bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3389/fonc.2018.00374

Prognostic Genes of Breast Cancer Identified by Gene Co-expression Network Analysis
Cited by: 178
Author(s): Jianing Tang, Deguang Kong, Qiuxia Cui, Kun Wang, Dan Zhang, Yan Gong
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-019-5795-x

Transcriptional analysis of renal dopamine-mediated Na+ homeostasis response to environmental salinity stress in Scatophagus argus
Cited by: 10
Author(s): Maoliang Su, Jia Zhou, Zhengyu Duan, Junbin Zhang
Software Mentions: 3
Published: over 7 years ago

10.3389/fonc.2020.00780

Identification and Validation of a Prognostic lncRNA Signature for Hepatocellular Carcinoma
Cited by: 36
Author(s): Wang Li, Qifeng Chen, Tao Huang, Peihong Wu, Lujun Shen, Zijing Huang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12958-021-00801-5

Trophoblast derived extracellular vesicles specifically alter the transcriptome of endometrial cells and may constitute a critical component of embryo-maternal communication
Cited by: 19
Author(s): Kasun Godakumara, James Ord, Freddy Lättekivi, Keerthie Dissanayake, Janeli Viil, Nageswara Rao Boggavarapu, Omid R. Faridani, Kersti Jääger, Agne Velthut-Meikas, Ülle Jaakma, Andres Salumets, Alireza Fazeli
Software Mentions: 3
Published: over 5 years ago

10.1038/sdata.2014.21

Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq
Cited by: 24
Author(s): Binsheng Gong, Charles Wang, Zhenqiang Su, Huasheng Hong, Jean Thierry‐Mieg, Danielle Thierry-Mieg, Leming Shi, Scott S. Auerbach, Weida Tong, Joshua Xu
Software Mentions: 3
Published: about 12 years ago

10.3389/fonc.2020.550986

MicroRNAs Expression Patterns Predict Tumor Mutational Burden in Colorectal Cancer
Cited by: 5
Author(s): Jiahao Huang, Haizhou Liu, Yang Zhao, Tao Luo, Jungang Liu, Junjie Liu, Xiaoyan Pan, Weizhong Tang
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-15-905

Limited sex-biased neural gene expression patterns across strains in Zebrafish (Danio rerio)
Cited by: 54
Author(s): Ryan Y. Wong, Melissa M McLeod, John Godwin
Software Mentions: 3
Published: almost 13 years ago

10.18632/aging.202410

Systems pharmacology dissection of Epimedium targeting tumor microenvironment to enhance cytotoxic T lymphocyte responses in lung cancer
Cited by: 11
Author(s): Chao Huang, Zhihua Li, Jinglin Zhu, Xuetong Chen, Yuanyuan Hao, Ruijie Yang, Ruifei Huang, Jun Zhou, Zhenzhong Wang, Wei Xiao, Chunli Zheng, Yonghua Wang
Software Mentions: 3
Published: almost 6 years ago

10.1042/BSR20202376

A six-gene-based signature for breast cancer radiotherapy sensitivity estimation
Cited by: 8
Author(s): Xing Chen, Junjie Zheng, Min Zhuo, Ailong Zhang, Zhebin You
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13287-021-02310-z

Hypoxic preconditioning induces epigenetic changes and modifies swine mesenchymal stem cell angiogenesis and senescence in experimental atherosclerotic renal artery stenosis
Cited by: 20
Author(s): Busra Isik, Roman Thaler, Busra B. Goksu, Sabena M. Conley, Hayder Al-Khafaji, Arjunmohan Mohan, Mohsen Afarideh, Abdelrhman Abumoawad, Xiang Yang Zhu, James D. Krier, Ishran M. Saadiq, Hui Tang, Alfonso Eirin, La Tonya J. Hickson, André J. van Wijnen, Stephen C. Textor, Lilach O. Lerman, Sandra M. Herrmann
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-015-2068-1

A novel approach identifies the first transcriptome networks in bats: a new genetic model for vocal communication
Cited by: 15
Author(s): Pedro Rodenas-Cuadrado, Xiaowei Sylvia Chen, Lutz Wiegrebe, Uwe Firzlaff, Sonja C. Vernes
Software Mentions: 3
Published: about 11 years ago

10.1186/s13287-019-1335-5

High temperature suppressed SSC self-renewal through S phase cell cycle arrest but not apoptosis
Cited by: 12
Author(s): Jia Wang, Wei-Jun Gao, Shoulong Deng, Lei Xiang, Jia Hua, Wenzhi Ma
Software Mentions: 3
Published: over 7 years ago

10.1186/s13287-019-1191-3

In vitro expansion affects the response of human bone marrow stromal cells to irradiation
Cited by: 8
Author(s): Yang Xiang, Chun Wu, Jiang Wu, Weili Quan, Chao Cheng, Jian Zhou, Li Chen, Lan Xiang, Fengjie Li, Kebin Zhang, Qian Ran, Yi Zhang, Zhongjun Li
Software Mentions: 3
Published: over 7 years ago

10.3389/fcell.2020.00807

The Pathogenic Effects of Fusobacterium nucleatum on the Proliferation, Osteogenic Differentiation, and Transcriptome of Osteoblasts
Cited by: 8
Author(s): Hui Gao, Tianyong Sun, Fanghong Yang, Jiakan Yuan, Mei Yang, Wenyan Kang, Di Tang, Jun Zhang, Qiang Feng
Software Mentions: 3
Published: about 6 years ago

10.1186/s13287-018-1104-x

Comparative analysis of mesenchymal stem cells derived from amniotic membrane, umbilical cord, and chorionic plate under serum-free condition
Cited by: 62
Author(s): Jiao Ma, Jun Wu, Han Liu, Xiangxiang Jiang, Yan Long, Jie Hao, Hongmei Wang
Software Mentions: 3
Published: almost 8 years ago

10.7554/eLife.53403

Zebrafish macrophage developmental arrest underlies depletion of microglia and reveals Csf1r-independent metaphocytes
Cited by: 36
Author(s): Laura E. Kuil, Nynke Oosterhof, Giuliano Ferrero, Tereza Mikulášová, Martina Hason, Jordy Dekker, Mireia Rovira, Herma C. van der Linde, Paulina Mh van Strien, Emma de Pater, Gerben Schaaf, Erik Mj Bindels, Valérie Wittamer, Tjakko J. van Ham
Software Mentions: 3
Published: over 6 years ago

10.1242/dev.199628

LncRNA HBL1 is required for genome-wide PRC2 occupancy and function in cardiogenesis from human pluripotent stem cells
Cited by: 8
Author(s): Juli Liu, Sheng Liu, Lei Han, Sheng Yi, Yucheng Zhang, Il-man Kim, Jun Wan, Lei Yang
Software Mentions: 3
Published: over 5 years ago

10.3390/biomedicines9060629

Activin-A Induces Early Differential Gene Expression Exclusively in Periodontal Ligament Fibroblasts from Fibrodysplasia Ossificans Progressiva Patients
Cited by: 8
Author(s): Ton Schoenmaker, Michal Mokrý, Dimitra Micha, Coen Netelenbos, Nathalie Bravenboer, Marjolijn Gilijamse, Elisabeth M. W. Eekhoff, Teun J. de Vries
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2020.00601

Circular RNA Expression Profiles in Nasopharyngeal Carcinoma by Sequence Analysis
Cited by: 17
Author(s): Jing Yang, Yongqian Gong, Qingshan Jiang, Lijun Liu, Shuyan Li, Quanjun Zhou, Fang Huang, Zhifeng Liu
Software Mentions: 3
Published: over 6 years ago

10.1186/s13287-016-0370-8

Identification and validation of multiple cell surface markers of clinical-grade adipose-derived mesenchymal stromal cells as novel release criteria for good manufacturing practice-compliant production
Cited by: 120
Author(s): Emily T. Camilleri, Michael P. Gustafson, Amel Dudakovic, Scott M. Riester, Catalina Galeano Garces, Christopher R. Paradise, Hideki Takai, Marcel Karperien, Simon M. Cool, Hee Jeong Im Sampen, A. Noelle Larson, Wenchun Qu, Jay Smith, Allan B. Dietz, André J. van Wijnen
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0184120

Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition
Cited by: 25
Author(s): Xuan Tao, Yan Liang, Xuemei Yang, Jianhui Pang, Zhijun Zhong, Xiaohui Chen, Yuekui Yang, Kai Zeng, Runming Kang, Yongjia Lei, Sancheng Ying, Jing Gong, Yiren Gu, Xuebin Lv
Software Mentions: 3
Published: about 9 years ago

10.1186/s12967-018-1593-5

A circRNA–miRNA–mRNA network identification for exploring underlying pathogenesis and therapy strategy of hepatocellular carcinoma
Cited by: 199
Author(s): Dandan Xiong, Yi‐Wu Dang, Peng Lin, Dong‐Yue Wen, Rong‐Quan He, Dan Luo, Zhaoyong Feng, Gang Chen
Software Mentions: 3
Published: about 8 years ago

10.3389/fcell.2021.685494

Novel Functional Genes Involved in Transdifferentiation of Canine ADMSCs Into Insulin-Producing Cells, as Determined by Absolute Quantitative Transcriptome Sequencing Analysis
Cited by: 2
Author(s): Pengxiu Dai, Jiakai Li, Yijing Chen, Luwen Zhang, Xinke Zhang, Jinglu Wang, Guixiang Qi, Yihua Zhang
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.3631

RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers
Cited by: 34
Author(s): Van L.T. Hoang, Lisa Tom, Xiu-Cheng Quek, Jean-Marie Tan, Elizabeth Payne, Lynlee L. Lin, Sudipta Sinnya, Anthony P. Raphael, Duncan Lambie, Ian H. Frazer, Marcel E. Dinger, H. Peter Soyer, Tarl W. Prow
Software Mentions: 3
Published: about 9 years ago

10.1111/acel.12795

Differential aging-related changes in neurophysiology and gene expression in IB4-positive and IB4-negative nociceptive neurons
Cited by: 5
Author(s): Malgorzata A. Mis, Mark F. Rogers, Aaron R. Jeffries, Anna Wilbrey, Lubin Chen, Yang Yang, Sulayman D. Dib‐Hajj, Stephen G. Waxman, Edward B. Stevens, Andrew D. Randall
Software Mentions: 3
Published: over 8 years ago

10.18632/oncotarget.27112

Drivers of topoisomerase II poisoning mimic and complement cytotoxicity in AML cells
Cited by: 2
Author(s): Piyush More, Ute Goedtel-Armbrust, Viral Shah, Marianne Mathaes, Thomas Kindler, Miguel A. Andrade‐Navarro, Leszek Wojnowski
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-021-98420-y

Short-term transcriptomic response to plasma membrane injury
Cited by: 3
Author(s): Swantje Christin Häger, Catarina Dias, Stine Lauritzen Sønder, André Vidas Olsen, Isabelle da Piedade, Anne Sofie Busk Heitmann, Elena Papaleo, Jesper Nylandsted
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-95698-w

PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients
Cited by: 9
Author(s): Kota Fujisawa, Mamoru Shimo, Y-h. Taguchi, Shinya Ikematsu, Ryota Miyata
Software Mentions: 3
Published: about 5 years ago

10.7717/peerj.8592

fRNAkenseq: a fully powered-by-CyVerse cloud integrated RNA-sequencing analysis tool
Cited by: 2
Author(s): Allen Hubbard, Matthew Bomhoff, Carl J. Schmidt
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2020.01765

Identification of TYROBP and C1QB as Two Novel Key Genes With Prognostic Value in Gastric Cancer by Network Analysis
Cited by: 26
Author(s): Junjie Jiang, Yongfeng Ding, Mengjie Wu, Xiadong Lyu, Haifeng Wang, Yanyan Chen, Haiyong Wang, Lisong Teng
Software Mentions: 3
Published: about 6 years ago

10.3389/fonc.2021.707066

Cystatin-B Negatively Regulates the Malignant Characteristics of Oral Squamous Cell Carcinoma Possibly Via the Epithelium Proliferation/Differentiation Program
Cited by: 3
Author(s): Tiantian Xu, Xiao‐Wen Zeng, Xinhong Wang, Luxi Yang, Gang Luo, Ting Yu
Software Mentions: 3
Published: about 5 years ago

10.3389/fonc.2021.659201

Prognostic Prediction of Cytogenetically Normal Acute Myeloid Leukemia Based on a Gene Expression Model
Cited by: 4
Author(s): Yang Liu, Houyu Zhang, Xue Yang, Ting Lu, Shihui Ma, Hui Cheng, Kuangyu Yen, Tao Cheng
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.04775

Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns
Cited by: 77
Author(s): Alexander S. Mikheyev, Timothy A. Linksvayer
Software Mentions: 3
Published: almost 12 years ago

10.1038/s41598-021-96150-9

Transcriptomic analysis of the mouse retina after acute and chronic normobaric and hypobaric hypoxia
Cited by: 10
Author(s): Lynn J. A. Ebner, Marijana Samardzija, Federica Storti, Vyara Todorova, Duygu Karademir, Julian Behr, Fraser Simpson, Markus Thiersch, Christian Grimm
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-95423-7

Evolutionary transition of doublesex regulation from sex-specific splicing to male-specific transcription in termites
Cited by: 14
Author(s): Shôzô Miyazaki, Kokuto Fujiwara, Keima Kai, Yudai Masuoka, Hiroki Gotoh, Teruyuki Niimi, Yoshinobu Hayashi, Shuji Shigenobu, Kazuyuki Maekawa
Software Mentions: 3
Published: about 5 years ago

10.3389/fonc.2020.01029

Abnormal Food Timing Promotes Alcohol-Associated Dysbiosis and Colon Carcinogenesis Pathways
Cited by: 5
Author(s): Faraz Bishehsari, Shirin Moossavi, Phillip A. Engen, Xiaohan Liu, Yue Zhang
Software Mentions: 3
Published: over 6 years ago

10.1186/s13195-019-0558-0

APOE2 orchestrated differences in transcriptomic and lipidomic profiles of postmortem AD brain
Cited by: 36
Author(s): Iliya Lefterov, Cody M. Wolfe, Nicholas F. Fitz, Kyong Nyon Nam, Florent Letronne, Richard J. Biedrzycki, Julia Kofler, Xianlin Han, Jianing Wang, Jonathan Schug, Radosveta Koldamova
Software Mentions: 3
Published: almost 7 years ago

10.7717/peerj.3640

Expression differences inAphidius ervi(Hymenoptera: Braconidae) females reared on different aphid host species
Cited by: 11
Author(s): Gabriel I. Ballesteros, Juergen Gadau, Fabrice Legeai, Angélica González-González, Blas Lavandero, Jean Simon, Christian C. Figueroa
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-021-07367-x

The semi-dwarfing gene Rht-dp from dwarf polish wheat (Triticum polonicum L.) is the "Green Revolution” gene Rht-B1b
Cited by: 12
Author(s): Songyue Chai, Yao Qin, Xu Zhang, Xue Xiao, Xing Fan, Jian Zeng, Sha Li, Houyang Kang, Haiqin Zhang, Jun Li, Yong‐Hong Zhou, Yi Wang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13195-021-00810-x

Comorbidity between Alzheimer’s disease and major depression: a behavioural and transcriptomic characterization study in mice
Cited by: 15
Author(s): Ana Martín‐Sánchez, Janet Piñero, Lara Nonell, Magdalena Arnal, Elena M. Ribé, Alejo J. Nevado‐Holgado, Simon Lovestone, Ferrán Sanz, Laura I. Furlong, Olga Valverde
Software Mentions: 3
Published: over 5 years ago

10.1038/s42003-021-02223-w

Single-cell RNA sequencing of human nail unit defines RSPO4 onychofibroblasts and SPINK6 nail epithelium
Cited by: 8
Author(s): Hyun Je Kim, Joon Ho Shim, Ji-Hye Park, Hyun Tae Shin, Kee–Taek Jang, Woong-Yang Park, Kyung-Hoon Lee, Eun Ji Kwon, Hyung-Suk Jang, Hanseul Yang, Jong Hee Lee, Jun‐Mo Yang, Dong‐Youn Lee
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-94386-z

An epigenetic GPI anchor defect impairs TLR4 signaling in the B cell transdifferentiation model for primary human monocytes BLaER1
Cited by: 3
Author(s): Julia Wegner, Thomas Zillinger, Thais Marina Schlee-Guimarães, Eva Bartok, Martin Schlee
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.27529

A viral protein promotes host SAMS1 activity and ethylene production for the benefit of virus infection
Cited by: 55
Author(s): Shanshan Zhao, Wei Hong, Jiang Wu, Yu Wang, Shaoyi Ji, Shuyi Zhu, Chunhong Wei, Jinsong Zhang, Yang Li
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-021-93142-7

Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing
Cited by: 3
Author(s): Zoltán Maróti, Dóra Tombácz, Norbert Moldován, Gábor Torma, Victoria A Jefferson, Zsolt Csabai, Gábor Gulyás, Ákos Dörmő, Miklós Boldogkői, Tibor Kalmár, Florencia Meyer, Zsolt Boldogköi
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.26300

Exosomes impact survival to radiation exposure in cell line models of nervous system cancer
Cited by: 52
Author(s): Oliver Mrowczynski, A. Madhankumar, Jeffrey M. Sundstrom, Yuanjun Zhao, Yuka Imamura Kawasawa, Becky Slagle‐Webb, Christine Mau, Russell Payne, Elias Rizk, Brad E. Zacharia, James R. Connor
Software Mentions: 3
Published: almost 8 years ago

10.1155/2019/8016120

Study on miRNAs in Pan-Cancer of the Digestive Tract Based on the Illumina HiSeq System Data Sequencing
Cited by: 11
Author(s): Cheng-Chou Lai, Xuzhi Liang, Xiu-Yun Liang, Shaolin Ma, Junguo Li, Mingfang Shi, Xu Zhu, Huihua Lan, Jiang‐Hui Zeng
Software Mentions: 3
Published: about 7 years ago

10.1007/s00125-017-4500-3

Systems biology of the IMIDIA biobank from organ donors and pancreatectomised patients defines a novel transcriptomic signature of islets from individuals with type 2 diabetes
Cited by: 121
Author(s): Michele Solimena, Anke M. Schulte, Lorella Marselli, Florian Ehehalt, Daniela Richter, Manuela Kleeberg, Hassan Mziaut, Klaus-Peter Knoch, Julia Parnis, Marco Bugliani, Afshan Siddiq, Anne Jörns, Frédéric Burdet, Robin Liechti, Mara Suleiman, Daniel Margerie, Farooq Syed, Marius Distler, Robert Grützmann, Enrico Petretto, Aida Moreno‐Moral, Carolin Wegbrod, Anke Sönmez, Katja Pfriem, Anne Friedrich, Jörn Meinel, Claes B. Wollheim, Gustavo Baretton, Raphaël Scharfmann, Everson Nogoceke, Ezio Bonifacio, Dorothée Sturm, Birgit Meyer‐Puttlitz, Ugo Boggi, Hans‐Detlev Saeger, Franco Filipponi, Mathias Lesche, Paolo Meda, Andreas Dahl, Leonore Wigger, Ioannis Xénarios, Mario Falchi, Bernard Thorens, Jürgen Weitz, Krister Bokvist, Sigurd Lenzen, Guy A. Rutter, Philippe Froguel, Manon von Bülow, Mark Ibberson, Piero Marchetti
Software Mentions: 3
Published: almost 9 years ago

10.1093/ajcn/nqz012

Transcriptional changes in prostate of men on active surveillance after a 12-mo glucoraphanin-rich broccoli intervention—results from the Effect of Sulforaphane on prostate CAncer PrEvention (ESCAPE) randomized controlled trial
Cited by: 61
Author(s): Μαρία Τράκα, Antonietta Melchini, Jack Coode‐Bate, Omar Al Kadhi, Shikha Saha, Marianne Defernez, Perla Troncoso‐Rey, Helen Kibblewhite, Carmel M. O’Neill, Federico Bernuzzi, Laura Mythen, Jackie C. Hughes, Paul W. Needs, J. Dainty, George M. Savva, Robert Mills, Richard Y. Ball, Christopher S. Cooper, Richard Mithen
Software Mentions: 3
Published: over 7 years ago

10.1155/2020/6827057

Development of a Ten-lncRNA Signature Prognostic Model for Breast Cancer Survival: A Study with the TCGA Database
Cited by: 11
Author(s): Wenqing Zhou, Yongkui Pang, Yunmin Yao, Huiying Qiao
Software Mentions: 3
Published: about 6 years ago

10.7717/peerj.2834

Transcriptome analysis of the oriental melon (Cucumis meloL. var.makuwa) during fruit development
Cited by: 26
Author(s): Ah-Young Shin, Yongmin Kim, Namjin Koo, Su‐Min Lee, Seok-Hyeon Nahm, Suk‐Yoon Kwon
Software Mentions: 3
Published: almost 10 years ago

10.7554/eLife.43821

HDAC3 restrains CD8-lineage genes to maintain a bi-potential state in CD4+CD8+ thymocytes for CD4-lineage commitment
Cited by: 23
Author(s): Rachael Laura Philips, Jeong Heon Lee, Krutika S. Gaonkar, Pritha Chanana, Ji Young Chung, Sinibaldo Romero Arocha, Aaron Schwab, Tamás Ördög, Virginia Smith Shapiro
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-021-90412-2

Axonopathy precedes cell death in ocular damage mediated by blast exposure
Cited by: 9
Author(s): Nickolas Boehme, Adam Hedberg-Buenz, Nicole Tatro, Michael Bielecki, William C Castonguay, Todd E. Scheetz, Michael G. Anderson, Laura M. Dutca
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.25998

Bladder cancer detection by urinary extracellular vesicle mRNA analysis
Cited by: 21
Author(s): Taku Murakami, Cindy M. Yamamoto, Tomoshige Akino, Hiroshi Tanaka, Nobuyuki Fukuzawa, Hiroyoshi Suzuki, Takahiro Osawa, Takeshi Tsuji, Toshimori Seki, Hiroshi Harada
Software Mentions: 3
Published: about 8 years ago

10.1186/s12859-018-2251-x

An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease
Cited by: 23
Author(s): Ryohei Eguchi, Mohammand Bozlul Karim, Pingzhao Hu, Tetsuo Sato, Naoaki Ono, Shigehiko Kanaya, Md. Altaf‐Ul‐Amin
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-021-89207-2

Cold-induction of afadin in brown fat supports its thermogenic capacity
Cited by: 2
Author(s): Morten Lundh, Ali Altıntaş, Marco Tozzi, Odile Fabre, Tao Ma, Farnaz Shamsi, Zachary Gerhart-Hines, Romain Barrès, Yu–Hua Tseng, Brice Emanuelli
Software Mentions: 3
Published: over 5 years ago

10.3390/genes12040545

A Complex Gene Network Mediated by Ethylene Signal Transduction TFs Defines the Flower Induction and Differentiation in Olea europaea L.
Cited by: 2
Author(s): Amelia Salimonti, Ivano Forgione, Tiziana Maria Sirangelo, Guglielmo Puccio, Antonio Mauceri, Francesco Mercati, Francesco Sunseri, Fabrizio Carbone
Software Mentions: 3
Published: over 5 years ago

10.1038/s42003-020-0873-9

Pan-cancer molecular analysis of the RB tumor suppressor pathway
Cited by: 47
Author(s): Erik S. Knudsen, Ram Nambiar, Spencer R. Rosario, Dominic J. Smiraglia, David W. Goodrich, Agnieszka K. Witkiewicz
Software Mentions: 3
Published: over 6 years ago

10.18632/oncotarget.25552

ERα-mediated cell cycle progression is an important requisite for CDK4/6 inhibitor response in HR+ breast cancer
Cited by: 9
Author(s): Karineh Petrossian, Noriko Kanaya, Chiao Lo, Pei-Yin Hsu, Duc T. Nguyen, Lixin Yang, Lu Yang, Charles Warden, Xiwei Wu, Raju Pillai, Lauren Bernal, Chiun‐Sheng Huang, Laura Kruper, Yuan Yuan, George Somlo, Joanne Mortimer, Shiuan Chen
Software Mentions: 3
Published: over 8 years ago

10.1098/rsob.190141

Identification of a novel regulatory pathway for PPARα by RNA-seq characterization of the endothelial cell lipid peroxidative injury transcriptome
Cited by: 4
Author(s): Fangfang Dou, Beiling Wu, Sun Liang, Jiulin Chen, Te Liu, Zhihua Yu, Chuan Chen
Software Mentions: 3
Published: almost 7 years ago

10.3389/fcell.2021.727183

A Novel Pyroptosis-Associated Long Non-coding RNA Signature Predicts Prognosis and Tumor Immune Microenvironment of Patients With Breast Cancer
Cited by: 29
Author(s): Liqin Ping, Kaiming Zhang, Xueqi Ou, Xingsheng Qiu, Xia Xiao
Software Mentions: 3
Published: about 5 years ago

10.1186/s13071-018-2817-5

Genetic variation associated with increased insecticide resistance in the malaria mosquito, Anopheles coluzzii
Cited by: 21
Author(s): Bradley J. Main, Amanda Everitt, Anthony J. Cornel, Fereydoun Hormozdiari, Gregory C. Lanzaro
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.25787

Repression by PRDM13 is critical for generating precision in neuronal identity
Cited by: 34
Author(s): Bishakha Mona, Ana Uruena, Rahul K. Kollipara, Zhenzhong Ma, Mark D. Borromeo, Joshua C. Chang, Jane E. Johnson
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-021-88029-6

Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn & Fayoumi)
Cited by: 4
Author(s): Venkata Krishna Vanamamalai, Priyanka Garg, Gautham Kolluri, Ravi Kumar Gandham, Itishree Jali, Shailesh Sharma
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-87955-9

Induced pluripotent stem cells from subjects with Lesch-Nyhan disease
Cited by: 5
Author(s): Diane Sutcliffe, Ashok R. Dinasarapu, Jasper E. Visser, Joery den Hoed, Fatemeh Seifar, Piyush Joshi, Irène Ceballos-Picot, Tejas Sardar, Ellen J. Hess, Yan V. Sun, Zhexing Wen, Michael E. Zwick, Hyder A. Jinnah
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-018-4488-1

Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes
Cited by: 38
Author(s): Mahsa Khorramdelazad, Ido Bar, Paul Whatmore, Gabrielle Smetham, Vijay Bhaaskaria, Yuedong Yang, Shahla Hosseini Bai, Nitin Mantri, Yaoqi Zhou, Rebecca Ford
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.50845

A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols
Cited by: 34
Author(s): Vayu Maini Rekdal, Paola Nol Bernadino, Michael U. Luescher, Sina Kiamehr, Cuong H. Le, Jordan E. Bisanz, Peter J. Turnbaugh, Elizabeth N. Bess, Emily P. Balskus
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-018-2107-4

Watchdog – a workflow management system for the distributed analysis of large-scale experimental data
Cited by: 20
Author(s): Michael Kluge, Caroline C. Friedel
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-021-87278-9

Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)
Cited by: 8
Author(s): Lingshu Han, Yuena Sun, Yue Cao, Peng Gao, Zijiao Quan, Yaqing Chang, Jun Ding
Software Mentions: 3
Published: over 5 years ago

10.3390/genes12091374

Identification of Long Non-Coding RNAs Involved in Porcine Fat Deposition Using Two High-Throughput Sequencing Methods
Cited by: 5
Author(s): Yibing Liu, Ying Yu, Ai Hong, Fengxia Zhang, Xitong Zhao, Huatao Liu, Yong Shi, Kai Xing, Chuduan Wang
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-86795-x

Distinct transcriptomic response to Newcastle disease virus infection during heat stress in chicken tracheal epithelial tissue
Cited by: 2
Author(s): Perot Saelao, Ying Wang, Ganrea Chanthavixay, Vivian M. Yu, Rodrigo A. Gallardo, Jack C. M. Dekkers, Susan J. Lamont, T. Ross Kelly, Huaijun Zhou
Software Mentions: 3
Published: over 5 years ago

10.1186/s12967-020-02497-4

Identification and validation of stemness-related lncRNA prognostic signature for breast cancer
Cited by: 59
Author(s): Xiaoying Li, Yang Li, Xinmiao Yu, Feng Jin
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2164-13-459

Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae
Cited by: 52
Author(s): Agnieszka Podolska, Christian Anthon, Mads Bak, Niels Tommerup, Kerstin Skovgaard, Peter M. H. Heegaard, Jan Gorodkin, Susanna Cirera, Merete Fredholm
Software Mentions: 3
Published: about 14 years ago

10.1590/1678-4685-GMB-2016-0101

A comprehensive transcriptome analysis of skeletal muscles in two Polish pig breeds differing in fat and meat quality traits
Cited by: 32
Author(s): Katarzyna Piórkowska, Kacper Żukowski, Katarzyna Ropka‐Molik, M. Tyra, Artur Gurgul
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-016-1111-9

multiDE: a dimension reduced model based statistical method for differential expression analysis using RNA-sequencing data with multiple treatment conditions
Cited by: 5
Author(s): Guangliang Kang, Lijun Du, Hong Zhang
Software Mentions: 3
Published: over 10 years ago

10.7717/peerj.12091

Transcriptome analysis reveals the mechanism of stromal cell-derived factor-1 and exendin-4 synergistically promoted periodontal ligament stem cells osteogenic differentiation
Cited by: 0
Author(s): Wenyan Kang, Liqing Du, Qianyu Liang, Rui Zhang, Chunxu Lv, Shaohua Ge
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-12-480

GC-Content Normalization for RNA-Seq Data
Cited by: 656
Author(s): Davide Risso, Katja Schwartz, Gavin Sherlock, Sandrine Dudoit
Software Mentions: 3
Published: almost 15 years ago

10.7554/eLife.63731

CEP78 functions downstream of CEP350 to control biogenesis of primary cilia by negatively regulating CP110 levels
Cited by: 24
Author(s): André Gonçalves, Sarah Kirstine Hasselbalch, Beinta Biskopstø Joensen, Sebastian Patzke, Pernille Martens, Signe Krogh Ohlsen, Mathieu Quinodoz, Konstantinos Nikopoulos, Reem Suleiman, Magnus Per Damsø Jeppesen, Catja Weiss, Søren Tvorup Christensen, Carlo Rivolta, Jens S. Andersen, Pietro Farinelli, Lotte B. Pedersen
Software Mentions: 3
Published: over 5 years ago

10.3390/pathogens9020131

Metabolic Changes of Mycobacterium tuberculosis during the Anti-Tuberculosis Therapy
Cited by: 9
Author(s): Julia Bespyatykh, Egor Shitikov, Dmitry Bespiatykh, Andrei Guliaev, Ksenia M. Klimina, Vladimir A. Veselovsky, Georgij Arapidi, Marine Dogonadze, Viacheslav Zhuravlev, Elena Ilina, Vadim M. Govorun
Software Mentions: 3
Published: over 6 years ago

10.3389/fcell.2020.583434

Human Fetal Scalp Dermal Papilla Enriched Genes and the Role of R-Spondin-1 in the Restoration of Hair Neogenesis in Adult Mouse Cells
Cited by: 9
Author(s): Elizabeth Weber, Yung-Chih Lai, Mingxing Lei, Ting‐Xin Jiang, Cheng‐Ming Chuong
Software Mentions: 3
Published: almost 6 years ago

10.3389/fcell.2020.603815

Genome-Wide Integrated Analysis Revealed Functions of lncRNA–miRNA–mRNA Interaction in Growth of Intermuscular Bones in Megalobrama amblycephala
Cited by: 14
Author(s): Yulong Chen, Shiming Wan, Qing Li, Xiaoru Dong, Jinghan Diao, Qing Liao, Guiying Wang, Zexia Gao
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2020.602493

The Identification of Plasma Exosomal miR-423-3p as a Potential Predictive Biomarker for Prostate Cancer Castration-Resistance Development by Plasma Exosomal miRNA Sequencing
Cited by: 29
Author(s): Tianyu Guo, Yang Wang, Jing Jia, Xueying Mao, Elżbieta Stankiewicz, Glenda Scandura, Edwina Burke, Lei Xu, Jacek Marzec, Caitlin R. Davies, Jiaying Lu, Prabhakar Rajan, Alistair Grey, K. H. Tipples, John Hines, Sakunthala C. Kudahetti, Tim Oliver, Thomas Powles, Constantine Alifrangis, Manish Kohli, Greg Shaw, Wen Wang, Na Feng, Jonathan Shamash, Daniel M. Berney, Liang Wang, Yong‐Jie Lu
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-021-84080-5

Persistent COUP-TFII expression underlies the myopathy and impaired muscle regeneration observed in resistance to thyroid hormone-alpha
Cited by: 1
Author(s): Paola Aguiari, Yanyun Liu, Astgik Petrosyan, Sheue-yann Cheng, Gregory A. Brent, Laura Perin, Anna Milanesi
Software Mentions: 3
Published: over 5 years ago

10.3390/pathogens10091127

Delineating the Role of Aedes aegypti ABC Transporter Gene Family during Mosquito Development and Arboviral Infection via Transcriptome Analyses
Cited by: 8
Author(s): Vijoy Kumar, Shilpi Garg, Lalita Gupta, Kuldeep Gupta, Cheikh Tidiane Diagne, Dorothée Missé, Julien Pompon, Sanjeev Kumar, Vishal Saxena
Software Mentions: 3
Published: about 5 years ago

10.1534/genetics.120.303155

Rif1 Functions in a Tissue-Specific Manner To Control Replication Timing Through Its PP1-Binding Motif
Cited by: 11
Author(s): Robin L. Armstrong, Souradip Das, Christina A. Hill, Robert J. Duronio, Jared Nordman
Software Mentions: 3
Published: over 6 years ago

10.1186/s12915-021-01049-6

Sexual conflict drives micro- and macroevolution of sexual dimorphism in immunity
Cited by: 21
Author(s): Basabi Bagchi, Quentin Corbel, Imroze Khan, Ellen Payne, D. Banerji, Johanna Liljestrand-Rönn, Ivain Martinossi‐Allibert, Julian Baur, Ahmed Sayadi, Elina Immonen, Göran Arnqvist, Irene Söderhäll, David Berger
Software Mentions: 3
Published: over 5 years ago

10.1016/j.gdata.2015.12.027

Transcriptional profiling of the epigenetic regulator Smchd1
Cited by: 12
Author(s): Ruijie Liu, Kelan Chen, Natasha Jansz, Marnie E. Blewitt, Matthew E. Ritchie
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-021-81639-0

Loss of Parkinson’s susceptibility gene LRRK2 promotes carcinogen-induced lung tumorigenesis
Cited by: 21
Author(s): Chandra B. Lebovitz, Nicole Wretham, Maryam Osooly, Katy Milne, Tia Dash, Shelby Thornton, Basile Tessier‐Cloutier, Paalini Sathiyaseelan, Svetlana Bortnik, Nancy E. Go, Elizabeth C. Halvorsen, Rachel A. Cederberg, Norman S. Chow, Nancy Dos Santos, Kevin L. Bennewith, Brad H. Nelson, Marcel B. Bally, Wan L. Lam, Sharon M. Gorski
Software Mentions: 3
Published: almost 6 years ago

10.3389/fcell.2021.580834

Construction of circRNA-miRNA-mRNA Network for Exploring Underlying Mechanisms of Lubrication Disorder
Cited by: 2
Author(s): Shengnan Cong, Jinlong Li, Jingjing Zhang, Jingyi Feng, Aixia Zhang, Lianjun Pan, Jianhua Ma
Software Mentions: 3
Published: over 5 years ago

10.1186/gb-2010-11-10-r106

Differential expression analysis for sequence count data
Cited by: 12,645
Author(s): Simon Anders, Wolfgang Huber
Software Mentions: 3
Published: about 16 years ago

10.3390/pathogens8030132

Whole Transcriptome Analysis of Aedes albopictus Mosquito Head and Thorax Post-Chikungunya Virus Infection
Cited by: 9
Author(s): Ravikiran Vedururu, Matthew J. Neave, Vinod Sundaramoorthy, Diane Green, Jennifer Harper, Paul R Gorry, Jean‐Bernard Duchemin, Prasad N. Paradkar
Software Mentions: 3
Published: about 7 years ago

10.7554/eLife.33057

ZFP36 RNA-binding proteins restrain T cell activation and anti-viral immunity
Cited by: 83
Author(s): Michael J. Moore, Nathalie E. Blachère, John Fak, Christopher Y. Park, Kirsty Sawicka, Salina Parveen, Ilana Zucker-Scharff, Bruno Moltedo, Alexander Y. Rudensky, Robert B. Darnell
Software Mentions: 3
Published: over 8 years ago

10.1186/gb-2012-13-11-r102

Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs
Cited by: 63
Author(s): Ana C. Marques, Jennifer Y. Tan, Sheena Lee, Lesheng Kong, Andreas Heger, Chris P. Ponting
Software Mentions: 3
Published: almost 15 years ago

10.3389/fcell.2020.00520

Multi-Omic Approach to Identify Phenotypic Modifiers Underlying Cerebral Demyelination in X-Linked Adrenoleukodystrophy
Cited by: 11
Author(s): Phillip A. Richmond, Frans van der Kloet, Frédéric M. Vaz, David T.S. Lin, Anuli Uzozie, Emma Graham, Michael S. Kobor, Sara Mostafavi, Perry D. Moerland, Philipp F. Lange, Antoine H. C. van Kampen, Wyeth W. Wasserman, Marc Engelen, Stephan Kemp, Clara van Karnebeek
Software Mentions: 3
Published: over 6 years ago

10.1186/gb-2013-14-8-r89

The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus
Cited by: 191
Author(s): Erich M. Schwarz, Pasi K. Korhonen, Bronwyn E. Campbell, Neil D. Young, Aaron R. Jex, Abdul Jabbar, Ross S. Hall, Alinda Mondal, Adina Howe, Jason Pell, Andreas Hofmann, Peter R. Boag, Xing‐Quan Zhu, T. Ryan Gregory, Alex Loukas, Brian A. Williams, Igor Antoshechkin, C. Titus Brown, Paul W. Sternberg, Robin B. Gasser
Software Mentions: 3
Published: almost 14 years ago

10.1038/s41598-021-81085-y

Early stability and late random tumor progression of a HER2-positive primary breast cancer patient-derived xenograft
Cited by: 6
Author(s): Lorena Landuzzi, Arianna Palladini, Claudio Ceccarelli, Sofia Asioli, Giordano Nicoletti, Veronica Giusti, Francesca Ruzzi, Marianna L. Ianzano, Laura Scalambra, Roberta Laranga, Tania Balboni, Maddalena Arigoni, Martina Olivero, Raffaele Calogero, Carla De Giovanni, Massimiliano Dall’Ora, Enrico Di Oto, Donatella Santini, Maria Pia Foschini, M.C. Cucchi, Simone Zanotti, Mario Taffurelli, Patrizia Nanni, Pier‐Luigi Lollini
Software Mentions: 3
Published: almost 6 years ago

10.3389/fcell.2021.663032

Phenotypically Anchored mRNA and miRNA Expression Profiling in Zebrafish Reveals Flame Retardant Chemical Toxicity Networks
Cited by: 6
Author(s): Subham Dasgupta, Cheryl L. Dunham, Lisa Truong, Michael T. Simonich, Christopher Sullivan, Robyn L Tanguay
Software Mentions: 3
Published: over 5 years ago

10.1042/BSR20210284

Expression level of long non-coding RNA colon adenocarcinoma hypermethylated serves as a novel prognostic biomarker in patients with thyroid carcinoma
Cited by: 5
Author(s): Yong Xiao, Youbing Tu, Yuantao Li
Software Mentions: 3
Published: over 5 years ago

10.3390/pathogens10020167

Characterization of the Rhipicephalus (Boophilus) microplus Sialotranscriptome Profile in Response to Theileria equi Infection
Cited by: 5
Author(s): Patrícia Gonzaga Paulino, Gabriela Lopes Vivas Vitari, Antônio Mauro Rezende, Joana Couto, Sandra Antunes, Ana Domingos, Maristela Peckle, Carlos Luiz Massard, Flávio Marcos Gomes Araújo, Huarrisson Azevedo Santos
Software Mentions: 3
Published: over 5 years ago

10.1186/s12915-018-0578-4

Cell type-specific expression profiling unravels the development and evolution of stinging cells in sea anemone
Cited by: 57
Author(s): Kartik Sunagar, Yaara Y Columbus-Shenkar, Arie Fridrich, Nadya Gutkovich, Reuven Aharoni, Yehu Moran
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-021-07536-y

Expression characteristics of pineal miRNAs at ovine different reproductive stages and the identification of miRNAs targeting the AANAT gene
Cited by: 1
Author(s): Ran Di, Qiu Yue Liu, Shu Hui Song, Dong Tian, Jian He, Ying Ge, Xiang Yu Wang, Wen Hu, Joram M. Mwacharo, Zhang Yuan Pan, Jian Dong Wang, Qing Ma, G. L. Cao, Hui Jin, Liang Xiao, M. X. Chu
Software Mentions: 3
Published: over 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568