bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3389/fonc.2021.663556

Identification of a Three-RNA Binding Proteins (RBPs) Signature Predicting Prognosis for Breast Cancer
Cited by: 14
Author(s): Yang Liu, Hefen Sun, Xuan Li, Qiqi Liu, Yuanyuan Zhao, Liangdong Li, Baojin Xu, Yifeng Hou, Wei Jin
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-021-01716-y

Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp
Cited by: 28
Author(s): Jianbo Yuan, Xiaojun Zhang, Min Wang, Yamin Sun, Xianhui Qin, Shihao Li, Yang Yu, Yi Gao, Fei Liu, Jie Kong, Guangyi Fan, Chengsong Zhang, Lu Feng, Jianhai Xiang, Fuhua Li
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-020-01398-y

Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation
Cited by: 2
Author(s): Michal Schwartz, Avital Sarusi Portugez, Bracha Zukerman Attia, Miriam Tannenbaum, Leslie E. Cohen, Olga Loza, Emily Chase, Yousef Turman, Tommy Kaplan, Zaidoun Salah, Ofir Hakim
Software Mentions: 5
Published: almost 6 years ago

10.7717/peerj.9658

A prognostic gene model of immune cell infiltration in diffuse large B-cell lymphoma
Cited by: 9
Author(s): Hao Zhou, Chang Zheng, Desheng Huang
Software Mentions: 5
Published: about 6 years ago

10.3389/fonc.2021.637733

Low Expression of ADCY4 Predicts Worse Survival of Lung Squamous Cell Carcinoma Based on Integrated Analysis and Immunohistochemical Verification
Cited by: 3
Author(s): Zhicong Liu, Lixin Ru, Zhenchao Ma
Software Mentions: 5
Published: over 5 years ago

10.3389/fonc.2021.745166

A Co-Expression Network Reveals the Potential Regulatory Mechanism of lncRNAs in Relapsed Hepatocellular Carcinoma
Cited by: 6
Author(s): Yuan Fang, Yang Yang, Xiaoli Zhang, Na Li, Bo Yuan, Li Jin, Sheng Bao, Mengge Li, Dan Zhao, Lingrui Li, Zhong Zeng, Hanfei Huang
Software Mentions: 5
Published: about 5 years ago

10.3389/fonc.2019.01497

Identification of Distinct Immune Subtypes in Colorectal Cancer Based on the Stromal Compartment
Cited by: 27
Author(s): Rongfang Shen, Ping Li, Bing Li, Botao Zhang, Feng Li, Shujun Cheng
Software Mentions: 5
Published: almost 7 years ago

10.3389/fonc.2021.616576

LncRNA FENDRR in Carcinoma-Associated Fibroblasts Regulates the Angiogenesis of Oral Squamous Cell Carcinoma Through the PI3K/AKT Pathway
Cited by: 4
Author(s): Yuming Xu, Erhui Jiang, Zhang Shao, Zhengjun Shang
Software Mentions: 5
Published: over 5 years ago

10.3389/fonc.2021.691372

Prognostic Signature of Hepatocellular Carcinoma and Analysis of Immune Infiltration Based on m6A-Related lncRNAs
Cited by: 6
Author(s): Ting Guo, Kun He, Yifei Wang, Jingjing Sun, Yong Chen, Zelong Yang
Software Mentions: 5
Published: about 5 years ago

10.3389/fcell.2020.588041

Identification of Differential Gene Groups From Single-Cell Transcriptomes Using Network Entropy
Cited by: 3
Author(s): Yanglan Gan, Shanshan Liang, Qingting Wei, Guobing Zou
Software Mentions: 5
Published: about 6 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: over 5 years ago

10.1007/s00018-021-03822-w

Immune cells lacking Y chromosome show dysregulation of autosomal gene expression
Cited by: 43
Author(s): Jan P. Dumanski, Jonatan Halvardson, Hanna Davies, Edyta Rychlicka-Buniowska, Jonas Mattisson, Behrooz Torabi Moghadam, Noémi Nagy, Kazimierz Węglarczyk, Karolina Bukowska-Straková, Marcus Danielsson, Paweł Olszewski, Arkadiusz Piotrowski, Erin Oerton, Aleksandra Ambicka, Marcin Przewoźnik, Łukasz Bełch, Tomasz Grodzicki, Piotr Chłosta, Stefan Imreh, Vilmantas Giedraitis, Lena Kilander, Jessica Nordlund, Adam Ameur, Ulf Gyllensten, Åsa Johansson, Alicja Józkowicz, Maciej Siedlar, Alicja Klich-Rączka, Janusz Jaszczyński, Stefan Enroth, Jarosław Baran, Martin Ingelsson, John Perry, Janusz Ryś, Lars A. Forsberg
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.609601

Identify and Validate the Transcriptomic, Functional Network, and Predictive Validity of FBXL19-AS1 in Hepatocellular Carcinoma
Cited by: 4
Author(s): Dingdong He, Xiaokang Zhang, Xinyu Zhu, Narayani Maharjan, Yingchao Wang, Ping Luo, Chunzi Liang, Jiancheng Tu
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0238420

Construction and analysis of a competing endogenous RNA network to reveal potential prognostic biomarkers for Oral Floor Squamous Cell Carcinoma
Cited by: 1
Author(s): Wenjing Zhang, Shuai Xu, Laner Shi, Zhangzhi Zhu, Xinying Xie
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2021.650828

Integrative Analysis of a Novel Eleven-Small Nucleolar RNA Prognostic Signature in Patients With Lower Grade Glioma
Cited by: 6
Author(s): Teng Deng, Yizhen Gong, Xiwen Liao, Xiangkun Wang, Xin Zhou, Guangzhi Zhu, Ligen Mo
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.556497

Landscape of N6-Methyladenosine Modification Patterns in Human Ameloblastoma
Cited by: 19
Author(s): Xing Niu, Jun Xu, Jinwen Liu, Lijie Chen, Xue Qin, Ming Zhong
Software Mentions: 4
Published: about 6 years ago

10.1186/s13619-021-00083-7

Defining cell identity beyond the premise of differential gene expression
Cited by: 2
Author(s): Hani Jieun Kim, Patrick Tam, Pengyi Yang
Software Mentions: 4
Published: over 5 years ago

10.1038/srep16238

IDH mutation status is associated with a distinct hypoxia/angiogenesis transcriptome signature which is non-invasively predictable with rCBV imaging in human glioma
Cited by: 243
Author(s): Philipp Kickingereder, Felix Sahm, Alexander Radbruch, Wolfgang Wick, Sabine Heiland, Andreas von Deimling, Martin Bendszus, Benedikt Wiestler
Software Mentions: 4
Published: almost 11 years ago

10.1038/srep17901

Identification of Genes Associated with Smad3-dependent Renal Injury by RNA-seq-based Transcriptome Analysis
Cited by: 19
Author(s): Qin Zhou, Yuanyan Xiong, Xiao Ru Huang, Patrick Ming‐Kuen Tang, Xueqing Yu, Hui‐Yao Lan
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0230566

Genetic compensation in a stable slc25a46 mutant zebrafish: A case for using F0 CRISPR mutagenesis to study phenotypes caused by inherited disease
Cited by: 35
Author(s): Elena Buglo, Evan Sarmiento, Nicole Belliard Martuscelli, David W. Sant, Matt C. Danzi, A. Jeanine Abrams, Julia E. Dallman, Stephan Züchner
Software Mentions: 4
Published: over 6 years ago

10.1016/j.celrep.2016.06.096

Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins
Cited by: 60
Author(s): Christian Hauer, Jana Sieber, Thomas Schwarzl, Ina Hollerer, Tomaž Curk, Anne-Marie Alleaume, Matthias W. Hentze, Andreas E. Kulozik
Software Mentions: 4
Published: over 10 years ago

10.1038/srep18630

De novo assembly and characterization of root transcriptome in two distinct morphotypes of vetiver, Chrysopogon zizaniodes (L.) Roberty
Cited by: 17
Author(s): Debasis Chakrabarty, Puneet Singh Chauhan, Abhishek Chauhan, Yuvraj Indoliya, U. C. Lavania, Puneet Singh Chauhan
Software Mentions: 4
Published: almost 11 years ago

10.3390/ijms20143583

Ureaplasma Species Modulate Cytokine and Chemokine Responses in Human Brain Microvascular Endothelial Cells
Cited by: 6
Author(s): Christine Silwedel, Christian P. Speer, Axel Haarmann, Markus Fehrholz, Heike Claus, Nicolas Schlegel, Kirsten Glaser
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms20143480

Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize
Cited by: 34
Author(s): Ziwen Li, Xianghai An, Taotao Zhu, Tingwei Yan, Wu Shu, Youhui Tian, Jinping Li, Xiangyuan Wan
Software Mentions: 4
Published: over 7 years ago

10.1016/j.celrep.2021.108860

COX2 regulates senescence secretome composition and senescence surveillance through PGE2
Cited by: 30
Author(s): S. Goncalves, Kai Yin, Yoko Itō, Adelyne Chan, Ioana Olan, Sarah Gough, Liam Cassidy, Eva M. Serrao, Stephen Smith, Andrew Young, Masashi Narita, Matthew Hoare
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms160921310

Gene Expression Variations of Red—White Skin Coloration in Common Carp (Cyprinus carpio)
Cited by: 19
Author(s): Xiaomin Li, Yijun Song, Gao Xiao, Bai-Han Zhu, Gui-Cai Xu, Mingyuan Sun, Jun Xiao, Shahid Mahboob, Khalid A. Al‐Ghanim, Xin Sun, Jiong-Tang Li
Software Mentions: 4
Published: about 11 years ago

10.1016/j.celrep.2021.109032

Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome
Cited by: 17
Author(s): Alejandro Brenes, Harunori Yoshikawa, Dalila Bensaddek, Bogdan Mirauta, Daniel D Seaton, Jens Hukelmann, Hao Jiang, Oliver Stegle, Angus I. Lamond
Software Mentions: 4
Published: over 5 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

10.1371/journal.pone.0123569

XomAnnotate: Analysis of Heterogeneous and Complex Exome- A Step towards Translational Medicine
Cited by: 5
Author(s): Asoke K. Talukder, Shashidhar Ravishankar, Krittika Sasmal, Santhosh Gandham, Jyothsna Prabhukumar, Prahalad Achutharao, Debmalya Barh, Francesco Blasi
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0125224

An Iterative Leave-One-Out Approach to Outlier Detection in RNA-Seq Data
Cited by: 31
Author(s): Nysia I. George, John F. Bowyer, Nathaniel M. Crabtree, Ching‐Wei Chang
Software Mentions: 4
Published: over 11 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

10.1038/srep22398

Gene dysregulation is restored in the Parkinson’s disease MPTP neurotoxic mice model upon treatment of the therapeutic drug CuII(atsm)
Cited by: 12
Author(s): Lesley Cheng, Camelia Quek, Lin W. Hung, Robyn A. Sharples, Nicki A. Sherratt, Kevin J. Barnham, Andrew F. Hill
Software Mentions: 4
Published: over 10 years ago

10.1038/srep24048

RXR controlled regulatory networks identified in mouse brain counteract deleterious effects of Aβ oligomers
Cited by: 27
Author(s): Kyong Nyon Nam, Anaïs Mounier, Nicholas F. Fitz, Cody M. Wolfe, Jonathan Schug, Iliya Lefterov, Radosveta Koldamova
Software Mentions: 4
Published: over 10 years ago

10.1038/srep24375

RNA-seq analysis for detecting quantitative trait-associated genes
Cited by: 33
Author(s): Minseok Seo, Kwondo Kim, Joon Yoon, Jin Young Jeong, Hyun-Jeong Lee, Seoae Cho, Heebal Kim
Software Mentions: 4
Published: over 10 years ago

10.3390/ijms20225710

The Biological Effects of Complete Gasoline Engine Emissions Exposure in a 3D Human Airway Model (MucilAirTM) and in Human Bronchial Epithelial Cells (BEAS-2B)
Cited by: 13
Author(s): Pavel Rőssner, Tereza Červená, Michal Vojtíšek-Lom, Kristýna Vrbová, Antonín Ambrož, Zuzana Nováková, Fatima Elzeinová, Hasmik Margaryan, V. Beránek, Martin Pechout, David Macoun, Jǐŕı Kléma, Andrea Rössnerová, Miroslav Cigánek, Jan Topinka
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0114461

Inference of the Oxidative Stress Network in Anopheles stephensi upon Plasmodium Infection
Cited by: 10
Author(s): Jatin Shrinet, Umesh K. Nandal, T. Adak, Raj K. Bhatnagar, Sujatha Sunil
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pone.0166862

Drosophila DDX3/Belle Exerts Its Function Outside of the Wnt/Wingless Signaling Pathway
Cited by: 1
Author(s): Fabian H. Jenny, Konrad Basler
Software Mentions: 4
Published: almost 10 years ago

10.1038/srep31558

De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure
Cited by: 32
Author(s): Camilla Beate Hill, Andrew Cassin, Gabriel Keeble‐Gagnère, Monika S. Doblin, Antony Bacic, Ute Roessner
Software Mentions: 4
Published: about 10 years ago

10.1038/srep33736

MBD3 expression and DNA binding patterns are altered in a rat model of temporal lobe epilepsy
Cited by: 4
Author(s): Joanna Bednarczyk, Konrad J. Dębski, Anna Bot, Katarzyna Łukasiuk
Software Mentions: 4
Published: about 10 years ago

10.3390/ijms20236040

Whole Genome Expression Analyses of miRNAs and mRNAs Suggest the Involvement of miR-320a and miR-155-3p and their Targeted Genes in Lithium Response in Bipolar Disorder
Cited by: 27
Author(s): Claudia Pisanu, Eleni Merkouri Papadima, Carla Melis, Donatella Congiu, Annalisa Loizedda, Nicola Orrù, Stefano Calza, Sandro Orrù, Carlo Carcassi, Giovanni Severino, Raffaella Ardau, Caterina Chillotti, Maria Del Zompo, Alessio Squassina
Software Mentions: 4
Published: almost 7 years ago

10.3389/fcell.2020.571501

Chromatin and Transcriptional Response to Loss of TBX1 in Early Differentiation of Mouse Cells
Cited by: 4
Author(s): Andrea Cirino, Ilaria Aurigemma, Monica Franzese, Gabriella Lania, Dario Righelli, Rosa Ferrentino, Elizabeth Illingworth, Claudia Angelini, Antonio Baldini
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.11820

Clinical and prognostic relevance of CXCL12 expression in acute myeloid leukemia
Cited by: 2
Author(s): Shi-sen Wang, Zi‐jun Xu, Yue Jin, Ji‐chun Ma, Pei‐hui Xia, Xiang‐mei Wen, Zhen-wei Mao, Lin Jiang, Jun Qian
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0188264

Wnt co-receptors Lrp5 and Lrp6 differentially mediate Wnt3a signaling in osteoblasts
Cited by: 25
Author(s): Aimy Sebastian, Nicholas R. Hum, Deepa K. Murugesh, Sarah Hatsell, Aris N. Economides, Gabriela G. Loots
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0115964

A Note on an Exon-Based Strategy to Identify Differentially Expressed Genes in RNA-Seq Experiments
Cited by: 12
Author(s): Asta Laiho, Laura L. Elo
Software Mentions: 4
Published: almost 12 years ago

10.7554/eLife.04235

Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype
Cited by: 43
Author(s): James C. McGann, Jon A. Oyer, Saurabh Garg, Huilan Yao, Jun Li, Xin Feng, Lujian Liao, John R. Yates, Gail Mandel
Software Mentions: 4
Published: about 12 years ago

10.1016/j.stem.2017.03.003

H3K4 Methylation-Dependent Memory of Somatic Cell Identity Inhibits Reprogramming and Development of Nuclear Transfer Embryos
Cited by: 85
Author(s): Eva Hörmanseder, Angela Simeone, George E. Allen, Charles R. Bradshaw, Magdalena Figlmüller, J. B. Gurdon, Jérôme Jullien
Software Mentions: 4
Published: over 9 years ago

10.1016/j.stem.2019.09.008

Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal
Cited by: 71
Author(s): Stephanie Z. Xie, Laura García‐Prat, Véronique Voisin, Raffaele Ferrari, Olga I. Gan, Elvin Wagenblast, Kerstin B. Kaufmann, Andy G.X. Zeng, Shin‐ichiro Takayanagi, Ishita Patel, Esther K. Lee, Joseph Jargstorf, Gareth D. Holmes, Guy Romm, Kristele Pan, Michelle Shoong, Aditi Vedi, Chiara Luberto, Mark D. Minden, Gary D. Bader, Elisa Laurenti, John E. Dick
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0190456

Mitochondrial DNA depletion by ethidium bromide decreases neuronal mitochondrial creatine kinase: Implications for striatal energy metabolism
Cited by: 18
Author(s): Emily B. Warren, Aidan Aicher, Joshua P. Fessel, Christine Konradi
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.47013

An evolutionary recent IFN/IL-6/CEBP axis is linked to monocyte expansion and tuberculosis severity in humans
Cited by: 27
Author(s): Murilo Delgobo, Daniel A G B Mendes, Edgar Kozlova, Edroaldo Lummertz da Rocha, Gabriela F. Rodrigues-Luiz, Lucas Mascarin, Greicy Brisa Malaquias Dias, Daniel de Oliveira Patricio, Tim Dierckx, Maíra A. Bicca, G Bretton, Yonne Karoline Tenório de Menezes, Márick R Starick, Darcita Büerger Rovaris, Joanita Del Moral, Daniel Santos Mansur, Johan Van Weyenbergh, André Báfica
Software Mentions: 4
Published: about 7 years ago

10.3389/fnmol.2018.00288

Dysregulation of MicroRNAs and Target Genes Networks in Peripheral Blood of Patients With Sporadic Amyotrophic Lateral Sclerosis
Cited by: 84
Author(s): Maria Liguori, Nicoletta Nuzziello, Alessandro Introna, Arianna Consiglio, Flavio Licciulli, Eustachio D’Errico, Antonio Scarafino, Eugenio Distaso, Isabella Laura Simone
Software Mentions: 4
Published: about 8 years ago

10.1128/mSphereDirect.00120-18

Zika Virus Infection Preferentially Counterbalances Human Peripheral Monocyte and/or NK Cell Activity
Cited by: 26
Author(s): Fok‐Moon Lum, David Lee, Tze-Kwang Chua, Jeslin J. L. Tan, Cheryl Yi‐Pin Lee, Xuan Li, Yongxiang Fang, Bernett Lee, Wearn‐Xin Yee, Natasha Y. Rickett, Po Ying Chia, Vanessa Lim, Yee‐Sin Leo, David A. Matthews, Julian A. Hiscox, Lisa F. P. Ng
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0164461

Responses of Bovine Innate Immunity to Mycobacterium avium subsp. paratuberculosis Infection Revealed by Changes in Gene Expression and Levels of MicroRNA
Cited by: 40
Author(s): M. Malvisi, Fiorentina Palazzo, Nicola Morandi, Barbara Lazzari, J. L. Williams, G. Pagnacco, Giulietta Minozzi
Software Mentions: 4
Published: about 10 years ago

10.3390/cells7120275

Activation of Polyamine Catabolism by N1,N11-Diethylnorspermine in Hepatic HepaRG Cells Induces Dedifferentiation and Mesenchymal-Like Phenotype
Cited by: 12
Author(s): О. Н. Иванова, Anastasiya V. Snezhkina, George S. Krasnov, Vladimir T. Valuev-Elliston, Olga A. Khomich, Alexey Khomutov, Tuomo A. Keinänen, Leena Alhonen, Birke Bartosch, Anna V. Kudryavtseva, Sergey N. Kochetkov, Alexander Ivanov
Software Mentions: 4
Published: almost 8 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

10.1093/gbe/evy041

Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee
Cited by: 19
Author(s): Jason Pizzollo, William Nielsen, Yoichiro Shibata, Alexias Safi, Gregory E. Crawford, Gregory A. Wray, Courtney C. Babbitt
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0164766

RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process
Cited by: 1
Author(s): Thanh Nguyen, Asim Bhatti, Samuel Yang, Saeid Nahavandi
Software Mentions: 4
Published: about 10 years ago

10.1093/gbe/evv115

Complete Dosage Compensation inAnopheles stephensiand the Evolution of Sex-Biased Genes in Mosquitoes
Cited by: 40
Author(s): Xiaofang Jiang, James K. Biedler, Yumin Qi, Andrew Brantley Hall, Zhijian Tu
Software Mentions: 4
Published: over 11 years ago

10.1038/s41598-019-47363-6

Whole transcriptome analysis reveals correlation of long noncoding RNA ZEB1-AS1 with invasive profile in melanoma
Cited by: 20
Author(s): Ádamo Davi Diógenes Siena, Jéssica Rodrigues Plaça, Luíza Ferreira de Araújo, Isabela Ichihara de Barros, Kamila Chagas Peronni, Greice Andreotti de Molfetta, Carlos Alberto Oliveira de Biagi, Enilza Maria Espreáfico, Josane F. Sousa, Wilson A. Silva
Software Mentions: 4
Published: about 7 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/s13071-019-3534-4

Eimeria maxima-induced transcriptional changes in the cecal mucosa of broiler chickens
Cited by: 15
Author(s): Charles Li, Xianghe Yan, Hyun S. Lillehoj, Seong-Hwan Oh, Liheng Liu, Zhifeng Sun, Changqin Gu, Youngsub Lee, Zhezi Xianyu, Hongyan Zhao
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-49446-w

De novo transcriptome provides insights into the growth behaviour and resveratrol and trans-stilbenes biosynthesis in Dactylorhiza hatagirea - An endangered alpine terrestrial orchid of western Himalaya
Cited by: 19
Author(s): Nisha Dhiman, Nitesh Kumar Sharma, Pooja Thapa, Isha Sharma, Mohit Kumar Swarnkar, Amit Chawla, Ravi Shankar, Amita Bhattacharya
Software Mentions: 4
Published: about 7 years ago

10.3390/cells10030692

CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
Cited by: 2
Author(s): Sweta Talyan, Samantha Filipów, Michael Ignarski, Magdalena Smieszek, He Chen, Lucas Kühne, Linus Butt, Heike Göbel, Karla Johanna Ruth Hoyer-Allo, Felix C. Koehler, Janine Altmüller, Paul Brinkkötter, Bernhard Schermer, Thomas Benzing, Martin Kann, Roman‐Ulrich Müller, Christoph Dieterich
Software Mentions: 4
Published: over 5 years ago

10.3390/cells9112452

Photochemotherapy Induces Interferon Type III Expression via STING Pathway
Cited by: 0
Author(s): Edyta Biskup, Brian D. Larsen, Leonor Rib, Lasse Folkersen, Omid Niazi, Maria R. Kamstrup, Claus Storgaard Sørensen
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-49829-z

Adenovirus infection is associated with altered gut microbial communities in a non-human primate
Cited by: 27
Author(s): . Wasimuddin, Victor M. Corman, Jörg U. Ganzhorn, Jacques Rakotondranary, Yedidya R. Ratovonamana, Christian Drosten, Simone Sommer
Software Mentions: 4
Published: about 7 years ago

10.3390/cells9081846

Caenorhabditis elegans Deficient in DOT-1.1 Exhibit Increases in H3K9me2 at Enhancer and Certain RNAi-Regulated Regions
Cited by: 6
Author(s): Ruben Esse, Alla Grishok
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-019-49915-2

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat
Cited by: 52
Author(s): Mir Asif Iquebal, Pradeep Sharma, Rahul Singh Jasrotia, Sarika Jaiswal, Amandeep Kaur, Monika Saroha, U. B. Angadi, Sonia Sheoran, Rajender Singh, Gyanendra Singh, Anil Rai, Ruchi Tiwari, Dinesh Kumar
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-50573-7

Genome-wide association study and whole-genome sequencing identify a deletion in LRIT3 associated with canine congenital stationary night blindness
Cited by: 14
Author(s): Gautami Das, Doreen Becker, Vidhya Jagannathan, Orly Goldstein, Evelyn Santana, Kendall Carlin, Raghavi Sudharsan, Tosso Leeb, Yuji Nishizawa, Mineo Kondo, Gustavo D. Aguirre, Keiko Miyadera
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-50271-4

Fractional Deletion of Compound Kushen Injection Indicates Cytokine Signaling Pathways are Critical for its Perturbation of the Cell Cycle
Cited by: 9
Author(s): Thazin Nwe Aung, Saeed Nourmohammadi, Zhibo Qu, Yuka Harata-Lee, Jingang Cui, Hao Shen, Andrea J. Yool, Tara L. Pukala, Hongling Du, R. Daniel Kortschak, Wenxin Wei, David L. Adelson
Software Mentions: 4
Published: about 7 years ago

10.3390/cells9122593

Induced Pluripotent Stem Cells to Understand Mucopolysaccharidosis. I: Demonstration of a Migration Defect in Neural Precursors
Cited by: 3
Author(s): Silvin Lito, Adama Sidibé, Sten Ilmjärv, Patricie Burda, Matthias R. Baumgartner, Bernhard Wehrle-Haller, Karl‐Heinz Krause, Antoine Marteyn
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-52903-1

Sperm DNA Methylation Epimutation Biomarkers for Male Infertility and FSH Therapeutic Responsiveness
Cited by: 46
Author(s): S. Luján Marco, Ettore Caroppo, Craig S. Niederberger, Joan‐Carles Arce, Ingrid Sadler‐Riggleman, Daniel Beck, Eric Nilsson, Michael K. Skinner
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13059-021-02369-0

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome
Cited by: 23
Author(s): Robin-Lee Troskie, Yohaann Jafrani, Tim R. Mercer, Adam D. Ewing, Geoffrey J. Faulkner, Seth W. Cheetham
Software Mentions: 4
Published: over 5 years ago

10.3390/cells7110205

The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations
Cited by: 25
Author(s): Tamar Segal, Mali Salmon‐Divon, Gabi Gerlitz
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-019-52841-y

Prospective validation in epithelial tumors of a gene expression predictor of liver metastasis derived from uveal melanoma
Cited by: 3
Author(s): Petros Tsantoulis, Mauro Delorenzi, Ivan Bièche, Sophie Vacher, Pascale Mariani, Nathalie Cassoux, Alexandre Houy, Marc‐Henri Stern, Sergio Román-Román, Pierre‐Yves Dietrich, Arnaud Roth, Wulfran Cacheux
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-54935-z

Identification of potential chemosignals in the European water vole Arvicola terrestris
Cited by: 8
Author(s): Patricia Nagnan‐Le Meillour, Amandine Descamps, Chrystelle Le Danvic, Maurane Grandmougin, Jean‐Michel Saliou, Christophe Klopp, Marine Milhes, Coralie Bompard, Didier Chesneau, Kévin Poissenot, Matthieu Keller
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-55852-x

Multi-parameter immune profiling of peripheral blood mononuclear cells by multiplexed single-cell mass cytometry in patients with early multiple sclerosis
Cited by: 34
Author(s): Chotima Böttcher, Camila Fernández-Zapata, Stephan Schlickeiser, Désirée Kunkel, Axel Schulz, Henrik E. Mei, Carl Weidinger, René M. Gieß, Susanna Asseyer, Britta Siegmund, Friedemann Paul, Klemens Ruprecht, Josef Priller
Software Mentions: 4
Published: almost 7 years ago

10.3389/fonc.2019.00606

Inactivation of Prostaglandin E2 as a Mechanism for UGT2B17-Mediated Adverse Effects in Chronic Lymphocytic Leukemia
Cited by: 10
Author(s): Éric P. Allain, Michèle Rouleau, Trang Le, Katrina Vanura, Lyne Villeneuve, Patrick Caron, Véronique Turcotte, Éric Lévesque, Chantal Guillemette
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms21218333

Transcriptional Effects of Psychoactive Drugs on Genes Involved in Neurogenesis
Cited by: 7
Author(s): Chiara C. Bortolasci, Briana Spolding, Srisaiyini Kidnapillai, Timothy Connor, Trang T. T. Truong, Zoe Liu, Bruna Panizzutti, Mark F. Richardson, Laura J. Gray, Michael Berk, Olivia Dean, Ken Walder
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.3859

How to normalize metatranscriptomic count data for differential expression analysis
Cited by: 31
Author(s): Heiner Klingenberg, Peter Meinicke
Software Mentions: 4
Published: about 9 years ago

10.3389/fnins.2020.00774

Lasting and Sex-Dependent Impact of Maternal Immune Activation on Molecular Pathways of the Amygdala
Cited by: 19
Author(s): Marissa R Keever, Pan Zhang, Courtni R. Bolt, Adrienne M. Antonson, Haley E Rymut, Megan P. Caputo, Alexandra K Houser, Álvaro Gonzalez Hernández, Bruce R. Southey, Laurie A. Rund, Rodney W. Johnson, Sandra L. Rodriguez-Zas
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-58711-2

Nucleus accumbens pathways control cell-specific gene expression in the medial prefrontal cortex
Cited by: 5
Author(s): Takatoshi Hikida, Shuhei Yao, Tom Macpherson, Ayumi Fukakusa, Maki Morita, Haruhide Kimura, Keisuke Hirai, Tatsuya Ando, Hiroyoshi Toyoshiba, Akira Sawa
Software Mentions: 4
Published: over 6 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: over 6 years ago

10.7717/peerj.7696

The co-expression networks of differentially expressed RBPs with TFs and LncRNAs related to clinical TNM stages of cancers
Cited by: 4
Author(s): Shuaibin Lian, Liansheng Li, Yongjie Zhou, Zixiao Liu, Lei Wang
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-020-59934-z

Immunosuppressive effect and global dysregulation of blood transcriptome in response to psychosocial stress in vervet monkeys (Chlorocebus sabaeus)
Cited by: 2
Author(s): Anna J. Jasinska, Ivona Pandrea, Tianyu He, Cassandra Benjamin, Maurice Newton, Jen‐Chieh Lee, Nelson B. Freimer, Giovanni Coppola, J. David Jentsch
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.7107

Characterization of bidirectional gene pairs in The Cancer Genome Atlas (TCGA) dataset
Cited by: 8
Author(s): Juchuanli Tu, Xiaolu Li, Jianjun Wang
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-61633-8

MicroRNA hsa-mir-3923 serves as a diagnostic and prognostic biomarker for gastric carcinoma
Cited by: 11
Author(s): Xiaohui Yang, Ze Zhang, Lichao Zhang, Li Zhou
Software Mentions: 4
Published: over 6 years ago

10.7150/thno.55645

Deciphering the autophagy regulatory network via single-cell transcriptome analysis reveals a requirement for autophagy homeostasis in spermatogenesis
Cited by: 18
Author(s): Mei Wang, Yanwen Xu, Yuncong Zhang, Yuhan Chen, Gang Chang, Geng An, Xinyan Yang, Caihong Zheng, Jiexiang Zhao, Zhaoting Liu, Dazhuang Wang, Masahiro Kai, Rao S, Meng Dai, Dong Wang, Xiaoyang Zhao
Software Mentions: 4
Published: almost 6 years ago

10.1093/hmg/ddab140

Human photoreceptor cells from different macular subregions have distinct transcriptional profiles
Cited by: 15
Author(s): Andrew P. Voigt, Nathaniel K. Mullin, S. Scott Whitmore, Adam P. DeLuca, Erin R Burnight, Xiuying Liu, Budd A. Tucker, Todd E. Scheetz, Edwin M Stone, Robert F. Mullins
Software Mentions: 4
Published: over 5 years ago

10.1038/tp.2016.67

Candidate gene networks and blood biomarkers of methamphetamine-associated psychosis: an integrative RNA-sequencing report
Cited by: 26
Author(s): Michael S. Breen, Anne Uhlmann, Christiane M. Nday, Stephen J. Glatt, Mario Mitt, A. Metsalpu, Dan J. Stein, Nicola Illing
Software Mentions: 4
Published: over 10 years ago

10.1038/s41398-017-0050-1

Gene expression associated with PTSD in World Trade Center responders: An RNA sequencing study
Cited by: 56
Author(s): Pei‐Fen Kuan, Monika A. Waszczuk, Roman Kotov, Sean Clouston, Xiaohua Yang, Prashant Singh, Sean T. Glenn, Eduardo Cortes Gomez, Jianmin Wang, Evelyn J. Bromet, Benjamin J. Luft
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41398-019-0472-z

DLPFC transcriptome defines two molecular subtypes of schizophrenia
Cited by: 26
Author(s): Elijah F. W. Bowen, Jack L. Burgess, Richard Granger, Joel E. Kleinman, C. Harker Rhodes
Software Mentions: 4
Published: over 7 years ago

10.1186/s13148-021-01050-4

Epigenetic evidence of an Ac/Dc axis by VPA and SAHA
Cited by: 10
Author(s): Sebastian Lunke, Scott Maxwell, Ishant Khurana, K N Harikrishnan, Jun Okabe, Keith Al-Hasani, Assam El‐Osta
Software Mentions: 4
Published: over 5 years ago

10.1128/mBio.02504-18

The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium
Cited by: 73
Author(s): Alexander J. Westermann, Elisa Venturini, Mikael E. Sellin, Konrad U. Förstner, Wolf‐Dietrich Hardt, Jörg Vogel
Software Mentions: 4
Published: over 7 years ago

10.1186/s13148-015-0086-0

Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis
Cited by: 26
Author(s): Warwick J. Locke, Elena Zotenko, Clare Stirzaker, Mark D. Robinson, Rebecca A. Hinshelwood, Andrew Stone, Roger R. Reddel, Lily I. Huschtscha, Susan J. Clark
Software Mentions: 4
Published: over 11 years ago

10.1128/mBio.00617-20

EspFu-Mediated Actin Assembly Enhances Enteropathogenic Escherichia coli Adherence and Activates Host Cell Inflammatory Signaling Pathways
Cited by: 12
Author(s): Fernando Henrique Martins, Ashwani Kumar, Cecília M. Abe, Enéas Carvalho, Milton Yutaka Nishiyama-Jr, Chao Xing, Vanessa Sperandio, Waldir P. Elias
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms21124453

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA
Cited by: 7
Author(s): Andreas Kloetgen, Sujitha Duggimpudi, Konstantin Schuschel, Kebria Hezaveh, Daniel Picard, Heiner Schaal, Marc Remke, Jan‐Henning Klusmann, Arndt Borkhardt, Alice C. McHardy, Jessica I. Hoell
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms21061910

NR2F2 Orphan Nuclear Receptor is Involved in Estrogen Receptor Alpha-Mediated Transcriptional Regulation in Luminal A Breast Cancer Cells
Cited by: 8
Author(s): Edina Erdős, Bálint László Bálint
Software Mentions: 4
Published: over 6 years ago

10.1128/mSphere.00231-18

Kinome Expansion in the Fusarium oxysporum Species Complex Driven by Accessory Chromosomes
Cited by: 28
Author(s): Gregory A. DeIulio, Li Guo, Yong Zhang, Jonathan M. Goldberg, H. Corby Kistler, Lijun Ma
Software Mentions: 4
Published: over 8 years ago

10.1186/s13148-020-00836-2

Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer
Cited by: 15
Author(s): Mitchell G. Lawrence, Ruth Pidsley, Birunthi Niranjan, Melissa Papargiris, Brooke A. Pereira, Michelle Richards, Linda Teng, Sam Norden, Andrew Ryan, Mark Frydenberg, Clare Stirzaker, Renea A. Taylor, Gail P. Risbridger, Susan J. Clark
Software Mentions: 4
Published: over 6 years ago

10.1128/mBio.00588-21

An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin
Cited by: 6
Author(s): Gabriela Balderrama-Gutierrez, Ana Milovic, Vanessa J. Cook, M. Nurul Islam, Youwen Zhang, Hippokratis Kiaris, John T. Belisle, A Mortazavi, Alan G. Barbour
Software Mentions: 4
Published: over 5 years ago

10.1186/s13148-020-00989-0

Identification and validation of methylated differentially expressed miRNAs and immune infiltrate profile in EBV-associated gastric cancer
Cited by: 4
Author(s): Man-Sheng Zhu, Qi Liang, Tao Chen, Qian Kong, Gengtai Ye, Shitong Yu, Xunjun Li, Qinglie He, Hao Líu, Yanfeng Hu, Jiang Yu, Guoxin Li
Software Mentions: 4
Published: almost 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568