bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-85669-6

Transcriptome of rhesus macaque (Macaca mulatta) exposed to total-body irradiation
Cited by: 12
Author(s): Yaoxiang Li, Jatinder Singh, Rency S. Varghese, Yubo Zhang, Oluseyi O. Fatanmi, Amrita K. Cheema, Vijay K. Singh
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-021-01037-6

When your host shuts down: larval diapause impacts host-microbiome interactions in Nasonia vitripennis
Cited by: 15
Author(s): Jessica Dittmer, Robert M. Brucker
Software Mentions: 5
Published: over 5 years ago

10.18632/oncotarget.23344

APOBEC-mediated mutagenesis in urothelial carcinoma is associated with improved survival, mutations in DNA damage response genes, and immune response
Cited by: 83
Author(s): Alexander Glaser, Damiano Fantini, Yiduo Wang, Yu Yu, Kalen Rimar, Joseph R. Podojil, Stephen D. Miller, Joshua J. Meeks
Software Mentions: 5
Published: almost 9 years ago

10.1186/1471-2164-14-230

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro
Cited by: 39
Author(s): Nicolas C. Nalpas, Stephen D. E. Park, David A. Magee, Maria Taraktsoglou, John A. Browne, Kevin M. Conlon, Kévin Rue-Albrecht, Kate E. Killick, Karsten Hokamp, Amanda J. Lohan, Brendan J. Loftus, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 5
Published: over 13 years ago

10.1371/journal.pbio.3000877

High-throughput mapping of the phage resistance landscape in E. coli
Cited by: 82
Author(s): Vivek K. Mutalik, Benjamin A. Adler, Harneet S. Rishi, Denish Piya, Crystal Zhong, Britt Koskella, Elizabeth Kutter, Richard Calendar, Pavel S. Novichkov, Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin
Software Mentions: 5
Published: about 6 years ago

10.1002/mbo3.1146

Deeper below the surface—transcriptional changes in selected genes of Clostridium beijerinckii in response to butanol shock
Cited by: 5
Author(s): Petra Patáková, Jan Kolek, Katerina Jureckova, Barbora Branská, Karel Sedlář, Maryna Vasylkivska, Ivo Provazník
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-020-60015-4

Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis
Cited by: 62
Author(s): Perrine Soret, Louise-Eva Vandenborght, F Francis, Noémie Coron, Raphaël Enaud, Marta Avalos, Thierry Schaeverbeke, Patrick Berger, Michaël Fayon, Rodolphe Thiébaut, Laurence Delhaès, Magali Chabé, Christophe Audebert, Isabelle Durand-Joly, Amale Boldron, Isabelle Pin, Odile Cognet, H Pelloux, A. Prévotat, B. Wallaert, N. Wizla, C. Thumerelle, Dominique Turck
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-015-0734-x

Errors in RNA-Seq quantification affect genes of relevance to human disease
Cited by: 128
Author(s): Christelle Robert, Michael Watson
Software Mentions: 5
Published: about 11 years ago

10.1371/journal.pone.0227303

Transcriptome analysis of Actinidia chinensis in response to Botryosphaeria dothidea infection
Cited by: 8
Author(s): Yuanxiu Wang, Guihong Xiong, Zhe He, Mingfeng Yan, M. Q. Zou, Junxi Jiang
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12864-020-07228-z

Differential gene expression analysis reveals pathways important in early post-traumatic osteoarthritis in an equine model
Cited by: 6
Author(s): Annette M. McCoy, Ann M. Kemper, M. Boyce, M. P. Brown, Troy N. Trumble
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-018-23195-8

Personalised drug repositioning for Clear Cell Renal Cell Carcinoma using gene expression
Cited by: 13
Author(s): Karel K.M. Koudijs, Anton G.T. Terwisscha van Scheltinga, Stefan Böhringer, Kirsten J. M. Schimmel, Henk‐Jan Guchelaar
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-019-44962-1

The human tubal lavage proteome reveals biological processes that may govern the pathology of hydrosalpinx
Cited by: 8
Author(s): Elizabeth Yohannes, Avedis Kazanjian, Morgan E. Lindsay, Dennis T. Fujii, Nicholas Ieronimakis, Gregory E. Chow, Ronald D. Beesley, Ryan J. Heitmann, Richard O. Burney
Software Mentions: 5
Published: over 7 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

10.1371/journal.pone.0252685

Expanded transcriptomic view of strawberry fruit ripening through meta-analysis
Cited by: 0
Author(s): Gibum Yi, Hosub Shin, Kyeonglim Min, Eun Jin Lee
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0119027

Comparative Transcriptome Analysis of Anthurium “Albama” and Its Anthocyanin-Loss Mutant
Cited by: 17
Author(s): Zhiying Li, Jiabin Wang, Xuequan Zhang, Li Xu
Software Mentions: 5
Published: over 11 years ago

10.1038/s41598-021-86544-0

An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
Cited by: 5
Author(s): Gabriel Jiménez-Domínguez, Patrice Ravel, Stéphan Jalaguier, Vincent Cavaillès, Jacques Colinge
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-019-45515-2

Open chromatin dynamics in prosensory cells of the embryonic mouse cochlea
Cited by: 13
Author(s): Brent A. Wilkerson, Alex Chitsazan, Leah S. VandenBosch, Matthew S. Wilken, Thomas A. Reh, Olivia Bermingham‐McDonogh
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-018-22734-7

Transcriptional landscape of human endogenous retroviruses (HERVs) and other repetitive elements in psoriatic skin
Cited by: 11
Author(s): Freddy Lättekivi, Sulev Kõks, Maris Keermann, Ene Reimann, Ele Prans, Kristi Abram, Helgi Silm, Gea Kõks, Külli Kingo
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-017-14595-3

UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq
Cited by: 27
Author(s): Zhifu Sun, Asha Nair, Xianfeng Chen, Naresh Prodduturi, Junwen Wang, Jean Pierre A. Kocher
Software Mentions: 5
Published: about 9 years ago

10.3389/fpls.2020.00132

Developmental Analysis of Mimulus Seed Transcriptomes Reveals Functional Gene Expression Clusters and Four Imprinted, Endosperm-Expressed Genes
Cited by: 9
Author(s): Miguel A. Flores‐Vergara, Elen Oneal, Mário Costa, Gonzalo H. Villarino, Caitlyn Roberts, María Angels de Luis Balaguer, Sı́lvia Coimbra, John H. Willis, Robert G. Franks
Software Mentions: 5
Published: over 6 years ago

10.3390/metabo10020066

EFMviz: A COBRA Toolbox Extension to Visualize Elementary Flux Modes in Genome-Scale Metabolic Models
Cited by: 6
Author(s): Chaitra Sarathy, Martina Kutmon, Michael Lenz, Michiel E. Adriaens, Chris T. Evelo, Ilja C. W. Arts
Software Mentions: 5
Published: over 6 years ago

10.1038/srep46156

Integrated host and viral transcriptome analyses reveal pathology and inflammatory response mechanisms to ALV-J injection in SPF chickens
Cited by: 18
Author(s): Xi Lan, Yan Wang, Kai Tian, Fei Ye, Huadong Yin, Xiaoling Zhao, Hengyong Xu, Yong Huang, Haibo Li, John Hsieh, Susan J. Lamont, Qing Zhu
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-017-08094-8

CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo
Cited by: 14
Author(s): D. Craig Ayre, Ian C. Chute, Andrew P. Joy, David A. Barnett, Andrew M. Hogan, Marc P. Grüll, Lourdes Peña‐Castillo, Andrew S. Lang, Stephen M. Lewis, Sherri L. Christian
Software Mentions: 5
Published: about 9 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

10.1093/jxb/eraa124

Transcriptomics in Erigeron canadensis reveals rapid photosynthetic and hormonal responses to auxin herbicide application
Cited by: 19
Author(s): Cara L. McCauley, Scott A. M. McAdam, Ketaki P. Bhide, Jyothi Thimmapuram, Jo Ann Banks, Bryan G. Young
Software Mentions: 5
Published: over 6 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/fneur.2019.00745

A Risk Classification System With Five-Gene for Survival Prediction of Glioblastoma Patients
Cited by: 26
Author(s): Yulin Wang, Xin Liu, Gefei Guan, Wenjin Zhao, Minghua Zhuang
Software Mentions: 5
Published: over 7 years ago

10.1038/srep46203

Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection
Cited by: 25
Author(s): Arun Kommadath, Hua Bao, Igseo Choi, James M. Reecy, James E. Koltes, Eric R. Fritz-Waters, Christopher J. Eisley, Jason R. Grant, R. Rowland, Christopher K. Tuggle, Jack C. M. Dekkers, Joan K. Lunney, Le Luo Guan, Paul Stothard, Graham Plastow
Software Mentions: 5
Published: over 9 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

10.1126/sciadv.abd7819

High-resolution 3D imaging uncovers organ-specific vascular control of tissue aging
Cited by: 54
Author(s): Junyu Chen, Unnikrishnan Sivan, Sin Lih Tan, Luciana Lippo, Jessica De Angelis, Rossella Labella, Amit Singh, Alexandros Chatzis, Stanley Cheuk, Mino Medhghalchi, Jesús Gil, Georg A. Holländer, Brian D. Marsden, R. J. P. Williams, Saravana K. Ramasamy, Anjali P. Kusumbe
Software Mentions: 5
Published: over 5 years ago

10.3389/fpls.2020.597589

Chloroplast Electron Chain, ROS Production, and Redox Homeostasis Are Modulated by COS-OGA Elicitation in Tomato (Solanum lycopersicum) Leaves
Cited by: 3
Author(s): Sophie Moreau, Géraldine van Aubel, Rekin’s Janky, Pierre Van Cutsem
Software Mentions: 5
Published: almost 6 years ago

10.1007/s00395-021-00887-3

LncRNA LncHrt preserves cardiac metabolic homeostasis and heart function by modulating the LKB1-AMPK signaling pathway
Cited by: 24
Author(s): Ning Liu, Masaharu Kataoka, Yingchao Wang, Linbin Pu, Xiaoxuan Dong, Xuyang Fu, Feng Zhang, Feng Gao, Tian Liang, Jianqiu Pei, Changchen Xiao, Qiongzi Qiu, TingTing Hong, Qiming Chen, Jing Zhao, Long‐Guan Zhu, Junhua He, Xiaoyun Hu, Yu Nie, Wei Zhu, Hong Yu, Douglas B. Cowan, Xinyang Hu, Jianan Wang, Dazhi Wang, Jinghai Chen
Software Mentions: 5
Published: about 5 years ago

10.1073/pnas.2005330117

Nuclear receptor REVERBα is a state-dependent regulator of liver energy metabolism
Cited by: 31
Author(s): Louise Hunter, Charlotte E Pelekanou, Antony Adamson, Polly Downton, Nichola J Barron, Thomas Cornfield, Toryn Poolman, Neil Humphreys, Peter Cunningham, Leanne Hodson, A. S. I. Loudon, Mudassar Iqbal, David A. Bechtold, David Ray
Software Mentions: 5
Published: about 6 years ago

10.1155/2020/3817573

Diet Modifies Pioglitazone’s Influence on Hepatic PPARγ-Regulated Mitochondrial Gene Expression
Cited by: 5
Author(s): Sakil Kulkarni, Jiansheng Huang, Eric Tycksen, Paul Cliften, David A. Rudnick
Software Mentions: 5
Published: about 6 years ago

10.1155/2021/6642939

Identification of a Potential PPAR-Related Multigene Signature Predicting Prognosis of Patients with Hepatocellular Carcinoma
Cited by: 7
Author(s): Wenfang Xu, Zhe Chen, Gang Liu, Yong Dai, Xuanfu Xu, Duan Ma, Lei Liu
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.ppat.1008986

Qualitative Differences Between the IFNα subtypes and IFNβ Influence Chronic Mucosal HIV-1 Pathogenesis
Cited by: 21
Author(s): Kejun Guo, Guannan Shen, Jon Kibbie, Tanía González, Stephanie M. Dillon, Harry A. Smith, Emily Cooper, Kerry J. Lavender, Kim J. Hasenkrug, Kathrin Sutter, Ulf Dittmer, Miranda Kroehl, Katerina Kechris, Cara C. Wilson, Mario L. Santiago
Software Mentions: 5
Published: about 6 years ago

10.1186/s13293-021-00368-1

Hepatic steatosis and steatohepatitis: a functional meta-analysis of sex-based differences in transcriptomic studies
Cited by: 16
Author(s): José F. Català-Senent, Marta R. Hidalgo, Marina Berenguer, Gopanandan Parthasarathy, Harmeet Malhi, Pablo Malmierca-Merlo, María de la Iglesia-Vayá, Francisco García‐García
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2019.00766

Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data
Cited by: 30
Author(s): Sharmin Akter, Dong Xu, Susan C. Nagel, John J. Bromfield, Katherine E. Pelch, Gilbert B Wilshire, Trupti Joshi
Software Mentions: 5
Published: about 7 years ago

10.1080/21655979.2020.1862527

The underlying molecular mechanism and identification of transcription factor markers for laryngeal squamous cell carcinoma
Cited by: 8
Author(s): Bin-Yu Mo, Guosheng Li, Su-Hua Huang, Wei-Ying He, Lu Xie, Zhu‐Xin Wei, Ya-Si Su, Liang Yue, Li Yang, Ya Cheng, Wei Dai, Run Lin
Software Mentions: 5
Published: almost 6 years ago

10.3389/fnins.2020.607215

Unraveling Targetable Systemic and Cell-Type-Specific Molecular Phenotypes of Alzheimer’s and Parkinson’s Brains With Digital Cytometry
Cited by: 5
Author(s): Marie Catherine Bordone, Nuno L. Barbosa‐Morais
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.60100

Sequential perturbations to mouse corticogenesis following in utero maternal immune activation
Cited by: 15
Author(s): Cesar P Canales, Myka L. Estes, Karol Cichewicz, Kartik Angara, John Paul Aboubechara, Scott A. Cameron, Kathryn Prendergast, Linda Su-Feher, Iva Zdilar, Ellie J Kreun, Emma C Connolly, Jin Myeong Seo, Jack B Goon, Kathleen Farrelly, Tyler W. Stradleigh, Deborah van der List, Lori Haapanen, Judy Van de Water, Daniel Vogt, A. Kimberley McAllister, A. Nord
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0153932

Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis
Cited by: 24
Author(s): Randy J. Hempel, John P. Bannantine, Judith R. Stabel
Software Mentions: 5
Published: over 10 years ago

10.1073/pnas.1822046116

Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination
Cited by: 47
Author(s): Diógenes Saulo de Lima, Lucas Esteves Cardozo, Vinicius Maracaja‐Coutinho, Andreas Suhrbier, Karim Mane, David Jeffries, Eduardo Lani Volpe da Silveira, Paulo Amaral, Rino Rappuoli, Thushan I. de Silva, Helder I. Nakaya
Software Mentions: 5
Published: about 7 years ago

10.1098/rsos.200792

Tissue-specific developmental regulation and isoform usage underlie the role ofdoublesexin sex differentiation and mimicry inPapilioswallowtails
Cited by: 13
Author(s): Riddhi Deshmukh, Dhanashree Lakhe, Krushnamegh Kunte
Software Mentions: 5
Published: about 6 years ago

10.3389/fnmol.2018.00481

Common CHD8 Genomic Targets Contrast With Model-Specific Transcriptional Impacts of CHD8 Haploinsufficiency
Cited by: 30
Author(s): A. Ayanna Wade, Kenneth J. Lim, Rinaldo Catta-Preta, Alexander Nord
Software Mentions: 5
Published: almost 8 years ago

10.3389/fnins.2018.00136

Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids
Cited by: 4
Author(s): Sofie Derycke, Loïc Kéver, Koen Herten, Koen Van Den Berge, Maarten Van Steenberge, Jeroen Van Houdt, Lieven Clement, Pascal Poncin, Éric Parmentier, Erik Verheyen
Software Mentions: 5
Published: over 8 years ago

10.1177/1177932219860817

Accurate Classification of Differential Expression Patterns in a Bayesian Framework With Robust Normalization for Multi-Group RNA-Seq Count Data
Cited by: 10
Author(s): Takayuki Osabe, Kentaro Shimizu, Koji Kadota
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-021-90797-0

Targeting of the CD80/86 proinflammatory axis as a therapeutic strategy to prevent severe COVID-19
Cited by: 9
Author(s): Antonio Julià, Irene Bonafonte-Pardàs, Antonio Gómez, María López-Lasanta, Mireia López-Corbeto, Sergio H Martínez-Mateu, Jordi Lladós, Iván Rodríguez-Nunez, R Myers, Sara Marsal
Software Mentions: 5
Published: over 5 years ago

10.3389/fmolb.2021.689037

Analyzing and Validating the Prognostic Value of a TNF-Related Signature in Kidney Renal Clear Cell Carcinoma
Cited by: 5
Author(s): Wenhao Zhang, Chang-Jiu Li, Fanding Wu, Ning Li, Yuwei Wang, Yixuan Hu, Tiantian Fang, Yuan Hui, Honghua He
Software Mentions: 5
Published: over 5 years ago

10.1186/s12936-019-2659-4

A fast and cost-effective microsampling protocol incorporating reduced animal usage for time-series transcriptomics in rodent malaria parasites
Cited by: 7
Author(s): Abhinay Ramaprasad, Amit Kumar Subudhi, Richard Culleton, Arnab Pain
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-021-92610-4

Identification of biological pathway and process regulators using sparse partial least squares and triple-gene mutual interaction
Cited by: 2
Author(s): Jun-Yan Hong, T.D.C.P. Gunasekara, Cheng He, Sanzhen Liu, Jianqin Huang, Hairong Wei
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-93845-x

Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma
Cited by: 12
Author(s): Priyanka Banerjee, Premanand Balraj, Nilesh Sudhakar Ambhore, S.A. Wicher, Rodney D. Britt, Christina M. Pabelick, Y. S. Prakash, Venkatachalem Sathish
Software Mentions: 5
Published: over 5 years ago

10.3390/genes12030385

Maternal Vitamin and Mineral Supplementation and Rate of Maternal Weight Gain Affects Placental Expression of Energy Metabolism and Transport-Related Genes
Cited by: 25
Author(s): Wellison J. S. Diniz, Lawrence P. Reynolds, P. P. Borowicz, Alison K Ward, Kevin K. Sedivec, Kacie L McCarthy, Cierrah J Kassetas, Friederike Baumgaertner, James D Kirsch, Sheri T. Dorsam, Tammi L Neville, J Chris Forcherio, Ronald Scott, J. S. Caton, Carl R Dahlen
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-93863-9

MYCN-induced nucleolar stress drives an early senescence-like transcriptional program in hTERT-immortalized RPE cells
Cited by: 6
Author(s): Sofia Zanotti, Suzanne Vanhauwaert, Christophe Van Neste, Volodimir Olexiouk, Jolien Van Laere, Marlies Verschuuren, Joni Van der Meulen, Liselot Mus, Kaat Durinck, Laurentijn Tilleman, Dieter Deforce, Filip Van Nieuwerburgh, Michael D. Hogarty, Bieke Decaesteker, Winnok H. De Vos, Frank Speleman
Software Mentions: 5
Published: over 5 years ago

10.3389/fnins.2019.00002

A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks
Cited by: 51
Author(s): Shradha Mukherjee, Christine Klaus, Mihaela Pricop-Jeckstadt, Jeremy A. Miller, Felix L Struebing
Software Mentions: 5
Published: almost 8 years ago

10.1172/JCI91363

The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes
Cited by: 70
Author(s): Bon Ham Yip, Violetta Steeples, Emmanouela Repapi, Richard N. Armstrong, Miriam Llorian, S. Roy, Jacqueline Shaw, Hamid Dolatshad, Stephen Taylor, Amit Verma, Matthias Bartenstein, Paresh Vyas, Nicholas C. P. Cross, Luca Malcovati, Mario Cazzola, Eva Hellström‐Lindberg, Seishi Ogawa, Christopher W.J. Smith, Andrea Pellagatti, Jacqueline Boultwood
Software Mentions: 5
Published: over 9 years ago

10.3390/jcm9092730

Metastatic Burden Defines Clinically and Biologically Distinct Subgroups of Stage 4 High-Risk Neuroblastoma
Cited by: 2
Author(s): Eun Seop Seo, Eun-Jin Lee, Boram Lee, Min Jae Shin, Young-Seok Cho, Hee Young Ju, Hee Won Cho, Hee Young Ju, Keon Hee Yoo, Hong Hoe Koo, Ji Won Lee, Ki Woong Sung
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-017-14942-4

Genome-wide profiling of nardilysin target genes reveals its role in epigenetic regulation and cell cycle progression
Cited by: 6
Author(s): Yusuke Morita, Mikiko Ohno, Kiyoto Nishi, Yutaka Hiraoka, Sayaka Saijo, Shintaro Matsuda, Toru Kita, Takeshi Kimura, Eiichiro Nishi
Software Mentions: 5
Published: about 9 years ago

10.1038/s41598-017-09335-6

Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis
Cited by: 85
Author(s): Julia Steinberg, Graham R. S. Ritchie, Theodoros I. Roumeliotis, Raveen L Jayasuriya, Matthew Clark, Roger A. Brooks, Abbie L. A. Binch, Karan M. Shah, Rachael Coyle, Mercedes Pardo, Christine Le Maitre, Yolande F M Ramos, Rob G H H Nelissen, Ingrid Meulenbelt, Andrew W. McCaskie, Jyoti S. Choudhary, J. Mark Wilkinson, Eleftheria Zeggini
Software Mentions: 5
Published: about 9 years ago

10.1111/jcmm.16799

Comprehensive characterization of pathological stage‐related genes of papillary thyroid cancer along with survival prediction
Cited by: 1
Author(s): Lei Xu, Liang Feng, Haiyan Li, Menglong Li, Yongmei Xie, Zhihui Li, Yanzhi Guo
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.65574

KLF10 integrates circadian timing and sugar signaling to coordinate hepatic metabolism
Cited by: 16
Author(s): Anthony A Ruberto, Aline Gréchez-Cassiau, Sabrina Guérin, Luc Martin, Johana S. Revel, Mohamed Mehiri, Malayannan Subramaniam, Franck Delaunay, Michèle Teboul
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pcbi.1006794

A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory
Cited by: 7
Author(s): Rodoniki Athanasiadou, Benjamin Neymotin, Nathan Brandt, Wei Wang, Lionel Christiaen, David Gresham, Daniel Tranchina
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pcbi.1002887

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling
Cited by: 46
Author(s): S. Huang, David Clarke, Sara J.C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger, Ernest Fraenkel
Software Mentions: 5
Published: over 13 years ago

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

10.1002/jcp.28522

Comprehensive analysis of a ceRNA network reveals potential prognostic cytoplasmic lncRNAs involved in HCC progression
Cited by: 84
Author(s): Yi Bai, Junyu Long, Zhisong Liu, Jianzhen Lin, Hanchan Huang, Dongxu Wang, Yang Xu, Fei Miao, Yilei Mao, Xinting Sang, Hong Zhao
Software Mentions: 5
Published: over 7 years ago

10.1186/s12934-015-0226-4

An analysis of the changes in soluble hydrogenase and global gene expression in Cupriavidus necator (Ralstonia eutropha) H16 grown in heterotrophic diauxic batch culture
Cited by: 17
Author(s): Bat-Erdene Jugder, Zhiliang Chen, Darren Tan Tek Ping, Hélène Lebhar, Jeffrey Welch, Christopher P. Marquis
Software Mentions: 5
Published: over 11 years ago

10.3390/cells8080919

The Combination of IFN β and TNF Induces an Antiviral and Immunoregulatory Program via Non-Canonical Pathways Involving STAT2 and IRF9
Cited by: 11
Author(s): Mélissa K. Mariani, Pouria Dasmeh, Audray Fortin, Élise Caron, Mario Kalamujic, Alexander N. Harrison, Diana Ioana Hotea, Dacquin M. Kasumba, Sandra Cervantes-Ortiz, Espérance Mukawera, Adrian W.R. Serohijos, Nathalie Grandvaux
Software Mentions: 5
Published: about 7 years ago

10.3390/biology9090251

Differential Expression and miRNA–Gene Interactions in Early and Late Mild Cognitive Impairment
Cited by: 20
Author(s): Leonardo Miranda Brito, Ândrea Ribeiro-dos-Santos, Amanda Ferreira Vidal, Gilderlanio Santana de Araújo
Software Mentions: 5
Published: about 6 years ago

10.1186/s12967-020-02233-y

IRGS: an immune-related gene classifier for lung adenocarcinoma prognosis
Cited by: 22
Author(s): Xiaoshun Shi, Ruidong Li, Xiaoying Dong, Allen M. Chen, Xiguang Liu, Di Lu, Siyang Feng, He Wang, Kaican Cai
Software Mentions: 5
Published: over 6 years ago

10.1186/s13148-020-00879-5

G9a regulates tumorigenicity and stemness through genome-wide DNA methylation reprogramming in non-small cell lung cancer
Cited by: 25
Author(s): Rajendra P. Pangeni, Lu Yang, Keqiang Zhang, Jinhui Wang, Wendong Li, Chao Guo, Xinwei Yun, Ting Sun, Jami Wang, Dan J. Raz
Software Mentions: 5
Published: over 6 years ago

10.1093/molbev/msaa110

Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum
Cited by: 10
Author(s): Rosa Fernández, Marina Marcet‐Houben, Fabrice Legeai, Gautier Richard, Stéphanie Robin, Valentin Wucher, Cinta Pegueroles, Toni Gabaldón, Denis Tagu
Software Mentions: 5
Published: over 6 years ago

10.3389/fimmu.2019.00330

Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression
Cited by: 37
Author(s): Florian Kirchner, Katharina Littringer, Simon Altmeier, Van Du T. Tran, Franziska Annett Schönherr, Christina Braunsdorf, Marco Pagni, Dominique Sanglard, Nicole Joller, Salomé LeibundGut‐Landmann
Software Mentions: 5
Published: over 7 years ago

10.18632/oncotarget.25330

Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma
Cited by: 14
Author(s): Michael Hamilton, Thomas Girke, Ernest Martinez
Software Mentions: 5
Published: over 8 years ago

10.1186/s13029-017-0063-4

DEApp: an interactive web interface for differential expression analysis of next generation sequence data
Cited by: 63
Author(s): Yan Li, Jorge Andrade
Software Mentions: 5
Published: almost 10 years ago

10.1186/s40064-016-2743-y

Identification of differentially expressed genes implicated in peel color (red and green) of Dimocarpus confinis
Cited by: 9
Author(s): Jun Fan, Xiuping Chen, Wen-shun Hu, Shaoquan Zheng
Software Mentions: 5
Published: over 10 years ago

10.1186/s12967-018-1707-0

Evaluation of the prognostic value of paraoxonase 1 in the recurrence and metastasis of hepatocellular carcinoma and establishment of a liver-specific predictive model of survival
Cited by: 18
Author(s): Zhenzhen Yu, Qifeng Ou, Chongxi Fan, Jiong Bi, Wen Li, Jiachi Ma, Rongchang Wang, Xiaohui Huang
Software Mentions: 5
Published: almost 8 years ago

10.1186/s12931-019-1085-z

Airway host-microbiome interactions in chronic obstructive pulmonary disease
Cited by: 82
Author(s): Zhang Wang, Barbara Maschera, Simon Lea, Umme Kolsum, David Michalovich, Stephanie Van Horn, Christopher Traini, James R. Brown, Edith M. Hessel, Dave Singh
Software Mentions: 5
Published: over 7 years ago

10.1093/bioinformatics/btv634

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes
Cited by: 54
Author(s): Sheida Nabavi, Daniel Schmolze, Mayinuer Maitituoheti, Sadhika Malladi, Andrew H. Beck
Software Mentions: 5
Published: about 11 years ago

10.1371/journal.pbio.3000481

Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias
Cited by: 45
Author(s): Shir Mandelboum, Zohar Manber, Orna Elroy‐Stein, Ran Elkon
Software Mentions: 5
Published: almost 7 years ago

10.3389/fgene.2015.00169

Identifying differential transcription factor binding in ChIP-seq
Cited by: 21
Author(s): Dai-Ying Wu, Danielle Bittencourt, Michael R. Stallcup, Kimberly D. Siegmund
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0103207

A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data
Cited by: 195
Author(s): Zong Hong Zhang, Dhanisha J. Jhaveri, Vikki M. Marshall, Denis C. Bauer, Janette Edson, Ramesh Narayanan, Gregory J. Robinson, Andreas E. Lundberg, Perry F. Bartlett, Naomi R. Wray, Qiongyi Zhao
Software Mentions: 5
Published: about 12 years ago

10.3389/fgene.2020.616998

Application of an Autophagy-Related Gene Prognostic Risk Model Based on TCGA Database in Cervical Cancer
Cited by: 16
Author(s): Huadi Shi, Fulan Zhong, Xiaoqiong Yi, Zhenyi Shi, Feiyan Ou, Zhonghua Xu, Yufang Zuo
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2020.00055

Establishment of a Prognostic Model Using Immune-Related Genes in Patients With Hepatocellular Carcinoma
Cited by: 14
Author(s): Wenjie Wang, Han Wang, Ting-yan Hua, Wei Song, Jie Zhu, Jingjing Wang, Yongzhen Huang, Zhi-Liang Ding
Software Mentions: 5
Published: over 6 years ago

10.3389/fphar.2020.599760

Modulation of the Gut Microbiota and Liver Transcriptome by Red Yeast Rice and Monascus Pigment Fermented by Purple Monascus SHM1105 in Rats Fed with a High-Fat Diet
Cited by: 10
Author(s): Hua Yang, Ronghua Pan, Jing Wang, Lizhong Zheng, Zhenjing Li, Qingbin Guo, Changlu Wang
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2021.663787

Integrated Analysis of Microarray and RNA-Seq Data for the Identification of Hub Genes and Networks Involved in the Pancreatic Cancer
Cited by: 10
Author(s): Maryum Nisar, Rehan Zafar Paracha, Iqra Arshad, Sidra Adil, Sabaoon Zeb, Rumeza Hanif, Mehak Rafiq, Zamir Hussain
Software Mentions: 5
Published: over 5 years ago

10.3389/fonc.2020.01088

MMP25 Regulates Immune Infiltration Level and Survival Outcome in Head and Neck Cancer Patients
Cited by: 8
Author(s): Yujie Liang, Chenyu Guan, Kan Li, Guanghui Zheng, Tao Wang, Sien Zhang, Guiqing Liao
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2021.634116

A Novel Six-mRNA Signature Predicts Survival of Patients With Glioblastoma Multiforme
Cited by: 8
Author(s): Zhentao Liu, Hao Zhang, Haitao Hu, Zengyu Cai, Chengyin Lu, Qiang Liang, Jun Qian, Chunhui Wang, Lei Jiang
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-68949-5

Capsidiol-related genes are highly expressed in response to Colletotrichum scovillei during Capsicum annuum fruit development stages
Cited by: 10
Author(s): Viviane Yumi Baba, Adrian F. Powell, Suzana Tiemi Ivamoto, Luiz Filipe Protásio Pereira, André Luís Laforga Vanzela, Renata Mussoi Giacomin, Susan R. Strickler, Lukas A. Mueller, Rosana Rodrigues, Leandro Simões Azeredo Gonçalves
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2021.648701

Multiomics Analysis Reveals Molecular Abnormalities in Granulosa Cells of Women With Polycystic Ovary Syndrome
Cited by: 14
Author(s): Ru-Song Zhao, Yonghui Jiang, Shigang Zhao, Han Zhao
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.625466

Zebrafish Chromosome 14 Gene Differential Expression in the fmr1hu2787 Model of Fragile X Syndrome
Cited by: 1
Author(s): Karissa Barthelson, Lachlan Baer, Yang Dong, Melanie L. Hand, Zac Pujic, Morgan Newman, Geoffrey J. Goodhill, Robert I. Richards, Stephen Pederson, Michael Lardelli
Software Mentions: 5
Published: over 5 years ago

10.3389/fonc.2020.01195

Multi-Omics Characterization of the 4T1 Murine Mammary Gland Tumor Model
Cited by: 82
Author(s): Barbara Schrörs, Sebastian Boegel, Christian Albrecht, Thomas Bukur, Valesca Bukur, Christoph Holtsträter, Christoph Ritzel, Katja Manninen, Arbel D. Tadmor, Mathias Vormehr, Uğur Şahin, Martin Löwer
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2018.00441

Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle
Cited by: 30
Author(s): Tassia M. Goncalves, Luciana Correia de Almeida Regitano, James E. Koltes, Aline Silva Mello Cesar, Sónia Cristina da Silva Andrade, Gérson Barreto Mourão, G. Gasparin, Gabriel Costa Monteiro Moreira, Eric R. Fritz-Waters, James M. Reecy
Software Mentions: 5
Published: about 8 years ago

10.3389/fgene.2021.730003

Identification of Autophagy Related circRNA-miRNA-mRNA-Subtypes Network With Radiotherapy Responses and Tumor Immune Microenvironment in Non-small Cell Lung Cancer
Cited by: 12
Author(s): Limin Fan, Baosheng Li, Li Zhao, Liang Sun
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2019.01207

Thermal Manipulation During Embryogenesis Impacts H3K4me3 and H3K27me3 Histone Marks in Chicken Hypothalamus
Cited by: 26
Author(s): Sarah-Anne David, Anaïs Vitorino Carvalho, Coralie Gimonnet, Aurélien Brionne, Christelle Hennequet-Antier, Benoît Piégu, Sabine Crochet, Nathalie Couroussé, Thierry Bordeau, Yves Bigot, Anne Collin, Vincent Coustham
Software Mentions: 5
Published: almost 7 years ago

10.1038/sdata.2018.290

Transcriptome profiling of a beach-adapted wild legume for dissecting novel mechanisms of salinity tolerance
Cited by: 5
Author(s): Hengyou Zhang, Christine Zuelsdorf, Darin S. Penneys, Shoujin Fan, Janice Kofsky, Bao‐Hua Song
Software Mentions: 5
Published: almost 8 years ago

10.1038/sdata.2018.136

A merged lung cancer transcriptome dataset for clinical predictive modeling
Cited by: 26
Author(s): Su Bin Lim, Swee Jin Tan, Wan-Teck Lim, Chwee Teck Lim
Software Mentions: 5
Published: over 8 years ago

10.3389/fonc.2021.626187

Dysregulation of Transcription Factor Networks Unveils Different Pathways in Human Papillomavirus 16-Positive Squamous Cell Carcinoma and Adenocarcinoma of the Uterine Cervix
Cited by: 9
Author(s): Saloê Bispo, Ticiana Della Justina Farias, Patrícia Savio de Araujo-Souza, Ricardo Cintra, Hellen Geremias dos Santos, Natasha Andressa Nogueira Jorge, Mauro A. A. Castro, Gabriel Wajnberg, Nicole de Miranda Scherer, Maria Luiza Nogueira Dias Genta, Jesus Paula Carvalho, Luísa Lina Villa, Laura Sichero, Fábio Passetti
Software Mentions: 5
Published: over 5 years ago

10.1038/sdata.2016.51

Comprehensive RNA-Seq profiling to evaluate lactating sheep mammary gland transcriptome
Cited by: 40
Author(s): Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Gwenola Tosser‐Klopp, J. J. Arranz
Software Mentions: 5
Published: over 10 years ago

10.3389/fonc.2021.640272

Identification of Novel Alternative Splicing Events Associated With Tumorigenesis, Protein Modification, and Immune Microenvironment in Early-Onset Gastric Cancer
Cited by: 4
Author(s): Jian Zhang, Ajay Goel, Lin Zhu
Software Mentions: 5
Published: over 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568