bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41438-021-00529-8

Chromatin accessibility and translational landscapes of tea plants under chilling stress
Cited by: 21
Author(s): Pengjie Wang, Shan Jin, Xuejin Chen, Lihua Wu, Yuanrun Zheng, Chuan Yue, Yan Guo, Xingtan Zhang, Jing Yang, Naixing Ye
Software Mentions: 5
Published: over 5 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

10.3389/fimmu.2019.01463

Contrasting Gene Expression Profiles of Monocytes and Lymphocytes From Peste-Des-Petits-Ruminants Virus Infected Goats
Cited by: 17
Author(s): Sajad A. Wani, Anamika Sahu, Raja Ishaq Nabi Khan, Awadh Bihari Pandey, Shikha Saxena, Neelima Hosamani, Waseem Akram Malla, Dheeraj Chaudhary, Sonam Kanchan, V. K. Sah, Kaushal Kishor Rajak, D. Muthuchelvan, Bina Mishra, Ashok Kumar Tiwari, Aditya Prasad Sahoo, Basavaraj Sajjanar, Yash Pal Singh, Ravi Kumar Gandham, Bishnu Prasad Mishra, Raj Kumar Singh
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0154531

Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq
Cited by: 63
Author(s): Shiva Marthandan, Mario Baumgart, Stefan Priebe, Marco Groth, Jonas Schaer, Christoph Kaether, Reinhard Guthke, Alessandro Cellerino, Matthias Platzer, Stephan Diekmann, Peter Hemmerich
Software Mentions: 5
Published: over 10 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/fimmu.2018.02055

Molecular and Cellular Response to Experimental Anisakis pegreffii (Nematoda, Anisakidae) Third-Stage Larval Infection in Rats
Cited by: 19
Author(s): Ivana Bušelić, Željka Trumbić, Jerko Hrabar, Anamarija Vrbatović, Ivana Bočina, Ivona Mladineo
Software Mentions: 5
Published: about 8 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

10.1038/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

10.3389/fimmu.2021.640837

Transcriptomic Analysis of Inflammatory Cardiomyopathy Identifies Molecular Signatures of Disease and Informs in silico Prediction of a Network-Based Rationale for Therapy
Cited by: 1
Author(s): Khushboo Singh, Hai Fang, Graham Davies, Benjamin Wright, Helen Lockstone, Richard O. Williams, Daniela Čiháková, Julian C. Knight, Shoumo Bhattacharya
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms22179228

SARS-CoV-2 Impairs Dendritic Cells and Regulates DC-SIGN Gene Expression in Tissues
Cited by: 13
Author(s): Guoshuai Cai, Mulong Du, Yohan Bossé, Helmut Albrecht, Fei Qin, Xizhi Luo, X Michelle Androulakis, Chao Cheng, Mitzi Nagarkatti, Mitzi Nagarkatti, David C. Christiani, Michael L. Whitfield, Christopher I. Amos, Feifei Xiao
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0197162

A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells
Cited by: 15
Author(s): Alexander Wolff, Michaela Bayerlová, Jochen Gaedcke, Dieter Kube, Tim Beißbarth
Software Mentions: 5
Published: over 8 years ago

10.3389/fimmu.2020.558036

The Novel Omega-6 Fatty Acid Docosapentaenoic Acid Positively Modulates Brain Innate Immune Response for Resolving Neuroinflammation at Early and Late Stages of Humanized APOE-Based Alzheimer's Disease Models
Cited by: 14
Author(s): Qiu-Lan Ma, Cansheng Zhu, Marco Morselli, Trent Su, Matteo Pelligrini, Zhengqi Lu, Mychica Jones, Paul Denver, Daniel Castro, Xiaohong Gu, Frances Relampagos, Kaitlin Caoili, Bruce Teter, Sally A. Frautschy, Gregory M. Cole
Software Mentions: 5
Published: about 6 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

10.3390/cancers12030702

STAT3 Mutation Is Associated with STAT3 Activation in CD30+ ALK− ALCL
Cited by: 16
Author(s): Emma Andersson, Oscar Brück, Till Braun, Susanna Mannisto, Leena Saikko, Sonja Lagström, Pekka Ellonen, Sirpa Leppä, Marco Herling, Panu E. Kovanen, Satu Mustjoki
Software Mentions: 5
Published: over 6 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

10.1038/s41598-017-11807-8

Genomic and transcriptomic analysis of the toluene degrading black yeast Cladophialophora immunda
Cited by: 36
Author(s): Barbara Blasi, Hakim Tafer, Christina Kustor, Caroline Poyntner, Ksenija Lopandić, Katja Sterflinger
Software Mentions: 5
Published: about 9 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

10.3390/ijms22042046

Dysregulated Provision of Oxidisable Substrates to the Mitochondria in ME/CFS Lymphoblasts
Cited by: 20
Author(s): Daniel Missailidis, Oana Sanislav, Claire Y. Allan, Paige K. Smith, Sarah J. Annesley, Paul R. Fisher
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0233077

Comparative transcriptomics of Diuraphis noxia and Schizaphis graminum fed wheat plants containing different aphid-resistance genes
Cited by: 2
Author(s): Lina Aguirre Rojas, Erin D. Scully, Laramy Enders, Alicia E. Timm, Deepak K. Sinha, C. Michael Smith
Software Mentions: 5
Published: over 6 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

10.1371/journal.pone.0167488

Cell-Based Systems Biology Analysis of Human AS03-Adjuvanted H5N1 Avian Influenza Vaccine Responses: A Phase I Randomized Controlled Trial
Cited by: 46
Author(s): Leigh M. Howard, Kristen L. Hoek, Johannes Goll, Parimal Samir, Allison C. Galassie, Tara M. Allos, Xinnan Niu, Laura E. Gordy, C. Buddy Creech, Nripesh Prasad, Travis L. Jensen, Heather Hill, Shawn Levy, Sebastian Joyce, Andrew J. Link, Kathryn M. Edwards
Software Mentions: 5
Published: almost 10 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

10.1038/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

10.3390/biology10010039

Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets
Cited by: 11
Author(s): Adeel Malik, Chang-Bae Kim
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41421-020-00214-5

Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progression
Cited by: 67
Author(s): Guohe Song, Yang Shi, Meiying Zhang, Shyamal Goswami, Saifullah Afridi, Ling Meng, Jiaqiang Ma, Yi Chen, Youpei Lin, Juan Zhang, Yuming Liu, Zijie Jin, Shenghong Yang, Dongning Rao, Shu Zhang, Aiwu Ke, Xiaoying Wang, Yang Cao, Jian Zhou, Jia Fan, Xiaoming Zhang, Ruibin Xi, Qiang Gao
Software Mentions: 5
Published: almost 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

10.1128/mSystems.00053-18

Balances: a New Perspective for Microbiome Analysis
Cited by: 173
Author(s): Javier Rivera Pinto, J. J. Egozcue, Vera Pawlowsky‐Glahn, Roger Paredes, Marc Noguera‐Julian, M. Luz Calle
Software Mentions: 5
Published: about 8 years ago

10.3390/cancers13092115

Chromatin-Directed Proteomics Identifies ZNF84 as a p53-Independent Regulator of p21 in Genotoxic Stress Response
Cited by: 8
Author(s): Anna Strzeszewska-Potyrała, Karolina Staniak, Joanna Czarnecka‐Herok, Mahmoud-Reza Rafiee, Marcin Herok, Grażyna Mosieniak, Jeroen Krijgsveld, Ewa Sikora
Software Mentions: 5
Published: over 5 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

10.1186/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

10.1038/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

10.1371/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/s41598-019-44962-1

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

10.1038/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/s41598-019-51379-3

Tissue- and Species-Specific Patterns of RNA metabolism in Post-Mortem Mammalian Retina and Retinal Pigment Epithelium
Cited by: 9
Author(s): Les Kallestad, Seth Blackshaw, Ahmad M. Khalil, Krzysztof Palczewski
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-019-57218-9

Immune gene signatures for predicting durable clinical benefit of anti-PD-1 immunotherapy in patients with non-small cell lung cancer
Cited by: 109
Author(s): Sohyun Hwang, Ah-Young Kwon, Jooyeon Jeong, Sewha Kim, Haeyoun Kang, Joon-Suk Park, Joo-Hang Kim, Ok Jin Han, Sun Min Lim, Hee Jung An
Software Mentions: 5
Published: almost 7 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

10.1371/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.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

10.3390/v13040553

Profile of Small RNAs, vDNA Forms and Viral Integrations in Late Chikungunya Virus Infection of Aedes albopictus Mosquitoes
Cited by: 11
Author(s): Michele Marconcini, Elisa Pischedda, Vincent Houé, Umberto Palatini, Nabor Lozada-Chávez, Davide Sogliani, Anna‐Bella Failloux, Mariangela Bonizzoni
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/s41419-021-03739-z

WNT/β-catenin-suppressed FTO expression increases m6A of c-Myc mRNA to promote tumor cell glycolysis and tumorigenesis
Cited by: 61
Author(s): Xueying Yang, Fei Shao, Dong Guo, Wei Wang, Juhong Wang, Rongxuan Zhu, Yibo Gao, Jie He, Zhimin Lu
Software Mentions: 5
Published: over 5 years ago

10.3390/v13061129

Evidence of Transcriptional Shutoff by Pathogenic Viral Haemorrhagic Septicaemia Virus in Rainbow Trout
Cited by: 4
Author(s): Irene Cano, Eduarda M. Santos, Karen Moore, Audrey Farbos, Ronny van Aerle
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pntd.0002905

Dual RNA-seq of Parasite and Host Reveals Gene Expression Dynamics during Filarial Worm–Mosquito Interactions
Cited by: 59
Author(s): Young Jun Choi, Matthew T. Aliota, George F. Mayhew, Sara M. Erickson, Bruce M. Christensen
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pntd.0003853

The Epigenome of Schistosoma mansoni Provides Insight about How Cercariae Poise Transcription until Infection
Cited by: 46
Author(s): David Roquis, Julie M. J. Lepesant, Marion Picard, Michael Freitag, Hugues Parrinello, Marco Groth, Rémi Emans, Céline Cosseau, Christoph Grunau
Software Mentions: 5
Published: about 11 years ago

10.1002/cti2.1093

Machine learning applied to whole‐blood RNA‐sequencing data uncovers distinct subsets of patients with systemic lupus erythematosus
Cited by: 39
Author(s): William A. Figgett, Katherine Monaghan, Milica Ng, Monther Alhamdoosh, Eugene Maraskovsky, Nicholas J. Wilson, Alberta Hoi, Eric F Morand, Fabienne Mackay
Software Mentions: 5
Published: almost 8 years ago

10.1186/s13148-021-01149-8

Transcriptional epigenetic regulation of Fkbp1/Pax9 genes is associated with impaired sensitivity to platinum treatment in ovarian cancer
Cited by: 7
Author(s): Javier Soto, Carlos Rodríguez-Antolín, Olga Vera, Olga Pernía, Isabel Esteban‐Rodríguez, María Dolores Diestro, Javier Benı́tez, Fátima Sánchez-Cabo, Rafael Álvarez, Javier de Castro
Software Mentions: 5
Published: about 5 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

10.1038/s41598-020-59808-4

Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation
Cited by: 29
Author(s): Ian M. Traniello, Syed Bukhari, Jessica L. Kevill, Amy Cash Ahmed, Adam R. Hamilton, Nicholas L. Naeger, Declan C. Schroeder, Gene E. Robinson
Software Mentions: 5
Published: over 6 years ago

10.3390/ijms22010382

Exosomal miRNAs as Potential Biomarkers to Monitor Phosphodiesterase 5 Inhibitor Induced Anti-Fibrotic Effects on CCl4 Treated Rats
Cited by: 9
Author(s): Andre Broermann, RM Schmid, Ogsen Gabrielyan, Marlene Sakowski, Claudia Eisele, Sascha Keller, Michael Wolff, Patrick Baum, Birgit Stierstorfer, J. Huber, Bernhard K. Krämer, Berthold Hocher, Ruediger Streicher, Denis Delić
Software Mentions: 5
Published: almost 6 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

10.1038/s41598-020-60065-8

Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation
Cited by: 7
Author(s): Jessica Schira‐Heinen, A. Czapla, Marion Hendricks, Andreas Kloetgen, Wasco Wruck, James Adjaye, Gesine Kögler, Hans Müller, Kai Stühler, Hans‐Ingo Trompeter
Software Mentions: 5
Published: over 6 years ago

10.1016/j.cell.2018.09.043

Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance
Cited by: 111
Author(s): Anastasiya Kazachenka, Tessa M. Bertozzi, Marcela K. Sjoberg-Herrera, N Walker, Joseph Gardner, Richard Gunning, Eleni Pahita, Sarah Adams, David J. Adams, Anne C. Ferguson-Smith
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pone.0184471

Genome-wide miRNA response to anacardic acid in breast cancer cells
Cited by: 14
Author(s): David J. Schultz, Penn Muluhngwi, Negin Alizadeh-Rad, Madelyn A. Green, Eric C. Rouchka, Sabine Waigel, Carolyn M. Klinge
Software Mentions: 5
Published: about 9 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/cells9091924

Microcurrent Stimulation Triggers MAPK Signaling and TGF-β1 Release in Fibroblast and Osteoblast-Like Cell Lines
Cited by: 14
Author(s): Evangelia Konstantinou, Zoi Zagoriti, Anastasia Pyriochou, Konstantinos Poulas
Software Mentions: 5
Published: about 6 years ago

10.1093/bioinformatics/btx631

Towards unified quality verification of synthetic count data with countsimQC
Cited by: 39
Author(s): Charlotte Soneson, Mark D. Robinson
Software Mentions: 5
Published: about 9 years ago

10.1016/j.cell.2016.09.006

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing
Cited by: 349
Author(s): Angelo Amabile, Alessandro Migliara, Paola Capasso, Mauro Biffi, Davide Cittaro, Luigi Naldini, Angelo Lombardo
Software Mentions: 5
Published: about 10 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

10.3390/toxins13080552

Bacterial Enrichment Cultures Biotransform the Mycotoxin Deoxynivalenol into a Novel Metabolite Toxic to Plant and Porcine Cells
Cited by: 4
Author(s): Ilse Vanhoutte, Caroline De Tender, Kristel Demeyere, Mohamed F. Abdallah, Sarah Ommeslag, Pieter Vermeir, Sarah De Saeger, Jane Debode, Evelyne Meyer, Siska Croubels, Kris Audenaert, Leen De Gelder
Software Mentions: 5
Published: about 5 years ago

10.1016/j.xcrm.2020.100039

Human Tumor-Infiltrating MAIT Cells Display Hallmarks of Bacterial Antigen Recognition in Colorectal Cancer
Cited by: 27
Author(s): Shamin Li, Yannick Simoni, Étienne Becht, Chiew Yee Loh, Naisi Li, Daniel M. Lachance, Si-Lin Koo, Teck Por Lim, Emile Tan, Ronnie Mathew, Andrew Nguyen, Justin Golovato, Julia D. Berkson, Martin Prlic, Bernett Lee, Samuel S. Minot, Niranjan Nagarajan, Neelendu Dey, Daniel S.W. Tan, Iain Bee Huat Tan, Evan W. Newell
Software Mentions: 5
Published: over 6 years ago

10.1016/j.tranon.2021.101107

3D heterospecies spheroids of pancreatic stroma and cancer cells demonstrate key phenotypes of pancreatic ductal adenocarcinoma
Cited by: 5
Author(s): Xinyuan Liu, Beate Gündel, Xidan Li, Jianping Liu, Andrew N. Wright, Matthias Löhr, Gustav Arvidsson, Rainer Heuchel
Software Mentions: 5
Published: over 5 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

10.1101/2020.04.24.059527

Consensus transcriptional regulatory networks of coronavirus-infected human cells
Cited by: 1
Author(s): Scott A. Ochsner, Rudolf T. Pillich, Neil J. McKenna
Software Mentions: 5
Published: over 6 years ago

10.1128/mBio.01193-19

Determination of an Interaction Network between an Extracellular Bacterial Pathogen and the Human Host
Cited by: 23
Author(s): Brad Griesenauer, Tuan M. Tran, Kate R. Fortney, Diane M. Janowicz, Paula A. Johnson, Hongyu Gao, Stephen Barnes, Landon Wilson, Yunlong Liu, Stanley M. Spinola
Software Mentions: 5
Published: over 7 years ago

10.1016/j.cell.2020.04.035

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues
Cited by: 1,817
Author(s): Carly G.K. Ziegler, Samuel J. Allon, Sarah K. Nyquist, Ian Mbano, Vincent N. Miao, Constantine N. Tzouanas, Yuming Cao, Ashraf S. Yousif, Julia Bals, Blake M. Hauser, Jared Feldman, Christoph Muus, Marc H. Wadsworth, Samuel W. Kazer, Travis Hughes, Benjamin Doran, G. James Gatter, Marko Vukovic, Faith Taliaferro, Benjamin E. Mead, Zhiru Guo, Jennifer Wang, Delphine Gras, Magali Plaisant, Meshal Ansari, Ilias Angelidis, Heiko Adler, Jennifer M.S. Sucre, Chase J. Taylor, Brian M. Lin, Avinash Waghray, Vanessa Mitsialis, Daniel F. Dwyer, Kathleen M. Buchheit, Joshua A. Boyce, Nora A. Barrett, Tanya M. Laidlaw, Shaina L. Carroll, Lucrezia Colonna, Victor Tkachev, Christopher W. Peterson, Alison Yu, Hengqi Zheng, Hannah P. Gideon, Caylin G. Winchell, Philana Ling Lin, Colin D. Bingle, Scott B. Snapper, Jonathan A. Kropski, Fabian J. Theis, Herbert B. Schiller, Laure‐Emmanuelle Zaragosi, Pascal Barbry, Alasdair Leslie, Hans–Peter Kiem, JoAnne L. Flynn, Sarah M. Fortune, Bonnie Berger, Robert W. Finberg, Leslie S. Kean, Manuel Garber, Aaron Schmidt, Daniel Lingwood, Alex K. Shalek, José Ordovás-Montañés, Nicholas E. Banovich, Alvis Brāzma, Tushar J. Desai, Thao Duong, Oliver Eickelberg, Christine S. Falk, Michael Farzan, Ian A. Glass, Muzlifah Haniffa, Péter Horváth, Deborah T. Hung, Naftali Kaminski, Mark A. Krasnow, Malte Kühnemund, Robert Lafyatis, Haeock Lee, Sylvie Leroy, Sten Linnarson, Joakim Lundeberg, Kerstin B. Meyer, Alexander V. Misharin, Martijn C. Nawijn, M Nikolíc, Dana Pe’er, Joseph E. Powell, Stephen R. Quake, Jay Rajagopal, Purushothama Rao Tata, Emma L. Rawlins, Aviv Regev, Paul A. Reyfman, Mauricio Rojas, Orit Rosen, Kourosh Saeb‐Parsy, Christos Samakovlis, Herbert B. Schiller, Joachim L. Schultze, Max A. Seibold, Douglas P. Shepherd, Jason R. Spence, Avrum Spira, Xin Sun, Sarah A. Teichmann, Fabian J. Theis, Alexander M. Tsankov, Maarten van den Berge, Michael von Papen, Jeffrey A. Whitsett, Ramnik J. Xavier, Yan Xu, Kun Zhang
Software Mentions: 5
Published: over 6 years ago

10.1016/j.cell.2019.05.047

Neutrophils Driving Unconventional T Cells Mediate Resistance against Murine Sarcomas and Selected Human Tumors
Cited by: 147
Author(s): Andrea Ponzetta, Roberta Carriero, Silvia Carnevale, Marialuisa Barbagallo, Martina Molgora, Chiara Perucchini, Elena Magrini, Francesca Gianni, Paolo Kunderfranco, Nadia Polentarutti, Fabio Pasqualini, Sabrina Di Marco, Domenico Supino, Clelia Peano, Ferdinando Carlo Maria Cananzi, Piergiuseppe Colombo, Silvana Pilotti, Suliman Yousef Alomar, Eduardo Bonavita, Maria Rosaria Galdiero, Cecília Garlanda, Alberto Mantovani, Sébastien Jaillon
Software Mentions: 5
Published: over 7 years ago

10.1002/1878-0261.12853

Genome‐scale CRISPR screening identifies cell cycle and protein ubiquitination processes as druggable targets for erlotinib‐resistant lung cancer
Cited by: 10
Author(s): Jieun Lee, Ahyoung Choi, Sung Yup Cho, Yukyung Jun, Deukchae Na, Ahra Lee, Giyong Jang, Jee Young Kwon, Jaesang Kim, Sanghyuk Lee, Charles Lee
Software Mentions: 5
Published: almost 6 years ago

10.3390/ijms221810006

Increased Autotaxin Levels in Severe COVID-19, Correlating with IL-6 Levels, Endothelial Dysfunction Biomarkers, and Impaired Functions of Dendritic Cells
Cited by: 14
Author(s): Ioanna Nikitopoulou, Dionysiοs Fanidis, Konstantinos Ntatsoulis, Panagiotis Moulos, George Mpekoulis, Maria Evangelidou, Alice G. Vassiliou, Vasiliki Dimakopoulou, Edison Jahaj, Stamatios Tsipilis, Stylianos E. Orfanos, Ioanna Dimopoulou, Emmanouil Angelakis, Karolina Akinosoglou, Niki Vassilaki, Argyrios Tzouvelekis, Αναστασία Κοτανίδου, Vassilis Aidinis
Software Mentions: 5
Published: about 5 years ago

10.1002/1878-0261.12314

Induced <scp>PTF</scp> 1a expression in pancreatic ductal adenocarcinoma cells activates acinar gene networks, reduces tumorigenic properties, and sensitizes cells to gemcitabine treatment
Cited by: 17
Author(s): Brad L. Jakubison, Patrick G. Schweickert, Sarah E. Moser, Yi Yang, Hongyu Gao, Kathleen M. Scully, Pamela Itkin-Ansari, Yunlong Liu, Stephen F. Konieczny
Software Mentions: 5
Published: over 8 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

10.1016/j.isci.2020.101249

Frequency of MicroRNA Response Elements Identifies Pathologically Relevant Signaling Pathways in Triple-Negative Breast Cancer
Cited by: 5
Author(s): Asha Nair, Xiaojia Tang, Kevin J. Thompson, Peter T. Vedell, Krishna R. Kalari, Subbaya Subramanian
Software Mentions: 5
Published: over 6 years ago

10.1002/1878-0261.12902

A novel prognostic mRNA/miRNA signature for esophageal cancer and its immune landscape in cancer progression
Cited by: 35
Author(s): Yue Zhao, Li Xu, Xinyu Wang, Shuai Niu, Hezhong Chen, Chunguang Li
Software Mentions: 5
Published: over 5 years ago

10.1016/j.cell.2020.09.062

M. tuberculosis Reprograms Hematopoietic Stem Cells to Limit Myelopoiesis and Impair Trained Immunity
Cited by: 126
Author(s): Nargis Khan, Jeffrey Downey, Joaquín Sanz, Eva Kaufmann, Birte Blankenhaus, Alain Pacis, Erwan Pernet, Eisha Ahmed, Sílvia Cardoso, Anastasia Nijnik, Bruce Mazer, Christopher M. Sassetti, Marcel A. Behr, Miguel P. Soares, Luis B. Barreiro, Maziar Divangahi
Software Mentions: 5
Published: about 6 years ago

10.1002/1878-0261.12138

<scp>APE</scp>1/Ref‐1 knockdown in pancreatic ductal adenocarcinoma – characterizing gene expression changes and identifying novel pathways using single‐cell <scp>RNA</scp> sequencing
Cited by: 26
Author(s): Fenil Shah, Emery Goossens, Nadia M. Atallah, Michelle Grimard, Mark R. Kelley, Melissa L. Fishel
Software Mentions: 5
Published: about 9 years ago

10.1186/s13024-018-0261-9

Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model
Cited by: 37
Author(s): Lodewijk J.A. Toonen, Maurice Overzier, Melvin M. Evers, Leticia G. León, Sander A.J. van der Zeeuw, Hailiang Mei, Szymon M. Kiełbasa, Jelle J. Goeman, Kristina Hettne, Ólafur Þ. Magnússon, Marion Poirel, Alexandre Seyer, Peter A.C. ’t Hoen, Willeke M. C. van Roon‐Mom
Software Mentions: 5
Published: over 8 years ago

10.1093/bioinformatics/btaa1063

ProkSeq for complete analysis of RNA-Seq data from prokaryotes
Cited by: 8
Author(s): A. K. M. Firoj Mahmud, Nicolas Delhomme, Soumyadeep Nandi, Maria Fällman
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12974-021-02154-7

Identification of aberrant innate and adaptive immunity based on changes in global gene expression in the blood of adults with autism spectrum disorder
Cited by: 11
Author(s): Fumie Horiuchi, Yuta Yoshino, Hiroshi Kumon, Rie Hosokawa, Kiwamu Nakachi, Kentaro Kawabe, Jun‐ichi Iga, Shu‐ichi Ueno
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-020-02048-6

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows
Cited by: 289
Author(s): Elena Denisenko, Belinda Guo, Matthew Jones, Rui Hou, Leanne de Kock, Timo Lassmann, Daniel Poppe, C Olivier, Rebecca K. Simmons, Ryan Lister, Alistair R.R. Forrest
Software Mentions: 5
Published: over 6 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

10.1016/j.molmet.2017.02.007

Heterogeneity of hypothalamic pro-opiomelanocortin-expressing neurons revealed by single-cell RNA sequencing
Cited by: 125
Author(s): Brian Y.H. Lam, Irène Cimino, Joseph Polex-Wolf, Sara Kohnke, Debra Rimmington, Valentine P. Iyemere, Nicholas Heeley, Chiara Cossetti, Reiner Schulte, Luís R. Saraiva, Darren W. Logan, Clémence Blouet, Stephen O’Rahilly, Anthony P. Coll, Giles S.H. Yeo
Software Mentions: 5
Published: over 9 years ago

10.1186/s13059-021-02464-2

Systematic functional interrogation of human pseudogenes using CRISPRi
Cited by: 11
Author(s): Ming Sun, Yunfei Wang, Caishang Zheng, Yanjun Wei, Jiakai Hou, Peng Zhang, Wei He, Xiangdong Lv, Yao Ding, Han Liang, Chung-Chau Hon, Xi Chen, Xu Han, Yiwen Chen
Software Mentions: 5
Published: about 5 years ago

10.1074/mcp.TIR119.001646

DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis
Cited by: 109
Author(s): Yong Zhu, Lukas M. Orre, Yan Zhou Tran, Georgios Mermelekas, Henrik J. Johansson, Alina Malyutina, Simon Anders, Janne Lehtiö
Software Mentions: 5
Published: over 6 years ago

10.1093/gbe/evz150

Evolution of Phototransduction Genes in Lepidoptera
Cited by: 26
Author(s): Aide Macias-Muñoz, Aline G. Rangel Olguin, Adriana D. Briscoe
Software Mentions: 5
Published: over 7 years ago

10.15252/msb.20209888

Gene expression profiling reveals insights into infant immunological and febrile responses to group B meningococcal vaccine
Cited by: 6
Author(s): Daniel O’Connor, Marta Pinto, Dylan Sheerin, Adriana Tomić, Ruth Drury, Samuel Channon‐Wells, Ushma Galal, Christina Dold, Hannah Robinson, Simon Kerridge, Emma Plested, Henry J. Hughes, Lisa Stockdale, Manish Sadarangani, Matthew D. Snape, Christine S. Rollier, Michael Levin, Andrew J. Pollard
Software Mentions: 5
Published: about 6 years ago

10.1093/gbe/evab145

High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady ButterflyVanessa cardui
Cited by: 7
Author(s): Linlin Zhang, Rachel Steward, Christopher W. Wheat, Robert D. Reed
Software Mentions: 5
Published: over 5 years ago

10.1093/bioinformatics/btaa1009

glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data
Cited by: 89
Author(s): Constantin Ahlmann-Eltze, Wolfgang Huber
Software Mentions: 5
Published: almost 6 years ago

10.1093/gbe/evab110

Transcriptomic Analysis of Skin Color in Anole Lizards
Cited by: 5
Author(s): Pietro Longo Hollanda de Mello, Paul M Hime, Richard E. Glor
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers13153764

Glioblastomas within the Subventricular Zone Are Region-Specific Enriched for Mesenchymal Transition Markers: An Intratumoral Gene Expression Analysis
Cited by: 5
Author(s): Diana J. Z. Dalemans, Sharon Berendsen, Kaspar Draaisma, Pierre A. Robe, Tom J. Snijders
Software Mentions: 5
Published: over 5 years ago

10.1186/s13073-016-0315-y

The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p
Cited by: 34
Author(s): Zsolt Czimmerer, Tamás Varga, Máté Kiss, Cesaré Ovando Vázquez, Quang Minh Doan‐Xuan, Dominik Rückerl, Sudhir Gopal Tattikota, Xin Yan, Zsuzsanna Nagy, Bence Dániel, Szilárd Póliska, Attila Horváth, Gergely Nagy, Éva Várallyay, Matthew N. Poy, Judith E. Allen, Zsolt Bacsó, Cei Abreu‐Goodger, László Nagy
Software Mentions: 5
Published: over 10 years ago

10.1186/s13073-016-0348-2

Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring
Cited by: 9
Author(s): José P. Silva, Guerline Lambert, Derek Van Booven, Claes Wahlestedt
Software Mentions: 5
Published: about 10 years ago

10.15252/msb.20199012

Sex‐dependent and sex‐independent regulatory systems of size variation in natural populations
Cited by: 4
Author(s): Hirokazu Okada, Ryuta Yagi, Vincent Gardeux, Bart Deplancke, Ernst Hafen
Software Mentions: 5
Published: about 7 years ago

10.1093/bioinformatics/btz089

How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in Arabidopsis thaliana
Cited by: 9
Author(s): Kimon Froussios, Nicholas J. Schurch, Katarzyna Mackinnon, Marek Gierliński, Céline Duc, Gordon G. Simpson, Geoffrey J. Barton
Software Mentions: 5
Published: over 7 years ago

10.1186/s13073-017-0432-2

Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes
Cited by: 33
Author(s): Leif Väremo, Tora Ida Henriksen, Camilla Schéele, Christa Broholm, Maria Pedersen, Mathias Uhlén, Bente Klarlund Pedersen, Jens Nielsen
Software Mentions: 5
Published: over 9 years ago

10.3390/ijms22062901

Age and Sex-Related Changes in Human First-Trimester Placenta Transcriptome and Insights into Adaptative Responses to Increased Oxygen
Cited by: 7
Author(s): Fulin Liu, Christelle Simasotchi, Françoise Vibert, Wencan Zhu, Sophie Gil, Séverine A. Degrelle, Thierry Fournier
Software Mentions: 5
Published: over 5 years ago

10.1186/s13073-017-0492-3

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists
Cited by: 63
Author(s): Xun Zhu, Thomas Wolfgruber, Austin Tasato, Cédric Arisdakessian, David Garmire, Lana X. Garmire
Software Mentions: 5
Published: almost 9 years ago

10.3390/ijms22052353

ATF3-Induced Mammary Tumors Exhibit Molecular Features of Human Basal-Like Breast Cancer
Cited by: 3
Author(s): Leqin Yan, Sally Gaddis, Luis Della Coletta, John Repass, Katherine Powell, Melissa S. Simper, Yueping Chen, Michelle Byrom, Yi Zhong, Kevin Lin, Bin Liu, Yao Lu, Jianjun Shen, Michael C. MacLeod
Software Mentions: 5
Published: over 5 years ago

10.1016/j.celrep.2018.10.072

Heart Regeneration in the Mexican Cavefish
Cited by: 78
Author(s): William T. Stockdale, Madeleine E. Lemieux, Abigail C. Killen, Juanjuan Zhao, Zhilian Hu, Joey Riepsaame, Noémie Hamilton, Tetsuhiro Kudoh, Paul R. Riley, Ronny van Aerle, Yoshiyuki Yamamoto, Mathilda T.M. Mommersteeg
Software Mentions: 5
Published: about 8 years ago

10.1186/s13073-020-00760-3

ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer
Cited by: 32
Author(s): Aileen P. Szczepanski, Zibo Zhao, Victoria Sosnowski, Young Ah Goo, Elizabeth T. Bartom, Lu Wang
Software Mentions: 5
Published: over 6 years ago

10.1093/gigascience/giy117

Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation
Cited by: 16
Author(s): Zhouchun Shang, Dongsheng Chen, Quanlei Wang, Shengpeng Wang, Qiuting Deng, Liang Wu, Chuanyu Liu, Xiangning Ding, Shiyou Wang, Junyan Zhong, Doudou Zhang, Xiaodong Cai, Shida Zhu, Huanming Yang, Longqi Liu, J. Lynn Fink, Fang Chen, Xiaoqing Liu, Zhengliang Gao, Xun Xu
Software Mentions: 5
Published: about 8 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568