bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-017-14673-6

Epigenetics and adaptive phenotypic variation between habitats in an asexual snail
Cited by: 50
Author(s): Jennifer L. M. Thorson, Mark W. Smithson, Daniel Beck, Ingrid Sadler‐Riggleman, Eric Nilsson, Mark F. Dybdahl, Michael K. Skinner
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0228078

Transcriptome analysis to identify candidate genes associated with the yellow-leaf phenotype of a Cymbidium mutant generated by γ-irradiation
Cited by: 8
Author(s): Sang Hoon Kim, Se Won Kim, Gah‐Hyun Lim, Jae Il Lyu, Hong‐Il Choi, Yeong Deuk Jo, Si-Yong Kang, Byoung-Cheorl Kang, Jin-Baek Kim
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0113091

Comparative Transcriptomic Analysis of the Response to Cold Acclimation in Eucalyptus dunnii
Cited by: 18
Author(s): Yiqing Liu, Yi Jiang, Jianbin Lan, Yong Zou, Junping Gao
Software Mentions: 1
Published: almost 12 years ago

10.1038/s41598-017-14736-8

Differential gene expression of Australian Cricotopus draysoni (Diptera: Chironomidae) populations reveals seasonal association in detoxification gene regulation
Cited by: 5
Author(s): Matt N. Krosch, Litticia M. Bryant, Sue Vink
Software Mentions: 1
Published: almost 9 years ago

10.3390/ani10030468

MiRNAs and mRNAs Analysis during Abdominal Preadipocyte Differentiation in Chickens
Cited by: 19
Author(s): Xiangfei Ma, Junwei Sun, Shuaipeng Zhu, Zhenwei Du, Donghua Li, Wenting Li, Zhuanjian Li, Yadong Tian, Xiangtao Kang, Guirong Sun
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-13999-5

The non-invasive exfoliated transcriptome (exfoliome) reflects the tissue-level transcriptome in a mouse model of NSAID enteropathy
Cited by: 19
Author(s): Canaan Whitfield-Cargile, Noah D. Cohen, Kejun He, Ivan Ivanov, Jennifer S. Goldsby, Ana M. Chamoun‐Emanuelli, Brad R. Weeks, Laurie A. Davidson, Robert S. Chapkin
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-015-2150-8

The comprehensive immunomodulation of NeurimmiRs in haemocytes of oyster Crassostrea gigas after acetylcholine and norepinephrine stimulation
Cited by: 25
Author(s): Hao Chen, Lingling Wang, Zhi Zhou, Zujun Hou, Zhaoqun Liu, Weilin Wang, Dahai Gao, Qiang Gao, Mengqiang Wang, Linsheng Song
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-017-14808-9

Antibiotics induce polarization of pleural macrophages to M2-like phenotype in patients with tuberculous pleuritis
Cited by: 13
Author(s): Sisi Wang, Jian Zhang, Liyan Sui, Hao Xu, Qianling Piao, Ying Liu, Xiangping Qu, Ying Sun, Lei Song, Dan Li, Liping Peng, Shucheng Hua, Guangan Hu, Jianzhu Chen
Software Mentions: 1
Published: almost 9 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: about 11 years ago

10.1186/s12864-020-07113-9

De novo transcriptome assembly from the gonads of a scleractinian coral, Euphyllia ancora: molecular mechanisms underlying scleractinian gametogenesis
Cited by: 11
Author(s): Yi‐Ling Chiu, Shinya Shikina, Yuki Yoshioka, Chuya Shinzato, Ching‐Fong Chang
Software Mentions: 1
Published: almost 6 years ago

10.1002/1878-0261.12629

Exosome‐delivered circRNA promotes glycolysis to induce chemoresistance through the miR‐122‐PKM2 axis in colorectal cancer
Cited by: 305
Author(s): Xinyi Wang, Haiyang Zhang, Hao Yang, Ming Bai, Tao Ning, Ting Deng, Rui Li, Qian Fan, Kegan Zhu, Jialu Li, Zhan Yang, Guoguang Ying, Yi Ba
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-14913-9

Differential transcriptome regulation by 3,5-T2 and 3′,3,5-T3 in brain and liver uncovers novel roles for thyroid hormones in tilapia
Cited by: 16
Author(s): Arturo Olverá, Christopher J. Martyniuk, Nicolas Buisine, Verónica Jiménez-Jacinto, Alejandro Sánchez-Flores, Laurent M. Sachs, Aurea Orozco
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-017-4097-4

Dual transcriptome of the immediate neutrophil and Candida albicans interplay
Cited by: 37
Author(s): Maria Joanna Niemiec, Christian Grumaz, David Ermert, Christiane Desel, Madhu Shankar, José Pedro Lopes, Ian G. Mills, Philip Stevens, Kai Sohn, Constantin F. Urban
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-15699-6

Transcriptomic analysis of the regulation of stalk development in flowering Chinese cabbage (Brassica campestris) by RNA sequencing
Cited by: 17
Author(s): Xinmin Huang, Yuling Lei, Hongling Guan, Yanwei Hao, Houcheng Liu, Guangwen Sun, Riyuan Chen, Shiwei Song
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2164-15-S5-S3

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees
Cited by: 18
Author(s): Lijun Liu, Victor Missirian, Matthew S. Zinkgraf, Andrew Groover, Vladimir Filkov
Software Mentions: 1
Published: about 12 years ago

10.1186/s12864-018-5181-0

Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle
Cited by: 23
Author(s): Majid Khansefid, J.E. Pryce, Sunduimijid Bolormaa, Yizhou Chen, Catriona A. Millen, Amanda J. Chamberlain, Christy J. Vander Jagt, Michael E. Goddard
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-017-3577-x

De novo transcriptome assembly reveals high transcriptional complexity in Pisum sativum axillary buds and shows rapid changes in expression of diurnally regulated genes
Cited by: 24
Author(s): Stephanie C. Kerr, Federico Gaiti, Christine A. Beveridge, Miloš Tanurdžić
Software Mentions: 1
Published: over 9 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

10.1038/s41598-017-16611-y

OCT4 supports extended LIF-independent self-renewal and maintenance of transcriptional and epigenetic networks in embryonic stem cells
Cited by: 10
Author(s): Runsheng He, Besa Xhabija, Batool Al‐Qanber, Benjamin L. Kidder
Software Mentions: 1
Published: almost 9 years ago

10.1002/mnfr.201500050

Egg ovotransferrin‐derived ACE inhibitory peptide IRW increases ACE2 but decreases proinflammatory genes expression in mesenteric artery of spontaneously hypertensive rats
Cited by: 66
Author(s): Kaustav Majumder, Guanxiang Liang, Yanhong Chen, Leluo Guan, Sandra T. Davidge, Jianping Wu
Software Mentions: 1
Published: about 11 years ago

10.1038/s41598-017-16472-5

Identification of a histone family gene signature for predicting the prognosis of cervical cancer patients
Cited by: 42
Author(s): Xiaofang Li, Run Tian, Hugh Gao, Yongkang Yang, Bryan R.G. Williams, Michael P. Gantier, Nigel A.J. McMillan, Dakang Xu, Yiqun Hu, Yue Gao
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-16930-0

MALE STERILE6021 (MS6021) is required for the development of anther cuticle and pollen exine in maize
Cited by: 27
Author(s): Youhui Tian, Senlin Xiao, Juan Liu, Yamuna Somaratne, Hua Zhang, Mingming Wang, Huairen Zhang, Li Zhao, Huabang Chen
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-17140-4

Transcriptome analysis of watermelon (Citrullus lanatus) fruits in response to Cucumber green mottle mosaic virus (CGMMV) infection
Cited by: 41
Author(s): Xiaodong Li, Mengnan An, Zihao Xia, Xiaojiao Bai, Yuanhua Wu
Software Mentions: 1
Published: almost 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

10.1042/BSR20203481

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

10.1007/s12035-020-02088-w

Large-Scale Analysis Reveals Gene Signature for Survival Prediction in Primary Glioblastoma
Cited by: 14
Author(s): Birbal Prasad, Yongji Tian, Xinzhong Li
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-017-17751-x

The transcriptome of Mycobacterium tuberculosis in a lipid-rich dormancy model through RNAseq analysis
Cited by: 34
Author(s): Diana A. Aguilar-Ayala, Laurentijn Tilleman, Filip Van Nieuwerburgh, Dieter Deforce, Juan Carlos Palomino, Peter Vandamme, Jorge A. González-y-Merchand, Anandi Martin
Software Mentions: 1
Published: over 8 years ago

10.1155/2017/4352450

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

10.1371/journal.pcbi.1006758

Augmenting subnetwork inference with information extracted from the scientific literature
Cited by: 0
Author(s): Sid Kiblawi, Deborah Chasman, Amanda N. Henning, Eunju Park, Hoifung Poon, Michael N. Gould, Paul Ahlquist, Mark Craven
Software Mentions: 1
Published: about 7 years ago

10.1080/19768354.2018.1487335

Time-series transcriptomic analysis of the kelp grouper Epinephelus moara in response to low salinity stress
Cited by: 5
Author(s): Qiang Gao, Yanfeng Yue, Minghua Min, Shi-Qing Peng, Zhaohong Shi, Jinbo Wang, Tao Zhang
Software Mentions: 1
Published: about 8 years ago

10.1007/s12035-018-0884-4

A Regulatory Circuitry Between Gria2, miR-409, and miR-495 Is Affected by ALS FUS Mutation in ESC-Derived Motor Neurons
Cited by: 29
Author(s): Davide Capauto, Alessio Colantoni, Lei Lü, Tiziana Santini, Giovanna Peruzzi, Silvia Biscarini, Mariangela Morlando, Neil A. Shneider, Elisa Caffarelli, Pietro Laneve, Irene Bozzoni
Software Mentions: 1
Published: over 8 years ago

10.1007/s11418-021-01505-1

Curcumin suppresses LGR5(+) colorectal cancer stem cells by inducing autophagy and via repressing TFAP2A-mediated ECM pathway
Cited by: 27
Author(s): Xiaohong Mao, Xin Zhang, Xiaowei Zheng, Yongwu Chen, Zixue Xuan, Ping Huang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-18607-0

Differentially expressed microRNAs between cattleyak and yak testis
Cited by: 23
Author(s): Cheng Xu, Shan Wu, Wangsheng Zhao, TserangDonko Mipam, Jingbo Liu, Wenjing Liu, Chuanping Yi, Mujahid Ali Shah, Shumin Yu, Xin Cai
Software Mentions: 1
Published: over 8 years ago

10.1007/s12035-019-01789-1

Inflammatory Responses Induced by the Rupture of Intracranial Aneurysms Are Modulated by miRNAs
Cited by: 14
Author(s): Michał Korostyński, Rafał Morga, Marcin Piechota, Dżesika Hoinkis, Sławomir Gołda, Tomasz Dziedzic, Agnieszka Słowik, Marek Moskała, Joanna Pera
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-016-2839-3

RNA-sequencing of the sturgeon Acipenser baeri provides insights into expression dynamics of morphogenic differentiation and developmental regulatory genes in early versus late developmental stages
Cited by: 12
Author(s): Wei Song, Keji Jiang, Fengying Zhang, Yuling Lin, Lan Ma
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-018-19200-9

Maternal whole blood cell miRNA-340 is elevated in gestational diabetes and inversely regulated by glucose and insulin
Cited by: 37
Author(s): Laura Stirm, Peter Huypens, Steffen Sass, Richa Batra, Louise Fritsche, Sara Y. Brucker, Harald Abele, Anita M. Hennige, Fabian J. Theis, Johannes Beckers, Martin Hrabé de Angelis, Andreas Fritsche, Hans‐Ulrich Häring, Harald Staiger
Software Mentions: 1
Published: over 8 years ago

10.18632/aging.202628

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

10.1038/s41598-018-19837-6

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

10.1038/s41598-018-19954-2

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

10.1186/s12864-015-1501-9

Incomplete meiotic sex chromosome inactivation in the domestic dog
Cited by: 14
Author(s): Federica Federici, Eskeatnaf Mulugeta, Sam Schoenmakers, Evelyne Wassenaar, Jos W. Hoogerbrugge, Godfried W. van der Heijden, Wiggert A. van Cappellen, Johan A. Slotman, Wilfred F. J. van IJcken, Joop S.E. Laven, J. Anton Grootegoed, Willy M. Baarends
Software Mentions: 1
Published: over 11 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

10.5713/ab.20.0751

Combined transcriptome and proteome analyses reveal differences in the longissimus dorsi muscle between Kazakh cattle and Xinjiang brown cattle
Cited by: 1
Author(s): Xin Yan, Jia Wang, Hongbo Li, Liang Gao, Juan Geng, Zhen Ma, Jianming Liu, Jinshan Zhang, Peng-Gui Xie, Lei Chen
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-019-5702-5

Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in Melilotus
Cited by: 0
Author(s): Shuhua Fu, Peter L. Chang, Maren Friesen, Natasha L. Teakle, Aaron M. Tarone, Sing Hoi Sze
Software Mentions: 1
Published: over 7 years ago

10.1016/j.molmet.2021.101290

Epigenetic rewiring of skeletal muscle enhancers after exercise training supports a role in whole-body function and human health
Cited by: 10
Author(s): Kristine Williams, Germán D. Carrasquilla, Lars R. Ingerslev, Mette Yde Hochreuter, Svenja Hansson, Nicolas Pillon, Ida Donkin, Soetkin Versteyhe, Juleen R. Zierath, Tuomas O. Kilpeläinen, Romain Barrès
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-018-21525-4

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

10.1371/journal.pcbi.1007873

Inferring the immune response from repertoire sequencing
Cited by: 20
Author(s): Maximilian Puelma Touzel, Aleksandra M. Walczak, Thierry Mora
Software Mentions: 1
Published: over 6 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

10.1186/s12864-019-6156-5

Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection
Cited by: 10
Author(s): Xuelian Ma, Xiaomin Zhao, Kaili Wang, Xiaoyi Tang, Jianxiong Guo, Mi Mi, Yanping Qi, Lingling Chang, Yong Huang, Dewen Tong
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-21371-4

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

10.1186/s12864-015-2029-8

Age and prior blood feeding of Anopheles gambiae influences their susceptibility and gene expression patterns to ivermectin-containing blood meals
Cited by: 33
Author(s): Jonathan A. Seaman, Haoués Alout, Jacob I. Meyers, Mark D. Stenglein, Roch K. Dabiré, Saúl Lozano-Fuentes, Timothy A. Burton, Wojtek Kuklinski, William C. Black, Brian D. Foy
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pbio.3001012

TMT-Opsins differentially modulate medaka brain function in a context-dependent manner
Cited by: 8
Author(s): Bruno M. Fontinha, Theresa Zekoll, M. Alrawi, Miguel Gallach, Florian Reithofer, Alison J. Barker, Maximilian Hofbauer, Roland Fischer, Arndt von Haeseler, Herwig Baier, Kristin Tessmar-Raible
Software Mentions: 1
Published: over 5 years ago

10.1155/2021/6646459

Identification and Analysis of Three Hub Prognostic Genes Related to Osteosarcoma Metastasis
Cited by: 8
Author(s): Jianye Tan, Huiying Liang, Bo Yang, Shuang Zhu, Guofeng Wu, Lutao Li, Zhengwei Liu, Lin Li, Weizhong Qi, Sijing Li, Lin Li
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pbio.3000471

Transcription-induced formation of extrachromosomal DNA during yeast ageing
Cited by: 63
Author(s): Ryan M. Hull, Michelle King, G Pizza, Felix Krueger, Xabier Vergara, Jonathan Houseley
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-23714-7

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

10.7554/eLife.50346

Disruption of entire Cables2 locus leads to embryonic lethality by diminished Rps21 gene expression and enhanced p53 pathway
Cited by: 2
Author(s): Tra Thi Huong Dinh, Hiroyoshi Iseki, Seiya Mizuno, Saori Iijima-Mizuno, Yoko Tanimoto, Yoko Daitoku, Kayoko Kato, Yuko Hamada, Ammar Shaker Hamed Hasan, Hayate Suzuki, Katsuyuki Murata, Masafumi Muratani, Masatsugu Ema, Jun-Dal Kim, Junji Ishida, Akiyoshi Fukamizu, Mitsuyasu Kato, Satoru Takahashi, Ken‐ichi Yagami, Valerie Wilson, Ruth M. Arkell, Fumihiro Sugiyama
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pbio.3000238

Fat body–specific vitellogenin expression regulates host-seeking behaviour in the mosquito Aedes albopictus
Cited by: 22
Author(s): Jessica Dittmer, Ayad Alafndi, Paolo Gabrieli
Software Mentions: 1
Published: over 7 years ago

10.3892/mmr.2019.10852

Long non‑coding RNA Unigene56159 promotes glioblastoma multiforme cell proliferation and invasion through negatively regulating microRNA‑194‑5p
Cited by: 2
Author(s): Guangyu Jiang, Hang Dong, Dao‐Yi Yu, Xinyu Yang
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-24284-4

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

10.1042/BSR20192706

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

10.1038/s41598-021-85394-0

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

10.7554/eLife.46012

CCN1 interlinks integrin and hippo pathway to autoregulate tip cell activity
Cited by: 34
Author(s): Myo-Hyeon Park, Ae kyung Kim, Sarala Manandhar, Su-Young Oh, Gil-Jin Jang, Kang Li, Dongwon Lee, Do Young Hyeon, Sunhee Lee, Hye-Eun Lee, Tae‐Lin Huh, Sang Heon Suh, Daehee Hwang, Kyunghee Byun, Hae-Chul Park, You Mie Lee
Software Mentions: 1
Published: about 7 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

10.1042/BSR20181640

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

10.1038/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

10.1155/2020/2671281

Identification and Analysis of Novel Biomarkers Involved in Chromophobe Renal Cell Carcinoma by Integrated Bioinformatics Analyses
Cited by: 2
Author(s): Wei Zhang, Yin Xu, Jinghan Zhang, Jun Wu
Software Mentions: 1
Published: over 6 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/s12864-016-2435-6

Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis
Cited by: 27
Author(s): Lisa Zondag, Kim Rutherford, Neil J. Gemmell, Megan J. Wilson
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-015-1246-5

Transcriptomic response to heat stress among ecologically divergent populations of redband trout
Cited by: 92
Author(s): Shawn R. Narum, Nathan R. Campbell
Software Mentions: 1
Published: over 11 years ago

10.7554/eLife.28415

Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions
Cited by: 54
Author(s): Jason A. Morrison, Rebecca McLennan, Lauren A. Wolfe, Madelaine Gogol, Samuel R. Meier, Mary Cathleen McKinney, Jessica M. Teddy, Laura Holmes, Craig L. Semerad, Andrew Box, Hua Li, Kathryn Hall, Anoja Perera, Paul M. Kulesa
Software Mentions: 1
Published: almost 9 years ago

10.3390/molecules22081364

Biochemical and Comparative Transcriptomic Analyses Identify Candidate Genes Related to Variegation Formation in Paeonia rockii
Cited by: 17
Author(s): Qianqian Shi, Long Li, Xiaoxiao Zhang, Jianrang Luo, Xiang Li, Lijuan Zhai, Li He, Yanlong Zhang
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pbio.3001387

Neutrophils promote T-cell activation through the regulated release of CD44-bound Galectin-9 from the cell surface during HIV infection
Cited by: 16
Author(s): Garett Dunsmore, Eliana Perez Rosero, Shima Shahbaz, Deanna M. Santer, Juan Jovel, Paige Lacy, Stan Houston, Shokrollah Elahi
Software Mentions: 1
Published: about 5 years ago

10.3390/molecules22081292

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

10.1186/s12864-020-07336-w

Regulation of the antennal transcriptome of the dengue vector, Aedes aegypti, during the first gonotrophic cycle
Cited by: 15
Author(s): Sharon R. Hill, Tanvi Taparia, Rickard Ignell
Software Mentions: 1
Published: over 5 years ago

10.3390/molecules23123276

Effect of Aspergillus flavus Fungal Elicitor on the Production of Terpenoid Indole Alkaloids in Catharanthus roseus Cambial Meristematic Cells
Cited by: 18
Author(s): Chuxin Liang, Chang Chen, Pengfei Zhou, Lv Xu, Jianhua Zhu, Jincai Liang, Jiachen Zi, Rongmin Yu
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22010364

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

10.15252/emmm.202114045

Asymptomatic COVID‐19: disease tolerance with efficient anti‐viral immunity against SARS‐CoV‐2
Cited by: 31
Author(s): Yi‐Hao Chan, Siew‐Wai Fong, Chek-Meng Poh, Guillaume Carissimo, Nicholas Kim‐Wah Yeo, Siti Naqiah Amrun, Yun Shan Goh, Jackwee Lim, Weili Xu, Rhonda Sin‐Ling Chee, Anthony Torres‐Ruesta, Cheryl Yi‐Pin Lee, Matthew Zirui Tay, Zi Wei Chang, Wen-Hsin Lee, Bei Wang, Seow‐Yen Tan, Shirin Kalimuddin, Barnaby Edward Young, Yee‐Sin Leo, Cheng‐I Wang, Bernett Lee, Olaf Rötzschke, David C. Lye, Laurent Rénia, Lisa F. P. Ng
Software Mentions: 1
Published: over 5 years ago

10.15252/emmm.202013524

Menin‐regulated Pbk controls high fat diet‐induced compensatory beta cell proliferation
Cited by: 6
Author(s): Jian Ma, Bowen Xing, Yan Cao, Xin He, Kate E Bennett, Chao Tong, Chiying An, Taylor Hojnacki, Zijie Feng, Sunbin Deng, Sunbin Ling, Gengchen Xie, Yuan Wu, Yue Ren, Ming Yu, Bryson W. Katona, Hongzhe Li, Ali Naji, Xianxin Hua
Software Mentions: 1
Published: over 5 years ago

10.1155/2019/7505260

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

10.1186/s12885-021-08482-4

CD36 promotes vasculogenic mimicry in melanoma by mediating adhesion to the extracellular matrix
Cited by: 11
Author(s): Carmela Martini, Mark O. DeNichilo, Danielle P. King, Michaelia P. Cockshell, Brenton Ebert, Brian Dale, Lisa M. Ebert, Anthony E. Woods, Claudine S. Bonder
Software Mentions: 1
Published: about 5 years ago

10.1186/s12885-021-07995-2

Comprehensive analysis of ceRNA networks reveals prognostic lncRNAs related to immune infiltration in colorectal cancer
Cited by: 25
Author(s): Jingyi Chen, Yuxuan Song, Mei Li, Yu Zhang, Ting-Ru Lin, Jie Sun, Di Wang, Yulan Liu, Junyu Guo, Weidong Yu
Software Mentions: 1
Published: over 5 years ago

10.15252/emmm.201606493

Activin promotes skin carcinogenesis by attraction and reprogramming of macrophages
Cited by: 24
Author(s): Maria Antsiferova, Aleksandra Piwko‐Czuchra, Michael Cangkrama, Mateusz S. Wietecha, Dilara Şahin, Katharina Birkner, Valerie C Amann, Mitchell P. Levesque, Daniel Hohl, Reinhard Dummer, Sabine Werner
Software Mentions: 1
Published: over 9 years ago

10.1186/s12885-020-07399-8

Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel
Cited by: 5
Author(s): Gregory B. Lim, Young-Ae Kim, Jihoon Seo, Hee Jin Lee, Gyungyub Gong, Sung Hee Park
Software Mentions: 1
Published: almost 6 years ago

10.21307/jofnem-2019-055

Identification of Suitable Meloidogyne spp. Housekeeping Genes
Cited by: 1
Author(s): Weiming Hu, Peter DiGennaro
Software Mentions: 1
Published: over 7 years ago

10.1111/acel.12373

Circulating micro <scp>RNA</scp> signature of genotype‐by‐age interactions in the long‐lived <scp>A</scp> mes dwarf mouse
Cited by: 50
Author(s): Berta Victoria, Joseph M. Dhahbi, Yury O. Nunez Lopez, Lina Spinel, Hani Atamna, Stephen R. Spindler, Michał M. Masternak
Software Mentions: 1
Published: about 11 years ago

10.15252/embj.2019103181

<scp>RNA</scp> m 6 A methylation regulates sorafenib resistance in liver cancer through <scp>FOXO</scp> 3‐mediated autophagy
Cited by: 230
Author(s): Ziyou Lin, Yi Niu, Arabella Wan, Dongshi Chen, Heng Liang, Xijun Chen, Lei Sun, Siyue Zhan, Liutao Chen, Chao Cheng, Xiaolei Zhang, Xianzhang Bu, Weiling He, Gang Wan
Software Mentions: 1
Published: over 6 years ago

10.18632/aging.202164

SNRPB-mediated RNA splicing drives tumor cell proliferation and stemness in hepatocellular carcinoma
Cited by: 19
Author(s): Yuting Zhan, Lei Li, Tingting Zeng, Ningning Zhou, Xin‐Yuan Guan, Yan Li
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pbio.1001732

A Downy Mildew Effector Attenuates Salicylic Acid–Triggered Immunity in Arabidopsis by Interacting with the Host Mediator Complex
Cited by: 167
Author(s): Marie‐Cécile Caillaud, Shuji Asai, Ghanasyam Rallapalli, Sophie J. M. Piquerez, Georgina Fabro, Jonathan D. G. Jones
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pbio.3001352

The antiviral state has shaped the CpG composition of the vertebrate interferome to avoid self-targeting
Cited by: 13
Author(s): Andrew Shaw, Suzannah J. Rihn, Nardus Mollentze, Arthur Wickenhagen, Douglas G. Stewart, Richard Orton, Srikeerthana Kuchi, Siddharth Bakshi, Milagros Rodriguez Collados, Matthew L. Turnbull, Joseph Busby, Quan Gu, Katherine Smollett, Connor Bamford, Elena Sugrue, Paul C. D. Johnson, Ana Filipe da Silva, Alfredo Castelló, Daniel G. Streicker, David L. Robertson, Massimo Palmarini, Sam J. Wilson
Software Mentions: 1
Published: almost 5 years ago

10.15252/emmm.202012409

Psoriatic skin inflammation is promoted by c‐Jun/AP‐1‐dependent CCL2 and IL‐23 expression in dendritic cells
Cited by: 35
Author(s): Philipp Novoszel, Martin Holcmann, Gabriel Stulnig, Cristiano De Sa Fernandes, Victoria Zyulina, Izabela Borek, Markus Linder, Alexandra Bogusch, Barbara Drobits, Thomas Bauer, Carmen Tam‐Amersdorfer, Patrick M. Brunner, Georg Stary, Latifa Bakiri, Erwin F. Wagner, Herbert Strobl, Maria Sibilia
Software Mentions: 1
Published: over 5 years ago

10.15252/embr.201948029

SUMOylated SNF2PH promotes variant surface glycoprotein expression in bloodstream trypanosomes
Cited by: 12
Author(s): Andreu Saura, Paula Ana Iribarren, Domingo I. Rojas-Barros, Jean-Mathieu Bart, Diana López‐Farfán, Eduardo Andrés-León, Isabel Vidal-Cobo, Cordula Boehm, Vanina E. Álvarez, Mark C. Field, Miguel Navarro
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12885-021-08345-y

Persistent Newcastle disease virus infection in bladder cancer cells is associated with putative pro-survival and anti-viral transcriptomic changes
Cited by: 6
Author(s): Lee-Chin Chan, Jeevanathan Kalyanasundram, Sze-Wei Leong, Mas Jaffri Masarudin, Abhi Veerakumarasivam, Khatijah Yusoff, Soon Choy Chan, Suet Lin Chia
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

10.3390/plants10091775

Comparative Transcriptomics of Non-Embryogenic and Embryogenic Callus in Semi-Recalcitrant and Non-Recalcitrant Upland Cotton Lines
Cited by: 8
Author(s): Sonika Kumar, Ashleigh Ruggles, Sam Logan, Alora Mazarakis, Tyson Thomas, Matthew Bates, Clayton Grosse, David L. Reed, Zhigang Li, Jane Grimwood, Jeremy Schmutz, Christopher Saski
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-017-3756-9

Integrated mRNA and microRNA transcriptome variations in the multi-tepal mutant provide insights into the floral patterning of the orchid Cymbidium goeringii
Cited by: 26
Author(s): Fengming Yang, Genfa Zhu, Zhen Wang, Hailin Liu, Qin Xu, Dan Huang, Chenkai Zhao
Software Mentions: 1
Published: over 9 years ago

10.21307/jofnem-2020-041

De novo transcriptome sequencing and analysis of Anisakis pegreffii (Nematoda: Anisakidae) third-stage and fourth stage larvae
Cited by: 5
Author(s): U‐Hwa Nam, Jong‐Oh Kim, Jeong-Ho Kim
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21249719

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

10.1186/s12885-019-5671-8

CRKL regulates alternative splicing of cancer-related genes in cervical cancer samples and HeLa cell
Cited by: 24
Author(s): Qingling Song, Fengtao Yi, Yuhong Zhang, Daniel K. Jun Li, Yaxun Wei, Han Yu, Yi Zhang
Software Mentions: 1
Published: over 7 years ago

10.3389/fgene.2021.598296

TRPM2, PDLIM5, BCL3, CD14, GBA Genes as Feasible Markers for Premature Coronary Heart Disease Risk
Cited by: 9
Author(s): Kriengchai Prasongsukarn, Wilanee Dechkhajorn, Surachet Benjathummarak, Yaowapa Maneerat
Software Mentions: 1
Published: over 5 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

10.3390/plants9060713

Transcriptome and Network Analyses of Heterostyly in Turnera subulata Provide Mechanistic Insights: Are S-Loci a Red-Light for Pistil Elongation?
Cited by: 8
Author(s): Paige M. Henning, Joel S. Shore, Andrew G. McCubbin
Software Mentions: 1
Published: over 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568