bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0222325

Fe limitation decreases transcriptional regulation over the diel cycle in the model diatom Thalassiosira pseudonana
Cited by: 13
Author(s): Johanna A. L. Goldman, Megan J. Schatz, Chris T. Berthiaume, Sacha Coesel, Mónica V. Orellana, E. Virginia Armbrust
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0226833

Effects of Allium hookeri on gut microbiome related to growth performance in young broiler chickens
Cited by: 15
Author(s): Sung-Hyen Lee, Sohyun Bang, Hyejeong Jang, Eun-Byeol Lee, Bong-Sang Kim, Seung-Hwan Kim, Sang-Hyun Kang, Kyung-Woo Lee, Dong-Wook Kim, Jung-Bong Kim, Jeong‐Sook Choe, Shin-Young Park, Hyun S. Lillehoj
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0236298

An in vitro model of chronic wounding and its implication for age-related macular degeneration
Cited by: 1
Author(s): Lindsay J. Bailey-Steinitz, Ying-Hsuan Shih, Monte J. Radeke, Peter Coffey
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0209300

Angiopoietin-2 promotes osteogenic differentiation of thoracic ligamentum flavum cells via modulating the Notch signaling pathway
Cited by: 9
Author(s): Xiaoxi Yang, Zhongqiang Chen, Xiangyu Meng, Chuiguo Sun, Mengtao Li, Shu Li, Dongwei Fan, Tianqi Fan, Ann Yehong Huang, Chi Zhang
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0242665

Genetic factors contributing to extensive variability of sex-specific hepatic gene expression in Diversity Outbred mice
Cited by: 12
Author(s): Tisha Melia, David J. Waxman
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0132310

Assessing Dissimilarity Measures for Sample-Based Hierarchical Clustering of RNA Sequencing Data Using Plasmode Datasets
Cited by: 20
Author(s): Pablo Reeb, Sergio Jorge Bramardi, Juan P. Steibel
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0155061

Comparative Analysis of Transcriptomes among Bombyx mori Strains and Sexes Reveals the Genes Regulating Melanic Morph and the Related Phenotypes
Cited by: 3
Author(s): Songzhen He, Xiaoling Tong, Kunpeng Lu, Yaru Lu, Jiangwen Luo, Wenhao Yang, Min Chen, Minjin Han, Hai Hu, Cheng Lü, Fangyin Dai
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0097821

PIWI Proteins Are Dispensable for Mouse Somatic Development and Reprogramming of Fibroblasts into Pluripotent Stem Cells
Cited by: 22
Author(s): Elaine Cheng, Dongwan Kang, Zhong Wang, Haifan Lin
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0098402

Blood Feeding and Plasmodium Infection Alters the miRNome of Anopheles stephensi
Cited by: 39
Author(s): Shanu Jain, Vandita Rana, Jatin Shrinet, Anil Sharma, T. Adak, Sujatha Sunil, Raj K. Bhatnagar
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0235575

Comparative gut transcriptome analysis of Diatraea saccharalis in response to the dietary source
Cited by: 4
Author(s): Daniel D. Noriega, Fabrício Barbosa Monteiro Arraes, José Dijair Antonino, Leonardo Lima Pepino Macedo, Fernando Fonseca, Roberto Coiti Togawa, Priscila Grynberg, Maria C. M. Silva, A. S. Negrisoli, Carolina Vianna Morgante, Maria Fátima Grossi-de-Sá
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0191096

Thyroid transcriptome analysis reveals different adaptive responses to cold environmental conditions between two chicken breeds
Cited by: 11
Author(s): Shanshan Xie, Xiufen Yang, Dehe Wang, Feng Zhu, Ning Yang, Zhuocheng Hou, Zhonghua Ning
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0130262

How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq
Cited by: 31
Author(s): Luis Fernando García-Ortega, Octavio Martínez
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0171694

An integrative study on the impact of highly differentially methylated genes on expression and cancer etiology
Cited by: 2
Author(s): Buğra Özer, Uğur Sezerman
Software Mentions: 3
Published: over 9 years ago

10.1038/s42003-019-0461-z

C/EBPβ-LIP induces cancer-type metabolic reprogramming by regulating the let-7/LIN28B circuit in mice
Cited by: 11
Author(s): Tobias Ackermann, Götz Hartleben, Christine Müller, Guido Mastrobuoni, Marco Groth, Britt A. Sterken, Mohamad Amr Zaini, Sameh A. Youssef, Hidde R. Zuidhof, Sara Russo Krauss, Gertrud Kortman, Gerald de Haan, Alain de Bruin, Zhao Qi Wang, Matthias Platzer, Stefan Kempa, Cornelis F. Calkhoven
Software Mentions: 3
Published: about 7 years ago

10.1038/s42003-019-0574-4

Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear
Cited by: 57
Author(s): Heiko T. Jansen, Shawn Trojahn, Michael W. Saxton, Corey R. Quackenbush, Brandon D. Evans Hutzenbiler, O. Lynne Nelson, Omar E. Cornejo, Charles T. Robbins, Joanna L. Kelley
Software Mentions: 3
Published: almost 7 years ago

10.1038/s42003-020-01235-2

Floral transcriptomes reveal gene networks in pineapple floral growth and fruit development
Cited by: 30
Author(s): Lulu Wang, Yang Li, Xingyue Jin, Liping Liu, Xiaozhuan Dai, Qing Liu, Lihua Zhao, Ping Zheng, Xiaomei Wang, Yeqiang Liu, Deshu Lin, Yuan Qin
Software Mentions: 3
Published: almost 6 years ago

10.1038/s42003-021-01925-5

Inhibiting LXRα phosphorylation in hematopoietic cells reduces inflammation and attenuates atherosclerosis and obesity in mice
Cited by: 2
Author(s): Maud Voisin, Elina Shrestha, Claire Rollet, Cyrus Nikain, Tatjana Josefs, Mélanie Mahé, Tessa Barrett, Hye Rim Chang, Rachel Ruoff, Jeffrey A. Schneider, Michela L. Garabedian, Chris Zoumadakis, Chi Sun Yun, Bara A. Badwan, Emily J. Brown, Adam C. Mar, Robert J. Schneider, Ira J. Goldberg, Inés Pineda-Torra, Edward A. Fisher
Software Mentions: 3
Published: over 5 years ago

10.1038/s42003-020-0873-9

Pan-cancer molecular analysis of the RB tumor suppressor pathway
Cited by: 47
Author(s): Erik S. Knudsen, Ram Nambiar, Spencer R. Rosario, Dominic J. Smiraglia, David W. Goodrich, Agnieszka K. Witkiewicz
Software Mentions: 3
Published: over 6 years ago

10.1038/s42003-021-02223-w

Single-cell RNA sequencing of human nail unit defines RSPO4 onychofibroblasts and SPINK6 nail epithelium
Cited by: 8
Author(s): Hyun Je Kim, Joon Ho Shim, Ji-Hye Park, Hyun Tae Shin, Kee–Taek Jang, Woong-Yang Park, Kyung-Hoon Lee, Eun Ji Kwon, Hyung-Suk Jang, Hanseul Yang, Jong Hee Lee, Jun‐Mo Yang, Dong‐Youn Lee
Software Mentions: 3
Published: about 5 years ago

10.1038/s42003-020-0775-x

Trypanosomatid parasite dynamically changes the transcriptome during infection and modifies honey bee physiology
Cited by: 24
Author(s): Qiushi Liu, Jing Lei, Alistair C. Darby, Tatsuhiko Kadowaki
Software Mentions: 3
Published: over 6 years ago

10.1155/2020/2018214

Construction and Comprehensive Analysis of Dysregulated Long Noncoding RNA-Associated Competing Endogenous RNA Network in Moyamoya Disease
Cited by: 2
Author(s): Xuefeng Gu, Da-Quan Jiang, Yanwen Yang, Peng Zhang, Guoqing Wan, Wangxian Gu, Junfeng Shi, Liying Jiang, Bing Chen, Yanjun Zheng, Dingsheng Liu, Shu Guo, Changlian Lu
Software Mentions: 3
Published: about 6 years ago

10.1155/2021/2203636

Identification of Novel COVID-19 Biomarkers by Multiple Feature Selection Strategies
Cited by: 2
Author(s): Shuai Zhang, Renliang Qu, Pengyan Wang, Shenghan Wang
Software Mentions: 3
Published: almost 5 years ago

10.1093/conphys/coaa013

Combined stress of ocean acidification and warming influence survival and drives differential gene expression patterns in the Antarctic pteropod, Limacina helicina antarctica
Cited by: 12
Author(s): Kevin M. Johnson, Gretchen E. Hofmann
Software Mentions: 3
Published: over 6 years ago

10.1016/j.dib.2017.10.019

Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana
Cited by: 11
Author(s): Daniel Lepe-Soltero, Alma Armenta-Medina, Daoquan Xiang, Raju Datla, C. Stewart Gillmor, Cei Abreu‐Goodger
Software Mentions: 3
Published: over 8 years ago

10.1093/database/baz086

Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms
Cited by: 12
Author(s): Jochen T. Bick, Shuqin Zeng, Mark D. Robinson, Susanne E. Ulbrich, Stefan Bauersachs
Software Mentions: 3
Published: over 7 years ago

10.3390/dj7020058

Effect of Dietary Fiber on the Composition of the Murine Dental Microbiome
Cited by: 10
Author(s): Lea M. Sedghi, Craig Byron, Ryan deM. Jennings, George E. Chlipala, Stefan J. Green, Laura Silo-Suh
Software Mentions: 3
Published: about 7 years ago

10.1242/dev.199628

LncRNA HBL1 is required for genome-wide PRC2 occupancy and function in cardiogenesis from human pluripotent stem cells
Cited by: 8
Author(s): Juli Liu, Sheng Liu, Lei Han, Sheng Yi, Yucheng Zhang, Il-man Kim, Jun Wan, Lei Yang
Software Mentions: 3
Published: about 5 years ago

10.1007/s00125-017-4500-3

Systems biology of the IMIDIA biobank from organ donors and pancreatectomised patients defines a novel transcriptomic signature of islets from individuals with type 2 diabetes
Cited by: 121
Author(s): Michele Solimena, Anke M. Schulte, Lorella Marselli, Florian Ehehalt, Daniela Richter, Manuela Kleeberg, Hassan Mziaut, Klaus-Peter Knoch, Julia Parnis, Marco Bugliani, Afshan Siddiq, Anne Jörns, Frédéric Burdet, Robin Liechti, Mara Suleiman, Daniel Margerie, Farooq Syed, Marius Distler, Robert Grützmann, Enrico Petretto, Aida Moreno‐Moral, Carolin Wegbrod, Anke Sönmez, Katja Pfriem, Anne Friedrich, Jörn Meinel, Claes B. Wollheim, Gustavo Baretton, Raphaël Scharfmann, Everson Nogoceke, Ezio Bonifacio, Dorothée Sturm, Birgit Meyer‐Puttlitz, Ugo Boggi, Hans‐Detlev Saeger, Franco Filipponi, Mathias Lesche, Paolo Meda, Andreas Dahl, Leonore Wigger, Ioannis Xénarios, Mario Falchi, Bernard Thorens, Jürgen Weitz, Krister Bokvist, Sigurd Lenzen, Guy A. Rutter, Philippe Froguel, Manon von Bülow, Mark Ibberson, Piero Marchetti
Software Mentions: 3
Published: almost 9 years ago

10.1155/2020/9369341

Nine Genes Mediate the Therapeutic Effects of Iodine-131 Radiotherapy in Thyroid Carcinoma Patients
Cited by: 6
Author(s): Shuwen Han, Yang Xi, Miao Da, Jingying Xu, Zhuang Jing, Gao Wei-li
Software Mentions: 3
Published: about 6 years ago

10.1016/j.ebiom.2018.02.017

Reciprocal modulation of mesenchymal stem cells and tumor cells promotes lung cancer metastasis
Cited by: 45
Author(s): Giulia Fregni, Mathieu Quinodoz, Emely Möller, Joanna A. Vuille, Sabine Galland, Carlo Fusco, Patricia Martin, Igor Letovanec, Paolo Provero, Carlo Rivolta, Nicolò Riggi, Ivan Stamenkovic
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2018.00294

Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline
Cited by: 23
Author(s): Shinya Tasaki, Chris Gaiteri, Sara Mostafavi, Lei Yu, Yanling Wang, Philip L. De Jager, David A. Bennett
Software Mentions: 3
Published: about 8 years ago

10.3389/fgene.2018.00610

Prenatal Alcohol Exposure: Profiling Developmental DNA Methylation Patterns in Central and Peripheral Tissues
Cited by: 26
Author(s): Alexandre A. Lussier, Tamara S. Bodnar, Matthew Mingay, Alexandre Morin, Martin Hirst, Michæl S. Kobor, Joanne Weinberg
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2021.583568

Aberrantly DNA Methylated-Differentially Expressed Genes in Pancreatic Cancer Through an Integrated Bioinformatics Approach
Cited by: 4
Author(s): Haifeng Sun, Rui Xin, Changjun Zheng, Ge Huang
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2019.00342

P-TEFb Regulates Transcriptional Activation in Non-coding RNA Genes
Cited by: 9
Author(s): Heeyoun Bunch, Hyeseung Choe, Jong Bum Kim, Doo Sin Jo, Soyeon Jeon, Sang-Hwa Lee, Dong‐Hyung Cho, Keunsoo Kang
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2021.620241

Integrated Transcriptomic and Epigenetic Study of PCOS: Impact of Map3k1 and Map1lc3a Promoter Methylation on Autophagy
Cited by: 11
Author(s): Yanmin Qin, Ting Li, Hui Zhao, Zhanrui Mao, Chunmei Ding, Yani Kang
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2020.00486

Expression Quantitative Trait Loci (eQTL) Mapping in Korean Patients With Crohn’s Disease and Identification of Potential Causal Genes Through Integration With Disease Associations
Cited by: 14
Author(s): Seulgi Jung, Wenting Liu, Jiwon Baek, Jung Won Moon, Byong Duk Ye, Ho‐Su Lee, Sang Hyoung Park, Suk Kyun Yang, Buhm Han, Jing Liu, Kyuyoung Song
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2021.574196

Identification of the Functions and Prognostic Values of RNA Binding Proteins in Bladder Cancer
Cited by: 18
Author(s): Yue Wu, Zheng Liu, Wa Xian, Huan Feng, Bintao Hu, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Shaogang Wang, Jihong Liu, Tao Wang
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2020.00321

Identification and Integrated Analysis of MicroRNA and mRNA Expression Profiles During Agonistic Behavior in Chinese Mitten Crab (Eriocheir sinensis) Using a Deep Sequencing Approach
Cited by: 4
Author(s): Yangyang Pang, Long He, Yameng Song, Xiaozhe Song, Jiahuan Lv, Yongxu Cheng, Xiaozhen Yang
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2015.00174

Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations
Cited by: 44
Author(s): Ovidiu D. Iancu, Alexandre M. Colville, Denesa Oberbeck, Priscila Darakjian, Shannon K. McWeeney, Robert Hitzemann
Software Mentions: 3
Published: over 11 years ago

10.3389/fgene.2019.00009

McImpute: Matrix Completion Based Imputation for Single Cell RNA-seq Data
Cited by: 60
Author(s): Aanchal Mongia, Debarka Sengupta, Angshul Majumdar
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2019.00752

Integration of Cross Species RNA-seq Meta-Analysis and Machine-Learning Models Identifies the Most Important Salt Stress–Responsive Pathways in Microalga Dunaliella
Cited by: 39
Author(s): Bahman Panahi, Mohammad Frahadian, Jacob T. Dums, Mohammad Amin Hejazi
Software Mentions: 3
Published: about 7 years ago

10.3389/fgene.2020.628539

Cell Type-Specific Predictive Models Perform Prioritization of Genes and Gene Sets Associated With Autism
Cited by: 7
Author(s): Jinting Guan, Yang Wang, Yiping Lin, Qingyang Yin, Yibo Zhuang, Guoli Ji
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2019.01215

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

10.3389/fgene.2018.00291

Transcriptome Analyses Reveal Adult Metabolic Syndrome With Intrauterine Growth Restriction in Pig Models
Cited by: 21
Author(s): Linyuan Shen, Mailin Gan, Shunhua Zhang, Jideng Ma, Guoqing Tang, Yanzhi Jiang, Mingzhou Li, Jinyong Wang, Xuewei Li, Lianqiang Che, Li Zhu
Software Mentions: 3
Published: about 8 years ago

10.3389/fgene.2020.00265

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

10.3389/fgene.2020.540094

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

10.3389/fmicb.2017.01784

Analyzing the Complex Regulatory Landscape of Hfq – an Integrative, Multi-Omics Approach
Cited by: 14
Author(s): Lucia Grenga, Govind Chandra, Gerhard Saalbach, Carla V. Galmozzi, Günter Krämer, Jacob G. Malone
Software Mentions: 3
Published: almost 9 years ago

10.3389/fmicb.2019.01914

Soil Metatranscriptomes Under Long-Term Experimental Warming and Drying: Fungi Allocate Resources to Cell Metabolic Maintenance Rather Than Decay
Cited by: 28
Author(s): Adriana L. Romero‐Olivares, Germán Meléndrez-Carballo, Asunción Lago‐Lestón, Kathleen K. Treseder
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2018.00445

Comparative mRNA-Seq Analysis Reveals the Improved EPS Production Machinery in Streptococcus thermophilus ASCC 1275 During Optimized Milk Fermentation
Cited by: 25
Author(s): Qinglong Wu, Nagendra P. Shah
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2020.01978

Sound Vibration-Triggered Epigenetic Modulation Induces Plant Root Immunity Against Ralstonia solanacearum
Cited by: 7
Author(s): Jihye Jung, Seon‐Kyu Kim, Sung‐Hee Jung, Mi‐Jeong Jeong, Choong-Min Ryu
Software Mentions: 3
Published: about 6 years ago

10.3389/fmolb.2021.625608

P23 Acts as Functional RBP in the Macrophage Inflammation Response
Cited by: 6
Author(s): Sebastian de Vries, Vladimı́r Beneš, Isabel S. Naarmann-de Vries, Cornelia Rücklé, Kathi Zarnack, Gernot Marx, Dirk H. Ostareck, Antje Ostareck-Lederer
Software Mentions: 3
Published: about 5 years ago

10.3389/fmolb.2021.678877

A Ferroptosis-Related lncRNAs Signature Predicts Prognosis and Immune Microenvironment for Breast Cancer
Cited by: 42
Author(s): Kaiming Zhang, Liqin Ping, Tian Du, Gehao Liang, Yun Huang, Zhiling Li, Rong Deng, Jun Tang
Software Mentions: 3
Published: about 5 years ago

10.3389/fmolb.2020.00030

Coexisting EGFR and TP53 Mutations in Lung Adenocarcinoma Patients Are Associated With COMP and ITGB8 Upregulation and Poor Prognosis
Cited by: 17
Author(s): Chang Zheng, Xuelian Li, Yong Ren, Zhihua Yin, Baosen Zhou
Software Mentions: 3
Published: over 6 years ago

10.3389/fmolb.2021.720370

Hydroxychloroquine Induces Apoptosis in Cholangiocarcinoma via Reactive Oxygen Species Accumulation Induced by Autophagy Inhibition
Cited by: 8
Author(s): Jiaqi Chen, Qiaoya Pan, Yang Bai, Xuepeng Chen, Yi Zhou
Software Mentions: 3
Published: almost 5 years ago

10.3389/fneur.2015.00045

Long Non-Coding RNA Expression during Aging in the Human Subependymal Zone
Cited by: 37
Author(s): Guy Barry, Boris Guennewig, Samantha J. Fung, Dominik C. Kaczorowski, Cynthia Shannon Weickert
Software Mentions: 3
Published: over 11 years ago

10.3389/fneur.2020.573575

Differential Glial Activation in Early Epileptogenesis—Insights From Cell-Specific Analysis of DNA Methylation and Gene Expression in the Contralateral Hippocampus
Cited by: 4
Author(s): Toni Berger, Magnus Dehli Vigeland, Hanne Sagsveen Hjorthaug, Cecilie G. Nome, Erik Taubøll, Kaja Kristine Selmer, Kjell Heuser
Software Mentions: 3
Published: almost 6 years ago

10.3389/fnins.2020.00538

Brainstem Organoids From Human Pluripotent Stem Cells
Cited by: 42
Author(s): Nobuyuki Eura, Takeshi K. Matsui, Joachim Luginbühl, Masaya Matsubayashi, Hitoki Nanaura, T. Shiota, Kaoru Kinugawa, Naohiko Iguchi, Takao Kiriyama, Canbin Zheng, Tsukasa Kouno, Yan Lan, Pornparn Kongpracha, Pattama Wiriyasermkul, Yoshihiko Sakaguchi, Riko Nagata, Tomoya Komeda, Naritaka Morikawa, Fumika Kitayoshi, Miyong Jong, Shinko Kobashigawa, Mari Nakanishi, Masatoshi Hasegawa, Yasuhiko Saito, Takashi Shiromizu, Yuhei Nishimura, Takahiko Kasai, Maiko Takeda, Hiroshi Kobayashi, Yusuke Inagaki, Yasuhito Tanaka, Manabu Makinodan, Toshifumi Kishimoto, Hiroki Kuniyasu, Shushi Nagamori, Alysson R. Muotri, Jay W. Shin, Kazuma Sugie, Eiichiro Mori
Software Mentions: 3
Published: about 6 years ago

10.3389/fnins.2021.606926

The Epidemiological and Mechanistic Understanding of the Neurological Manifestations of COVID-19: A Comprehensive Meta-Analysis and a Network Medicine Observation
Cited by: 6
Author(s): Jason Shen, Yuan Hou, Yadi Zhou, Reena Mehra, Lara Jehi, Feixiong Cheng
Software Mentions: 3
Published: over 5 years ago

10.3389/fnins.2019.00297

Regeneration Enhances Metastasis: A Novel Role for Neurovascular Signaling in Promoting Melanoma Brain Metastasis
Cited by: 13
Author(s): Roshini Prakash, Sivan Izraely, Nikita S. Thareja, Rex H. Lee, Maya Rappaport, Riki Kawaguchi, Orit Sagi‐Assif, Shlomit Ben‐Menachem, Tsipi Meshel, Michał Machnicki, Shuichi Ohe, Dave S. B. Hoon, Giovanni Coppola, Isaac P. Witz, S. Thomas Carmichael
Software Mentions: 3
Published: over 7 years ago

10.3389/fonc.2020.554759

Integrated Analysis of lncRNA–Mediated ceRNA Network in Lung Adenocarcinoma
Cited by: 90
Author(s): Xianxian Wu, Zhilin Sui, Hongdian Zhang, Ying Wang, Zhentao Yu
Software Mentions: 3
Published: almost 6 years ago

10.3389/fonc.2020.00215

A Novel Long Non-coding RNA, MSTRG.51053.2 Regulates Cisplatin Resistance by Sponging the miR-432-5p in Non-small Cell Lung Cancer Cells
Cited by: 24
Author(s): Jie Zhang, Chuanqin Xu, Y Gao, Yi Wang, Zongli Ding, Yueming Zhang, Wenyi Shen, Yulong Zheng, Yufeng Wan
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2021.553594

Comprehensive In Silico Analysis of a Novel Serum Exosome-Derived Competitive Endogenous RNA Network for Constructing a Prognostic Model for Glioblastoma
Cited by: 9
Author(s): Zihao Wang, Xin Ji, Lu Gao, Xiaopeng Guo, Wei Lian, Kan Deng, Bing Xing
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2020.533616

Expression Profile of Circular RNAs in Oral Squamous Cell Carcinoma
Cited by: 19
Author(s): Yanxiong Shao, Yuhan Song, Shuying Xu, Siyi Li, Huifang Zhou
Software Mentions: 3
Published: almost 6 years ago

10.3389/fonc.2020.602555

Development of an Immune-Related Gene Signature for Prognosis in Melanoma
Cited by: 13
Author(s): Mengli Zhang, Xu Zhou, Dan Huang, Chao Luan, Heng Gu, Ju Mei, Kun Chen
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2020.00871

A Radiosensitivity Gene Signature and XPO1 Predict Clinical Outcomes for Glioma Patients
Cited by: 5
Author(s): Shan Wu, Qiao Qiao, Guang Li
Software Mentions: 3
Published: about 6 years ago

10.3389/fonc.2018.00374

Prognostic Genes of Breast Cancer Identified by Gene Co-expression Network Analysis
Cited by: 178
Author(s): Jianing Tang, Deguang Kong, Qiuxia Cui, Kun Wang, Dan Zhang, Yan Gong
Software Mentions: 3
Published: almost 8 years ago

10.3389/fonc.2020.00780

Identification and Validation of a Prognostic lncRNA Signature for Hepatocellular Carcinoma
Cited by: 36
Author(s): Wang Li, Qifeng Chen, Tao Huang, Peihong Wu, Lujun Shen, Zijing Huang
Software Mentions: 3
Published: about 6 years ago

10.3389/fonc.2020.550986

MicroRNAs Expression Patterns Predict Tumor Mutational Burden in Colorectal Cancer
Cited by: 5
Author(s): Jiahao Huang, Haizhou Liu, Yang Zhao, Tao Luo, Jungang Liu, Junjie Liu, Xiaoyan Pan, Weizhong Tang
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2020.00601

Circular RNA Expression Profiles in Nasopharyngeal Carcinoma by Sequence Analysis
Cited by: 17
Author(s): Jing Yang, Yongqian Gong, Qingshan Jiang, Lijun Liu, Shuyan Li, Quanjun Zhou, Fang Huang, Zhifeng Liu
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2020.01765

Identification of TYROBP and C1QB as Two Novel Key Genes With Prognostic Value in Gastric Cancer by Network Analysis
Cited by: 26
Author(s): Junjie Jiang, Yongfeng Ding, Mengjie Wu, Xiadong Lyu, Haifeng Wang, Yanyan Chen, Haiyong Wang, Lisong Teng
Software Mentions: 3
Published: almost 6 years ago

10.3389/fonc.2021.707066

Cystatin-B Negatively Regulates the Malignant Characteristics of Oral Squamous Cell Carcinoma Possibly Via the Epithelium Proliferation/Differentiation Program
Cited by: 3
Author(s): Tiantian Xu, Xiao‐Wen Zeng, Xinhong Wang, Luxi Yang, Gang Luo, Ting Yu
Software Mentions: 3
Published: about 5 years ago

10.3389/fonc.2021.659201

Prognostic Prediction of Cytogenetically Normal Acute Myeloid Leukemia Based on a Gene Expression Model
Cited by: 4
Author(s): Yang Liu, Houyu Zhang, Xue Yang, Ting Lu, Shihui Ma, Hui Cheng, Kuangyu Yen, Tao Cheng
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2020.01029

Abnormal Food Timing Promotes Alcohol-Associated Dysbiosis and Colon Carcinogenesis Pathways
Cited by: 5
Author(s): Faraz Bishehsari, Shirin Moossavi, Phillip A. Engen, Xiaohan Liu, Yue Zhang
Software Mentions: 3
Published: about 6 years ago

10.1534/g3.117.042440

Transcriptional Profiling of Biofilm Regulators Identified by an Overexpression Screen in Saccharomyces cerevisiae
Cited by: 14
Author(s): Gareth A. Cromie, Zhihao Tan, Michelle Hays, Amy Sirr, Eric Jeffery, Andrew T. Dudley
Software Mentions: 3
Published: about 9 years ago

10.1534/g3.117.300318

Pas de deux: An Intricate Dance of Anther Smut and Its Host
Cited by: 5
Author(s): Su San Toh, Zehua Chen, Eric C. Rouchka, David J. Schultz, Christina A. Cuomo, Michael H. Perlin
Software Mentions: 3
Published: over 8 years ago

10.1534/g3.118.200910

Sex-Specific Co-expression Networks and Sex-Biased Gene Expression in the Salmonid Brook Charr Salvelinus fontinalis
Cited by: 18
Author(s): Ben J. G. Sutherland, Jenni M. Prokkola, Céline Audet, Louis Bernatchez
Software Mentions: 3
Published: over 7 years ago

10.1534/g3.118.201012

Global Shifts in Gene Expression Profiles Accompanied with Environmental Changes in Cnidarian-Dinoflagellate Endosymbiosis
Cited by: 8
Author(s): Yuu Ishii, Shinichiro Maruyama, Hiroshi Takahashi, Yoko Aihara, Takeshi Yamaguchi, Katsushi Yamaguchi, Shuji Shigenobu, Masakado Kawata, Naoto Ueno, Jun Minagawa
Software Mentions: 3
Published: about 7 years ago

10.1534/g3.119.400340

Differentially and Co-expressed Genes in Embryo, Germ-Line and Somatic Tissues ofTribolium castaneum
Cited by: 8
Author(s): Sher Afzal Khan, Heather Eggleston, K.M. Myles, Zach N. Adelman
Software Mentions: 3
Published: about 7 years ago

10.1534/g3.119.400365

Evolutionary and Experimental Loss of Gene Body Methylation and Its Consequence to Gene Expression
Cited by: 38
Author(s): Adam J. Bewick, Yinwen Zhang, Jered M. Wendte, Xiaoyu Zhang, Robert J. Schmitz
Software Mentions: 3
Published: about 7 years ago

10.1534/g3.120.401188

MYCs and PIFs Act Independently in Arabidopsis Growth Regulation
Cited by: 6
Author(s): Chunmei Li, Kazunari Nozue, Julin Maloof
Software Mentions: 3
Published: over 6 years ago

10.1534/g3.120.401516

Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus
Cited by: 20
Author(s): Javier F. Tabima, Ian A. Trautman, Ying Chang, Yan Wang, Stephen J. Mondo, Alan Kuo, Asaf Salamov, Igor V. Grigoriev, Jason E. Stajich, Joseph W. Spatafora
Software Mentions: 3
Published: almost 6 years ago

10.3390/genes8100257

Hybrid Sequencing of Full-Length cDNA Transcripts of Stems and Leaves in Dendrobium officinale
Cited by: 18
Author(s): Li He, Shuhua Fu, Zhichao Xu, Jun Yan, Jiang Xu, Hong Zhou, Jianguo Zhou, Xinlian Chen, Ying Liu, Kin Fai Au, Hui Yao
Software Mentions: 3
Published: almost 9 years ago

10.3390/genes8120357

Non-Additive Transcriptomic Responses to Inoculation with Rhizobia in a Young Allopolyploid Compared with Its Diploid Progenitors
Cited by: 6
Author(s): Adrian F. Powell, Jeff J. Doyle
Software Mentions: 3
Published: over 8 years ago

10.3390/genes8120383

Differential Expression of Serum MicroRNAs Supports CD4+ T Cell Differentiation into Th2/Th17 Cells in Severe Equine Asthma
Cited by: 33
Author(s): Alicja Pacholewska, Matthias Kraft, Vinzenz Gerber, Vidhya Jagannathan
Software Mentions: 3
Published: over 8 years ago

10.3390/genes9060294

Tissue Specificity and Dynamics of Sex-Biased Gene Expression in a Common Frog Population with Differentiated, Yet Homomorphic, Sex Chromosomes
Cited by: 22
Author(s): Wen‐Juan Ma, Paris Veltsos, Melissa A. Toups, Nicolas Rodrigues, Roberto Sermier, Daniel L. Jeffries, Nicolas Perrin
Software Mentions: 3
Published: about 8 years ago

10.3390/genes9060269

Landscape of Transposable Elements Focusing on the B Chromosome of the Cichlid Fish Astatotilapia latifasciata
Cited by: 29
Author(s): Rafael Luiz Buogo Coan, Cesar Martins
Software Mentions: 3
Published: over 8 years ago

10.3390/genes10020074

Macrophages from Susceptible and Resistant Chicken Lines have Different Transcriptomes following Marek’s Disease Virus Infection
Cited by: 17
Author(s): Pankaj Chakraborty, Richard Kuo, Lonneke Vervelde, Bernadette M. Dutia, Pete Kaiser, Jacqueline Smith
Software Mentions: 3
Published: over 7 years ago

10.3390/genes10050348

Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver
Cited by: 6
Author(s): Yu Luan, Lu Zhang, Mingyang Hu, Yongming Xu, Ye Hou, Xinyun Li, Zhao Song, Yi‐Fang Zhao, Changchun Li
Software Mentions: 3
Published: over 7 years ago

10.3390/genes10070515

The Farmed Atlantic Salmon (Salmo salar) Skin–Mucus Proteome and Its Nutrient Potential for the Resident Bacterial Community
Cited by: 25
Author(s): Giusi Minniti, Simen Rød Sandve, János Tamás Padra, Live Heldal Hagen, Sara K. Lindén, Phillip B. Pope, Magnus Ø. Arntzen, Gustav Vaaje‐Kolstad
Software Mentions: 3
Published: about 7 years ago

10.3390/genes10080606

Transcriptomic Analysis of the Influence of Methanol Assimilation on the Gene Expression in the Recombinant Pichia pastoris Producing Hirudin Variant 3
Cited by: 8
Author(s): Tao Li, Jian-Gang Ma, Zehua Xu, Shuang Wang, Nan Wang, Shulin Shao, Wei Yang, Lin Huang, Yihan Liu
Software Mentions: 3
Published: about 7 years ago

10.3390/genes10100795

Identification of Long Non-Coding RNA-Associated Competing Endogenous RNA Network in the Differentiation of Chicken Preadipocytes
Cited by: 21
Author(s): Lan Chen, Tao Zhang, Shanshan Zhang, Jen‐Wei Huang, Genxi Zhang, Kaizhou Xie, Jinyu Wang, Haiqing Wang, Guojun Dai
Software Mentions: 3
Published: almost 7 years ago

10.3390/genes10110946

Coding and Non-Coding RNA Abnormalities in Bipolar Disorder
Cited by: 22
Author(s): Jurjen J. Luykx, Fabrizio Giuliani, Giuliano Giuliani, Jan H. Veldink
Software Mentions: 3
Published: almost 7 years ago

10.3390/genes11030324

Genome-Wide Transcriptomic Analysis Reveals a Regulatory Network of Oxidative Stress-Induced Flowering Signals Produced in Litchi Leaves
Cited by: 8
Author(s): Xingyu Lu, Shanlin Yu, Peitao Lü, Houbin Chen, Silin Zhong, Biyan Zhou
Software Mentions: 3
Published: over 6 years ago

10.3390/genes11070787

Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System
Cited by: 11
Author(s): Cécile Fruchard, Hélène Badouin, David Latrasse, Ravi Suresh Devani, Aline Muyle, Bénédicte Rhoné, Susanne S. Renner, Anjan K. Banerjee, Abdelhafid Bendahmane, Gabriel Marais
Software Mentions: 3
Published: about 6 years ago

10.1111/imm.13341

Modified recombinant human IgG1‐Fc is superior to natural intravenous immunoglobulin at inhibiting immune‐mediated demyelination
Cited by: 1
Author(s): Christine Baksmeier, Patricia A. Blundell, Julia Steckel, Verena Schultz, Quan Gu, Ana da Silva Filipe, Alain Kohl, Chris Linnington, Dongli Lu, Anne Dell, Stuart M. Haslam, Jiabin Wang, Dan Czajkowsky, Norbert Goebels, Richard J. Pleass
Software Mentions: 3
Published: over 5 years ago

10.1093/insilicoplants/diaa005

Within- and cross-species predictions of plant specialized metabolism genes using transfer learning
Cited by: 7
Author(s): Bethany M. Moore, Peipei Wang, Pengxiang Fan, Aaron Lee, Bryan J. Leong, Yann‐Ru Lou, Craig A. Schenck, Koh‐ichi Sugimoto, Melissa D. Lehti-Shiu, Cornelius S. Barry, Shin-Han Shiu
Software Mentions: 3
Published: over 6 years ago

10.3390/insects11110820

Transcriptomics-Based Approach Identifies Spinosad-Associated Targets in the Colorado Potato Beetle, Leptinotarsa decemlineata
Cited by: 10
Author(s): Pierre Bastarache, Gabriel Wajnberg, Pascal Dumas, Simi Chacko, Jacynthe Lacroix, Nicolas Crapoulet, Chandra E. Moffat, Pier Jr Morin
Software Mentions: 3
Published: almost 6 years ago

10.1172/jci.insight.141690

Aging imparts cell-autonomous dysfunction to regulatory T cells during recovery from influenza pneumonia
Cited by: 20
Author(s): Luisa Morales‐Nebreda, Kathryn A. Helmin, Manuel A. Torres Acosta, Nikolay S. Markov, Jennifer Yuan Shih Hu, Anthony M. Joudi, Raul Piseaux‐Aillon, Hiam Abdala‐Valencia, Yuliya Politanska, Benjamin D. Singer
Software Mentions: 3
Published: over 5 years ago

10.1172/jci.insight.147929

Adipocyte-like signature in ovarian cancer minimal residual disease identifies metabolic vulnerabilities of tumor initiating cells
Cited by: 2
Author(s): Mara Artibani, Kenta Masuda, Zhiyuan Hu, Pascal C. Rauher, Garry Mallett, Nina Wietek, Matteo Morotti, Kay Y. Chong, Mohammad KaramiNejadRanjbar, Christos E. Zois, Sunanda Dhar, Salma El-Sahhar, Leticia Campo, Sarah P. Blagden, Stephen Damato, Pubudu Pathiraja, Shibani Nicum, Fergus Gleeson, A Laios, Abdulkhaliq Alsaadi, Laura Santana González, Takeshi Motohara, Ashwag Albukhari, Zhen Lü, Robert C. Bast, Adrian L. Harris, Christer S. Ejsing, Robin W. Klemm, Christopher Yau, Tatjana Sauka‐Spengler, Ashfaq Ahmed
Software Mentions: 3
Published: over 5 years ago

10.1172/jci.insight.145607

A surgical method for continuous intraportal infusion of gut microbial metabolites in mice
Cited by: 5
Author(s): Danny Orabi, Lucas J Osborn, Kevin Fung, William Massey, Anthony Horak, Federico Aucejo, Ibrahim Choucair, Beckey DeLucia, Zeneng Wang, Jan Claesen, J. Mark Brown
Software Mentions: 3
Published: over 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568