bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-67432-5

Differential expression of polyamine biosynthetic pathways in skin lesions and in plasma reveals distinct profiles in diffuse cutaneous leishmaniasis
Cited by: 7
Author(s): Hayna Malta‐Santos, Jaqueline França‐Costa, Amanda Ferreira Macedo, Artur T. L. Queiroz, Kiyoshi F. Fukutani, Sandra Márcia Muxel, Ricardo Khouri, Johan Van Weyenbergh, Viviane Boaventura, Aldina Barral, Jackson Maurício Lopes Costa, Eny Iochevet Segal Floh, Bruno B. Andrade, Lucile Maria Floeter‐Winter, Valéria M. Borges
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-66309-x

Comparative targeting analysis of KLF1, BCL11A, and HBG1/2 in CD34+ HSPCs by CRISPR/Cas9 for the induction of fetal hemoglobin
Cited by: 35
Author(s): Andrés Lamsfus‐Calle, Alberto Daniel‐Moreno, Justin S. Antony, Thomas Epting, Lukas Heumos, Praveen Baskaran, Jakob Admard, Nicolas Casadei, Ngadhnjim Latifi, Darina M. Siegmund, Michael Kormann, Rupert Handgretinger, Markus Mezger
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-66556-y

WNT and inflammatory signaling distinguish human Fallopian tube epithelial cell populations
Cited by: 9
Author(s): Ian M. Rose, Mallikarjun Bidarimath, Alex Webster, Andrew K. Godwin, Andrea Flesken‐Nikitin, Alexander Yu. Nikitin
Software Mentions: 4
Published: about 6 years ago

10.1186/s12967-021-02846-x

Eleven immune-gene pairs signature associated with TP53 predicting the overall survival of gastric cancer: a retrospective analysis of large sample and multicenter from public database
Cited by: 9
Author(s): Junyu Huo, Liqun Wu, Yunjin Zang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-64514-2

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype
Cited by: 12
Author(s): Sharon A. McGrath‐Morrow, Roland Ndeh, Kathryn A. Helmin, Basil Khuder, Cynthia Rothblum-Oviatt, Joseph M. Collaco, Jonathan H. Wright, Paul A. Reyfman, Howard M. Lederman, Benjamin D. Singer
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-61177-x

RNA-seq analysis reveals TRPC genes to impact an unexpected number of metabolic and regulatory pathways
Cited by: 10
Author(s): Karina Formoso, Sebastián Susperreguy, Marc Freichel, Lutz Birnbaumer
Software Mentions: 4
Published: over 6 years ago

10.1093/bib/bbv019

Optimization of miRNA-seq data preprocessing
Cited by: 100
Author(s): Susan H. Tam, Ming‐Sound Tsao, John Douglas Mcpherson
Software Mentions: 4
Published: over 11 years ago

10.1093/bib/bbx080

‘Multi-omic’ data analysis using O-miner
Cited by: 13
Author(s): Ajanthah Sangaralingam, Abu Z. Dayem Ullah, Jacek Marzec, Emanuela Gadaleta, A. Nagano, Helen Ross-Adams, Jun Wang, Nick R. Lemoine, Claude Chelala
Software Mentions: 4
Published: about 9 years ago

10.3389/fnbeh.2017.00069

Persistent Effects of Developmental Exposure to 17α-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior
Cited by: 26
Author(s): Tove Porseryd, Kristina Volkova, Nasim Reyhanian Caspillo, Thomas Källman, Patrik Dinnétz, Inger Porsch Hällström
Software Mentions: 4
Published: over 9 years ago

10.3389/fbioe.2020.00348

Analysis of Gene Signatures of Tumor Microenvironment Yields Insight Into Mechanisms of Resistance to Immunotherapy
Cited by: 4
Author(s): Ben Wang, Mengmeng Liu, Zhujie Ran, Xin Li, Jie Li, Yunsheng Ou
Software Mentions: 4
Published: about 6 years ago

10.1111/cns.13470

Bioinformatic analysis identifies key transcriptome signatures in temporal lobe epilepsy
Cited by: 22
Author(s): Qinglan Chen, Lu Xia, Shian Zhong, Qiang Wang, Jing Ding, Xin Wang
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.ccell.2018.04.004

Molecular, Pathological, Radiological, and Immune Profiling of Non-brainstem Pediatric High-Grade Glioma from the HERBY Phase II Randomized Trial
Cited by: 136
Author(s): Alan Mackay, Anna Burford, Valeria Molinari, David Jones, Elisa Izquierdo, Jurriaan Brouwer‐Visser, Felice Giangaspero, Christine Haberler, Torsten Pietsch, Thomas S. Jacques, Dominique Figarella‐Branger, Daniel Rodriguez, Paul S. Morgan, Pichai Raman, Angela J. Waanders, Adam Resnick, Maura Massimino, Maria Luisa Garré, Smith Hw, David Capper, Stefan M. Pfister, Thomas Würdinger, Rachel Tam, Josep Garcia, Meghna Das Thakur, Gilles Vassal, Jacques Grill, Tim Jaspan, Pascale Varlet, Chris Jones
Software Mentions: 4
Published: over 8 years ago

10.3389/fcell.2021.657917

PSMC5 Promotes Proliferation and Metastasis of Colorectal Cancer by Activating Epithelial–Mesenchymal Transition Signaling and Modulating Immune Infiltrating Cells
Cited by: 8
Author(s): Zengyou He, Xiao Yang, Ling Huang, Leqi Zhou, Sen Zhang, Jing Ping Sun, Min Zheng, Junjun Ma, Bo Feng, Lu Zang
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-017-19072-5

Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs
Cited by: 45
Author(s): Yuliaxis Ramayo-Caldas, María Ballester, Juan Pablo Sánchez, Olga González‐Rodríguez, Manuel Revilla, Henry Reyer, Klaus Wimmers, D. Torrallardona, Raquel Quintanilla
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-017-18480-x

RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients
Cited by: 51
Author(s): Jungmok You, Susan M. Corley, Li Wen, Chris Hodge, Roland Hӧllhumer, Michele C. Madigan, Marc R. Wilkins, Gerard Sutton
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-017-17996-6

Identification of long non-coding RNAs in the immature and mature rat anterior pituitary
Cited by: 19
Author(s): Dong-Xu Han, Xiaolong Sun, Yao Fu, Changjiang Wang, Jianbo Li, Hao Jiang, Yan Gao, Chengzhen Chen, Bao Yuan, Jiabao Zhang
Software Mentions: 4
Published: over 8 years ago

10.3389/fcell.2020.00688

The Construction and Analysis of ceRNA Network and Patterns of Immune Infiltration in Colon Adenocarcinoma Metastasis
Cited by: 30
Author(s): Zhengyan Chang, Runzhi Huang, Wanting Fu, Jiehan Li, Guo Ji, Jinglei Huang, Weijun Shi, Huabin Yin, Weifeng Wang, Tong Meng, Zongqiang Huang, Qing Wei, Huanlong Qin
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-017-16520-0

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis
Cited by: 130
Author(s): Thomas P. Quinn, Mark F. Richardson, David Lovell, Tamsyn M. Crowley
Software Mentions: 4
Published: over 8 years ago

10.3389/fcell.2021.607121

Loss of Ciliary Gene Bbs8 Results in Physiological Defects in the Retinal Pigment Epithelium
Cited by: 7
Author(s): Sandra Schneider, Rossella De Cegli, Jayapriya Nagarajan, Viola Kretschmer, Peter Andreas Matthiessen, Daniela Intartaglia, Nathan Hotaling, Marius Ueffing, Karsten Boldt, Iván Conte, Helen May-Simera
Software Mentions: 4
Published: over 5 years ago

10.1186/s12935-021-01928-6

Construction of a prognostic model with histone modification-related genes and identification of potential drugs in pancreatic cancer
Cited by: 8
Author(s): Chen Yuan, Ruiyuan Xu, Rexiati Ruze, Jinshou Yang, Huanyu Wang, Jianlu Song, Lei You, Yuming Wang, Yupei Zhao
Software Mentions: 4
Published: about 5 years ago

10.1186/s12935-019-0953-4

Effect of hyperoside on cervical cancer cells and transcriptome analysis of differentially expressed genes
Cited by: 22
Author(s): Guo Wei, Hui Yu, Lu Zhang, Xiuwei Chen, Yunduo Liu, Yaoxian Wang, Yunyan Zhang
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12935-021-01792-4

Identification of a prognostic and therapeutic immune signature associated with hepatocellular carcinoma
Cited by: 42
Author(s): Yanan Peng, Chang Liu, Mengting Li, Wenjie Li, Mengna Zhang, Xiang Jiang, Ying Chang, Lan Liu, Wei Fan, Qiu Zhao
Software Mentions: 4
Published: over 5 years ago

10.3389/fcell.2020.00808

Integrated Microarray and RNAseq Transcriptomic Analysis of Retinal Pigment Epithelium/Choroid in Age-Related Macular Degeneration
Cited by: 10
Author(s): Dhanach Dhirachaikulpanich, Xin Li, Louise F. Porter, Luminita Paraoan
Software Mentions: 4
Published: about 6 years ago

10.3389/fcell.2021.591754

Scaffold-Mediated Developmental Effects on Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Are Preserved After External Support Removal
Cited by: 1
Author(s): Jun Li, Jong-Kook Lee, Keiko Miwa, Yuki Kuramoto, Kiyoshi Masuyama, Hideki Yasutake, Satoki Tomoyama, Hiroyuki Nakanishi, Yasushi Sakata
Software Mentions: 4
Published: over 5 years ago

10.3389/fcell.2021.670854

Integrative Analysis of DNA Methylation and Transcriptome Identifies a Predictive Epigenetic Signature Associated With Immune Infiltration in Gliomas
Cited by: 7
Author(s): Jianlei Zhang, Yin Jiang, Li Luo, Dongzhou Huang, Dongfeng Zhai, Ge Wang, Ning Xu, Minqiang Yang, Ying Song, Guopei Zheng, Qiong Zhang
Software Mentions: 4
Published: about 5 years ago

10.3389/fcimb.2021.723481

Dual RNASeq Reveals NTHi-Macrophage Transcriptomic Changes During Intracellular Persistence
Cited by: 6
Author(s): Jodie Ackland, Ashley Heinson, David W. Cleary, Myron Christodoulides, Tom Wilkinson, Karl J. Staples
Software Mentions: 4
Published: about 5 years ago

10.3389/fcimb.2016.00193

Genome-Wide Transcriptional and Post-transcriptional Regulation of Innate Immune and Defense Responses of Bovine Mammary Gland to Staphylococcus aureus
Cited by: 41
Author(s): Lingzhao Fang, Yali Hou, Jinpeng An, Bingjie Li, Mengyuan Song, Xiao Wang, Peter Sørensen, Yichun Dong, Chao Liu, Yachun Wang, Huabin Zhu, Shengli Zhang, Ying Yu
Software Mentions: 4
Published: over 9 years ago

10.3389/fcimb.2020.561761

LL-37-Induced Autophagy Contributed to the Elimination of Live Porphyromonas gingivalis Internalized in Keratinocytes
Cited by: 12
Author(s): Xue Yang, Li Na Niu, Yaping Pan, Xiaodong Feng, Jie Liu, Yan Guo, Chunyu Pan, Fei Geng, Xiaolin Tang
Software Mentions: 4
Published: almost 6 years ago

10.3389/fcimb.2021.652837

Potential Roles of Oral Microbiota in the Pathogenesis of Immunoglobin A Nephropathy
Cited by: 6
Author(s): Jiawei He, Xu‐Jie Zhou, Ping Hou, Yan-Na Wang, Tao Gan, Yang Li, Yang Liu, Lijun Liu, Sufang Shi, Li Zhu, Jicheng Lv, Hong Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fncel.2021.629279

Validation of Induced Microglia-Like Cells (iMG Cells) for Future Studies of Brain Diseases
Cited by: 24
Author(s): Atoshi Banerjee, Yujie Lu, Kenny Do, Travis Mize, Xiaogang Wu, Xiangning Chen, Jingchun Chen
Software Mentions: 4
Published: over 5 years ago

10.1186/s12935-019-0950-7

A six-gene prognostic model predicts overall survival in bladder cancer patients
Cited by: 37
Author(s): Liwei Wang, Jiazhong Shi, Yaqin Huang, Sha Li, Jingqi Zhang, Hua Ding, Jin Yang, Zhiwen Chen
Software Mentions: 4
Published: almost 7 years ago

10.3389/fendo.2019.00840

Role of MicroRNAs in the Regulation of Subcutaneous White Adipose Tissue in Individuals With Obesity and Without Type 2 Diabetes
Cited by: 17
Author(s): Olga Brovkina, А Г Никитин, Д. С. Ходырев, Ekaterina A. Shestakova, Igor A. Sklyanik, Anna S. Panevina, Iurii Stafeev, Mikhail Menshikov, Anastasiya A. Kobelyatskaya, Anatoliy Yurasov, V. S. Fedenko, Yu I Yashkov, М. В. Шестакова
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.15807

Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease
Cited by: 39
Author(s): Magnus Tobiasson, Hani Abdulkadir, Andreas Lennartsson, Shintaro Katayama, Francesco Marabita, Annick De Paepe, Mohsen Karimi, Kaarel Krjutškov, Elisabet Einarsdottir, Michael Grövdal, Monika Jansson, Asmaa Ben Azenkoud, Lina Corddedu, Sören Lehmann, Karl Ekwall, Juha Kere, Eva Hellström‐Lindberg, Johanna Ungerstedt
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-019-5428-4

New insights in the control of antioxidants accumulation in tomato by transcriptomic analyses of genotypes exhibiting contrasting levels of fruit metabolites
Cited by: 20
Author(s): Adriana Sacco, Assunta Raiola, Roberta Calafiore, Amalia Barone, Maria Manuela Rigano
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2021.658736

A Prognostic Model Based on the Immune-Related lncRNAs in Colorectal Cancer
Cited by: 16
Author(s): Fen Qin, Houxi Xu, Guoli Wei, Ji Yi, Jialin Yu, Canhong Hu, Chunyi Yuan, Yuzhu Ma, Jun Qian, Lingchang Li, Jiege Huo
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2019.00603

Genome-Wide Identification of Circular RNAs Revealed the Dominant Intergenic Region Circularization Model in Apostichopus japonicus
Cited by: 15
Author(s): Xuelin Zhao, Xuemei Duan, Jianping Fu, Yina Shao, Weiwei Zhang, Ming Guo, Chenghua Li
Software Mentions: 4
Published: about 7 years ago

10.3389/fgene.2020.551065

Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice
Cited by: 11
Author(s): Fang Cao, Yu Guo, Qiang Zhang, Yinchun Fan, Qian Liu, Jiancheng Song, Hua Zhong, Shengtao Yao
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.729359

Construction of Interferon-Gamma-Related Gene Signature to Characterize the Immune-Inflamed Phenotype of Glioblastoma and Predict Prognosis, Efficacy of Immunotherapy and Radiotherapy
Cited by: 9
Author(s): Hang Ji, Yixu Ba, Shuai Ma, Kezuo Hou, Shan Mi, Xin Gào, Jiaqi Jin, Qingguo Gong, Ting Liu, Fang Wang, Zhihui Liu, Shupeng Li, Jianyang Du, Shaoshan Hu
Software Mentions: 4
Published: almost 5 years ago

10.18632/oncotarget.13806

Bronchial airway gene expression signatures in mouse lung squamous cell carcinoma and their modulation by cancer chemopreventive agents
Cited by: 20
Author(s): Donghai Xiong, Jing Pan, Qi Zhang, Éva Szabó, Mark Steven Miller, Ronald A. Lubet, Ming You, Yian Wang
Software Mentions: 4
Published: over 9 years ago

10.1186/s13568-021-01225-5

Manipulating the soil microbiomes during a community recovery process with plant beneficial species for the suppression of Fusarium wilt of watermelon
Cited by: 14
Author(s): Xu Zhang, Cong Xue, D. C. Fang, Xiangming He, Mengyu Wei, Chenjin Zhuo, Junyao Jin, Biao Shen, Rong Li, Ning Ling, Qirong Shen
Software Mentions: 4
Published: about 5 years ago

10.1099/acmi.0.000082

Transcriptome analysis of Brucella abortus S19∆per immunized mouse spleen revealed activation of MHC-I and MHC-II pathways
Cited by: 2
Author(s): K. S. Solanki, Ravikumar Gandham, Prasad Thomas, Pallab Chaudhuri
Software Mentions: 4
Published: over 6 years ago

10.1007/s00401-020-02230-x

Epigenomic, genomic, and transcriptomic landscape of schwannomatosis
Cited by: 21
Author(s): Sheila Mansouri, Suganth Suppiah, Yasin Mamatjan, Irene Paganini, Jeffrey Liu, Shirin Karimi, Vikas Patil, Farshad Nassiri, Olivia Singh, Yogi Sundaravadanam, Pramod C. Rath, Roberta Sestini, Francesca Gensini, Sameer Agnihotri, Jaishri O. Blakeley, Kimberly Laskie Ostrow, David A. Largaespada, Scott R. Plotkin, Anat Stemmer‐Rachamimov, Marcela Maria Ferrer, Trevor J. Pugh, Kenneth Aldape, Laura Papi, Gelareh Zadeh
Software Mentions: 4
Published: almost 6 years ago

10.1007/s00401-019-02109-6

Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases
Cited by: 37
Author(s): Elena Perenthaler, Anita Nikoncuk, Soheil Yousefi, Woutje M. Berdowski, Maysoon Alsagob, Ivan Čapo, Herma C. van der Linde, Paul van den Berg, Edwin H. Jacobs, Darija Putar, Mehrnaz Ghazvini, Eleonora Aronica, Wilfred F. J. van IJcken, Walter G. de Valk, Evita Medici-van den Herik, Marjon van Slegtenhorst, Lauren Brick, Mariya Kozenko, Jennefer N. Kohler, Jonathan A. Bernstein, Kristin G. Monaghan, Amber Begtrup, Rebecca Torene, Amna Al Futaisi, Fathiya Al Murshedi, Renjith Mani, Faisal Al Azri, Erik‐Jan Kamsteeg, Majid Mojarrad, Atieh Eslahi, Zaynab Khazaei, Fateme Massinaei Darmiyan, Mohammad Doosti, Ehsan Ghayoor Karimiani, Jana Vandrovcová, Faisal Zafar, Nuzhat Rana, Krishna Kumar Kandaswamy, Jozef Hertecant, Péter Bauer, Mohammed A. AlMuhaizea, Mustafa A. Salih, Mazhor Aldosary, Rawan Almass, Laila AlQuait, Wafa Qubbaj, Serdar Coşkun, Khaled O. Alahmadi, Muddathir H. Hamad, Salem Alwadaee, Khalid Awartani, Anas Dababo, Futwan Al‐Mohanna, Dilek Çolak, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Murat Günel, A. Gülhan Ercan-Şençiçek, Gouri Rao Passi, Huma Arshad Cheema, Stéphanie Efthymiou, Henry Houlden, Aida M. Bertoli‐Avella, Alice S. Brooks, Kyle Retterer, Reza Maroofian, Namik Kaya, Tjakko J. van Ham, Tahsin Stefan Barakat
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.102820

Development and validation of a prognostic classifier based on HIF-1 signaling for hepatocellular carcinoma
Cited by: 22
Author(s): Feiwen Deng, Chen Dong, Xiaoli Wei, Shilin Lu, Xuan Luo, Jincan He, Junting Liu, Tiebao Meng, Anli Yang, Huanwei Chen
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.103454

Weighted correlation gene network analysis reveals a new stemness index-related survival model for prognostic prediction in hepatocellular carcinoma
Cited by: 14
Author(s): Qiujing Zhang, Jia Wang, Menghan Liu, Qingqing Zhu, Qiang Li, Chao Xie, Congcong Han, Yali Wang, Min Gao, Jie Liu
Software Mentions: 4
Published: about 6 years ago

10.18632/aging.101751

miRNA-mRNA crosstalk in myocardial ischemia induced by calcified aortic valve stenosis
Cited by: 12
Author(s): Chenyang Duan, Zhijun Cao, Fuqin Tang, Jian Zhao, Chunshui Liang, Hong Liu, Xiao Ye, Liangming Liu, Rong Ma
Software Mentions: 4
Published: over 7 years ago

10.18632/aging.203322

Identification of prognostic long non-coding RNA signature with potential drugs in hepatocellular carcinoma
Cited by: 0
Author(s): Fang Hao, Nan Wang, Xiang Wang, Yongjun Chen, Junqing Wang
Software Mentions: 4
Published: about 5 years ago

10.18632/aging.202780

circRNA expression profiling of colon tissue from mesalazine-treated mouse of inflammatory bowel disease reveals an important circRNA-miRNA-mRNA pathway
Cited by: 8
Author(s): Wei Zhou, Haiyin Zhang, Y. B. Pan, Yingbin Xu, Yongqing Cao
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.202950

Multiomics integrative analysis identifies APOE allele-specific blood biomarkers associated to Alzheimer’s disease etiopathogenesis
Cited by: 13
Author(s): Laura Madrid, Sonia Moreno‐Grau, Shahzad Ahmad, Antonio González‐Pérez, Itziar de Rojas, Rui Xia, Pamela Victoria Martino Adami, Pablo García‐González, Luca Kleineidam, Qiong Yang, Vincent Damotte, Joshua C. Bis, Fuensanta Noguera-Perea, Céline Bellenguez, Xueqiu Jian, Juan Marín-Muñoz, Benjamin Grenier‐Boley, Adela Orellana, M. Arfan Ikram, Philippe Amouyel, Claudia L. Satizábal, Alzheimer’s Disease Neuroimaging Initiative, Luis Miguel Real, Carmen Antúnez-Almagro, Anita L. DeStefano, Alfredo Cabrera-Socorro, Rebecca Sims, Cornelia M. van Duijn, Eric Boerwinkle, Alfredo Ramı́rez, Myriam Fornage, Jean‐Charles Lambert, Julie Williams, Sudha Seshadri, Janina S. Ried, Agustín Ruiz, María Eugenia Sáez
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.103083

Nudix hydrolase 1 is a prognostic biomarker in hepatocellular carcinoma
Cited by: 6
Author(s): Qifeng Ou, Ning Ma, Zhenzhen Yu, Rongchang Wang, Yucheng Hou, Ziming Wang, Fan Chen, Wen Li, Jiong Bi, Jiachi Ma, Longjuan Zhang, Shan Qiao, Xiaohui Huang
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.102190

Long non-coding RNA CASC19 is associated with the progression and prognosis of advanced gastric cancer
Cited by: 23
Author(s): Wenjie Wang, Changan Guo, Rui Li, Zipeng Xu, Jianping Yu, Ye Yan, Jun Zhao, Jing Wang, Wen-An Wang, An Zhang, Hongtao Li, Chen Wang, Hongbin Liu
Software Mentions: 4
Published: about 7 years ago

10.1111/acel.12352

Eicosapentaenoic acid but not docosahexaenoic acid restores skeletal muscle mitochondrial oxidative capacity in old mice
Cited by: 50
Author(s): Matthew L. Johnson, Antigoni Z. Lalia, Surendra Dasari, Maximilian Pallauf, Mark Fitch, Marc K. Hellerstein, Ian R. Lanza
Software Mentions: 4
Published: about 11 years ago

10.1111/acel.13195

Growth differentiation factor 15 protects against the aging‐mediated systemic inflammatory response in humans and mice
Cited by: 59
Author(s): Ji Sun Moon, Ludger Goeminne, Jung Tae Kim, Jing Tian, Seok Hwan Kim, Ha Thi Nga, Sun Hyung Kang, Baeki E. Kang, Jin Seok Byun, Young‐Sun Lee, Jae‐Han Jeon, Minho Shong, Johan Auwerx, Dongryeol Ryu, Hyon‐Seung Yi
Software Mentions: 4
Published: about 6 years ago

10.1111/acel.13178

The inherited methylome landscape is directly altered with paternal aging and associated with offspring neurodevelopmental disorders
Cited by: 27
Author(s): Michelle M. Denomme, Mary E. Haywood, Jason C. Parks, William B. Schoolcraft, Mandy G. Katz‐Jaffe
Software Mentions: 4
Published: about 6 years ago

10.1186/1748-7188-7-5

A normalization strategy for comparing tag count data
Cited by: 72
Author(s): Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu
Software Mentions: 4
Published: over 14 years ago

10.3390/ani11082241

Transcriptomic Response under Heat Stress in Chickens Revealed the Regulation of Genes and Alteration of Metabolism to Maintain Homeostasis
Cited by: 8
Author(s): Hana Kim, Hye‐Ran Kim, Pil‐Nam Seong, D. K. Arora, Donghyun Shin, Woncheoul Park, Jong-Eun Park
Software Mentions: 4
Published: about 5 years ago

10.3390/ani11082165

Comprehensive Transcriptomic Comparison between Porcine CD8− and CD8+ Gamma Delta T Cells Revealed Distinct Immune Phenotype
Cited by: 7
Author(s): Sang–Wook Kim, Bee-Oh Lim, Sameer-ul-Salam Mattoo, Eunyoung Oh, Chang-Gi Jeong, Won-Il Kim, Kyung-Tai Lee, Sang-Myeong Lee, Junmo Kim
Software Mentions: 4
Published: about 5 years ago

10.3390/ani11092705

Ruminal and Fecal Bacteriome of Dairy Calves Fed Different Levels and Sources of NDF
Cited by: 2
Author(s): Gercino Ferreira Virgínio Júnior, Ana Paula da Silva, Ariany Faria de Toledo, Milaine Poczynek, Amanda Moelemberg Cezar, Horácio Montenegro, Luiz Lehmann Coutinho, Carla Maris Machado Bittar
Software Mentions: 4
Published: almost 5 years ago

10.3390/antiox10091380

NRF2 Mediates Therapeutic Resistance to Chemoradiation in Colorectal Cancer through a Metabolic Switch
Cited by: 7
Author(s): Séan M. O’Cathail, Chieh‐Hsi Wu, Russell J. Thomas, M. Hawkins, Tim Maughan, Annabelle Lewis
Software Mentions: 4
Published: almost 5 years ago

10.1128/AEM.02177-20

Identification of Natural Mutations Responsible for Altered Infection Phenotypes of Salmonella enterica Clinical Isolates by Using Cell Line Infection Screens
Cited by: 5
Author(s): Rafał Kolenda, Michał Burdukiewicz, Marcjanna Wimonć, Adrianna Aleksandrowicz, Aamir Ali, István Szabó, Karsten Tedin, Josefin Bartholdson Scott, Derek Pickard, Peter Schierack
Software Mentions: 4
Published: over 5 years ago

10.1007/s00404-019-05336-0

Changes in intestinal microflora in digestive tract diseases during pregnancy
Cited by: 20
Author(s): Min Jin, Dong Li, Rui Ji, Wen Li, Xiaofei Xu, Yanqing Li
Software Mentions: 4
Published: over 6 years ago

10.31557/APJCP.2020.21.6.1787

Risk Scoring System based on lncRNA Expression for Predicting Survival in Hepatocellular Carcinoma with Cirrhosis
Cited by: 13
Author(s): Jiaxiang Ye, Haixia Li, Jiazhang Wei, Yue Luo, Hongmei Li, Jinyan Zhang, Xi Luo
Software Mentions: 4
Published: about 6 years ago

10.31557/APJCP.2020.21.9.2593

Transcriptome Related to Avoiding Immune Destruction in Nasopharyngeal Cancer in Indonesian Patients Using Next-Generation Sequencing
Cited by: 2
Author(s): Risky Hiskia Poluan, Digdo Sudigyo, Gisti Rahmawati, Dicka Wahyu Setiasari, Salsabila Luthfi Sesotyosari, Tirta Wardana, Indwiani Astuti, Didik Setyo Heriyanto, Sagung Rai Indrasari, Cita Herawati, FNU Afiahayati, Sofia Mubarika Haryana
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12859-016-1276-2

dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data
Cited by: 87
Author(s): Sergi Sayols, Denise Scherzinger, H. Klein
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12859-020-03888-6

Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data
Cited by: 1
Author(s): Noel‐Marie Plonski, Emily Johnson, Madeline Frederick, Heather Mercer, Gail Fraizer, Richard S. Meindl, Gemma Casadesús, Helen Piontkivska
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-015-0859-7

Effects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling
Cited by: 9
Author(s): Marcella Vacca, Kumar Parijat Tripathi, Luisa Speranza, Riccardo Aiese Cigliano, Francesco Scalabrì, Federico Marracino, Michele Madonna, Walter Sanseverino, Carla Perrone-Capano, Mario Rosario Guarracino, Maurizio D’Esposito
Software Mentions: 4
Published: over 10 years ago

10.1186/1471-2105-15-91

Differential meta-analysis of RNA-seq data from multiple studies
Cited by: 88
Author(s): Andrea Rau, Guillemette Marot, Florence Jaffrézic
Software Mentions: 4
Published: over 12 years ago

10.1186/s12859-019-2623-x

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations
Cited by: 2
Author(s): Aleksandra Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh, Jonathan D. Wren
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2105-12-323

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Cited by: 14,016
Author(s): Bo Li, Colin N. Dewey
Software Mentions: 4
Published: about 15 years ago

10.1186/s12859-021-04061-3

ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries
Cited by: 2
Author(s): Liangliang Zhang, Yushu Shi, Kim Anh, Christine B. Peterson, Robert R. Jenq
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-019-3072-2

HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis
Cited by: 3
Author(s): Hongryul Ahn, Il Bong Jung, Han–Jung Chae, Dong‐Won Kang, Wi Hoon Jung, Sun Kim
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-020-3450-9

Data-based RNA-seq simulations by binomial thinning
Cited by: 19
Author(s): David Gerard
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-017-1648-2

Power analysis for RNA-Seq differential expression studies
Cited by: 27
Author(s): Lianbo Yu, Soledad Fernández, Guy Brock
Software Mentions: 4
Published: over 9 years ago

10.1186/s12859-019-2916-0

A multivariate Poisson-log normal mixture model for clustering transcriptome sequencing data
Cited by: 26
Author(s): Anjali Silva, Steven J. Rothstein, Paul D. McNicholas, Sanjeena Subedi
Software Mentions: 4
Published: about 7 years ago

10.1186/s12859-019-3140-7

Multiplatform biomarker identification using a data-driven approach enables single-sample classification
Cited by: 5
Author(s): Ling Zhang, Ishwor Thapa, Christian Haas, Dhundy Bastola
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12859-019-2734-4

Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data
Cited by: 73
Author(s): Hao Yang, Daixi Li, Yong Xu, Jian Ouyang, Yongkun Wang, Yuqi Zhang, Baoguo Li, Lu Xie, Guangrong Qin
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2105-15-81

spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data
Cited by: 89
Author(s): Kristoffer Vitting-Seerup, Bo T. Porse, Albin Sandelin, Johannes Waage
Software Mentions: 4
Published: over 12 years ago

10.1186/s12859-018-2191-5

RnaSeqSampleSize: real data based sample size estimation for RNA sequencing
Cited by: 54
Author(s): Shilin Zhao, Chung I. Li, Yan Guo, Quanhu Sheng, Yu Shyr
Software Mentions: 4
Published: about 8 years ago

10.1186/s12859-018-2261-8

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods
Cited by: 43
Author(s): Thomas P. Quinn, Tamsyn M. Crowley, Mark F. Richardson
Software Mentions: 4
Published: about 8 years ago

10.1186/s12915-019-0646-4

Enabling cell-type-specific behavioral epigenetics in Drosophila: a modified high-yield INTACT method reveals the impact of social environment on the epigenetic landscape in dopaminergic neurons
Cited by: 15
Author(s): Pavan Agrawal, Phuong Chung, Ulrike Heberlein, Clement F. Kent
Software Mentions: 4
Published: over 7 years ago

10.1186/s12915-018-0569-5

Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance
Cited by: 16
Author(s): Jessica M Stringer, Samuel C. Forster, Zhibo Qu, Lexie Prokopuk, Moira K O'Bryan, David K. Gardner, Stefan J. White, David L. Adelson, Patrick Western
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12896-015-0207-z

A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq
Cited by: 22
Author(s): Kevin Lambirth, Adam M. Whaley, Ivory C. Blakley, Jessica A. Schlueter, Kenneth L. Bost, Ann E. Loraine, Kenneth J. Piller
Software Mentions: 4
Published: almost 11 years ago

10.1186/1471-2407-14-977

Identification of a candidate prognostic gene signature by transcriptome analysis of matched pre- and post-treatment prostatic biopsies from patients with advanced prostate cancer
Cited by: 41
Author(s): Prabhakar Rajan, Jacqueline Stockley, Ian Sudbery, Janis Fleming, Ann Hedley, Gabriela Kalna, David Sims, Chris P. Ponting, Andreas Heger, Craig Robson, R. McMenemin, Ian Pedley, Hing Y. Leung
Software Mentions: 4
Published: over 11 years ago

10.1186/s12885-021-07911-8

Construction of the optimization prognostic model based on differentially expressed immune genes of lung adenocarcinoma
Cited by: 6
Author(s): Yuanliang Zhai, Bin Zhao, Yuzhen Wang, Lina Li, Jingjin Li, Li Xu, Linhan Chang, Qian Chen, Zhijun Liao
Software Mentions: 4
Published: over 5 years ago

10.1186/s12885-018-4757-z

Association of tamoxifen resistance and lipid reprogramming in breast cancer
Cited by: 98
Author(s): Susanne Hultsch, Matti Kankainen, Lassi Paavolainen, Ruusu-Maaria Kovanen, Elina Ikonen, Sara Kangaspeska, Vilja Pietiäinen, Olli Kallioniemi
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12885-020-6513-4

Immunogenomic pathways associated with cytotoxic lymphocyte infiltration and survival in colorectal cancer
Cited by: 8
Author(s): Yuanyuan Shen, Yue Guan, Justin Hummel, Chi‐Ren Shyu, Jonathan B. Mitchem
Software Mentions: 4
Published: over 6 years ago

10.1186/s12872-020-01838-x

Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms
Cited by: 4
Author(s): Siwei Bi, Ruiqi Liu, Linfeng He, Jingyi Li, Jun Gu
Software Mentions: 4
Published: over 5 years ago

10.1186/s12862-017-1087-8

Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria
Cited by: 21
Author(s): Melania Abrahamian, Meenakshi S. Kagda, Audrey M. V. Ah‐Fong, Howard S. Judelson
Software Mentions: 4
Published: over 8 years ago

10.1186/s12862-014-0260-6

At the brink of eusociality: transcriptomic correlates of worker behaviour in a small carpenter bee
Cited by: 59
Author(s): Sandra M. Rehan, Ali J. Berens, Amy L. Toth
Software Mentions: 4
Published: over 11 years ago

10.1186/s12862-018-1288-9

Evolutionary diversity and novelty of DNA repair genes in asexual Bdelloid rotifers
Cited by: 16
Author(s): Bette Hecox-Lea, David B. Mark Welch
Software Mentions: 4
Published: over 7 years ago

10.1186/s12862-017-1103-z

De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus
Cited by: 11
Author(s): Alexey Moskalev, Anna V. Kudryavtseva, Alexander S. Graphodatsky, Violetta R. Beklemisheva, Natalia A. Serdyukova, Konstantin V. Krutovsky, Vadim V. Sharov, Ivan V. Kulakovskiy, Andrey S. Lando, Artem S. Kasianov, Dmitry A. Kuzmin, Yuliya A. Putintseva, Sergey Feranchuk, Mikhail Shaposhnikov, Vadim E. Fraifeld, Dmitri Toren, А. В. Снежкина, Vasily Sitnik
Software Mentions: 4
Published: over 8 years ago

10.1186/s12863-019-0790-4

Transcriptome, physiological and biochemical analysis of Triarrhena sacchariflora in response to flooding stress
Cited by: 17
Author(s): Jia Wang, Hao Sun, Jiajin Sheng, Surong Jin, Fangjian Zhou, Zhongli Hu, Youxiang Diao
Software Mentions: 4
Published: over 6 years ago

10.1186/s12863-018-0608-9

RNA-seq analysis of lncRNA-controlled developmental gene expression during puberty in goat & rat
Cited by: 21
Author(s): Xiaoxiao Gao, Jing Ye, Chen Yang, Lei Luo, Ya Liu, Jianping Ding, Yunhai Zhang, Yinghui Ling, Weiping Huang, Xiaorong Zhang, Kaifa Zhang, Xiumei Li, Jie Zhou, Fugui Fang, Zubing Cao
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-017-3797-0

Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols
Cited by: 20
Author(s): Susan M. Corley, Karen L. MacKenzie, Annemiek Beverdam, Louise F. Roddam, Marc R. Wilkins
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-017-4359-1

A next generation sequencing based approach to identify extracellular vesicle mediated mRNA transfers between cells
Cited by: 19
Author(s): Jialiang Yang, Jacob Hagen, Kalyani V. P. Guntur, Kimaada Allette, Sarah Schuyler, Jyoti Ranjan, Francesca Petralia, Stéphane Gesta, Robert Sebra, Milind Mahajan, Bin Zhang, Jun Zhu, Sander M. Houten, Andrew Kasarskis, Vivek K. Vishnudas, Viatcheslav R. Akmaev, Rangaprasad Sarangarajan, Niven R. Narain, Eric E. Schadt, Carmen Argmann, Zhidong Tu
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-016-3345-3

TRPM2 SNP genotype previously associated with susceptibility to Rhodococcus equi pneumonia in Quarter Horse foals displays differential gene expression identified using RNA-Seq
Cited by: 6
Author(s): Cole M. McQueen, Canaan Whitfield-Cargile, Kranti Konganti, Glenn P. Blodgett, Scott V. Dindot, Noah D. Cohen
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-020-07327-x

Gene expression patterns of red sea urchins (Mesocentrotus franciscanus) exposed to different combinations of temperature and pCO2 during early development
Cited by: 5
Author(s): Juliet M. Wong, Gretchen E. Hofmann
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-14-S8-S1

Interdisciplinary dialogue for education, collaboration, and innovation: Intelligent Biology and Medicine in and beyond 2013
Cited by: 49
Author(s): Bing Zhang, Yufei Huang, Jason McDermott, Rebecca H Posey, Hua Xu, Zhongming Zhao
Software Mentions: 4
Published: over 13 years ago

10.1186/s12864-015-1767-y

Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq
Cited by: 132
Author(s): Anto P. Rajkumar, Per Qvist, Ross Lazarus, Francesco Lescai, Jia Ju, Mette Nyegaard, Ole Mors, Anders D. Børglum, Qibin Li, Jane H. Christensen
Software Mentions: 4
Published: about 11 years ago

10.1186/s12864-016-3130-3

Differential gene expression in Varroa jacobsoni mites following a host shift to European honey bees (Apis mellifera)
Cited by: 15
Author(s): Gladys K. Andino, Michael Gribskov, Denis L. Anderson, Jay D. Evans, Greg J. Hunt
Software Mentions: 4
Published: almost 10 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568