNA in human colorectal cancer
Cited by: 10
Author(s): Ji Won Hong, Jung Min Kim, Jeong Eun Kim, Hee Cho, Dasol Kim, Wankyu Kim, Jisun Oh, Ho Jeong Kwon
Software Mentions: 1
Published: over 6 years ago

10.3390/cancers13133131

Deregulated miRNAs Contribute to Silencing of B-Cell Specific Transcription Factors and Activation of NF-κB in Classical Hodgkin Lymphoma
Cited by: 2
Author(s): Julia Paczkowska, Joanna Janiszewska, Adam Ustaszewski, Julia Bein, Marcin Skalski, Agnieszka Dzikiewicz‐Krawczyk, Natalia Rozwadowska, Martin‐Leo Hansmann, Sven Hartmann, Maciej Giefing
Software Mentions: 1
Published: about 5 years ago

10.3390/nu12123762

Sasa quelpaertensis Leaf Extract Ameliorates Dyslipidemia, Insulin Resistance, and Hepatic Lipid Accumulation in High-Fructose-Diet-Fed Rats
Cited by: 2
Author(s): Jeong Yong Park, Mi Jang, Jung Min Oh, Hee-Chul Ko, Sung‐Pyo Hur, Jae-Won Kim, Songyee Baek, Se-Jae Kim
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

10.3390/cancers12113090

USP1 Regulates TAZ Protein Stability Through Ubiquitin Modifications in Breast Cancer
Cited by: 29
Author(s): Ashley L. Mussell, He Shen, Yanmin Chen, Michalis Mastri, Kevin H. Eng, Wiam Bshara, Costa Frangou, Jianmin Zhang
Software Mentions: 1
Published: almost 6 years ago

10.3390/cancers11091273

Etiology-Specific Analysis of Hepatocellular Carcinoma Transcriptome Reveals Genetic Dysregulation in Pathways Implicated in Immunotherapy Efficacy
Cited by: 9
Author(s): Wei Tse Li, Angela E. Zou, Christine O. Honda, Hao Zheng, Xiao Qi Wang, Tatiana Kisseleva, Eric Y. Chang, Weg M. Ongkeko
Software Mentions: 1
Published: about 7 years ago

10.3390/cancers11121919

The Landscape of Long Non-Coding RNA Dysregulation and Clinical Relevance in Muscle Invasive Bladder Urothelial Carcinoma
Cited by: 4
Author(s): Haotian Shen, Lauren Wong, Wei Tse Li, Megan Chu, Rachel High, Eric Y. Chang, Jessica Wang‐Rodriguez, Weg M. Ongkeko
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms22094910

Extracellular Vesicles in Synovial Fluid from Rheumatoid Arthritis Patients Contain miRNAs with Capacity to Modulate Inflammation
Cited by: 15
Author(s): Andrew D Foers, Alexandra L. Garnham, Simon Chatfield, Gordon K. Smyth, Lesley Cheng, Andrew F. Hill, Ian P. Wicks, Ken C Pang
Software Mentions: 1
Published: over 5 years ago

10.3390/cancers13153812

A Yes-Associated Protein (YAP) and Insulin-Like Growth Factor 1 Receptor (IGF-1R) Signaling Loop Is Involved in Sorafenib Resistance in Hepatocellular Carcinoma
Cited by: 9
Author(s): Mai Huong Thi Ngo, Sue Wei Peng, Yung Che Kuo, Chun‐Yen Lin, Ming–Heng Wu, Chia Hsien Chuang, Cheng Xiang Kao, Han Yin Jeng, Gee Way Lin, Thai-Yen Ling, Te‐Sheng Chang, Yen Hua Huang
Software Mentions: 1
Published: about 5 years ago

10.3390/nu7085297

Dietary Selenium Levels Affect Selenoprotein Expression and Support the Interferon-γ and IL-6 Immune Response Pathways in Mice
Cited by: 63
Author(s): Petra A. Tsuji, Bradley A. Carlson, Christine B. Anderson, Harold E. Seifried, Dolph L. Hatfield, Michael Howard
Software Mentions: 1
Published: about 11 years ago

10.1038/s41598-020-59691-z

Transcriptomic response to soybean meal-based diets as the first formulated feed in juvenile yellow perch (Perca flavescens)
Cited by: 14
Author(s): Megan M. Kemski, Chad A. Rappleye, Konrad Dąbrowski, Richard S. Bruno, Macdonald Wick
Software Mentions: 1
Published: over 6 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

10.3390/cancers13153854

Quantitative Assessment and Prognostic Associations of the Immune Landscape in Ovarian Clear Cell Carcinoma
Cited by: 9
Author(s): Saira Khalique, Sarah H. Nash, David Mansfield, Julian Wampfler, Ayoma D. Attygale, Katherine Vroobel, Harriet Kemp, Richard Buus, Hannah Cottom, Ioannis Roxanis, Thomas R. Jones, Katharina von Loga, Dipa Begum, Naomi Guppy, Pradeep Ramagiri, Kerry Fenwick, Nik Matthews, Michael Hubank, Christopher J. Lord, Syed Haider, Alan Melcher, Susana Banerjee, Rachael Natrajan
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-60351-5

Inner Mongolian Cashmere Goat Secondary Follicle Development Regulation Research Based on mRNA-miRNA Co-analysis
Cited by: 22
Author(s): Wenjing Han, Feng Yang, Zhihong Wu, Fei Guo, Junjie Zhang, Erhan Hai, Fangzheng Shang, Rui Su, Ruijun Wang, Zhiying Wang, Zhihong Liu, Yunlong Zhao, Zhixin Wang, Yanjun Zhang, Jinquan Li
Software Mentions: 1
Published: over 6 years ago

10.3390/cancers12020339

TGF-Beta-Activated Cancer-Associated Fibroblasts Limit Cetuximab Efficacy in Preclinical Models of Head and Neck Cancer
Cited by: 37
Author(s): Ksenia M. Yegodayev, Ofra Novoplansky, Artemiy Golden, Manu Prasad, Liron Levin, Sankar Jagadeeshan, Jonathan Zorea, Orr Dimitstein, Ben‐Zion Joshua, Limor Cohen, Ekaterina Khrameeva, Moshe Elkabets
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms22105088

Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of AtENO2 Regulating Seed Germination
Cited by: 5
Author(s): Yu Wu, Lamei Zheng, Bing Jie, Huimin Liu, Genfa Zhang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0111006

Comparative Analysis and Modeling of the Severity of Steatohepatitis in DDC-Treated Mouse Strains
Cited by: 11
Author(s): Vikash Pandey, Marc Sultan, Karl Kashofer, Markus Ralser, Vyacheslav Amstislavskiy, Julia Starmann, Ingrid Osprian, Christina Grimm, Hendrik Hache, Marie–Laure Yaspo, Holger Sültmann, Michael Trauner, Helmut Denk, Kurt Zatloukal, Hans Lehrach, Christoph Wierling
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41598-020-62111-x

Combined transcriptomic and metabolomic analyses uncover rearranged gene expression and metabolite metabolism in tobacco during cold acclimation
Cited by: 26
Author(s): Jianing Xu, Zheng Chen, Fazhan Wang, Wei Jia, Zicheng Xu
Software Mentions: 1
Published: over 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: about 6 years ago

10.1038/s41598-020-62255-w

microRNA and Metabolite Signatures Linked to Early Consequences of Lethal Radiation
Cited by: 11
Author(s): Nabarun Chakraborty, Aarti Gautam, Gregory P. Holmes-Hampton, Vidya P. Kumar, Swapan Kumar Biswas, Raina Kumar, Dana Hamad, George Dimitrov, Ayodele O. Olabisi, Rasha Hammamieh, Sanchita Ghosh
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-62507-9

Genetic and genomic analysis for cocoon yield traits in silkworm
Cited by: 11
Author(s): Shou-Min Fang, Qi Zhou, Qiuhan Yu, Ze Zhang
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

10.3390/ijms22115877

The miR-106b/NR2F2-AS1/PLEKHO2 Axis Regulates Migration and Invasion of Colorectal Cancer through the MAPK Pathway
Cited by: 4
Author(s): Shuzhen Liu, Guoyan An, Qing Cao, Tong Li, Xinyu Jia, Lei Lei
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22115959

Nuclear Magnetic Resonance Therapy Modulates the miRNA Profile in Human Primary OA Chondrocytes and Antagonizes Inflammation in Tc28/2a Cells
Cited by: 4
Author(s): Bibiane Steinecker-Frohnwieser, Birgit Lohberger, Nicole Eck, Anda Mann, Cornelia Kratschmann, Andreas Leithner, W. Kullich, Lukas Weigl
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22116013

Epithelial Regeneration Ability of Crohn’s Disease Assessed Using Patient-Derived Intestinal Organoids
Cited by: 12
Author(s): Chansu Lee, Sung Noh Hong, Eun Ran Kim, Dong Kyung Chang, Young‐Ho Kim
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0130328

Asian Citrus Psyllid Expression Profiles Suggest Candidatus Liberibacter Asiaticus-Mediated Alteration of Adult Nutrition and Metabolism, and of Nymphal Development and Immunity
Cited by: 75
Author(s): Meenal Vyas, Tonja W. Fisher, Rong He, William M. Nelson, Guohua Yin, Joseph M. Cicero, Mark R. Willer, Ryan Kim, Robin Kramer, Greg A. May, John A. Crow, Carol Soderlund, David R. Gang, Judith K. Brown
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0017820

Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays
Cited by: 206
Author(s): Daniel Bottomly, Nicole A.R. Walter, Jessica Ezzell Hunter, Priscila Darakjian, Sunita Kawane, Kari J. Buck, Robert P. Searles, Michael A. Mooney, Shannon K. McWeeney, Robert Hitzemann
Software Mentions: 1
Published: over 15 years ago

10.1038/s41598-021-85394-0

Differential normal skin transcriptomic response in total body irradiated mice exposed to scattered versus scanned proton beams
Cited by: 4
Author(s): Alexandre Leduc, Samia Chaouni, Frédéric Pouzoulet, Ludovic De Marzi, Frédérique Mégnin-Chanet, Erwan Corre, Dinu Stefan, Jean‐Louis Habrand, François Sichel, Carine Laurent
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0104541

De Novo Transcriptome Assembly and Comparative Analysis of Differentially Expressed Genes in Prunus dulcis Mill. in Response to Freezing Stress
Cited by: 54
Author(s): S. A. Mousavi, Arghavan Alisoltani, Behrouz Shiran, Hossein Fallahi, Esmaeil Ebrahimie, Ali Imani, S. Houshmand
Software Mentions: 1
Published: about 12 years ago

10.1038/s41598-021-85480-3

Transcriptional regulation of dosage compensation in Carica papaya
Cited by: 4
Author(s): Juan Liu, Jennifer Han, Anupma Sharma, Ching Man Wai, Ray Ming, Qingyi Yu
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0034940

Transcriptome Responses of Insect Fat Body Cells to Tissue Culture Environment
Cited by: 16
Author(s): Naoya Ogata, Takeshi Yokoyama, Kikuo Iwabuchi
Software Mentions: 1
Published: over 14 years ago

10.1038/s41598-021-85886-z

Comparative transcriptome analysis during developmental stages of direct somatic embryogenesis in Tilia amurensis Rupr
Cited by: 9
Author(s): Hyein Kang, Chae-Bin Lee, Sae-Hyuk Kwon, Jimin Park, Kyu-Suk Kang, Donghwan Shim
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

10.1038/s41598-021-86465-y

Powerful p-value combination methods to detect incomplete association
Cited by: 25
Author(s): Susan A. Yoon, Bukyung Baik, Taesung Park, Dougu Nam
Software Mentions: 1
Published: over 5 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

10.1371/journal.pone.0186173

The transcriptomes of cave and surface populations of Gammarus minus (Crustacea: Amphipoda) provide evidence for positive selection on cave downregulated transcripts
Cited by: 24
Author(s): David B. Carlini, Daniel W. Fong
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0256875

Transcriptome characterization and expression profile of Coix lacryma-jobi L. in response to drought
Cited by: 9
Author(s): Guidong Miao, Yan Qin, Jihua Guo, Qingxia Zhang, Yingying Bao
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22126218

Integrative Analyses of Circulating Small RNAs and Kidney Graft Transcriptome in Transplant Glomerulopathy
Cited by: 8
Author(s): Canan Kuscu, Manjari Kiran, Akram Mohammed, Cem Kuscu, Sarthak Satpathy, Aaron R. Wolen, Elissa Bardhi, Amandeep Bajwa, James D. Eason, Daniel G. Maluf, Valeria R. Mas, Enver Akalin
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0206159

Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs
Cited by: 45
Author(s): Mathilde Le Sciellour, Étienne Labussière, Olivier Zemb, David Renaudeau
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-14-19

Transcriptome analysis of rice root heterosis by RNA-Seq
Cited by: 118
Author(s): Rongrong Zhai, Feng Yue, Huimin Wang, Xiaodeng Zhan, Xihong Shen, Weiming Wu, Yingxin Zhang, Daibo Chen, Gaoxing Dai, Yang Zhou, Shifeng Cheng
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0084386

Genetic Analysis of Benzothiophene Biodesulfurization Pathway of Gordonia terrae Strain C-6
Cited by: 31
Author(s): Wei Wang, Ting Ma, Kehui Lian, Yue Zhang, Huimei Tian, Kaihua Ji, Guoqiang Li
Software Mentions: 1
Published: over 12 years ago

10.3390/ijms22126430

Null cyp1b1 Activity in Zebrafish Leads to Variable Craniofacial Defects Associated with Altered Expression of Extracellular Matrix and Lipid Metabolism Genes
Cited by: 5
Author(s): Susana Alexandre-Moreno, Juan-Manuel Bonet-Fernández, Raquel Atienzar-Aroca, José-Daniel Aroca-Aguilar, Julio Escribano
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0103567

De Novo Assembly of the Perennial Ryegrass Transcriptome Using an RNA-Seq Strategy
Cited by: 44
Author(s): Jacqueline D. Farrell, Stephen Byrne, Cristiana Paina, Torben Asp
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0242179

MiR-424-5p regulates cell cycle and inhibits proliferation of hepatocellular carcinoma cells by targeting E2F7
Cited by: 24
Author(s): Yichao Zhao, Chaoqian Zhu, Qing Chang, Peng Peng, Jie Yang, Chunmei Liu, Yang Liu, Xiaonan Chen, Yuanguang Liu, Ran Cheng, Yijie Wu, Xiaotang Wu, Liang Hu, Jun Yin
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0135670

Transcriptomic Profiling of Spleen in Grass-Fed and Grain-Fed Angus Cattle
Cited by: 9
Author(s): Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Jianan Liu, George E. Liu, Zan Liu, Jiuzhou Song
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0169177

Transcriptome Analysis of Taxillusi chinensis (DC.) Danser Seeds in Response to Water Loss
Cited by: 27
Author(s): Shugen Wei, Xiaojun Ma, Limei Pan, Miao Jin, Jine Fu, Longhua Bai, Zhonglian Zhang, Yanjun Guan, Changming Mo, Hao Huang, Maoshan Chen
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0245613

A transcriptomic analysis of sugarcane response to Leifsonia xyli subsp. xyli infection
Cited by: 7
Author(s): Kai Zhu, Li‐Tao Yang, Chengxi Li, Prakash Lakshmanan, Yong‐Xiu Xing, Yang–Rui Li
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-87991-5

Genome-wide identification, evolutionary relationship and expression analysis of AGO, DCL and RDR family genes in tea
Cited by: 9
Author(s): Debasish B. Krishnatreya, Pooja Moni Baruah, Bhaskar Dowarah, Soni Chowrasia, Tapan Kumar Mondal, Niraj Agarwala
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0156780

Comparative Analyses between Skeletal Muscle miRNAomes from Large White and Min Pigs Revealed MicroRNAs Associated with Postnatal Muscle Hypertrophy
Cited by: 11
Author(s): Xihui Sheng, Ligang Wang, Hemin Ni, Lixian Wang, Xiaolong Qi, Shuhan Xing, Yong Guo
Software Mentions: 1
Published: over 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

10.1371/journal.pone.0199264

A CRISPR screen identifies MAPK7 as a target for combination with MEK inhibition in KRAS mutant NSCLC
Cited by: 15
Author(s): Nicholas Dompe, Christiaan Klijn, Sara A. Watson, Katherine R. Welker Leng, Jenna Port, Trinna Cuellar, Colin Watanabe, Benjamin Haley, Richard M. Neve, Marie Evangelista, David Stokoe
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-021-88874-5

ATHB2 is a negative regulator of germination in Arabidopsis thaliana seeds
Cited by: 3
Author(s): Rocío Soledad Tognacca, Monica Carabelli, Giorgio Morelli, Ida Ruberti, Javier Francisco Botto
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0196681

Identification of cancer-related miRNA-lncRNA biomarkers using a basic miRNA-lncRNA network
Cited by: 51
Author(s): Guangle Zhang, Cong Pian, Zhi Chen, Jin Zhang, Mei‐Ling Xu, Liangyun Zhang, Yuanyuan Chen
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

10.1371/journal.pone.0193009

Evidence of sex-bias in gene expression in the brain transcriptome of two populations of rainbow trout (Oncorhynchus mykiss) with divergent life histories
Cited by: 12
Author(s): Matthew C. Hale, Garrett J. McKinney, Frank P. Thrower, Krista M. Nichols
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-021-89948-0

The chemical defensome of five model teleost fish
Cited by: 15
Author(s): Marta Eide, Xiaokang Zhang, Odd André Karlsen, Jeffrey Goldstone, John J. Stegeman, Inge Jonassen, Anders Goksøyr
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

10.1371/journal.pone.0210414

The transcriptome sequencing and functional analysis of eyestalk ganglions in Chinese mitten crab (Eriocheir sinensis) treated with different photoperiods
Cited by: 4
Author(s): Yangyang Pang, Cong Zhang, Minjie Xu, Genyong Huang, Yongxu Cheng, Xiaozhen Yang
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22137025

Extending the Toolkit for Beauty: Differential Co-Expression of DROOPING LEAF-Like and Class B MADS-Box Genes during Phalaenopsis Flower Development
Cited by: 7
Author(s): Francesca Lucibelli, Maria Carmen Valoroso, Günter Theißen, Susanne Nolden, Mariana Mondragón-Palomino, Serena Aceto
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

10.1371/journal.pone.0149067

Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton
Cited by: 27
Author(s): Hisao Koga, Haruka Fujitani, Yoshiaki Morino, Norio Miyamoto, Jun Tsuchimoto, Tomoko Shibata, Masahiro Nozawa, Shuji Shigenobu, Atsushi Ogura, Kazunori Tachibana, Masato Kiyomoto, Shonan Amemiya, Hiroshi Wada
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-017-3596-7

Transcriptome analysis of lentil (Lens culinaris Medikus) in response to seedling drought stress
Cited by: 88
Author(s): Dharmendra Singh, Chandan Kumar Singh, Jyoti Taunk, R. S. Tomar, Ashish Chaturvedi, Kishor Gaikwad, Madan Pal
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-017-3585-x

RNA-seq of life stages of the oomycete Phytophthora infestans reveals dynamic changes in metabolic, signal transduction, and pathogenesis genes and a major role for calcium signaling in development
Cited by: 70
Author(s): Audrey M. V. Ah‐Fong, Kyoung Su Kim, Howard S. Judelson
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0039914

A Retinoblastoma Orthologue Is a Major Regulator of S-Phase, Mitotic, and Developmental Gene Expression in Dictyostelium
Cited by: 11
Author(s): Kimchi Strasser, Gareth Bloomfield, Asa MacWilliams, Adriano Ceccarelli, Harry K. MacWilliams, Adrian Tsang
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0118002

LSD1 Overexpression Is Associated with Poor Prognosis in Basal-Like Breast Cancer, and Sensitivity to PARP Inhibition
Cited by: 61
Author(s): Satoi Nagasawa, Anna S. Sedukhina, Yuko Nakagawa, Ichiro Maeda, Manabu Kubota, Shigeko Ohnuma, Koichiro Tsugawa, Tomohiko Ohta, Marta Roche-Molina, Juan A. Bernal, A.J. Narvaez, Anand D. Jeyasekharan, Ko Sato
Software Mentions: 1
Published: over 11 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

10.1038/s41598-021-90982-1

Analysis of the role of Purα in the pathogenesis of Alzheimer's disease based on RNA-seq and ChIP-seq
Cited by: 4
Author(s): Xiaoguang Shi, Shuanglai Ren, Bingying Zhang, Shanshan Guo, Wenxin He, Chengmin Yuan, Xiaofan Yang, Kevin Ig-lzevbekhai, Tao Sun, Qinwen Wang, Jianqi Cui
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-019-6370-1

Combining transcriptomics and metabolomics to reveal the underlying molecular mechanism of ergosterol biosynthesis during the fruiting process of Flammulina velutipes
Cited by: 14
Author(s): Ruihong Wang, Pengda Ma, Chen Li, Lingang Xiao, Zongsuo Liang, Juane Dong
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0110548

In-Depth Transcriptome Analysis of the Red Swamp Crayfish Procambarus clarkii
Cited by: 61
Author(s): Huangxuan Shen, Yacheng Hu, Yuanchao Ma, Xin Zhou, Zenghong Xu, Shui Yu, Chunyan Li, Peng Xu, Xin Sun
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0239617

Comparative transcriptome analysis reveals candidate genes related to cadmium accumulation and tolerance in two almond mushroom (Agaricus brasiliensis) strains with contrasting cadmium tolerance
Cited by: 3
Author(s): Penghu Liu, Zaixing Huang, Xuhui Luo, Hua Cai, Weng Bo-qi, Yixiang Wang, Li‐Song Chen
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0137726

Social Regulation of Gene Expression in Threespine Sticklebacks
Cited by: 23
Author(s): Anna K. Greenwood, Catherine L. Peichel
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-021-92489-1

Identification of potential microRNAs and KEGG pathways in denervation muscle atrophy based on meta-analysis
Cited by: 2
Author(s): Xinyi Gu, Bo Jin, Zhidan Qi, Xiaofeng Yin
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-93128-5

Introducing the novel Cytoscape app TimeNexus to analyze time-series data using temporal MultiLayer Networks (tMLNs)
Cited by: 5
Author(s): Michaël Pierrelée, Ana Reynders, Fabrice Lopez, Aziz Moqrich, Laurent Tichit, Bianca Habermann
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0130885

Transcriptome Profiling of Tomato Fruit Development Reveals Transcription Factors Associated with Ascorbic Acid, Carotenoid and Flavonoid Biosynthesis
Cited by: 65
Author(s): Jie Ye, Tixu Hu, Congmei Yang, Hanxia Li, Mingze Yang, Raina Ijaz, Zhibiao Ye, Yuyang Zhang
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0198221

AmpliSeq transcriptome analysis of human alveolar and monocyte-derived macrophages over time in response to Mycobacterium tuberculosis infection
Cited by: 34
Author(s): Audrey C. Papp, Abul K. Azad, Maciej Pietrzak, Amanda Williams, Samuel K. Handelman, Robert P. Igo, Catherine M. Stein, Katherine E. Hartmann, Larry S. Schlesinger, Wolfgang Sadée
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0219976

Comparative transcriptome analysis of translucent flesh disorder in mangosteen (Garcinia mangostana L.) fruits in response to different water regimes
Cited by: 8
Author(s): Deden Derajat Matra, Toshinori Kozaki, Kazuo Ishii, Roedhy Poerwanto, Eiichi Inoue
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0154156

Abnormal Osmotic Avoidance Behavior in C. elegans Is Associated with Increased Hypertonic Stress Resistance and Improved Proteostasis
Cited by: 11
Author(s): Elaine C. Lee, Heejung Kim, Jennifer Ditano, Dacie Manion, Benjamin L. King, Kevin Strange
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0116935

Transcriptional Regulation and Adaptation to a High-Fiber Environment in Bacillus subtilis HH2 Isolated from Feces of the Giant Panda
Cited by: 11
Author(s): Ziyao Zhou, Xiaoxiao Zhou, Li Jin, Zhijun Zhong, Wei Li, Xuehan Liu, Furui Liu, Huaiyi Su, Yongjiu Luo, Wuyang Gu, Chengdong Wang, Hemin Zhang, Desheng Li, Tiantian He, Hualin Fu, Suizhong Cao, Jinjiang Shi, Guangneng Peng
Software Mentions: 1
Published: over 11 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

10.1371/journal.pone.0084311

The MicroRNA Expression Signature of Bladder Cancer by Deep Sequencing: The Functional Significance of the miR-195/497 Cluster
Cited by: 130
Author(s): Toshihiko Iwamoto, Naohiko Seki, Hirofumi Yoshino, Takeshi Chiyomaru, Takahiro Yamasaki, Hideo Hidaka, Tomokazu Yonezawa, Nijiro Nohata, Takashi Kinoshita, Masayuki Nakagawa, Hideki Enokida
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0169595

Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis
Cited by: 33
Author(s): Suzana Tiemi Ivamoto, Osvaldo Reis, Douglas Silva Domingues, Tiago Benedito dos Santos, Fernanda Freitas de Oliveira, David Pot, Thierry Leroy, Luiz Gonzaga Esteves Vieira, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, Luiz Filipe Protásio Pereira
Software Mentions: 1
Published: over 9 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

10.1371/journal.pone.0159295

Transcriptome Profiling Reveals Disruption of Innate Immunity in Chronic Heavy Ethanol Consuming Female Rhesus Macaques
Cited by: 29
Author(s): Suhas Sureshchandra, Maham Rais, Cara Stull, Kathleen A. Grant, Ilhem Messaoudi
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0090895

Scanning of Transposable Elements and Analyzing Expression of Transposase Genes of Sweet Potato [Ipomoea batatas]
Cited by: 9
Author(s): Yan Ling, Yinghong Gu, Tao Xiang, Xianjun Lai, Yizheng Zhang, Xuemei Tan, Haiyan Wang
Software Mentions: 1
Published: over 12 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

10.1371/journal.pone.0208459

Gene landscape and correlation between B-cell infiltration and programmed death ligand 1 expression in lung adenocarcinoma patients from The Cancer Genome Atlas data set
Cited by: 18
Author(s): Kuo‐Hao Ho, Chih‐Ju Chang, Tsung-Hui Huang, Chwen‐Ming Shih, Ann‐Jeng Liu, Peng-Hsu Chen, Kur‐Ta Cheng, Ku‐Chung Chen
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-021-93381-8

The coordination of major events in C4 photosynthesis evolution in the genus Flaveria
Cited by: 12
Author(s): Ming‐Ju Amy Lyu, Udo Gowik, Steven Kelly, Sarah Covshoff, Julian M. Hibberd, Rowan F. Sage, Martha Ludwig, Gane Ka Shu Wong, Peter Westhoff, Xin Guang Zhu
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-015-2082-3

New global analysis of the microRNA transcriptome of primary tumors and lymph node metastases of papillary thyroid cancer
Cited by: 51
Author(s): Manuel Saiselet, David Gacquer, Alex Spinette, Ligia Craciun, Myriam Decaussin‐Petrucci, Guy Andry, Vincent Detours, Carine Maenhaut
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0226338

Transcriptome landscape of Rafflesia cantleyi floral buds reveals insights into the roles of transcription factors and phytohormones in flower development
Cited by: 10
Author(s): Safoora Amini, Khadijah Rosli, Mohd-Faizal Abu-Bakar, Hamidah Alias, Mohd-Noor Mat-Isa, Mohd-Afiq-Aizat Juhari, Jumaat Haji-Adam, Hoe-Han Goh, Kiew Lian Wan
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0147527

Use of De Novo Transcriptome Libraries to Characterize a Novel Oleaginous Marine Chlorella Species during the Accumulation of Triacylglycerols
Cited by: 16
Author(s): Cresten Mansfeldt, Lubna V. Richter, Beth A. Ahner, William P. Cochlan, Ruth Richardson
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-021-95403-x

Identification of intima-to-media signals for flow-induced vascular remodeling using correlative gene expression analysis
Cited by: 4
Author(s): John Kolega, Kerry E. Poppenberg, Hee‐Woong Lim, Liza Gutierrez, Sricharan S. Veeturi, Adnan H. Siddiqui, Hamidreza Rajabzadeh-Oghaz, Vincent M. Tutino
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-96046-8

Functional genomics study of Pseudomonas putida to determine traits associated with avoidance of a myxobacterial predator
Cited by: 4
Author(s): Shukria Akbar, D. Cole Stevens
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0175622

Correlation of EGFR or KRAS mutation status with 18F-FDG uptake on PET-CT scan in lung adenocarcinoma
Cited by: 19
Author(s): Kazuya Takamochi, Kaoru Mogushi, Hideya Kawaji, Kota Imashimizu, Manabu Fukui, Shiaki Oh, Masayoshi Itoh, Yoshihide Hayashizaki, Weijey Ko, Masao Akeboshi, Kenji Suzuki
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-021-95938-z

Signaling pathway perturbation analysis for assessment of biological impact of cigarette smoke on lung cells
Cited by: 3
Author(s): Hongyu Chen, Xi Chen, Yifei Shen, Xinxin Yin, FangJie Liu, Lu Liu, Jie Yao, Qinjie Chu, Yaqin Wang, Hongyan Qi, Michael P. Timko, Weijia Fang, Longjiang Fan
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0179881

Loss of prion protein induces a primed state of type I interferon-responsive genes
Cited by: 15
Author(s): Giulia Malachin, Malin Rokseth Reiten, Øyvind Salvesen, Håvard Aanes, Jorke H. Kamstra, Kerstin Skovgaard, Peter M. H. Heegaard, Cecilie Ersdal, Arild Espenes, Michael A. Tranulis, Maren Bakkebø
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0213149

Genome-wide profiling of piRNAs in the whitefly Bemisia tabaci reveals cluster distribution and association with begomovirus transmission
Cited by: 7
Author(s): Md. Shamimuzzaman, Daniel K. Hasegawa, Wenbo Chen, Alvin M. Simmons, Zhangjun Fei, Kai-Shu Ling
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0120388

A Genome-Wide Scan Reveals Important Roles of DNA Methylation in Human Longevity by Regulating Age-Related Disease Genes
Cited by: 37
Author(s): Fu-Hui Xiao, Yonghan He, Qi-Gang Li, Huan Wu, Longhai Luo, Qing‐Peng Kong
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0175315

Transcriptomic variation of eyestalk reveals the genes and biological processes associated with molting in Portunus trituberculatus
Cited by: 26
Author(s): Jianjian Lv, Longtao Zhang, Ping Liu, Jian Li
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms22158197

Waterlogging-Stress-Responsive LncRNAs, Their Regulatory Relationships with miRNAs and Target Genes in Cucumber (Cucumis sativus L.)
Cited by: 8
Author(s): Kinga Kęska, Michał Wojciech Szcześniak, Adela Adamus, Małgorzata Czernicka
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-98323-y

Primate-specific stress-induced transcription factor POU2F1Z protects human neuronal cells from stress
Cited by: 2
Author(s): А. Г. Степченко, Т. Н. Порцева, И. А. Глухов, А. П. Котнова, B. M. Lyanova, С. Г. Георгиева, Е. В. Панкратова
Software Mentions: 1
Published: almost 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

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Papers Mentioning edgeR 6,568