bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.7717/peerj.8930

Transcriptome analysis revealed key prognostic genes and microRNAs in hepatocellular carcinoma
Cited by: 24
Author(s): Xi Ma, Lin Zhou, Shusen Zheng
Software Mentions: 3
Published: over 6 years ago

The Transcriptome of Cunninghamia lanceolata male/female cone reveal the association between MIKC MADS-box genes and reproductive organs development
Cited by: 12
Author(s): Dandan Wang, Zhaodong Hao, Xiaofei Long, Zhanjun Wang, Xianrui Zheng, Daiquan Ye, Peng Ye, Weihuang Wu, Xiangyang Hu, Guibin Wang, Renhua Zheng, Jisen Shi, Jinhui Chen
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-020-06870-x

Shedding light on cashmere goat hair follicle biology: from morphology analyses to transcriptomic landascape
Cited by: 8
Author(s): Cristina Nocelli, Katia Cappelli, Stefano Capomaccio, Luisa Pascucci, Francesca Mercati, Irene Pazzaglia, Samanta Mecocci, Marco Antonini, Carlo Renieri
Software Mentions: 3
Published: about 6 years ago

10.1038/srep37536

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle
Cited by: 24
Author(s): Alejandra Rougon‐Cardoso, Mitzi Flores-Ponce, Hilda E. Ramos-Aboites, Christian E. Martínez-Guerrero, Youjin Hao, Luís Cunha, Jonathan Alejandro Rodríguez-Martínez, Cesaré Ovando-Vázquez, José Roberto Bermúdez-Barrientos, Cei Abreu‐Goodger, Noelina Hernández, Nélson Simões, Rafaél Montiel
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13195-019-0558-0

APOE2 orchestrated differences in transcriptomic and lipidomic profiles of postmortem AD brain
Cited by: 36
Author(s): Iliya Lefterov, Cody M. Wolfe, Nicholas F. Fitz, Kyong Nyon Nam, Florent Letronne, Richard J. Biedrzycki, Julia Kofler, Xianlin Han, Jianing Wang, Jonathan Schug, Radosveta Koldamova
Software Mentions: 3
Published: over 6 years ago

10.1186/s13195-021-00810-x

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

10.1186/s12974-020-02011-z

Complement peptide C3a receptor 1 promotes optic nerve degeneration in DBA/2J mice
Cited by: 27
Author(s): Jeffrey M. Harder, Pete A. Williams, Catherine E. Braine, Hongtian Yang, Jocelyn M. Thomas, Nicole E. Foxworth, Simon W. M. John, Gareth R. Howell
Software Mentions: 3
Published: almost 6 years ago

10.1038/srep33296

Global analysis of differential gene expression related to long-term sperm storage in oviduct of Chinese Soft-Shelled Turtle Pelodiscus sinensis
Cited by: 23
Author(s): Tengfei Liu, Ping Yang, Hong Chen, Yufei Huang, Yi Liu, Yasir Waqas, Nisar Ahmed, Xia Chu, Qiusheng Chen
Software Mentions: 3
Published: almost 10 years ago

10.1038/srep33151

De novo Transcriptome Analysis Reveals Distinct Defense Mechanisms by Young and Mature Leaves of Hevea brasiliensis (Para Rubber Tree)
Cited by: 37
Author(s): Yuxiao Fang, Hailiang Mei, Binhui Zhou, Xiaohu Xiao, Meng Yang, Yacheng Huang, Xiangyu Long, Songnian Hu, Chaorong Tang
Software Mentions: 3
Published: almost 10 years ago

10.7717/peerj.10576

A novel similarity score based on gene ranks to reveal genetic relationships among diseases
Cited by: 3
Author(s): Dongmei Luo, Chengdong Zhang, Liwan Fu, Yuening Zhang, Yue‐Qing Hu
Software Mentions: 3
Published: over 5 years ago

10.1038/srep31150

Schistosome sex matters: a deep view into gonad-specific and pairing-dependent transcriptomes reveals a complex gender interplay
Cited by: 99
Author(s): Zhigang Lu, Florian Sessler, Nancy Holroyd, Steffen Hahnel, Thomas Quack, Matthew Berriman, Christoph G. Grevelding
Software Mentions: 3
Published: about 10 years ago

10.1186/s12870-017-1187-z

De novo transcriptome assembly from flower buds of dioecious, gynomonoecious and chemically masculinized female Coccinia grandis reveals genes associated with sex expression and modification
Cited by: 16
Author(s): Ravi Suresh Devani, Sangram Sinha, Jayeeta Banerjee, Rabindra Kumar Sinha, Abdelhafid Bendahmane, Anjan K. Banerjee
Software Mentions: 3
Published: over 8 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: over 8 years ago

10.1186/s12864-016-3009-3

Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat
Cited by: 79
Author(s): Siyuan Zhan, Yao Dong, Wei Zhao, Jiazhong Guo, Tao Zhong, Linjie Wang, Li Li, Hongping Zhang
Software Mentions: 3
Published: about 10 years ago

10.1093/ajcn/nqz012

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

10.1038/srep28702

Global transcriptome changes in perennial ryegrass during early infection by pink snow mould
Cited by: 12
Author(s): Mallikarjuna Rao Kovi, Mohamed Abdelhalim, Anil Kunapareddy, Åshild Ergon, Anne Marte Tronsmo, May Bente Brurberg, Ingerd Skow Hofgaard, Torben Asp, Odd Arne Rognli
Software Mentions: 3
Published: about 10 years ago

10.1038/srep27043

Differences in DNA Repair Capacity, Cell Death and Transcriptional Response after Irradiation between a Radiosensitive and a Radioresistant Cell Line
Cited by: 33
Author(s): Mireia Borràs-Fresneda, Joan Francesc Barquinero, Maria Gomolka, Sabine Hornhardt, Ute Rößler, Gemma Armengol, Leonardo Barrios
Software Mentions: 3
Published: about 10 years ago

10.1038/s41388-019-0845-z

The protein secretion modulator TMED9 drives CNIH4/TGFα/GLI signaling opposing TMED3-WNT-TCF to promote colon cancer metastases
Cited by: 34
Author(s): Sasmita Mishra, Carolina Bernal, Marianna Silvano, Santosh Anand, Ariel Ruiz i Altaba
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-018-4627-8

Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse
Cited by: 44
Author(s): Paula Fagundes de Gouvêa, Aline Vianna Bernardi, Luís Eduardo Gerolamo, Emerson de Souza Santos, Diego Mauricio Riaño‐Pachón, Sérgio Akira Uyemura, Taísa Magnani Dinamarco
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-016-2704-4

Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health
Cited by: 30
Author(s): Nikol Voutsina, Adrienne Payne, Robert D. Hancock, Graham J. J. Clarkson, Steve D. Rothwell, Mark A. Chapman, Gail Taylor
Software Mentions: 3
Published: over 10 years ago

10.7717/peerj.8260

qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data
Cited by: 4
Author(s): Necla Koçhan, G. Yazgı Tütüncü, Gordon K. Smyth, Luke C. Gandolfo, Göknur Giner
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-4521-4

Lineage-specific duplications of NBS-LRR genes occurring before the divergence of six Fragaria species
Cited by: 20
Author(s): Yan Zhong, Xiaohui Zhang, Zong‐Ming Cheng
Software Mentions: 3
Published: over 8 years ago

10.1038/srep26114

Comparative analysis of the integument transcriptomes of the black dilute mutant and the wild-type silkworm Bombyx mori
Cited by: 17
Author(s): Songyuan Wu, Xiaoling Tong, Chenxing Peng, Xiong Guan, Kunpeng Lu, Hai Hu, Tan D, Chunlin Li, Minjin Han, Cheng Lü, Fangyin Dai
Software Mentions: 3
Published: over 10 years ago

10.1155/2020/6827057

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

10.1038/srep25474

Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells
Cited by: 41
Author(s): Pamela Milani, Renan Escalante-Chong, Brandon Shelley, Natasha L. Patel-Murray, Xin X, Miriam Adam, Berhan Mandefro, Dhruv Sareen, Clive N. Svendsen, Ernest Fraenkel
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-017-4170-z

Transcript expression plasticity as a response to alternative larval host plants in the speciation process of corn and rice strains of Spodoptera frugiperda
Cited by: 35
Author(s): Karina Lucas Silva‐Brandão, Renato J. Horikoshi, Daniel Bernardi, Celso Omoto, Antônio Figueira, Marcelo Mendes Brandão
Software Mentions: 3
Published: almost 9 years ago

10.1038/srep24964

Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection
Cited by: 34
Author(s): Guanxiang Liang, Nilusha Malmuthuge, Yongjuan Guan, Yan Ren, Philip Griebel, Le Luo Guan
Software Mentions: 3
Published: over 10 years ago

10.1002/cam4.3006

Downregulated hsa_circ_0077837 and hsa_circ_0004826, facilitate bladder cancer progression and predict poor prognosis for bladder cancer patients
Cited by: 31
Author(s): Chong Shen, Zhouliang Wu, Yujie Wang, Shen Gao, La Da, Linguo Xie, Yunkai Qie, Dan Tian, Hailong Hu
Software Mentions: 3
Published: over 6 years ago

10.1038/srep24061

Empirical insights into the stochasticity of small RNA sequencing
Cited by: 5
Author(s): Li‐Xuan Qin, Thomas Tuschl, Samuel Singer
Software Mentions: 3
Published: over 10 years ago

10.1016/j.isci.2021.102741

Derepression of inflammation-related genes link to microglia activation and neural maturation defect in a mouse model of Kleefstra syndrome
Cited by: 3
Author(s): Ayumi Yamada, Takae Hirasawa, Kayako Nishimura, Chikako Shimura, Naomi Kogo, Kei Fukuda, Madoka Kato, Masaki Yokomori, Tetsutaro Hayashi, Mana Umeda, Mika Yoshimura, Yoichiro Iwakura, Itoshi Nikaido, Shigeyoshi Itohara, Yoichi Shinkai
Software Mentions: 3
Published: about 5 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: over 6 years ago

10.1186/s12870-019-1802-2

Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube
Cited by: 8
Author(s): Zhang Zhong, C.K. Kang, Shuyi Zhang, Xingang Li
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pntd.0006410

Sialome diversity of ticks revealed by RNAseq of single tick salivary glands
Cited by: 61
Author(s): Jan Perner, Sára Kropáčková, Petr Kopáček, José M. C. Ribeiro
Software Mentions: 3
Published: over 8 years ago

10.1038/srep20837

Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model
Cited by: 15
Author(s): Els Willems, Carlos Guerrero-Bosagna, Eddy Decuypere, Steven Janssens, Johan Buyse, Nadine Buys, Per Jensen, Nadia Everaert
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-020-6570-8

MicroRNA expression profile analysis in sperm reveals hsa-mir-191 as an auspicious omen of in vitro fertilization
Cited by: 37
Author(s): Hua Xu, Xin Wang, Zhikai Wang, Jianhui Li, Zhiming Xu, Maohua Miao, Guowu Chen, Xiang-Dong Lei, Jun Wu, Huijuan Shi, Ke Wang, Tiancheng Zhang, Xiaoxi Sun
Software Mentions: 3
Published: over 6 years ago

10.1038/srep18399

Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing
Cited by: 56
Author(s): Aroa Suárez-Vega, Christophe Klopp, Christèle Robert-Granié, Gwenola Tosser‐Klopp, Juan José Arranz
Software Mentions: 3
Published: over 10 years ago

10.1038/srep13456

TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability
Cited by: 15
Author(s): Lamiaa Bahnassawy, Thanneer M. Perumal, Laura González-Cano, Anna-Lena Hillje, Leila Taher, Wojciech Makałowski, Yutaka Suzuki, Georg Fuellen, Antonio del Sol, Jens Christian Schwamborn
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pntd.0009797

A gene expression panel for estimating age in males and females of the sleeping sickness vector Glossina morsitans
Cited by: 1
Author(s): Eric R. Lucas, Alistair C. Darby, Stephen J. Torr, Martin J. Donnelly
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0161987

De Novo Assembly and Transcriptome Analysis of Bulb Onion (Allium cepa L.) during Cold Acclimation Using Contrasting Genotypes
Cited by: 25
Author(s): Jeongsukhyeon Han, Senthil Kumar Thamilarasan, Sathishkumar Natarajan, Jong-In Park, Mi-Young Chung, Ill–Sup Nou
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0242970

Chronic IL-1 exposure drives LNCaP cells to evolve androgen and AR independence
Cited by: 8
Author(s): Haley Dahl, Mohammed Kanchwala, Shayna E. Thomas‐Jardin, Amrit Sandhu, Preethi Kanumuri, Afshan F. Nawas, Chao Xing, Chenchu Lin, Daniel E. Frigo, Nikkí A. Delk
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.37182

A selective gut bacterial bile salt hydrolase alters host metabolism
Cited by: 156
Author(s): Lina Yao, Sarah C. Seaton, Sula Ndousse-Fetter, Arijit A. Adhikari, Nicholas DiBenedetto, Amir I. Mina, Alexander S. Banks, Lynn Bry, A. Sloan Devlin
Software Mentions: 3
Published: about 8 years ago

10.1186/1471-2164-15-337

Transcriptome differences between two sister desert poplar species under salt stress
Cited by: 36
Author(s): Jian Zhang, Jiexiong Feng, Jing Lü, Yongzhi Yang, Xu Zhang, Dongshi Wan, Jianquan Liu
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-016-2376-0

Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen Pectobacterium atrosepticum
Cited by: 19
Author(s): Stanford Kwenda, Vladimir Gorshkov, Aiyagari Ramesh, Sanushka Naidoo, Enrico Rubagotti, Paul R. J. Birch, Lucy N. Moleleki
Software Mentions: 3
Published: over 10 years ago

10.1186/s12866-020-02020-1

Berberine alters gut microbial function through modulation of bile acids
Cited by: 10
Author(s): Patricia G. Wolf, Saravanan Devendran, Heidi L. Doden, Lindsey K. Ly, Tyler Moore, Hiroyuki Takei, Hiroshi Nittono, Tsuyoshi Murai, Takao Kurosawa, George E. Chlipala, Stefan J. Green, Genta Kakiyama, Purna C. Kashyap, Vance J. McCracken, H. Rex Gaskins, Patrick M. Gillevet, Jason M. Ridlon
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0174236

Enhancement of Arabidopsis growth characteristics using genome interrogation with artificial transcription factors
Cited by: 7
Author(s): Niels van Tol, Martijn Rolloos, Johan E. Pinas, Christiaan V. Henkel, Dieuwertje Augustijn, Paul J. J. Hooykaas, Bert J. van der Zaal
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0091041

Variation in RNA-Seq Transcriptome Profiles of Peripheral Whole Blood from Healthy Individuals with and without Globin Depletion
Cited by: 70
Author(s): Heesun Shin, Casey P. Shannon, Nick Fishbane, Jian Ruan, Mi Zhou, Robert Balshaw, J. Wilson-McManus, Raymond T. Ng, Bruce M. McManus, Scott J. Tebbutt
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-021-07478-5

Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs
Cited by: 13
Author(s): Christine N Goldfarb, David J. Waxman
Software Mentions: 3
Published: over 5 years ago

10.1038/srep02898

Soft truncation thresholding for gene set analysis of RNA-seq data: Application to a vaccine study
Cited by: 15
Author(s): Brooke L. Fridley, Gregory D. Jenkins, Diane E. Grill, Richard B. Kennedy, Gregory A. Poland, Ann L. Oberg
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12866-020-1722-1

Integrative analysis of outer membrane vesicles proteomics and whole-cell transcriptome analysis of eravacycline induced Acinetobacter baumannii strains
Cited by: 19
Author(s): Dinesh Kumar Kesavan, Aparna Vasudevan, Liang Wu, Jianguo Chen, Zhaoliang Su, Shengjun Wang, Huaxi Xu
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-021-07584-4

Identification of co-expression network correlated with different periods of adipogenic and osteogenic differentiation of BMSCs by weighted gene co-expression network analysis (WGCNA)
Cited by: 13
Author(s): Yu Liu, Markus Tingart, Sophie Lecouturier, Jianzhang Li, Jörg Eschweiler
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-019-5502-y

Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes
Cited by: 2
Author(s): Hao Cai, Xiangyu Li, Jun He, Wenbin Zhou, Kai Song, You Guo, Huaping Liu, Qingzhou Guan, Haidan Yan, Xianlong Wang, Zheng Guo
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-018-4679-9

Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles
Cited by: 39
Author(s): Andrea Grilli, Rossella Bengalli, Eleonora Longhin, Laura Capasso, Maria Carla Proverbio, Mattia Forcato, Silvio Bicciato, Maurizio Gualtieri, Cristina Battaglia, Marina Camatini
Software Mentions: 3
Published: over 8 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

10.1186/s12920-019-0580-x

A comprehensive genome-wide profiling comparison between HBV and HCV infected hepatocellular carcinoma
Cited by: 21
Author(s): Suofeng Sun, Yuan Li, Sun‐Young Han, Huiying Jia, Xiuling Li, Xiaofang Li
Software Mentions: 3
Published: almost 7 years ago

10.3390/ani9060313

Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs
Cited by: 11
Author(s): Xin Liu, Jianfei Gong, Ligang Wang, Xinhua Hou, Hongmei Gao, Yan Hua, Fuping Zhao, Longchao Zhang, Lixian Wang
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0230249

Proteomic changes during experimental de- and remyelination in the corpus callosum
Cited by: 6
Author(s): Gabor T. Szilagyi, Arkadiusz Nawrocki, Krisztián Erős, J. Schmidt, Katalin Fekete, Maria L. Elkjaer, K. H. Hyrlov, Martin R. Larsen, Zsolt Illés, Ferenc Gallyas
Software Mentions: 3
Published: over 6 years ago

10.1038/s41597-020-00628-6

Consensus transcriptional regulatory networks of coronavirus-infected human cells
Cited by: 23
Author(s): Scott A. Ochsner, Rudolf T. Pillich, Neil J. McKenna
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12870-019-2169-0

Differential gene expression among three sex types reveals a MALE STERILITY 1 (CpMS1) for sex differentiation in papaya
Cited by: 11
Author(s): Dessireé Zerpa‐Catanho, Jennifer Wai, Ming Li Wang, Liang Yu, Julie Nguyen, Ray Ming
Software Mentions: 3
Published: over 6 years ago

10.1038/s41597-019-0117-3

Metagenomics and transcriptomics data from human colorectal cancer
Cited by: 5
Author(s): Tina Visnovska, Patrick J. Biggs, Frank Frizelle, Rachel Purcell
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0162402

Comprehensive Transcriptome Analyses of the Fructose-Fed Syrian Golden Hamster Liver Provides Novel Insights into Lipid Metabolism
Cited by: 8
Author(s): Ziyang Li, Chaoliang Xiong, Suo Mo, Haiying Tian, Mengqian Yu, Tingting Mao, Qian Chen, Huai‐Rong Luo, Quan-Zhen Li, Jianxin Lü, Yi Zhao, Wei Li
Software Mentions: 3
Published: almost 10 years ago

10.3390/ani10111944

Overexpression of PLIN1 Promotes Lipid Metabolism in Bovine Adipocytes
Cited by: 12
Author(s): Shijun Li, Sayed Haidar Abbas Raza, Chunping Zhao, Gong Chen, Zan Liu
Software Mentions: 3
Published: almost 6 years ago

10.18632/aging.203425

ADAM15 correlates with prognosis, immune infiltration and apoptosis in hepatocellular carcinoma
Cited by: 9
Author(s): Jun Xu, Yong Guan, Yi Chao Zhang, Zhendong Qiu, Yu Zhou, Chen Chen, Jie-Ping Yu, Weixing Wang
Software Mentions: 3
Published: about 5 years ago

10.1038/sdata.2017.163

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system
Cited by: 4
Author(s): Margherita Francescatto, Marina Lizio, Ingrid H.C.H.M. Philippens, Luba M. Pardo, Ronald E. Bontrop, Mizuho Sakai, Shoko Watanabe, Masayoshi Itoh, Akira Hasegawa, Timo Lassmann, Jessica Severin, Jayson Harshbarger, Imad Abugessaisa, Takeya Kasukawa, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Hideya Kawaji, Patrizia Rizzu, Peter Heutink
Software Mentions: 3
Published: almost 9 years ago

10.1038/sdata.2017.118

A gene expression atlas of adult Schistosoma mansoni and their gonads
Cited by: 44
Author(s): Zhigang Lu, Florian Sessler, Nancy Holroyd, Steffen Hahnel, Thomas Quack, Matthew Berriman, Christoph G. Grevelding
Software Mentions: 3
Published: about 9 years ago

10.1038/sdata.2017.20

Genome-wide barcoded transposon screen for cancer drug sensitivity in haploid mouse embryonic stem cells
Cited by: 11
Author(s): Stephen J. Pettitt, Dragomir B. Krastev, Helen Pemberton, Yari Fontebasso, Jessica Frankum, Farah L. Rehman, Rachel Brough, Feifei Song, Ilirjana Bajrami, Rumana Rafiq, Fredrik Wållberg, Iwanka Kozarewa, Kerry Fenwick, Javier Armisen-Garrido, Amanda Swain, Aditi Gulati, James Campbell, Alan Ashworth, Christopher J. Lord
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0170779

Correlated 5-Hydroxymethylcytosine (5hmC) and Gene Expression Profiles Underpin Gene and Organ-Specific Epigenetic Regulation in Adult Mouse Brain and Liver
Cited by: 50
Author(s): I‐Hsuan Lin, Yifan Chen, Ming Hsu
Software Mentions: 3
Published: over 9 years ago

10.1186/s12979-015-0038-8

Hormetic effect of rotenone in primary human fibroblasts
Cited by: 13
Author(s): Shiva Marthandan, Stefan Priebe, Marco Groth, Reinhard Guthke, Matthias Platzer, Peter Hemmerich, Stephan Diekmann
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-017-4374-2

A survey on cellular RNA editing activity in response to Candida albicans infections
Cited by: 3
Author(s): Yao‐Wei Huang, Yingying Cao, Jiarui Li, Yuanhua Liu, Zhong Wu, Xuan Li, Chen Chen, Pei Hao
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0184003

Honokiol induces superoxide production by targeting mitochondrial respiratory chain complex I in Candida albicans
Cited by: 38
Author(s): Libo Sun, Kai Liao, Dayong Wang
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41438-020-0287-3

Transcriptome analysis and metabolic profiling reveal the key role of carotenoids in the petal coloration of Liriodendron tulipifera
Cited by: 39
Author(s): Zhaodong Hao, Siqin Liu, Lingfeng Hu, Jisen Shi, Jinhui Chen
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0234029

An investigation into the beneficial effects and molecular mechanisms of humic acid on foxtail millet under drought conditions
Cited by: 8
Author(s): Jie Shen, Meijun Guo, Yuguo Wang, Xiangyang Yuan, Shuqi Dong, Xi-e Song, Peng Guo
Software Mentions: 3
Published: about 6 years ago

10.1007/s00401-013-1168-8

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy
Cited by: 162
Author(s): Katja Kobow, Antony Kaspi, K N Harikrishnan, K. Kiese, Mark Ziemann, Ishant Khurana, Ina Fritzsche, Jan Hauke, Eric Hahnen, Roland Coras, Angelika Mühlebner, Assam El‐Osta, Ingmar Blümcke
Software Mentions: 3
Published: almost 13 years ago

10.1038/s41438-020-0269-5

A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae)
Cited by: 9
Author(s): Ting Xue, Xinqing Zheng, Duo Chen, Limin Liang, Nan Chen, Zhen Huang, Wenfang Fan, Jiannan Chen, Chengsong Wan, Shuai Chen, Jinmao Zhu, Binghua Chen, Xingtan Zhang, Youqiang Chen
Software Mentions: 3
Published: over 6 years ago

10.1038/s41438-018-0020-7

Divergence in the transcriptional landscape between low temperature and freeze shock in cultivated grapevine (Vitis vinifera)
Cited by: 49
Author(s): Jason P. Londo, Alisson P. Kovaleski, Jacquelyn Lillis
Software Mentions: 3
Published: over 8 years ago

10.1038/s41438-020-00452-4

Induced defense response in red mango fruit against Colletotrichum gloeosporioides
Cited by: 22
Author(s): Sudheeran Pradeep Kumar, Noa Sela, Mira Carmeli-Weissberg, Rinat Ovadia, Sayantan Panda, Oleg Feygenberg, Dalia Maurer, Michal Oren-Shamir, Asaph Aharoni, Noam Alkan
Software Mentions: 3
Published: over 5 years ago

10.3390/antibiotics9100715

Aureolic Acid Group of Agents as Potential Antituberculosis Drugs
Cited by: 2
Author(s): Julia Bespyatykh, Dmitry Bespiatykh, Maja V. Malakhova, Ksenia M. Klimina, Andrey Bespyatykh, Anna M. Varizhuk, Anna N. Tevyashova, Tatiana A Nikolenko, Galina E. Pozmogova, Elena N. Ilina, Egor Shitikov
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-5795-x

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

10.1371/journal.pone.0180842

RNA sequencing to determine the contribution of kinase receptor transactivation to G protein coupled receptor signalling in vascular smooth muscle cells
Cited by: 15
Author(s): Danielle Kamato, Venkata Vijayanand Bhaskarala, Nitin Mantri, Tae Gyu Oh, Dora Ling, Reearna Janke, Wenhua Zheng, Peter J. Little, Narin Osman
Software Mentions: 3
Published: about 9 years ago

10.1038/s41388-020-01435-4

The proapoptotic gene interferon regulatory factor-1 mediates the antiproliferative outcome of paired box 2 gene and tamoxifen
Cited by: 2
Author(s): Shixiong Wang, Venkata S. Somisetty, Baoyan Bai, Igor Chernukhin, Henri Niskanen, Minna U. Kaikkonen, Meritxell Bellet, Jason S. Carroll, Antoni Hurtado
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0128041

Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions
Cited by: 85
Author(s): Lei Gong, Hongxia Zhang, Xiaoyan Gan, Li Zhang, Yuchao Chen, Fengjie Nie, Lei Shi, Miao Li, Zhiqian Guo, Guohui Zhang, Song Yao
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0188285

DEclust: A statistical approach for obtaining differential expression profiles of multiple conditions
Cited by: 7
Author(s): Yoshimasa Aoto, Tsuyoshi Hachiya, Kazuhiro Okumura, Sumitaka Hase, Kengo Sato, Yuichi Wakabayashi, Yasubumi Sakakibara
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0238594

High accuracy gene expression profiling of sorted cell subpopulations from breast cancer PDX model tissue
Cited by: 1
Author(s): Warren Porter, Eileen Snowden, Friedrich Hahn, Mitchell Ferguson, Frances Tong, W. Shannon Dillmore, Rainer Blaesius
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms22189719

Genome-Wide Analysis of LncRNA in Bovine Mammary Epithelial Cell Injuries Induced by Escherichia Coli and Staphylococcus Aureus
Cited by: 11
Author(s): Changjie Lin, Yifan Zhu, Zhiyu Hao, Haojun Xu, Ting Li, Jinghan Yang, Xi Chen, Yingyu Chen, Aizhen Guo, Changmin Hu
Software Mentions: 3
Published: almost 5 years ago

10.1002/hed.25537

Association between loss of Y chromosome and poor prognosis in male head and neck squamous cell carcinoma
Cited by: 21
Author(s): Robert Hollows, Wenbin Wei, Jean‐Baptiste Cazier, Hisham Mehanna, Gabriella Parry, Graham Halford, Paul G. Murray
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-905

Limited sex-biased neural gene expression patterns across strains in Zebrafish (Danio rerio)
Cited by: 54
Author(s): Ryan Y. Wong, Melissa M McLeod, John Godwin
Software Mentions: 3
Published: over 12 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

10.1371/journal.pone.0251868

Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem
Cited by: 3
Author(s): Stephanie Lam, Arun Kommadath, Ó. López-Campos, Nuria Prieto, J. L. Aalhus, M. Juárez, M. E. R. Dugan, Payam Vahmani
Software Mentions: 3
Published: over 5 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: almost 6 years ago

10.1093/gigascience/giaa009

De novo genome assembly and Hi-C analysis reveal an association between chromatin architecture alterations and sex differentiation in the woody plant Jatropha curcas
Cited by: 15
Author(s): Maosheng Chen, Longjian Niu, Miaomiao Zhao, Chuan-Jia Xu, Bang-Zhen Pan, Qi Fu, Yongfu Tao, Hua He, Chaoqi Hou, Zeng-Fu Xu
Software Mentions: 3
Published: over 6 years ago

10.1155/2017/8027626

Transcriptome Analysis of Two Different Developmental Stages of <i>Paeonia lactiflora</i> Seeds
Cited by: 7
Author(s): Yong-Lei Ma, Jinqiu Cui, Xiujun Lu, Lijie Zhang, Zhijing Chen, Riwen Fei, Xiulan Sun
Software Mentions: 3
Published: over 9 years ago

10.1093/gigascience/giz020

MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs
Cited by: 14
Author(s): Stuart M. Brown, Hao Chen, Yuhan Hao, Bobby Peter Laungani, Thahmina Ali, Changsu Dong, Carlos Lijeron, Baekdoo Kim, Claudia Wultsch, Zhiheng Pei, Konstantinos Krampis
Software Mentions: 3
Published: over 7 years ago

10.1093/gigascience/giy027

Whole-genome resequencing reveals signatures of selection and timing of duck domestication
Cited by: 70
Author(s): Zebin Zhang, Yaxiong Jia, Pedro Almeida, Judith E. Mank, Marcel van Tuinen, Qiong Wang, Zhihua Jiang, Yu Chen, Kai Zhan, Shuisheng Hou, Zhengkui Zhou, Huifang Li, Fan Yang, Yong He, Zhonghua Ning, Ning Yang, Lujiang Qu
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-019-5745-7

Cold acclimation triggers major transcriptional changes in Drosophila suzukii
Cited by: 29
Author(s): Thomas Enriquez, Hervé Colinet
Software Mentions: 3
Published: over 7 years ago

10.1155/2021/3984463

Identification of Potential lncRNAs and miRNAs as Diagnostic Biomarkers for Papillary Thyroid Carcinoma Based on Machine Learning
Cited by: 14
Author(s): Fei Yang, Jie Zhang, Baokun Li, Zhao Zhi-gang, Yan Liu, Zhen Zhao, Jing Shao, Guiying Wang
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0225080

Identifying candidate diagnostic markers for early stage of non-small cell lung cancer
Cited by: 1
Author(s): Zhen Wu, Xu Zhang, Zhijun He, Liyun Hou
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-017-4285-2

ENCoRE: an efficient software for CRISPR screens identifies new players in extrinsic apoptosis
Cited by: 15
Author(s): Dietrich Trümbach, Susanne Pfeiffer, Manuel Poppe, Hagen Scherb, Sebastian Doll, Wolfgang Wurst, Joel Schick
Software Mentions: 3
Published: almost 9 years ago

10.3390/ijms22189693

Fetal Brain Elicits Sexually Conflicting Transcriptional Response to the Ablation of Uterine Forkhead Box A2 (Foxa2) in Mice
Cited by: 5
Author(s): Pramod Dhakal, Monica Strawn, Ananya Samal, Susanta K. Behura
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12870-021-03009-2

Genome-wide association analysis reveals quantitative trait loci and candidate genes involved in yield components under multiple field environments in cotton (Gossypium hirsutum)
Cited by: 8
Author(s): Guozhong Zhu, Shuang Hou, Xiaohui Song, Xing Wang, Wei Wang, Quanjia Chen, Wangzhen Guo
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0237400

Whole-blood transcriptome profiling reveals signatures of metformin and its therapeutic response
Cited by: 14
Author(s): Monta Ustinova, Laura Ansone, Ivars Silamiķelis, Vita Rovīte, Ilze Elbere, Laila Silamiķele, Ineta Kalniņa, Dāvids Fridmanis, Jeļizaveta Sokolovska, Ilze Konrāde, Valdis Pīrāgs, Jānis Kloviņš
Software Mentions: 3
Published: about 6 years ago

10.1186/s12920-019-0548-x

Placental microRNAs in pregnancies with early onset intrauterine growth restriction and preeclampsia: potential impact on gene expression and pathophysiology
Cited by: 72
Author(s): Zain Awamleh, Gregory B. Gloor, V. K. M. Han
Software Mentions: 3
Published: about 7 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

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Papers Mentioning edgeR 6,568