bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1186/s12864-021-07402-x

Impacts of fludioxonil resistance on global gene expression in the necrotrophic fungal plant pathogen Sclerotinia sclerotiorum
Cited by: 6
Author(s): Akeem Owolabi Taiwo, Lincoln A. Harper, Mark Derbyshire
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-016-2552-2

De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.)
Cited by: 43
Author(s): Ming Li, Zhaoxu Liang, Yuan Zeng, Yan Ji, Kai–Chao Wu, Jun Liang, Shikun He, Guanyu Wang, Zhanghong Mo, Feiquan Tan, Li Song, Wang LunWang
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-015-1555-8

An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data
Cited by: 10
Author(s): Yejun Wang, Keith D. MacKenzie, Aaron P. White
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-13-278

Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers
Cited by: 86
Author(s): Ying Wang, Vinayak Brahmakshatriya, Blanca Lupiani, Sanjay M. Reddy, Benjamin Soibam, Ashley Benham, Preethi H. Gunaratne, Hsiao‐Ching Liu, Nares Trakooljul, Nancy H. Ing, Ron Okimoto, Huaijun Zhou
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-14-763

Comparative transcriptome analysis of geographically distinct virulent and attenuated Babesia bovis strains reveals similar gene expression changes through attenuation
Cited by: 50
Author(s): Monica J. Pedroni, Kerry S. Sondgeroth, Gina M Gallego-López, Ignacio Echaide, Audrey O.T. Lau
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-015-1667-1

De novo assembly of the Carcinus maenas transcriptome and characterization of innate immune system pathways
Cited by: 46
Author(s): Bas Verbruggen, Lisa K. Bickley, Eduarda M. Santos, Charles R. Tyler, Grant D. Stentiford, Kelly S. Bateman, Ronny van Aerle
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-018-5318-1

Differential responses of Lasiopodomys mandarinus and Lasiopodomys brandtii to chronic hypoxia: a cross-species brain transcriptome analysis
Cited by: 13
Author(s): Qianqian Dong, Luye Shi, Yangwei Li, Mengwan Jiang, Hong Sun, Baishi Wang, Han Cheng, Yifeng Zhang, Tian Shao, Yuhua Shi, Zhenlong Wang
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-020-6494-3

Transcriptomic analysis of the testicular fusion in Spodoptera litura
Cited by: 5
Author(s): Yaqing Chang, Jun Ou, Yucheng Liu, Qiong Wu, Liang Wen, Sichun Zheng, Li Sheng, Qili Feng, Lin Liu
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-021-07879-6

Analyzing the gonadal transcriptome of the frog Hoplobatrachus rugulosus to identify genes involved in sex development
Cited by: 5
Author(s): Yun Tang, Jing-Yi Chen, Guohua Ding, Lin Zhen-shan
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-6082-6

A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression
Cited by: 13
Author(s): Stewart T. G. Burgess, Edward J Marr, Kathryn Bartley, Francesca Nunn, Rachel E. Down, Robert J. Weaver, Jessica C. Prickett, J. A. Dunn, Stéphane Rombauts, Thomas Van Leeuwen, Yves Van de Peer, Alasdair J. Nisbet
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2164-14-400

The acute transcriptional response of the coral Acropora millepora to immune challenge: expression of GiMAP/IAN genes links the innate immune responses of corals with those of mammals and plants
Cited by: 43
Author(s): Yvonne Weiss, Sylvain Forêt, David C. Hayward, Tracy D. Ainsworth, Rob King, Eldon E. Ball, David J. Miller
Software Mentions: 1
Published: over 13 years ago

10.1186/s12864-020-06869-4

Comparative RNA-Seq transcriptome analyses reveal dynamic time-dependent effects of 56Fe, 16O, and 28Si irradiation on the induction of murine hepatocellular carcinoma
Cited by: 5
Author(s): Anna M. Nia, Kamil Khanipov, Brooke L. Barnette, Robert L. Ullrich, George Golovko
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-017-3515-y

Transcriptome profiling of the floating-leaved aquatic plant Nymphoides peltata in response to flooding stress
Cited by: 7
Author(s): Juanxia Wu, Huabin Zhao, Dan Yu, Xinglong Xu
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-021-07825-6

Maternal cold exposure induces distinct transcriptome changes in the placenta and fetal brown adipose tissue in mice
Cited by: 3
Author(s): Sujoy Ghosh, Chul‐Hong Park, Jisu Lee, Nathan Lee, Rui Zhang, Clara Huesing, Dorien Reijnders, Jenny L. Sones, Heike Münzberg, Leanne M. Redman, Jason Y. Chang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-5823-x

Understanding the liver under heat stress with statistical learning: an integrated metabolomics and transcriptomics computational approach
Cited by: 15
Author(s): Allen Hubbard, Xiaoke Zhang, Sara Jastrebski, Abhyudai Singh, Carl J. Schmidt
Software Mentions: 1
Published: over 7 years ago

10.1186/s12865-021-00439-3

Differential long non-coding RNA expression profile and function analysis in primary Sjogren’s syndrome
Cited by: 7
Author(s): Xiaochan Chen, Qi Cheng, Yan Du, Lei Liu, Huaxiang Wu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12865-019-0292-1

Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in HeLa cells
Cited by: 25
Author(s): Yue Tu, Xiongfei Wu, Fengyun Yu, Jianzhong Dang, Juan Wang, Yaxun Wei, Zhitao Cai, Zhipeng Zhou, Wenbiao Liao, Lian Li, Yi Zhang
Software Mentions: 1
Published: over 7 years ago

10.1186/s12881-019-0936-2

POLE mutations improve the prognosis of endometrial cancer via regulating cellular metabolism through AMF/AMFR signal transduction
Cited by: 19
Author(s): Yiran Li, Yiding Bian, Kai Wang, Xiaoping Wan
Software Mentions: 1
Published: almost 7 years ago

10.1093/brain/awab123

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

10.3390/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

10.3390/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

10.1186/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

10.1186/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

10.1186/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/s12935-021-01839-6

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

10.1186/s12935-021-01808-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/s12935-021-02075-8

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

10.1186/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

10.1186/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/s12935-019-1040-6

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

10.1186/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

10.1186/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

10.1186/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/s12935-020-01388-4

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/s12935-020-01483-6

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/s12935-018-0704-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/s12935-019-0901-3

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/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

10.1002/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

10.1002/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

10.1002/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/cam4.719

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/cam4.3963

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

10.1002/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/cam4.2089

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/cam4.432

<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

10.1002/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

10.1186/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

10.1186/2049-3002-1-11

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

10.26508/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

10.26508/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

10.26508/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.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

10.3390/v13071325

Virus-Targeted Transcriptomic Analyses Implicate Ranaviral Interaction with Host Interferon Response in Frog Virus 3-Infected Frog Tissues
Cited by: 1
Author(s): Yun Tian, Francisco De Jesús Andino, Collins N. Khwatenge, Jiuyi Li, Jacques Robert, Yongming Sang
Software Mentions: 1
Published: over 5 years ago

10.3390/v13071293

Transcriptome and Proteomic Analysis Reveals Up-Regulation of Innate Immunity-Related Genes Expression in Caprine Herpesvirus 1 Infected Madin Darby Bovine Kidney Cells
Cited by: 0
Author(s): Hao Fei, Xing Xie, Maojun Liu, Mao Li, Wenliang Li, Woonsung Na
Software Mentions: 1
Published: over 5 years ago

10.1186/s12957-021-02362-8

Effects of EFNA1 on cell phenotype and prognosis of esophageal carcinoma
Cited by: 2
Author(s): Yongqiang Zhang, Jinning Zhang, Guanlong Pan, Tianhao Guan, Changhao Zhang, A. Hao, Yan Li, Hai Ren
Software Mentions: 1
Published: about 5 years ago

10.1186/s13071-020-04155-6

Glucose transporter GLUT1 influences Plasmodium berghei infection in Anopheles stephensi
Cited by: 4
Author(s): Mengfei Wang, Jingwen Wang
Software Mentions: 1
Published: over 6 years ago

10.1186/s13071-016-1856-z

Preliminary analysis of Psoroptes ovis transcriptome in different developmental stages
Cited by: 15
Author(s): Manli He, Jing Xu, Ran He, Nengxing Shen, Xiaobin Gu, Xuerong Peng, Guangyou Yang
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13071-021-04624-6

Time-resolved transcriptional profiling of Trichinella-infected murine myocytes helps to elucidate host–pathogen interactions in the muscle stage
Cited by: 1
Author(s): Xiaoxiang Hu, Xiaolei Liu, Chen Li, Zhang Yu-lu, Chengyao Li, Yanfeng Li, Yingxi Chen, Hao Guo, Xue Bai, Mingyuan Liu
Software Mentions: 1
Published: over 5 years ago

10.1186/s13071-017-2312-4

Sialotranscriptomics of Rhipicephalus zambeziensis reveals intricate expression profiles of secretory proteins and suggests tight temporal transcriptional regulation during blood-feeding
Cited by: 20
Author(s): Minique H. de Castro, Daniël de Klerk, Ronel Pienaar, D. J. G. Rees, Ben J. Mans
Software Mentions: 1
Published: about 9 years ago

10.1186/s13071-020-04173-4

Catalogue of stage-specific transcripts in Ixodes ricinus and their potential functions during the tick life-cycle
Cited by: 10
Author(s): Pavlína Věchtová, Zoltán Füssy, Radim Čegan, Ján Štěrba, Jan Erhart, Vladimı́r Beneš, Libor Grubhoffer
Software Mentions: 1
Published: over 6 years ago

10.1186/s13071-020-04457-9

RNA sequencing analysis of altered expression of long noncoding RNAs associated with Schistosoma japonicum infection in the murine liver and spleen
Cited by: 9
Author(s): Tianqi Xia, Bikash Ranjan Giri, Jingyi Liu, Pengfei Du, Xue Li, Xuxin Li, Shun Li, Guofeng Cheng
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13071-020-3910-0

Expanded complement of Niemann-Pick type C2-like protein genes in Clonorchis sinensis suggests functions beyond sterol binding and transport
Cited by: 3
Author(s): Marziyeh Anari, Andreas J. Stroehlein, Ross S. Hall, Bill C.H. Chang, Robin B. Gasser, Neil D. Young
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13071-020-3914-9

Proteins involved in the biosynthesis of lipophosphoglycan in Leishmania: a comparative genomic and evolutionary analysis
Cited by: 6
Author(s): Lucas Gentil Azevedo, Artur T. L. Queiroz, Aldina Barral, Luciane Amorim Santos, Pablo Ivan Pereira Ramos
Software Mentions: 1
Published: over 6 years ago

10.3390/pathogens6040068

Prebiotic Oligosaccharides Potentiate Host Protective Responses against L. Monocytogenes Infection
Cited by: 20
Author(s): Poyin Chen, Taylor Reiter, Bihua C. Huang, Nguyet Kong, Bart C. Weimer
Software Mentions: 1
Published: almost 9 years ago

10.1016/j.patter.2021.100246

Quantum processor-inspired machine learning in the biomedical sciences
Cited by: 14
Author(s): Richard Y. Li, Sharvari Gujja, Sweta R. Bajaj, Omar Gamel, Nicholas A. Cilfone, Jeffrey R. Gulcher, Daniel A. Lidar, Thomas Chittenden
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.3529

Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity
Cited by: 11
Author(s): Michael Gerth, Gregory D. D. Hurst
Software Mentions: 1
Published: over 9 years ago

10.7717/peerj.11239

Integrated metabolome and transcriptome revealed the flavonoid biosynthetic pathway in developing Vernonia amygdalina leaves
Cited by: 9
Author(s): Lanya Shui, Kaisen Huo, Yan Chen, Zilin Zhang, Yanfang Li, Jun Niu
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.7743

Transcriptomic responses of hypothalamus to acute exercise in type 2 diabetic Goto-Kakizaki rats
Cited by: 3
Author(s): Shuang Fu, Yuhuan Meng, Shudai Lin, Wenlu Zhang, Yuting He, Lizhen Huang, Hongli Du
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.8403

Differentially expressed genes and key molecules of BRCA1/2-mutant breast cancer: evidence from bioinformatics analyses
Cited by: 12
Author(s): Yue Li, Xiaoyan Zhou, Jiali Liu, Yin Yang, Xin Yuan, Rui Yang, Qi Wang, Jing Ji, Qian He
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.8035

Transcriptome sequencing of Verticillium dahliae from a cotton farm reveals positive correlation between virulence and tolerance of sugar-induced hyperosmosis
Cited by: 0
Author(s): Jin Li, Juan Perucho, Yuanyuan Liu, Wenwen Xia, Fengfeng Cheng, Wenhui Tian, Lin Zhang, Jianbo Zhu, Aiying Wang
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.1549

In plantacomparative transcriptomics of host-adapted strains ofRalstonia solanacearum
Cited by: 25
Author(s): Florent Ailloud, Tiffany M. Lowe, Isabelle Robène, Stéphane Cruveiller, Caitilyn Allen, Philippe Prior
Software Mentions: 1
Published: almost 11 years ago

10.7717/peerj.7261

Comparative transcriptomic and proteomic analyses of the green and white parts of chimeric leaves in Ananas comosus var. bracteatus
Cited by: 10
Author(s): Ying Xue, Jun Ma, Yehua He, Shuang Yu, Zhen Yuan Lin, Yingyuan Xiong, Fatima Rafique, Fuxing Jiang, Lina Sun, Min Ma, Yujue Zhou, Xi Li, Zhuo Huang
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.6402

In silico analysis reveals a shared immune signature in CASP8-mutated carcinomas with varying correlations to prognosis
Cited by: 7
Author(s): Yashoda Ghanekar, Subhashini Sadasivam
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.2977

Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genusMacrobrachium: identification and expression validation in a model species (M. koombooloomba)
Cited by: 26
Author(s): Rahi Lifat, Shorash Amin, Peter B. Mather, David A. Hurwood
Software Mentions: 1
Published: over 9 years ago

10.7717/peerj.4500

Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq
Cited by: 30
Author(s): Liuxin Xiang, Chaowei Cai, Jieru Cheng, Lu Wang, Chaofeng Wu, Yùzhēn Shí, Jingzhi Luo, Lin He, Yushan Deng, Xiao Zhang, Yǒulù Yuán, Yingfan Cai
Software Mentions: 1
Published: over 8 years ago

10.7717/peerj.8368

Genome-wide analysis of lncRNAs, miRNAs, and mRNAs forming a prognostic scoring system in esophageal squamous cell carcinoma
Cited by: 12
Author(s): Xun Shi, You Li, Yehuan Sun, Xu Zhao, Xin Sun, Tuotuo Gong, Zhinan Liang, Yuan Ma, Xiaozhi Zhang
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.3959

Comparative analysis of the microRNA transcriptome between yak and cattle provides insight into high-altitude adaptation
Cited by: 37
Author(s): Jiuqiang Guan, Keren Long, Jideng Ma, Jinwei Zhang, Dafang He, Long Jin, Qianzi Tang, Anan Jiang, Xun Wang, Yaodong Hu, Shilin Tian, Zhi Jiang, Mingzhou Li, Xiaolin Luo
Software Mentions: 1
Published: almost 9 years ago

10.7717/peerj.7442

Integrated mRNA and miRNA profiling in NIH/3T3 cells in response to bovine papillomavirus E6 gene expression
Cited by: 4
Author(s): Feng Pang, Mengmeng Zhang, Guohua Li, Zhenxing Zhang, Haifeng Huang, Baobao Li, Chengqiang Wang, Xiaohong Yang, Yiying Zheng, Q. An, Luyin Zhang, Lijun Du, Fengyang Wang
Software Mentions: 1
Published: about 7 years ago

10.7717/peerj.11135

Combining transcriptome analysis and GWAS for identification and validation of marker genes in the Physalis peruviana-Fusarium oxysporum pathosystem
Cited by: 0
Author(s): Gina A. Garzón-Martínez, Francy Liliana García Arias, Felix E. Enciso-Rodríguez, Mauricio Soto‐Suárez, Carolina González, Aureliano Bombarely, Luz Stella Barrero, Jaime A. Osorio Guarín
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.10328

Deregulation of lysophosphatidic acid metabolism in oral cancer promotes cell migration via the up-regulation of COX-2
Cited by: 3
Author(s): Mariati Abdul Rahman, Malcolm Tan, Steven P. Johnson, Robert Hollows, Wen Lin Chai, Jason Peter Mansell, Lee Fah Yap, Ian C. Paterson
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.5307

A novel long non-coding RNA, AC012456.4, as a valuable and independent prognostic biomarker of survival in oral squamous cell carcinoma
Cited by: 11
Author(s): Xuegang Hu, Zailing Qiu, Jianchai Zeng, Tingting Xiao, Zhihong Ke, Hongbing Lyu
Software Mentions: 1
Published: about 8 years ago

10.7717/peerj.11755

Identification and expression profile of the soil moisture and Ralstonia solanacearum response CYPome in ginger (Zingiber officinale)
Cited by: 2
Author(s): Mengjun Huang, Haitao Xing, Zhexin Li, Honglei Li, Lin Wu, Yi Jiang
Software Mentions: 1
Published: about 5 years ago

10.7717/peerj.10654

Freshwater sponge hosts and their green algae symbionts: a tractable model to understand intracellular symbiosis
Cited by: 9
Author(s): Chelsea Hall, Sara Camilli, Henry Dwaah, Benjamin Kornegay, Christie A. Lacy, Malcolm Hill, Andrew P. Hill
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.1591

The Iflaviruses Sacbrood virus and Deformed wing virus evoke different transcriptional responses in the honeybee which may facilitate their horizontal or vertical transmission
Cited by: 54
Author(s): Eugene V. Ryabov, Jessica Fannon, Jonathan D. Moore, Graham R. Wood, David J. Evans
Software Mentions: 1
Published: almost 11 years ago

10.7717/peerj.8609

Genome sequencing of Aspergillus glaucus ‘CCHA’ provides insights into salt-stress adaptation
Cited by: 4
Author(s): Wenmin Qiu, Jingen Li, Wei Yi, Fan Feng, Jing Jiang, Mingying Liu, Xiaojiao Han, Chaoguang Tian, Shihong Zhang, Renying Zhuo
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.10668

An integrated analysis of lncRNA and mRNA expression profiles in the kidneys of mice with lupus nephritis
Cited by: 4
Author(s): Juan Wang, Xiongfei Wu, Yue Tu, Jianzhong Dang, Zhitao Cai, Wenjing Liao, Weili Quan, Yaxun Wei
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.7102

Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots
Cited by: 1
Author(s): Wang Wei, Sunil Kumar Singh, Xiwen Li, Hui Sun, Yu Ye, Min Jiang, Hailing Zi, Renyi Liu, Huiming Zhang, Zhaoqing Chu
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.8776

Physiological parameters and differential expression analysis of N-phenyl-N′-[6-(2-chlorobenzothiazol)-yl] urea-induced callus of Eucalyptus urophylla × Eucalyptus grandis
Cited by: 4
Author(s): Lejun Ouyang, Zechen Wang, Limei Li, Baoling Chen
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.8379

Comparative transcriptome analysis revealed genes involved in the fruiting body development ofOphiocordyceps sinensis
Cited by: 12
Author(s): Xuhui Tong, Han Zhang, Fang Wang, Zhengyao Xue, Jing Cao, Cheng Peng, Jianbin Guo
Software Mentions: 1
Published: almost 7 years ago

10.7717/peerj.8394

LINC00844 promotes proliferation and migration of hepatocellular carcinoma by regulating NDRG1 expression
Cited by: 11
Author(s): Zhou Wei, Kang Huang, Qiuyan Zhang, Shaojun Ye, Zibiao Zhong, Cheng Zeng, Guizhu Peng, Ling Li, Qifa Ye
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.10223

Transcriptome and gene expression analysis ofRhynchophorus ferrugineus(Coleoptera: Curculionidae) during developmental stages
Cited by: 8
Author(s): Hui Yang, Danping Xu, Zhihang Zhuo, Jingjing Hu, Binfeng Lu
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.2520

A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)
Cited by: 26
Author(s): Moshtaghi Azam, Md. Lifat Rahi, Tuan Viet Nguyen, Peter B. Mather, David A. Hurwood
Software Mentions: 1
Published: about 10 years ago

10.7717/peerj.9262

Identification of gene expression and DNA methylation of SERPINA5 and TIMP1 as novel prognostic markers in lower-grade gliomas
Cited by: 8
Author(s): Wenjing Zeng, Yang Yi, Zhipeng Wen, Peng Chen, Xiaoping Chen, Zhicheng Gong
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.4276

Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungusPecoramyces ruminantiumstrain C1A
Cited by: 17
Author(s): Shelby Calkins, Nicole C. Elledge, Katherine E. Mueller, Stephen M. Marek, Matthew Brian Couger, Mostafa S. Elshahed, Noha H. Youssef
Software Mentions: 1
Published: over 8 years ago

10.7717/peerj.10249

Prognostic model of invasive ductal carcinoma of the breast based on differentially expressed glycolysis-related genes
Cited by: 2
Author(s): Xiaoping Li, Qihe Yu, Jishang Chen, Hui Huang, Zhuangsheng Liu, Chengxing Wang, Yuan He, Xin Zhang, Weiwen Li, Chao Li, Jinglin Zhao, Wansheng Long
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.10976

Transcriptome profiling reveals histone deacetylase 1 gene overexpression improves flavonoid, isoflavonoid, and phenylpropanoid metabolism in Arachis hypogaea hairy roots
Cited by: 2
Author(s): Liangchen Su, Shuai Liu, Xing Liu, Baihong Zhang, Meijuan Li, Lidan Zeng, Ling Li
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.11781

Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris
Cited by: 5
Author(s): Sandra Cervantes, Jaana Vuosku, Tanja Pyhäjärvi
Software Mentions: 1
Published: about 5 years ago

10.7717/peerj.9021

Identification of exosomal miRNAs associated with the anthracycline-induced liver injury in postoperative breast cancer patients by small RNA sequencing
Cited by: 14
Author(s): Yue Zhang, Di Wang, Di Shen, Yang Luo, Yi‐Qun Che
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0116437

Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle
Cited by: 19
Author(s): Yaokun Li, José A. Carrillo, Yi Ding, Yanghua He, Chunping Zhao, Zan Liu, Jiuzhou Song
Software Mentions: 1
Published: over 11 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568