bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-65947-5

De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress
Cited by: 13
Author(s): Elham Younesi-Melerdi, Ghorbanali Nematzadeh, Ali Pakdin Parizi, Mohammad Reza Bakhtiarizadeh, Seyed Abolfazl Motahari
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2018.01026

Comparative Methylome Analysis Reveals Perturbation of Host Epigenome in Chestnut Blight Fungus by a Hypovirus
Cited by: 10
Author(s): Ru Li, Sisi Zhou, Yongbing Li, Xiaorui Shen, Qinnan Wang, Baoshan Chen
Software Mentions: 3
Published: over 8 years ago

10.1002/advs.201902040

Deubiquitylase OTUD6B Governs pVHL Stability in an Enzyme‐Independent Manner and Suppresses Hepatocellular Carcinoma Metastasis
Cited by: 27
Author(s): Xinxin Liu, Xiaoli Zhang, Zhiqiang Peng, Chunnan Li, Ze Wang, Chanjuan Wang, Zhikang Deng, Bo Wu, Yu Cui, Zhanxin Wang, Chun-Ping Chu, Ming‐Hua Zheng, Lingqiang Zhang
Software Mentions: 3
Published: over 6 years ago

10.1186/s12935-019-0744-y

Up-regulated lncRNA XIST contributes to progression of cervical cancer via regulating miR-140-5p and ORC1
Cited by: 66
Author(s): Xing Chen, Dongsheng Xiong, Liya Ye, Kai Wang, Lingfei Huang, Shuangshuang Mei, Jinhong Wu, Shanshan Chen, Xiaoli Lai, Lingzhi Zheng, Meifen Wang
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-019-5460-4

RNA-sequencing analysis of shell gland shows differences in gene expression profile at two time-points of eggshell formation in laying chickens
Cited by: 22
Author(s): Samiullah Khan, Shu‐Biao Wu, Juliet R. Roberts
Software Mentions: 3
Published: almost 8 years ago

10.18632/aging.102652

Integrated transcriptome expression profiling reveals a novel lncRNA associated with L-DOPA-induced dyskinesia in a rat model of Parkinson’s disease
Cited by: 8
Author(s): Chunlei Han, Yunpeng Liu, Yun‐Peng Sui, Ning Chen, Tingting Du, Ying Jiang, Chenjia Guo, Kailiang Wang, Qiao Wang, Shiying Fan, Michio Shimabukuro, Fangang Meng, Yuan Fang, Jianguo Zhang
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-020-6721-y

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments
Cited by: 50
Author(s): Alemu Takele Assefa, Jo Vandesompele, Olivier Thas
Software Mentions: 3
Published: over 6 years ago

10.1186/s12885-015-1955-9

The genomic and transcriptomic landscape of anaplastic thyroid cancer: implications for therapy
Cited by: 51
Author(s): Katayoon Kasaian, Sam M. Wiseman, Blair Walker, Jacqueline E. Schein, Yongjun Zhao, Martin Hirst, Richard A. Moore, Andrew J. Mungall, Marco A. Marra, Steven J.M. Jones
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12885-021-08539-4

A methylation-based nomogram for predicting survival in patients with lung adenocarcinoma
Cited by: 5
Author(s): Xuelong Wang, Bin Zhou, Yuxin Xia, Jianjun Zuo, Yanchao Liu, Xin Bi, Xiong Luo, Chengwei Zhang
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-63263-6

Circulating MicroRNA Profiling in Non-ST Elevated Coronary Artery Syndrome Highlights Genomic Associations with Serial Platelet Reactivity Measurements
Cited by: 14
Author(s): Kristian C. Becker, Lydia Coulter Kwee, Megan L. Neely, Elizabeth Grass, Joseph A. Jakubowski, Keith Fox, Harvey D. White, Simon Gregory, Paul A. Gurbel, Leonardo de Pinto Carvalho, Richard C. Becker, E. Magnus Ohman, Matthew T. Roe, Svati H. Shah, Mark Y. Chan
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-62286-3

Fabrication of Perfusable Vascular Channels and Capillaries in 3D Liver-like Tissue
Cited by: 20
Author(s): Nobuhito Mori, Yuka Akagi, Yukiko Imai, Yoichiro Takayama, Yasuyuki S. Kida
Software Mentions: 3
Published: over 6 years ago

10.1186/s12935-021-01970-4

A novel autophagy-related genes prognostic risk model and validation of autophagy-related oncogene VPS35 in breast cancer
Cited by: 5
Author(s): Xiaoying Li, Yu Cao, Xinmiao Yu, Feng Jin, Yang Li
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-61857-8

De novo transcriptome assembly and analysis of Phragmites karka, an invasive halophyte, to study the mechanism of salinity stress tolerance
Cited by: 18
Author(s): Soumya Shree Nayak, Seema Pradhan, Dinabandhu Sahoo, Ajay Parida
Software Mentions: 3
Published: over 6 years ago

10.1186/s12935-021-01901-3

Construction of a long noncoding RNA-based competing endogenous RNA network and prognostic signatures of left- and right-side colon cancer
Cited by: 2
Author(s): Kezhi Li, Yuqing Yin, Yanping Tang, Long Long, Min Xie, Jilin Li, Ke Ding, Bang-li Hu
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-61420-5

Eosinophil accumulation in postnatal lung is specific to the primary septation phase of development
Cited by: 17
Author(s): Lucas F. Loffredo, Mackenzie E. Coden, Brian M. Jeong, Matthew T. Walker, Kishore R. Anekalla, Ton C. Doan, Raul I. Rodriguez, M.J. Browning, Ki-Won Nam, James J. Lee, Hiam Abdala‐Valencia, Sergejs Berdnikovs
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-63040-5

Circulating RNA Transcriptome of Pregnant Women with TSH Just Above the Trimester-Specific Reference and its Correlation with the Hypertensive Phenotype
Cited by: 2
Author(s): Andréa Harumy de Lima Hirata, Luiz Antônio de Jesus Rocha, Valdelena Alessandra da Silva, Rafael Fernandes Almeida, Lucas dos Santos Bacigalupo, Patrícia Siqueira Varela, Leonardo Martins Silva, João Bosco Pesquero, Humberto Dellê, Cleber Camacho
Software Mentions: 3
Published: over 6 years ago

10.1186/s12935-021-01784-4

Re-expression of miR-200s in claudin‐low mammary tumor cells alters cell shape and reduces proliferation and invasion potentially through modulating other miRNAs and SUZ12 regulated genes
Cited by: 8
Author(s): Kaitlyn E. Simpson, Garret Conquer-Van Heumen, Katrina L. Watson, Majesta J Roth, Courtney J. Martin, Roger A. Moorehead
Software Mentions: 3
Published: over 5 years ago

10.1186/s12935-019-1052-2

Identification and analysis of long non-coding RNA related miRNA sponge regulatory network in bladder urothelial carcinoma
Cited by: 28
Author(s): Jiawu Wang, Chengyao Zhang, Yan Wu, Weiyang He, Xin Gou
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2020.01921

The Role of Testosterone and Gibberellic Acid in the Melanization of Cryptococcus neoformans
Cited by: 4
Author(s): Jamila S Tucker, Tiffany Guess, Erin E. McClelland
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-55896-z

System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster
Cited by: 7
Author(s): Julia Bespyatykh, Egor Shitikov, Andrei Guliaev, Alexander Smolyakov, Ksenia M. Klimina, Vladimir A. Veselovsky, М В Малахова, Georgij Arapidi, Marine Dogonadze, Olga Manicheva, Dmitry Bespiatykh, Igor Mokrousov, Viacheslav Zhuravlev, Elena N. Ilina, Vadim M. Govorun
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-55132-8

Tissue-type plasminogen activator-primed human iPSC-derived neural progenitor cells promote motor recovery after severe spinal cord injury
Cited by: 7
Author(s): Yasuhiro Shiga, Akina Shiga, Pinar Mesci, HyoJun Kwon, Coralie Brifault, Jung Hyun Kim, Jacob Jeziorski, Chanond A. Nasamran, Seiji Ohtori, Alysson R. Muotri, Steven L. Gonias, W. Marie Campana
Software Mentions: 3
Published: almost 7 years ago

10.18632/aging.202989

Integrated analysis of long noncoding RNAs and mRNA expression profiles reveals the potential role of lncRNAs in early stage of post-peripheral nerve injury in Sprague-Dawley rats
Cited by: 3
Author(s): Yujing Zhang, Zhaowei Zhu, Xiangxia Liu, Shuqia Xu, Yi Zhang, Yangbin Xu, Bo He
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-56790-4

Fetal androgen exposure is a determinant of adult male metabolic health
Cited by: 16
Author(s): Katarzyna Siemienowicz, Panagiotis Filis, Sophie Shaw, Alex Douglas, Jessica Thomas, Sally Mulroy, Forbes Howie, Paul A. Fowler, W. Colin Duncan, Michael T. Rae
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12935-019-0905-z

Identification of circRNA–miRNA–mRNA regulatory network in gastric cancer by analysis of microarray data
Cited by: 74
Author(s): Yongjun Guan, Jianying Ma, Wei Song
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-54180-4

A framework for identification of on- and off-target transcriptional responses to drug treatment
Cited by: 23
Author(s): Yi Huang, Masaaki Furuno, Takahiro Arakawa, Satoshi Takizawa, Michiel de Hoon, Harukazu Suzuki, Erik Arner
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12935-020-01472-9

Significance of tumor mutation burden combined with immune infiltrates in the progression and prognosis of ovarian cancer
Cited by: 45
Author(s): Fangfang Bi, Ying Chen, Qing Yang
Software Mentions: 3
Published: about 6 years ago

10.1186/s12885-018-4594-0

Chromoanasynthesis is a common mechanism that leads to ERBB2 amplifications in a cohort of early stage HER2+ breast cancer samples
Cited by: 13
Author(s): George Vasmatzis, Xue Wang, James B. Smadbeck, Stephen J. Murphy, Katherine B. Geiersbach, Sarah H. Johnson, Athanasios Gaitatzes, Yan W. Asmann, Farhad Kosari, Mitesh J. Borad, Daniel J. Serie, Sarah A. McLaughlin, Jennifer M. Kachergus, Brian M. Necela, E. Aubrey Thompson
Software Mentions: 3
Published: over 8 years ago

10.3389/fmed.2020.00056

A Robust 6-lncRNA Prognostic Signature for Predicting the Prognosis of Patients With Colorectal Cancer Metastasis
Cited by: 22
Author(s): Shuyuan Li, Shuo Chen, Boxue Wang, Lin Zhang, Yinan Su, Xipeng Zhang
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2017.02121

Different Non-Saccharomyces Yeast Species Stimulate Nutrient Consumption in S. cerevisiae Mixed Cultures
Cited by: 57
Author(s): José Antonio Curiel, Pilar Morales, Ramón González, Jordi Tronchoni
Software Mentions: 3
Published: about 9 years ago

10.3389/fmicb.2018.02259

The MADS-box Transcription Factor PsMAD1 Is Involved in Zoosporogenesis and Pathogenesis of Phytophthora sojae
Cited by: 19
Author(s): Long Lin, Wenwu Ye, Jiawei Wu, Mingrun Xuan, Yufei Li, Jian Gao, Yonglin Wang, Yan Wang, Suomeng Dong, Yuanchao Wang
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-020-58709-w

Nanocatalytic activity of clean-surfaced, faceted nanocrystalline gold enhances remyelination in animal models of multiple sclerosis
Cited by: 44
Author(s): Andrew P. Robinson, Joanne Zhongyan Zhang, Haley E. Titus, Molly Karl, Mikhail Merzliakov, Adam R. Dorfman, Stephen J. Karlik, Michael G. Stewart, Richard K. Watt, Benjin D. Facer, Jon D. Facer, Noah D. Christian, Karen S. Ho, Michael T. Hotchkin, Mark G. Mortenson, Robert H. Miller, Stephen D. Miller
Software Mentions: 3
Published: over 6 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

10.1038/s41598-019-50718-8

The role of extracellular matrix in mouse and human corneal neovascularization
Cited by: 19
Author(s): Marco Barbariga, F. Vallone, Ettore Mosca, Fabio Bignami, Cinzia Magagnotti, Phillippe Fonteyne, Federica Chiappori, Luciano Milanesi, Paolo Rama, Annapaola Andolfo, Giulio Ferrari
Software Mentions: 3
Published: about 7 years ago

10.3389/fimmu.2020.582358

Transcriptional Memory-Like Imprints and Enhanced Functional Activity in γδ T Cells Following Resolution of Malaria Infection
Cited by: 7
Author(s): Rasika Kumarasingha, Lisa J Ioannidis, Waruni Abeysekera, Stephanie I Studniberg, Dinidu S Wijesurendra, Ramin Mazhari, Daniel P. Poole, Ivo Müeller, Louis Schofield, Diana S. Hansen, Emily M. Eriksson
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2407-14-880

Deep Sequencing the microRNA profile in rhabdomyosarcoma reveals down-regulation of miR-378 family members
Cited by: 55
Author(s): Francesca Megiorni, Samantha Cialfi, Heather P. McDowell, Armando Felsani, Simona Camero, Alessandro Guffanti, Barry Pizer, Aldo Clerico, Alessandra De Grazia, Antonio Pizzuti, Anna Moles, Carlo Dominici
Software Mentions: 3
Published: almost 12 years ago

10.18632/aging.104004

Integrated analysis of transcriptomic and metabolomic data demonstrates the significant role of pyruvate carboxylase in the progression of ovarian cancer
Cited by: 9
Author(s): Hongjing Shang, Jianfeng Zheng, Jinyi Tong
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-52375-3

A New Strategy for Identifying Mechanisms of Drug-drug Interaction Using Transcriptome Analysis: Compound Kushen Injection as a Proof of Principle
Cited by: 4
Author(s): Hao Shen, Zhibo Qu, Yuka Harata-Lee, Jingang Cui, Thazin Nwe Aung, Wei Wang, R. Daniel Kortschak, David L. Adelson
Software Mentions: 3
Published: almost 7 years ago

10.1016/j.ccell.2018.08.015

The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation
Cited by: 75
Author(s): N Martinez-Soria, Lynsey McKenzie, Julia Draper, Anetta Ptasińska, Hasan Issa, Sandeep Potluri, Helen J. Blair, Anna Pickin, Asmida Isa, Paulynn Suyin Chin, Ricky Tirtakusuma, Dan Coleman, Sirintra Nakjang, Salam A. Assi, Victoria J. Forster, Mojgan Reza, Edward Law, Philip Berry, Dorothée Mueller, Cameron S. Osborne, Alex Elder, Simon Bomken, Deepali Pal, James M. Allan, Gareth J. Veal, Peter N. Cockerill, Christian Wichmann, Josef Vormoor, Georges Lacaud, Constanze Bonifer, Olaf Heidenreich
Software Mentions: 3
Published: about 8 years ago

10.1155/2019/9107806

Circ_MDM2_000139, Circ_ATF2_001418, Circ_CDC25C_002079, and Circ_BIRC6_001271 Are Involved in the Functions of XAV939 in Non-Small Cell Lung Cancer
Cited by: 8
Author(s): Haixiang Yu, Liping Xu, Zhengjia Liu, Bo Guo, Zhifeng Han, Xin Hua
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-016-2906-9

An integrative genomics approach for identifying novel functional consequences of PBRM1 truncated mutations in clear cell renal cell carcinoma (ccRCC)
Cited by: 18
Author(s): Yuanyuan Wang, Xingyi Guo, Michael J. Bray, Zhiyong Ding, Zhongming Zhao
Software Mentions: 3
Published: over 10 years ago

10.3389/fimmu.2019.01960

Differential Impact of Co-expressed SP-A1/SP-A2 Protein on AM miRNome; Sex Differences
Cited by: 16
Author(s): Nithyananda Thorenoor, Yuka Imamura Kawasawa, Chintan K. Gandhi, Xuesheng Zhang, Joanna Floros
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-52559-x

Transcriptomic Analysis of mRNA-lncRNA-miRNA Interactions in Hepatocellular Carcinoma
Cited by: 35
Author(s): Xia Tang, Delong Feng, Min Li, Jinxue Zhou, Xiaoyuan Li, Dachun Zhao, Bingtao Hao, Dewei Li, Keyue Ding
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-50229-6

Model-based clustering for identifying disease-associated SNPs in case-control genome-wide association studies
Cited by: 8
Author(s): Yan Xu, Li Xing, Jessica Su, Xuekui Zhang, Weiliang Qiu
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2164-14-171

Transcriptomics of morphological color change in polychromatic Midas cichlids
Cited by: 76
Author(s): Frederico Henning, Julia C. Jones, Paolo Franchini, Axel Meyer
Software Mentions: 3
Published: over 13 years ago

10.1038/s41598-019-49647-3

Comparative transcriptome analysis of the human endocervix and ectocervix during the proliferative and secretory phases of the menstrual cycle
Cited by: 7
Author(s): Sampurna Mukhopadhyay, Yupu Liang, Hong Hur, G. Villegas, Giulia Calenda, Alexandra Reis, Lily Millen, Patrick Barnable, Lisa Mamkina, Narender Kumar, Tamara Kalir, Rhoda Sperling, Natalia Teleshova
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-50310-0

Comparative transcriptomics between species attributes reactogenicity pathways induced by the capsular group B meningococcal vaccine, 4CMenB, to the membrane-bound endotoxin of its outer membrane vesicle component
Cited by: 9
Author(s): Dylan Sheerin, Daniel O’Connor, Christina Dold, Elizabeth A. Clutterbuck, Moustafa Attar, Christine S. Rollier, Manish Sadarangani, Andrew J. Pollard
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-015-2088-x

De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum
Cited by: 22
Author(s): Valeria Petrella, Serena Aceto, Francesco Musacchia, Vincenza Colonna, Mark D. Robinson, Vladimı́r Beneš, G. Cicotti, Gioia Bongiorno, Luigi Gradoni, Petr Volf, Marco Salvemini
Software Mentions: 3
Published: about 11 years ago

10.1093/bib/bbx149

Developing a ‘personalome’ for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes
Cited by: 20
Author(s): Francesca Vitali, Haiquan Li, A. Grant Schissler, Joanne Berghout, Colleen Kenost, Yves A. Lussier
Software Mentions: 3
Published: almost 9 years ago

10.3389/fimmu.2021.678699

The Zinc Nutritional Immunity of Epinephelus coioides Contributes to the Importance of znuC During Pseudomonas plecoglossicida Infection
Cited by: 12
Author(s): Lixing Huang, Yanfei Zuo, Yingxue Qin, Lingmin Zhao, Mao Lin, Qingpi Yan
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-48741-w

SerpinB2 inhibits migration and promotes a resolution phase signature in large peritoneal macrophages
Cited by: 24
Author(s): Wayne A. Schroder, Thiago Dominguez Crespo Hirata, Thuy T. Le, Joy Gardner, Glen M. Boyle, Jonathan Ellis, Eri Nakayama, Dilan Pathirana, Helder I. Nakaya, Andreas Suhrbier
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-49440-2

Transgenerational Self-Reconstruction of Disrupted Chromatin Organization After Exposure To An Environmental Stressor in Mice
Cited by: 23
Author(s): Carlos Díaz-Castillo, Raquel Chamorro-García, Toshihiro Shioda, Bruce Blumberg
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-016-2574-9

De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood
Cited by: 12
Author(s): Abbot O. Oghenekaro, Tommaso Raffaello, Andriy Kovalchuk, Fred O. Asiegbu
Software Mentions: 3
Published: over 10 years ago

10.3389/fimmu.2021.656846

Expression of Senescence Marker TIGIT Identifies Polyfunctional Donor-Reactive CD4+ T Cells Preferentially Lost After Kidney Transplantation
Cited by: 12
Author(s): Amy C. J. van der List, Nicolle H.R. Litjens, Mariska Klepper, M. Betjes
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.203102

Alterations in the RTK/Ras/PI3K/AKT pathway serve as potential biomarkers for immunotherapy outcome of diffuse gliomas
Cited by: 11
Author(s): Song Han, Pengfei Wang, Hong‐Qing Cai, Jinghai Wan, Shouwei Li, Ze-Huan Lin, Chunmei Yu, Yan Chen
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-46473-5

Differential expression of individual transcript variants of PD-1 and PD-L2 genes on Th-1/Th-2 status is guaranteed for prognosis prediction in PCNSL
Cited by: 22
Author(s): Yasuo Takashima, Atsushı Kawaguchi, Ryuichi Sato, Kenichi Yoshida, Azusa Hayano, Jumpei Homma, Junya Fukai, Yasuo Iwadate, Koji Kajiwara, Shin Ishizawa, Hiroaki Hondoh, Masakazu Nakano, Seishi Ogawa, Kei Tashiro
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-45821-9

Skeletal muscle in MuRF1 null mice is not spared in low-gravity conditions, indicating atrophy proceeds by unique mechanisms in space
Cited by: 39
Author(s): Samuel M. Cadena, Yunyu Zhang, Jian Fang, Sophie Brachat, Pia Kuss, E. Giorgetti, Louis S. Stodieck, Michaela Kneissel, David J. Glass
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-015-1461-0

GRACOMICS: software for graphical comparison of multiple results with omics data
Cited by: 7
Author(s): Minseok Seo, Joon Yoon, Taesung Park
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-019-45665-3

Deep transcriptome analysis using RNA-Seq suggests novel insights into molecular aspects of fat-tail metabolism in sheep
Cited by: 32
Author(s): Mohammad Reza Bakhtiarizadeh, Abdolreza Salehi, Ali A. Alamouti, Rostam Abdollahi-Arpanahi, Seyed Alireza Salami
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2018.00879

Cord Blood CD8+ T Cells Have a Natural Propensity to Express IL-4 in a Fatty Acid Metabolism and Caspase Activation-Dependent Manner
Cited by: 11
Author(s): Yuxia Zhang, Jovana Maksimovic, Bing Huang, David P. De Souza, Gaetano Naselli, Huan Chen, Li Zhang, Kai Weng, Hanquan Liang, Yanhui Xu, John M. Wentworth, Nicholas D. Huntington, Alicia Oshlack, Sitang Gong, Axel Kallies, Peter Vuillermin, Min Yang, Leonard C. Harrison
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-019-45528-x

Loss of MafA and MafB expression promotes islet inflammation
Cited by: 13
Author(s): Tania Singh, Jesper K. Colberg, Luis Sarmiento, Patrícia Chaves, Lars Bolvig Hansen, Sara Bsharat, Luis Rodrigo Cataldo, Monika Dudenhöffer-Pfeifer, Malin Fex, David Bryder, Dan Holmberg, Ewa Sitnicka, Corrado Cilio, Rashmi B. Prasad, Isabella Artner
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-44600-w

Genome-wide identification and characterization of long non-coding RNAs expressed during sheep fetal and postnatal hair follicle development
Cited by: 27
Author(s): Ablat Sulayman, Kechuan Tian, Xixia Huang, Yuezhen Tian, Xinming Xu, Xuefeng Fu, Bi Zhao, Weiwei Wu, Dan Wang, Aynur Yasin, Hanikezi Tulafu
Software Mentions: 3
Published: over 7 years ago

10.1186/s12915-016-0311-0

Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation
Cited by: 18
Author(s): David S. Rabiger, Jennifer Taylor, Andrew Spriggs, Melanie L. Hand, Steven T. Henderson, Susan D. Johnson, Karsten Oelkers, Mária Hrmová, Keisuke Saito, Go Suzuki, Yasuhiko Mukai, Bernard J. Carroll, Anna M. Koltunow
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-019-44924-7

Whole-blood transcriptomic signatures induced during immunization by chloroquine prophylaxis and Plasmodium falciparum sporozoites
Cited by: 23
Author(s): Tuan M. Tran, Else M. Bijker, Mariëlle C. Haks, Tom H. M. Ottenhoff, Leo G. Visser, Remko Schats, Pratap Venepally, Hernán Lorenzi, Peter D. Crompton, Robert W. Sauerwein
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-44944-3

Detection of novel biomarkers for early detection of Non-Muscle-Invasive Bladder Cancer using Competing Endogenous RNA network analysis
Cited by: 35
Author(s): Morteza Kouhsar, Sadegh Azimzadeh Jamalkandi, Ali Moeini, Ali Masoudi‐Nejad
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-47389-w

Electrical stimulation shifts healing/scarring towards regeneration in a rat limb amputation model
Cited by: 30
Author(s): Karla Mychellyne Costa Oliveira, John H. Barker, Eugène Berezikov, Lukas Pindur, S Kynigopoulos, Maria Eischen-Loges, Zhongchao Han, Mit Balvantray Bhavsar, Dirk Henrich, Liudmila Leppik
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-43354-9

Analysis by RNA-seq of transcriptomic changes elicited by heat shock in Leishmania major
Cited by: 20
Author(s): Alberto Rastrojo, Laura Corvo, Rodrigo Lombraña, José Carlos Solana, Begoña Aguado, José Marı́a Requena
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-42680-2

Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts
Cited by: 31
Author(s): Yuanhang Liu, Pritha Chanana, Jaime Davila, Xiaonan Hou, Valentina Zanfagnin, Cordelia D. McGehee, Ellen L. Goode, Eric C. Polley, Paul Haluska, S. John Weroha, Chen Wang
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-43135-4

The transgenerational effects of oocyte mitochondrial supplementation
Cited by: 11
Author(s): Justin C. St. John, Yogeshwar Makanji, Jacqueline L. Johnson, Te-Sha Tsai, Simone Lagondar, Fleur Rodda, Xin Sun, Mulyoto Pangestu, Penny Chen, Peter Temple-Smith
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-43075-z

A universal transcriptomic signature of age reveals the temporal scaling of Caenorhabditis elegans aging trajectories
Cited by: 35
Author(s): Andrei E. Tarkhov, Ramani Alla, Srinivas Ayyadevara, Mikhail A. Pyatnitskiy, L. I. Men’shikov, Robert J. Shmookler Reis, П. О. Федичев
Software Mentions: 3
Published: over 7 years ago

10.1186/s12915-020-00886-1

The CBP KIX domain regulates long-term memory and circadian activity
Cited by: 18
Author(s): Snehajyoti Chatterjee, Christopher C. Angelakos, Ethan Bahl, Joshua D. Hawk, Marie E. Gaine, Shane G. Poplawski, Anne Schneider‐Anthony, Manish Kumar Yadav, Giulia S. Porcari, Jean‐Christophe Cassel, K. Peter Giese, Jacob J. Michaelson, Lisa C. Lyons, Anne‐Laurence Boutillier, Ted Abel
Software Mentions: 3
Published: about 6 years ago

10.1038/s41408-021-00440-4

Relapsed multiple myeloma demonstrates distinct patterns of immune microenvironment and malignant cell-mediated immunosuppression
Cited by: 22
Author(s): Alissa Visram, Surendra Dasari, Emilie Anderson, Shaji Kumar, Taxiarchis Kourelis
Software Mentions: 3
Published: over 5 years ago

10.1186/s13068-019-1612-7

Common metabolic networks contribute to carbon sink strength of sorghum internodes: implications for bioenergy improvement
Cited by: 7
Author(s): Yin Li, Min Tu, Yaping Feng, Wenqing Wang, Joachim Messing
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-019-43862-8

CRISPR/Cas9-mediated ablation of elovl2 in Atlantic salmon (Salmo salar L.) inhibits elongation of polyunsaturated fatty acids and induces Srebp-1 and target genes
Cited by: 53
Author(s): Alex K. Datsomor, Nikola Zic, Keshuai Li, Rolf Erik Olsen, Yang Jin, Jon Olav Vik, Rolf B. Edvardsen, Fabian Grammes, Anna Wargelius, Per Winge
Software Mentions: 3
Published: over 7 years ago

10.1186/s13068-020-01758-0

Comparative transcriptome analyses define genes and gene modules differing between two Populus genotypes with contrasting stem growth rates
Cited by: 14
Author(s): Xiao Han, Yi An, Yangyan Zhou, Chao Liu, Weilun Yin, Xinli Xia
Software Mentions: 3
Published: about 6 years ago

10.3389/fimmu.2018.03071

Protection Against Marburg Virus Using a Recombinant VSV-Vaccine Depends on T and B Cell Activation
Cited by: 34
Author(s): Andrea Marzi, Andrea Menicucci, Flora Engelmann, Julie Callison, Eva Horne, Friederike Feldmann, Allen Jankeel, Heinz Feldmann, Ilhem Messaoudi
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13068-019-1630-5

Responses of Methanosarcina barkeri to acetate stress
Cited by: 21
Author(s): Pinjing He, Haowen Duan, Wenfeng Han, Yang Liu, Liming Shao
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-019-5525-4

Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon
Cited by: 22
Author(s): Amin R. Mohamed, Klara L. Verbyla, Hawlader Abdullah Al-Mamun, Sean McWilliam, Bradley S. Evans, Hilary King, Peter D. Kube, James W. Kijas
Software Mentions: 3
Published: over 7 years ago

10.1186/s13068-021-01880-7

CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate
Cited by: 14
Author(s): Friederike Gutmann, Cosimo Jann, Filipa Pereira, Anders Johansson, Lars M. Steinmetz, Kiran Raosaheb Patil
Software Mentions: 3
Published: over 5 years ago

10.1186/1754-6834-6-72

Comparative transcriptome analysis to investigate the high starch accumulation of duckweed (Landoltia punctata) under nutrient starvation
Cited by: 79
Author(s): Tao Xiang, Yang Fang, Yao Xiao, Yanling Jin, Xinrong Ma, Yun Zhao, Kai He, Hai Zhao, Haiyan Wang
Software Mentions: 3
Published: over 13 years ago

10.1038/s41598-019-43935-8

GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data
Cited by: 105
Author(s): Naim Al Mahi, Mehdi Fazel Najafabadi, Marcin Pilarczyk, Michal Kouril, Mario Medvedovic
Software Mentions: 3
Published: over 7 years ago

10.1186/s12915-018-0579-3

Food perception without ingestion leads to metabolic changes and irreversible developmental arrest in C. elegans
Cited by: 14
Author(s): Rebecca E. W. Kaplan, Amy K. Webster, Rojin Chitrakar, Joseph A. Dent, L. Ryan Baugh
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-019-39880-1

MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions
Cited by: 25
Author(s): Bruno Arcà, Alessio Colantoni, Carmine Fiorillo, Francesco Severini, Vladimír Beneš, Marco Di Luca, Raffaele Calogero, Fabrizio Lombardo
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2020.540094

Identification of RNA Transcript Makers Associated With Prognosis of Kidney Renal Clear Cell Carcinoma by a Competing Endogenous RNA Network Analysis
Cited by: 16
Author(s): Qiwei Yang, Weiwei Chu, Wei Yang, Yan-Qiong Cheng, Chuanmin Chu, Xiuwu Pan, Jianqing Ye, Jun Cao, Sishun Gan, Xingang Cui
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-019-6223-y

Comparative transcriptomics in Syllidae (Annelida) indicates that posterior regeneration and regular growth are comparable, while anterior regeneration is a distinct process
Cited by: 23
Author(s): Rannyele Passos Ribeiro, Guillermo Ponz‐Segrelles, Christoph Bleidorn, M. Teresa Aguado
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-37669-2

Molecular evidence for distinct modes of nutrient acquisition between visceral and neurotropic schistosomes of birds
Cited by: 10
Author(s): Roman Leontovyč, Neil D. Young, Pasi K. Korhonen, Ross S. Hall, Jana Bulantová, Veronika Jeřábková, Martin Kašný, Robin B. Gasser, Petr Horák
Software Mentions: 3
Published: over 7 years ago

10.1186/1741-7007-12-42

RNA-seq: impact of RNA degradation on transcript quantification
Cited by: 327
Author(s): Irene Gallego Romero, Athma A. Pai, Jenny Tung, Yoav Gilad
Software Mentions: 3
Published: over 12 years ago

10.3390/antiox9090884

The Transcriptomic Response of the Murine Thyroid Gland to Iodide Overload and the Role of the Nrf2 Antioxidant System
Cited by: 7
Author(s): Dionysios V. Chartoumpekis, Panos G. Ziros, Ilias Georgakopoulos-Soares, Alexander Smith, Ana C. Marques, Mark Ibberson, Peter Kopp, Ioannis Habeos, Ioannis P. Trougakos, Nicholas K.H. Khoo, Gerasimos P. Sykiotis
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-40016-8

Whole transcriptome targeted gene quantification provides new insights on pulmonary sarcomatoid carcinomas
Cited by: 10
Author(s): Greta Alì, Rossella Bruno, Anello Marcello Poma, Ornella Affinito, Antonella Monticelli, Paolo Piaggi, Sara Ricciardi, Marco Lucchi, Franca Melfi, Antonio Chella, Sérgio Cocozza, Gabriella Fontanini
Software Mentions: 3
Published: over 7 years ago

10.18632/aging.103683

Profiling of circular RNAs in age-related cataract reveals circZNF292 as an antioxidant by sponging miR-23b-3p
Cited by: 27
Author(s): Shijie Liang, Shengqian Dou, Wenfeng Li, Yusen Huang
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2020.00265

Modulator-Dependent RBPs Changes Alternative Splicing Outcomes in Kidney Cancer
Cited by: 12
Author(s): Yan Wang, Steven Chen, Xi Rao, Yunlong Liu
Software Mentions: 3
Published: over 6 years ago

10.3390/antiox9121190

Differential Sex-Dependent Regulation of the Alveolar Macrophage miRNome of SP-A2 and co-ex (SP-A1/SP-A2) and Sex Differences Attenuation after 18 h of Ozone Exposure
Cited by: 7
Author(s): Nithyananda Thorenoor, David S. Phelps, Joanna Floros
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-40754-9

Genome analysis of Pseudomonas syringae pv. actinidiae biovar 6, which produces the phytotoxins, phaseolotoxin and coronatine
Cited by: 34
Author(s): Takashi Fujikawa, Hiroyuki Sawada
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-016-2720-4

Genome-wide analysis of the transcriptional response to porcine reproductive and respiratory syndrome virus infection at the maternal/fetal interface and in the fetus
Cited by: 27
Author(s): Jamie M. Wilkinson, Hua Bao, Andrea Ladinig, Linjun Hong, Paul Stothard, Joan K. Lunney, Graham Plastow, John C. S. Harding
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-018-36866-3

Marine biogenics in sea spray aerosols interact with the mTOR signaling pathway
Cited by: 12
Author(s): Jana Asselman, Emmanuel Van Acker, Maarten De Rijcke, Laurentijn Tilleman, Filip Van Nieuwerburgh, Jan Mees, Karel A.C. De Schamphelaere, Colin R. Janssen
Software Mentions: 3
Published: almost 8 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

10.3389/fgene.2020.628539

Cell Type-Specific Predictive Models Perform Prioritization of Genes and Gene Sets Associated With Autism
Cited by: 7
Author(s): Jinting Guan, Yang Wang, Yiping Lin, Qingyang Yin, Yibo Zhuang, Guoli Ji
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-36059-y

Genome-Wide Transcriptome Landscape of Embryonic Brain-Derived Neural Stem Cells Exposed to Alcohol with Strain-Specific Cross-Examination in BL6 and CD1 Mice
Cited by: 22
Author(s): Wayne Xu, Vichithra R. B. Liyanage, Aaron MacAulay, Romina D. Levy, Kyle Curtis, Carl O. Olson, Robby M. Zachariah, Shayan Amiri, Marjorie Buist, Geoffrey Hicks, James R. Davie, Mojgan Rastegar
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-34636-9

Gene set enrichment analysis of the bronchial epithelium implicates contribution of cell cycle and tissue repair processes in equine asthma
Cited by: 13
Author(s): Laurence Tessier, Olivier Côté, Mary E. Clark, Laurent Viel, Andrés Diaz-Méndez, Simon Anders, Dorothee Bienzle
Software Mentions: 3
Published: almost 8 years ago

10.1042/BSR20202463

Explore prognostic biomarker of bladder cancer based on competing endogenous network
Cited by: 6
Author(s): Faping Li, Hui Guo, Bin Liu, Nian Liu, Zhixiang Xu, Yishu Wang, Honglan Zhou
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2019.01215

Expression Quantitative Trait Loci in Equine Skeletal Muscle Reveals Heritable Variation in Metabolism and the Training Responsive Transcriptome
Cited by: 8
Author(s): Gabriella Farries, Kenneth Bryan, C. L. McGivney, Paul A. McGettigan, K. F. Gough, John A. Browne, David E. MacHugh, Lisa Katz, Emmeline W. Hill
Software Mentions: 3
Published: almost 7 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568