bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3389/fphys.2012.00339

A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells
Cited by: 18
Author(s): Justyna Józefczuk, Karl Kashofer, Ramesh Ummanni, Frauke Henjes, Samrina Rehman, Suzanne Geenen, Wasco Wruck, Christian Regenbrecht, Andriani Daskalaki, Christoph Wierling, Paola Turano, Ivano Bertini, Ulrike Korf, Kurt Zatloukal, Hans V. Westerhoff, Hans Lehrach, James Adjaye
Software Mentions: 2
Published: over 14 years ago

10.3389/fphys.2017.00723

N-acetylcysteine Counteracts Adipose Tissue Macrophage Infiltration and Insulin Resistance Elicited by Advanced Glycated Albumin in Healthy Rats
Cited by: 10
Author(s): Karolline S. da Silva, Paula Ramos Pinto, N. Fabre, Diogo Bugano Diniz Gomes, Karina Thieme, Lígia Shimabukuro Okuda, Rodrigo Tallada Iborra, Vanessa G. Freitas, Maria Heloísa Massola Shimizu, Walcy Rosolia Teodoro, Suely Kazue Nagahashi Marie, Tom M. Woods, Margaret A. Brimble, Russell Pickford, Kerry‐Anne Rye, Maristela Mitiko Okamoto, Sérgio Catanozi, Maria L. Correa-Giannela, Ubiratan Fabres Machado, Marisa Passarelli
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pgen.1000142

Efficient Genetic Method for Establishing Drosophila Cell Lines Unlocks the Potential to Create Lines of Specific Genotypes
Cited by: 55
Author(s): Amanda Simcox, Srabani Mitra, Sharon L. Truesdell, Litty Paul, Ting Chen, Jonathan P. Butchar, Steven E. Justiniano
Software Mentions: 2
Published: about 18 years ago

10.1186/s12935-021-01830-1

The immune‐related biomarker TEK inhibits the development of clear cell renal cell carcinoma (ccRCC) by regulating AKT phosphorylation
Cited by: 10
Author(s): Siming Chen, Mengxue Yu, Lingao Ju, Gang Wang, Kaiyu Qian, Yu Xiao, Xinghuan Wang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1009186

Autocrine insulin pathway signaling regulates actin dynamics in cell wound repair
Cited by: 5
Author(s): Mitsutoshi Nakamura, Jeffrey M. Verboon, Tessa E. Allen, María Teresa Abreu-Blanco, Raymond Liu, Andrew N. M. Dominguez, Jeffrey J. Delrow, Susan M. Parkhurst
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2021.724676

A Global Analysis of Photoreceptor-Mediated Transcriptional Changes Reveals the Intricate Relationship Between Central Metabolism and DNA Repair in the Filamentous Fungus Trichoderma atroviride
Cited by: 7
Author(s): Enrique Pola-Sánchez, José Manuel Villalobos-Escobedo, Nohemí Carreras-Villaseñor, Pedro Martı́nez-Hernández, Emma Beatriz Beltrán-Hernández, Edgardo Ulises Esquivel-Naranjo, Alfredo Herrera‐Estrella
Software Mentions: 2
Published: about 5 years ago

10.3389/fphys.2020.629542

Calcium-Sensing Receptor Participates in High Glucose-Induced EndMT in Primary Human Aortic Endothelial Cells
Cited by: 2
Author(s): Cheng Yuan, Lihua Ni, Xianqin Yang, Changjiang Zhang, Xiaoyan Wu
Software Mentions: 2
Published: over 5 years ago

10.1038/s41398-019-0589-0

Integrated genome-wide methylation and expression analyses reveal functional predictors of response to antidepressants
Cited by: 30
Author(s): Chelsey Ju, Laura M. Fiori, Raoul Belzeaux, Jean-François Théroux, Gary Gang Chen, Zahia Aouabed, Pierre Blier, Faranak Farzan, Benício N. Frey, Peter Giacobbe, Raymond W. Lam, Francesco Leri, Glenda MacQueen, Roumen Milev, Daniel J. Müller, Sagar V. Parikh, Susan Rotzinger, Cláudio N. Soares, Rudolf Uher, Qingqin Li, Jane A. Foster, Sidney H. Kennedy, Gustavo Turecki
Software Mentions: 2
Published: almost 7 years ago

10.3390/v9100271

Antiviral Properties of Chemical Inhibitors of Cellular Anti-Apoptotic Bcl-2 Proteins
Cited by: 37
Author(s): Daria Bulanova, Aleksandr Ianevski, А. Н. Бугай, Yevhen Akimov, Suvi Kuivanen, Henrik Paavilainen, Laura Kakkola, Jatin Nandania, Laura Turunen, Tiina Öhman, Hanna Ala-Hongisto, Hanna M Pesonen, Marika Kuisma, Anni Honkimaa, Emma Louise Walton, Valentyn Oksenych, Martina B. Lorey, Dmitry Guschin, Jungmin Shim, Jinhee Kim, Thoa Thi Than, So Young Chang, Veijo Hukkanen, Evgeny Kulesskiy, Varpu Marjomäki, Ilkka Julkunen, Tuula A. Nyman, Sampsa Matikainen, Jani Saarela, Famara Sané, Didier Hober, Gülşah Gabriel, Jef K. De Brabander, Miika Martikainen, Marc P. Windisch, Ji-Young Min, Roberto Bruzzone, Tero Aittokallio, Markus Vähä‐Koskela, Olli Vapalahti, Arto Pulk, Vidya Velagapudi, Denis E. Kainov
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12882-020-02142-8

Identification of biomarkers and pathways in hypertensive nephropathy based on the ceRNA regulatory network
Cited by: 8
Author(s): Zhen Wang, Zhongjie Liu, Yong Yang, Kang Lei
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12967-015-0384-5

DNA methylation patterns in newborns exposed to tobacco in utero
Cited by: 70
Author(s): Carmen Ivorra, Mario F. Fraga, Gustavo F. Bayón, Agustín F. Fernández, Consuelo García-Vicent, Felipe Javier Chaves, Josep Redón, Empar Lurbe
Software Mentions: 2
Published: over 11 years ago

10.1038/s41398-020-0800-3

Genome-wide DNA methylation analysis of heavy cannabis exposure in a New Zealand longitudinal cohort
Cited by: 24
Author(s): Amy J. Osborne, John Pearson, Alison Noble, Neil J. Gemmell, L. John Horwood, Joseph M. Boden, Miles C. Benton, Donia Macartney-Coxson, Martin A. Kennedy
Software Mentions: 2
Published: over 6 years ago

10.1186/s12882-017-0600-z

Serum micro-rna profiles in patients with autosomal dominant polycystic kidney disease according to hypertension and renal function
Cited by: 18
Author(s): İsmail Koçyiğit, Serpil Taheri, Elif Funda Şener, Eray Eroğlu, Fahir Öztürk, Aydın Ünal, Kezban Korkmaz, Gökmen Zararsız, Murat Hayri Sipahioğlu, Yusuf Özkul, Bülent Tokgöz, Oktay Oymak, Tevfik Ecder, Jonas Axelsson
Software Mentions: 2
Published: over 9 years ago

10.1080/19490976.2019.1651596

Mucosal IgG in inflammatory bowel disease – a question of (sub)class?
Cited by: 10
Author(s): Tomas Castro‐Dopico, Menna R. Clatworthy
Software Mentions: 2
Published: about 7 years ago

10.1186/s12870-019-1935-3

Rpv3–1 mediated resistance to grapevine downy mildew is associated with specific host transcriptional responses and the accumulation of stilbenes
Cited by: 35
Author(s): Birgit Eisenmann, Stefan Czemmel, Tobias Ziegler, Günther Buchholz, A. Kortekamp, Oliver Trapp, Thomas Rausch, Ian B. Dry, Jochen Bogs
Software Mentions: 2
Published: about 7 years ago

10.3390/ijms22031423

Diabetes Induces a Transcriptional Signature in Bone Marrow–Derived CD34+ Hematopoietic Stem Cells Predictive of Their Progeny Dysfunction
Cited by: 4
Author(s): Yuri D’Alessandra, Mattia Chiesa, Vera Vigorelli, Veronica Ricci, Erica Rurali, Angela Raucci, Gualtiero I. Colombo, Giulio Pompilio, Maria Vinci
Software Mentions: 2
Published: over 5 years ago

10.1038/s41398-021-01323-9

Transcriptomic signaling pathways involved in a naturalistic model of inflammation-related depression and its remission
Cited by: 8
Author(s): Marie‐Pierre Moisan, Aline Foury, Sandra Dexpert, Steve W. Cole, Cédric Beau, Damien Forestier, Patrick Ledaguenel, Eric Magne, Lucile Capuron
Software Mentions: 2
Published: over 5 years ago

10.1038/s41398-021-01373-z

Cell-type-specific expression quantitative trait loci associated with Alzheimer disease in blood and brain tissue
Cited by: 27
Author(s): Devanshi Patel, Xiaoling Zhang, John Farrell, Jaeyoon Chung, Thor D. Stein, Kathryn L. Lunetta, Lindsay A. Farrer
Software Mentions: 2
Published: over 5 years ago

10.1002/hsr2.202

A prognostic risk model based on immune‐related genes predicts overall survival of patients with hepatocellular carcinoma
Cited by: 2
Author(s): Banglun Pan, Lin Liu, Wei Li
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41398-021-01528-y

Conserved immunomodulatory transcriptional networks underlie antipsychotic-induced weight gain
Cited by: 5
Author(s): Rizaldy C. Zapata, Besma Chaudry, Mariela Lopez Valencia, Dinghong Zhang, Scott A. Ochsner, Neil J. McKenna, Olivia Osborn
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2020.01635

DNA-Binding and Transcription Activation by Unphosphorylated Response Regulator AgrR From Cupriavidus metallidurans Involved in Silver Resistance
Cited by: 11
Author(s): Muntasir Ali, Ann Provoost, Kristel Mijnendonckx, Rob Van Houdt, Daniël Charlier
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2019.00092

Exposure to Sub-inhibitory Concentrations of the Chemosensitizer 1-(1-Naphthylmethyl)-Piperazine Creates Membrane Destabilization in Multi-Drug Resistant Klebsiella pneumoniae
Cited by: 19
Author(s): João Anes, Sathesh K Sivasankaran, Dechamma Mundanda Muthappa, Séamus Fanning, Shabarinath Srikumar
Software Mentions: 2
Published: over 7 years ago

10.3390/v4101844

miRNA Profiles of Monocyte-Lineage Cells Are Consistent with Complicated Roles in HIV-1 Restriction
Cited by: 31
Author(s): Jeanne M. Sisk, Janice E. Clements, Kenneth W. Witwer
Software Mentions: 2
Published: almost 14 years ago

10.1002/hep.29877

Impact of Interferon Lambda 4 Genotype on Interferon‐Stimulated Gene Expression During Direct‐Acting Antiviral Therapy for Hepatitis C
Cited by: 17
Author(s): Narayan Ramamurthy, Emanuele Marchi, Azim Ansari, Vincent Pedergnana, Angela R. McLean, Emma Hudson, Rory Bowden, Chris C. A. Spencer, Eleanor Barnes, Paul Klenerman
Software Mentions: 2
Published: about 8 years ago

10.3906/biy-2009-56

Transcriptome profiles associated with selenium-deficiency-dependent oxidative stress identify potential diagnostic and therapeutic targets in liver cancer cells
Cited by: 0
Author(s): Damla Gözen, Deniz Cansen Kahraman, Kübra Narci, Huma Shehwana, Özlen Konu, Rengül Çetin-Atalay
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0013451

A Molecular Signature of Proteinuria in Glomerulonephritis
Cited by: 63
Author(s): Heather N. Reich, David Tritchler, Daniel C. Cattran, Andrew M. Herzenberg, Felix Eichinger, Anissa Boucherot, Anna Henger, Céline C. Berthier, Viji Nair, Clemens D. Cohen, James W. Scholey, Matthias Kretzler
Software Mentions: 2
Published: almost 16 years ago

10.3389/fpls.2017.01006

Key Components of Different Plant Defense Pathways Are Dispensable for Powdery Mildew Resistance of the Arabidopsis mlo2 mlo6 mlo12 Triple Mutant
Cited by: 35
Author(s): Harald Kühn, Justine Lorek, Mark Kwaaitaal, Chiara Consonni, Katia Becker, Cristina Micali, Emiel Ver Loren van Themaat, Paweł Bednarek, Tom M. Raaymakers, Michela Appiano, Yuling Bai, Dorothea Meldau, Stephani Baum, Uwe Conrath, Ivo Feußner, Ralph Panstruga
Software Mentions: 2
Published: about 9 years ago

10.1186/s12967-020-02509-3

LTBP1 plays a potential bridge between depressive disorder and glioblastoma
Cited by: 7
Author(s): Xiaojun Fu, Pei Zhang, Hongwang Song, Chenxing Wu, Shengzhen Li, Shouwei Li, Yan Chen
Software Mentions: 2
Published: almost 6 years ago

10.1128/mBio.01593-17

Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms
Cited by: 41
Author(s): Brett M. Babin, Lydia Atangcho, Mark B. van Eldijk, Michael J. Sweredoski, Annie Moradian, Sonja Hess, Tim Tolker‐Nielsen, Dianne K. Newman, David A. Tirrell
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12935-020-01572-6

Integrated analysis of immune-related genes in endometrial carcinoma
Cited by: 9
Author(s): Yiru Wang, Yunduo Liu, Yue Guan, Hao Li, Yuan Liu, Mengjun Zhang, Ping Cui, Dan Kong, Xiuwei Chen, Hang Yin
Software Mentions: 2
Published: almost 6 years ago

10.3390/nu7053370

Low Folate and Selenium in the Mouse Maternal Diet Alters Liver Gene Expression Patterns in the Offspring after Weaning
Cited by: 15
Author(s): Matthew P. G. Barnett, Emma N. Bermingham, Wayne Young, Shalome A. Bassett, John E. Hesketh, Anabel Maciel-Dominguez, Warren C. McNabb, Nicole C. Roy
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0017900

Transcriptome Analysis of the Vernalization Response in Barley (Hordeum vulgare) Seedlings
Cited by: 53
Author(s): Aaron G. Greenup, Shahryar Sasani, Sandra N. Oliver, Sally A. Walford, Anthony A. Millar, Ben Trevaskis
Software Mentions: 2
Published: over 15 years ago

10.3389/fpls.2017.01905

Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases
Cited by: 24
Author(s): J. Alberto Romero Navarro, Wilbert Phillips‐Mora, Adriana Arciniegas-Leal, Allan Mata-Quirós, Niina Haiminen, Guiliana Mustiga, Donald Livingstone, Harm van Bakel, David N. Kuhn, Laxmi Parida, Andrew Kasarskis, Juan Carlos Motamayor
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijms22115895

In-Silico Evaluation of Genetic Alterations in Ovarian Carcinoma and Therapeutic Efficacy of NSC777201, as a Novel Multi-Target Agent for TTK, NEK2, and CDK1
Cited by: 8
Author(s): Harshita Khedkar, Yu-Chi Wang, Vijesh Kumar Yadav, Prateeti Srivastava, Bashir Lawal, Ntlotlang Mokgautsi, Maryam Rachmawati Sumitra, Alexander T.H. Wu, Hsu-Shan Huang
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2014.00402

Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification
Cited by: 36
Author(s): David H. Keating, Yaoping Zhang, Irene M. Ong, Sean J. McIlwain, Eduardo Morales, Jeffrey A. Grass, Mary Tremaine, William Bothfeld, Alan Higbee, Arne Ulbrich, Allison J. Balloon, Michael S. Westphall, Josh Aldrich, Mary Lipton, Joonhoon Kim, Oleg V. Moskvin, Yury V. Bukhman, Joshua J. Coon, Patricia J. Kiley, Donna M. Bates, Robert Landick
Software Mentions: 2
Published: about 12 years ago

10.3389/fpls.2018.00023

GSHR, a Web-Based Platform Provides Gene Set-Level Analyses of Hormone Responses in Arabidopsis
Cited by: 1
Author(s): Xiaojuan Ran, Jian Liu, Meifang Qi, Yuejun Wang, Jingfei Cheng, Yijing Zhang
Software Mentions: 2
Published: over 8 years ago

10.3389/fpls.2015.01157

Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice
Cited by: 57
Author(s): Shuchi Smita, Amit Katiyar, Viswanathan Chinnusamy, Dev Mani Pandey, Kailash C. Bansal
Software Mentions: 2
Published: over 10 years ago

10.1186/s12920-021-00908-z

Identification of major depressive disorder disease-related genes and functional pathways based on system dynamic changes of network connectivity
Cited by: 6
Author(s): Ruijie Geng, Xiao Huang
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2229-12-100

Reprogramming of gene expression during compression wood formation in pine: Coordinated modulation of S-adenosylmethionine, lignin and lignan related genes
Cited by: 56
Author(s): David P. Villalobos, Sara M. Díaz-Moreno, El-Sayed S Said, Rafael A. Cañas, Daniel Osuna, Sonia H E Van Kerckhoven, Rocío Bautista, M. Gonzalo Claros, Francisco M. Cánovas, Francisco R. Cantón
Software Mentions: 2
Published: about 14 years ago

10.3389/fmicb.2019.02303

Caecal Microbiota of Experimentally Campylobacter jejuni-Infected Chickens at Different Ages
Cited by: 18
Author(s): Julia Hankel, Klaus Jung, Henrike Kuder, Birgit Keller, Christoph A. Keller, Eric Galvez, Till Strowig, Christian Visscher
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0077936

Profiling Circulating MicroRNA Expression in Experimental Sepsis Using Cecal Ligation and Puncture
Cited by: 56
Author(s): Shao-Chun Wu, Johnson Chia‐Shen Yang, Cheng-Shyuan Rau, Yi‐Chun Chen, Tsu-Hsiang Lu, Ming‐Wei Lin, Siou-Ling Tzeng, Yi-Chan Wu, Chi‐Chuan Wu, Ching‐Hua Hsieh
Software Mentions: 2
Published: almost 13 years ago

10.1128/mBio.00867-21

Analysis of the Oxidative Stress Regulon Identifies soxS as a Genetic Target for Resistance Reversal in Multidrug-Resistant Klebsiella pneumoniae
Cited by: 11
Author(s): João Anes, Katherine Dever, Athmanya K. Eshwar, Scott V. Nguyen, Yu Cao, Sathesh K Sivasankaran, Sandra Sakalauskaitė, Angelika Lehner, Stéphanie Devineau, Rimantas Daugelavičius, Roger Stephan, Séamus Fanning, Shabarinath Srikumar
Software Mentions: 2
Published: about 5 years ago

10.1186/s12935-021-01797-z

MicroRNA-1182 and let-7a exert synergistic inhibition on invasion, migration and autophagy of cholangiocarcinoma cells through down-regulation of NUAK1
Cited by: 16
Author(s): Xin Pan, Gang Wang, Baoming Wang
Software Mentions: 2
Published: over 5 years ago

10.1186/s13567-015-0286-9

Transcriptional analysis of porcine intestinal mucosa infected with Salmonella Typhimurium revealed a massive inflammatory response and disruption of bile acid absorption in ileum
Cited by: 28
Author(s): Júber Herrera-Uribe, Melania Collado-Romero, Sara Zaldívar‐López, Cristina Arce, Rocío Bautista, Ana Carvajal, Susanna Cirera, M. Gonzalo Claros, Juan J. Garrido
Software Mentions: 2
Published: over 10 years ago

10.1038/s41438-019-0119-5

What makes turnips: anatomy, physiology and transcriptome during early stages of its hypocotyl-tuber development
Cited by: 23
Author(s): Mengyang Li, Niccolò Bassetti, Stefan Petrasch, Ningwen Zhang, Johan Bucher, Shuxing Shen, Zhao Jian-jun, Guusje Bonnema
Software Mentions: 2
Published: over 7 years ago

10.1038/s41438-019-0212-9

Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage (Brassica rapa)
Cited by: 10
Author(s): Xiaoxue Sun, Ram Kumar Basnet, Zhichun Yan, Johan Bucher, Chengcheng Cai, Jianjun Zhao, Guusje Bonnema
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12935-020-1140-3

Identification of molecular markers associated with the progression and prognosis of endometrial cancer: a bioinformatic study
Cited by: 12
Author(s): Jinhui Liu, Mingming Feng, Siyue Li, Song Nie, Hui Wang, Shan Wu, Jiangnan Qiu, Jie Zhang, Wenjun Cheng
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms221910556

Lipidomic and Proteomic Alterations Induced by Even and Odd Medium-Chain Fatty Acids on Fibroblasts of Long-Chain Fatty Acid Oxidation Disorders
Cited by: 4
Author(s): Khaled I. Alatibi, Stefan Tholen, Zeinab Wehbe, Judith Hagenbuchner, Daniela Karall, Michael J. Ausserlechner, Oliver Schilling, Sarah C. Grünert, Jerry Vockley, Sara Tucci
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2229-12-185

Grape berry ripening delay induced by a pre-véraison NAA treatment is paralleled by a shift in the expression pattern of auxin- and ethylene-related genes
Cited by: 84
Author(s): F. Ziliotto, Massimiliano Corso, Fabio Massimo Rizzini, Angela Rasori, Alessandro Botton, Claudio Bonghi
Software Mentions: 2
Published: almost 14 years ago

10.1128/mSphere.00824-19

Rectal Microbiome Composition Correlates with Humoral Immunity to HIV-1 in Vaccinated Rhesus Macaques
Cited by: 12
Author(s): Sonny R. Elizaldi, Anil Verma, Korey A. Walter, Matthew Rolston, Ashok R. Dinasarapu, Blythe Durbin‐Johnson, Matthew L. Settles, Pamela A. Kozlowski, Reben Raeman, Smita S. Iyer
Software Mentions: 2
Published: over 6 years ago

10.1128/mSphere.00276-20

Genomewide Stabilization of mRNA during a “Feast-to-Famine” Growth Transition in Escherichia coli
Cited by: 10
Author(s): Manon Morin, Brice Enjalbert, Delphine Ropers, Laurence Girbal, Muriel Cocaign‐Bousquet
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2021.680101

Dysbiosis of Gut Microbiota in Patients With Acute Myocardial Infarction
Cited by: 38
Author(s): Ying Han, Zhaowei Gong, Guizhi Sun, Jing Xu, Changlu Qi, Weiju Sun, Huijie Jiang, Peigang Cao, Hong Ju
Software Mentions: 2
Published: about 5 years ago

10.1128/mSystems.00142-16

Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO 2 Levels
Cited by: 37
Author(s): Jennifer Levering, Christopher L. Dupont, Andrew E. Allen, Bernhard Ø. Palsson, Karsten Zengler
Software Mentions: 2
Published: over 9 years ago

10.3389/fimmu.2020.00194

Rheumatoid Arthritis Patients, Both Newly Diagnosed and Methotrexate Treated, Show More DNA Methylation Differences in CD4+ Memory Than in CD4+ Naïve T Cells
Cited by: 14
Author(s): Kari Guderud, Line Hagen Sunde, Siri Tennebø Flåm, Marthe Thoresen Mæhlen, Maria D Mjaavatten, Siri Lillegraven, Anna‐Birgitte Aga, Ida Marie Evenrød, Ellen Sauar Norli, Bettina Kulle Andreassen, Sören Franzenburg, André Franke, Espen A. Haavardsholm, Simon Rayner, Kristina Gervin, Benedicte A. Lie
Software Mentions: 2
Published: over 6 years ago

10.1128/mSystems.00808-19

Systematic Localization of Escherichia coli Membrane Proteins
Cited by: 20
Author(s): Anna Sueki, Frank Stein, Mikhail M. Savitski, Joel Selkrig, Athanasios Typas
Software Mentions: 2
Published: over 6 years ago

10.1186/s12935-021-01789-z

Construction of a competitive endogenous RNA network and analysis of potential regulatory axis targets in glioblastoma
Cited by: 5
Author(s): Kai Yu, Huan Yang, Qiao‐Li Lv, Li-chong Wang, Zilong Tan, Zhe Zhang, Yulong Ji, Qian-xia Lin, Junjun Chen, Wei He, Zhe Chen, Xiaoli Shen
Software Mentions: 2
Published: over 5 years ago

10.1186/s12935-019-0977-9

Inactivation of the Wnt/β-catenin signaling pathway underlies inhibitory role of microRNA-129-5p in epithelial–mesenchymal transition and angiogenesis of prostate cancer by targeting ZIC2
Cited by: 19
Author(s): Zhenming Jiang, Yuxi Zhang, Xi Chen, Pingeng Wu, Dong Chen
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12935-020-01488-1

Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme
Cited by: 18
Author(s): Xiaolong Zhu, Lan Jiang, Hui Yang, Tianbing Chen, Xiang Wu, Kun Lv
Software Mentions: 2
Published: about 6 years ago

10.1186/s12935-021-02138-w

NCAPG promotes the progression of lung adenocarcinoma via the TGF-β signaling pathway
Cited by: 20
Author(s): Yun Wu, Ying Lin, Junfan Pan, Xunwei Tu, Yiquan Xu, Hongru Li, Yu‐Sheng Chen
Software Mentions: 2
Published: about 5 years ago

10.1186/s12935-020-1141-2

Depletion of histone methyltransferase KMT9 inhibits lung cancer cell proliferation by inducing non-apoptotic cell death
Cited by: 18
Author(s): Hannah Maria Baumert, Eric Metzger, Matthias Fahrner, Julie George, Roman K. Thomas, Oliver Schilling, Roland Schüle
Software Mentions: 2
Published: over 6 years ago

10.3389/fpls.2019.01704

Dual Transcriptome and Metabolic Analysis of Vitis vinifera cv. Pinot Noir Berry and Botrytis cinerea During Quiescence and Egressed Infection
Cited by: 20
Author(s): Zeraye Mehari Haile, G. Malacarne, S. Pilati, Paolo Sonego, Marco Moretto, Domenico Masuero, Urška Vrhovšek, Kristof Engelen, Elena Baraldi, C. Moser
Software Mentions: 2
Published: over 6 years ago

10.1186/s12935-021-01824-z

Immune subtyping for pancreatic cancer with implication in clinical outcomes and improving immunotherapy
Cited by: 13
Author(s): Jing-Kai Liu, Qiaofei Liu, Xiang Zhang, Ming Cui, Tong Li, Yalu Zhang, Quan Liao
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0146257

Time-Course Analysis of Brain Regional Expression Network Responses to Chronic Intermittent Ethanol and Withdrawal: Implications for Mechanisms Underlying Excessive Ethanol Consumption
Cited by: 44
Author(s): Maren L. Smith, Marcelo F. López, Kellie J. Archer, Aaron R. Wolen, Howard C. Becker, Michael F. Miles
Software Mentions: 2
Published: over 10 years ago

10.1186/s12935-018-0640-x

Identification of critical genes to predict recurrence and death in colon cancer: integrating gene expression and bioinformatics analysis
Cited by: 14
Author(s): Xuan Long, Zhigang Deng, Guoqiang Li, Ziwei Wang
Software Mentions: 2
Published: about 8 years ago

10.3389/fmicb.2021.663019

Pathological Features of Enterovirus 71-Associated Brain and Lung Damage in Mice Based on Quantitative Proteomic Analysis
Cited by: 9
Author(s): Yuefei Jin, Dong Liu, Tiantian Sun, Yue Du, Yanlei Gao, Ronghua Ding, Wangquan Ji, Weiguo Zhang, Haiyan Yang, Shuaiyin Chen, Guangcai Duan
Software Mentions: 2
Published: over 5 years ago

10.1186/1479-7364-7-24

Transcriptomics to study the effect of a Mediterranean-inspired diet on inflammation in Crohn's disease patients
Cited by: 151
Author(s): Gareth Marlow, Stephanie Ellett, Isobel Ferguson, Shuotun Zhu, Nishi Karunasinghe, Amalini Jesuthasan, Dug Yeo Han, Alan G. Fraser, Lynnette R. Ferguson
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0166147

SLC7A5 Functions as a Downstream Target Modulated by CRKL in Metastasis Process of Gastric Cancer SGC-7901 Cells
Cited by: 13
Author(s): Junqing Wang, Xiaochun Fei, Wenjun Wu, Xuehua Chen, Liping Su, Zhenggang Zhu, Yunyun Zhou
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0246650

Global blood gene expression profiles following a breast cancer diagnosis—Clinical follow-up in the NOWAC post-genome cohort
Cited by: 3
Author(s): Karina Standahl Olsen, Matthew T. G. Holden, Jean-Christophe Thalabard, Lill-Tove Busund, Eiliv Lund, Lars Holden
Software Mentions: 2
Published: over 5 years ago

10.1038/s41396-020-00831-8

Elevated CO2 and nitrate levels increase wheat root-associated bacterial abundance and impact rhizosphere microbial community composition and function
Cited by: 28
Author(s): Alla Usyskin-Tonne, Yitzhak Hadar, Uri Yermiyahu, Dror Minz
Software Mentions: 2
Published: almost 6 years ago

10.3390/nu13051683

Methylation and Expression of FTO and PLAG1 Genes in Childhood Obesity: Insight into Anthropometric Parameters and Glucose–Lipid Metabolism
Cited by: 11
Author(s): Wojciech Czogała, Małgorzata Czogała, Wojciech Strojny, Gracjan Wątor, Paweł Wołkow, Małgorzata Wójcik, Mirosław Bik-Multanowski, Przemysław Tomasik, Andrzej Wędrychowicz, Wojciech Kowalczyk, Karol Miklusiak, Agnieszka Łazarczyk, Przemysław Hałubiec, Szymon Skoczeń
Software Mentions: 2
Published: over 5 years ago

10.1002/iid3.375

Data mining combined with experiments to validate CEP55 as a prognostic biomarker in colorectal cancer
Cited by: 8
Author(s): Lin Kang, Xiaojian Zhu, Chen Luo, Fanqin Bu, Jinfeng Zhu, Zhengming Zhu
Software Mentions: 2
Published: almost 6 years ago

10.1177/1352458520943768

Methylome and transcriptome signature of bronchoalveolar cells from multiple sclerosis patients in relation to smoking
Cited by: 11
Author(s): Mikael V. Ringh, Michael Hagemann-Jensen, Maria Needhamsen, Susanna Kullberg, Jan Wahlström, Johan Grünewald, Boel Brynedal, Maja Jagodic, Tomas J. Ekström, Johan Öckinger, Lara Kular
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2229-8-32

Spatial distribution of transcript changes in the maize primary root elongation zone at low water potential
Cited by: 92
Author(s): William G. Spollen, Wen-Jing Tao, Babu Valliyodan, Kegui Chen, Lindsey G. Hejlek, Jong-Joo Kim, Mary E. LeNoble, Jinming Zhu, Hans J. Bohnert, David A. Henderson, Daniel P. Schachtman, Georgia Davis, Gordon K. Springer, Robert E. Sharp, Henry T. Nguyen
Software Mentions: 2
Published: over 18 years ago

10.7150/ijbs.56357

Targeting HLA-F suppresses the proliferation of glioma cells via a reduction in hexokinase 2-dependent glycolysis
Cited by: 8
Author(s): Xin Chen, Na Sun, Rongqin Li, Xuejia Sang, Xueqin Li, Jie Zhao, Jing Han, Jing Yang, Takayuki Ikezoe
Software Mentions: 2
Published: over 5 years ago

10.1186/s12935-020-01331-7

Identification of methylation-driven genes related to the prognosis of papillary renal cell carcinoma: a study based on The Cancer Genome Atlas
Cited by: 13
Author(s): Zeyu Liu, Yuxiang Wan, Ming Yang, Xuewei Qi, Zhenzhen Dong, Jinchang Huang, Jingnan Xu
Software Mentions: 2
Published: over 6 years ago

10.1111/imcb.12399

GPR43 regulates marginal zone B‐cell responses to foreign and endogenous antigens
Cited by: 9
Author(s): Leona Rohrbeck, Mónika Ádori, Shan Wang, Chenfei He, Christopher Andrew Tibbitt, Mark Chernyshev, Madle Sirel, Ulf Ribacke, Ben Murrell, Mohammad Bohlooly‐Y, Mikael C. I. Karlsson, Gunilla B. Karlsson Hedestam, Jonathan M. Coquet
Software Mentions: 2
Published: almost 6 years ago

10.7150/ijbs.58876

Prognostic value of LRRC4C in Colon and Gastric Cancers correlates with Tumour Microenvironment Immunity
Cited by: 5
Author(s): Xiaofeng Yang, Purun Lei, Lijun Huang, X. Tang, Bo Wei, Wei H
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2015.00171

Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study
Cited by: 24
Author(s): Andreas Dix, Kerstin Hünniger, Michael Weber, Reinhard Guthke, Oliver Kurzai, Jörg Linde
Software Mentions: 2
Published: over 11 years ago

10.2196/18387

Personal Health Information Inference Using Machine Learning on RNA Expression Data from Patients With Cancer: Algorithm Validation Study
Cited by: 4
Author(s): Solbi Kweon, Jeong Hoon Lee, Younghee Lee, Yu Rang Park
Software Mentions: 2
Published: about 6 years ago

10.3390/ijms21239029

An Automated Functional Annotation Pipeline That Rapidly Prioritizes Clinically Relevant Genes for Autism Spectrum Disorder
Cited by: 1
Author(s): Olivia J. Veatch, Merlin G. Butler, Sarah H. Elsea, Beth A. Malow, James S. Sutcliffe, Jason H. Moore
Software Mentions: 2
Published: almost 6 years ago

10.3389/fimmu.2019.01535

IL-6 Mediated Transcriptional Programming of Naïve CD4+ T Cells in Early Rheumatoid Arthritis Drives Dysregulated Effector Function
Cited by: 14
Author(s): Laura A. Ridgley, Amy E. Anderson, Nicola J Maney, Najib Naamane, Andrew Skelton, Catherine A. Lawson, Paul Emery, John D. Isaacs, Ruaidhrı́ J. Carmody, Arthur G. Pratt
Software Mentions: 2
Published: about 7 years ago

10.3389/fpls.2019.01323

Transcriptome Analysis of the Hierarchical Response of Histone Deacetylase Proteins That Respond in an Antagonistic Manner to Salinity Stress
Cited by: 13
Author(s): Minoru Ueda, Atsushi Matsui, S. Watanabe, Makoto Kobayashi, Kazuki Saito, Maho Tanaka, Junko Ishida, Miyako Kusano, Mitsunori Seo, Motoaki Seki
Software Mentions: 2
Published: almost 7 years ago

10.1186/s11689-018-9237-x

Strong correlation of downregulated genes related to synaptic transmission and mitochondria in post-mortem autism cerebral cortex
Cited by: 43
Author(s): Matthew Schwede, Shailender Nagpal, Michael J. Gandal, Neelroop N. Parikshak, Károly Mirnics, Daniel H. Geschwind, Eric M. Morrow
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0249374

Tumor microenvironment characterization in cervical cancer identifies prognostic relevant gene signatures
Cited by: 6
Author(s): Linyu Peng, Gati Hayatullah, Haïyan Zhou, Shuzhen Chang, Liya Liu, Haifeng Qiu, Xiaoran Duan, Han Liang
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2016.00326

Influence of Light and Temperature on Gene Expression Leading to Accumulation of Specific Flavonol Glycosides and Hydroxycinnamic Acid Derivatives in Kale (Brassica oleracea var. sabellica)
Cited by: 46
Author(s): Susanne Neugart, Angelika Krumbein, Rita Zrenner
Software Mentions: 2
Published: over 10 years ago

10.3390/nu9020116

Effects of an Encapsulated Fruit and Vegetable Juice Concentrate on Obesity-Induced Systemic Inflammation: A Randomised Controlled Trial
Cited by: 25
Author(s): Evan J. Williams, Katherine J. Baines, Bronwyn S. Berthon, Lisa G. Wood
Software Mentions: 2
Published: over 9 years ago

10.1038/s41385-019-0209-6

Impact of chemokine C–C ligand 27, foreskin anatomy and sexually transmitted infections on HIV-1 target cell availability in adolescent South African males
Cited by: 11
Author(s): Clive M. Gray, Kyle Leonard O’Hagan, Ramón Lorenzo-Redondo, Abraham J. Olivier, Sylvie Amu, Nyaradzo T. L. Chigorimbo‐Murefu, Rushil Harryparsad, Shorok Sebaa, Lungile Maziya, Janan Dietrich, Kennedy Otwombe, Neil Martinson, Selena Ferrian, Nonhlanhla N. Mkhize, David A. Lewis, Dirk Lang, Ann M. Carias, Heather B. Jaspan, Douglas P. Wilson, Marcus McGilvray, Gianguido C. Cianci, Meegan R. Anderson, Minh Dinh, Anna‐Lise Williamson, Jo Ann S Passmore, Francesca Chiodi, Thomas J. Hope
Software Mentions: 2
Published: over 6 years ago

10.1186/s12935-021-01854-7

Pentraxin 3 is a diagnostic and prognostic marker for ovarian epithelial cancer patients based on comprehensive bioinformatics and experiments
Cited by: 9
Author(s): Xiaolin Chang, Dan Li, Chang Liu, Zhe Zhang, Tao Wang
Software Mentions: 2
Published: over 5 years ago

10.1038/s41385-020-0277-7

Deficiency in the glycosyltransferase Gcnt1 increases susceptibility to tuberculosis through a mechanism involving neutrophils
Cited by: 17
Author(s): Kaori L. Fonseca, Ana Raquel Maceiras, Rita Matos, Luísa Simões-Costa, Jeremy Sousa, Baltazar Cá, Leandro Barros, Ana Fernandes, Stefan Mereiter, R. L. Reis, Joana Gomes, Gustavo Tapia, Paula Rodríguez-Martínez, Montse Martín-Céspedes, Sergo Vashakidze, Shota Gogishvili, Keti Nikolaishvili, Rui Appelberg, Fátima Gärtner, Pedro Rodrigues, Cristina Vilaplana, Celso A. Reis, Ana Magalhães, Margarida Saraiva
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0001200

Covert Genetic Selections to Optimize Phenotypes
Cited by: 0
Author(s): Di Wu, Elizabeth Townsley, Alan M. Tartakoff
Software Mentions: 2
Published: almost 19 years ago

10.3389/fpls.2016.01055

Phytochrome and Ethylene Signaling Integration in Arabidopsis Occurs via the Transcriptional Regulation of Genes Co-targeted by PIFs and EIN3
Cited by: 22
Author(s): Jinkil Jeong, Keunhwa Kim, Mi Eon Kim, Hye Gi Kim, Gwi Suk Heo, Ohkmae Kim Park, Youn‐Il Park, Giltsu Choi, Eunkyoo Oh
Software Mentions: 2
Published: about 10 years ago

10.1172/jci.insight.93739

Neonatal and adult recent thymic emigrants produce IL-8 and express complement receptors CR1 and CR2
Cited by: 43
Author(s): Marcin Ł. Pękalski, Arcadio Rubio Garćıa, Ricardo C. Ferreira, Daniel B. Rainbow, Deborah J. Smyth, Meghavi Mashar, Jane Brady, Natalia Savinykh, Xaquín Castro Dopico, Sumiyya Mahmood, Simon Duley, Helen Stevens, Neil Walker, Antony J. Cutler, Frank Waldron‐Lynch, David B. Dunger, Claire Shannon-Lowe, Alasdair Coles, Joanne L. Jones, Chris Wallace, John A. Todd, Linda S. Wicker
Software Mentions: 2
Published: about 9 years ago

10.1186/s13046-020-01624-9

Long non-coding RNA CASC9 promotes tumor growth and metastasis via modulating FZD6/Wnt/β-catenin signaling pathway in bladder cancer
Cited by: 29
Author(s): Yonghao Zhan, Lianghao Zhang, Shuanbao Yu, Jianguo Wen, Yuchen Liu, Xuepei Zhang
Software Mentions: 2
Published: about 6 years ago

10.1186/1742-2094-5-48

Neurological and behavioral abnormalities, ventricular dilatation, altered cellular functions, inflammation, and neuronal injury in brains of mice due to common, persistent, parasitic infection
Cited by: 175
Author(s): Gretchen Hermes, James W. Ajioka, Krystyna A. Kelly, Ernest Mui, Fiona Roberts, Kristen Kasza, Thomas Mayr, Michael J. Kirisits, Robert L. Wollmann, David J. P. Ferguson, Craig W. Roberts, Jong Hee Hwang, Toria Trendler, Richard P. Kennan, Yasuhiro Suzuki, Catherine A. Reardon, William F. Hickey, Lieping Chen, Rima McLeod
Software Mentions: 2
Published: almost 18 years ago

10.1186/s13046-020-01646-3

IFI6 depletion inhibits esophageal squamous cell carcinoma progression through reactive oxygen species accumulation via mitochondrial dysfunction and endoplasmic reticulum stress
Cited by: 44
Author(s): Zhenchuan Liu, Shaorui Gu, Tiancheng Lu, Kaiqing Wu, Lei Li, Chunyan Dong, Yilu Zhou
Software Mentions: 2
Published: about 6 years ago

10.1186/s12935-020-01180-4

Identification of novel biomarkers affecting the metastasis of colorectal cancer through bioinformatics analysis and validation through qRT-PCR
Cited by: 10
Author(s): Wenping Lian, Jin Huang, Jingjing Cao, Xinyu Zhang, Tao Zhu, Shuai Zhao, Sujuan Wu, Kailu Zou, Xinyun Zhang, Mingliang Zhang, Xiaoli Zheng, Mengle Peng
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2019.00023

Identification of Important Effector Proteins in the FOXJ1 Transcriptional Network Associated With Ciliogenesis and Ciliary Function
Cited by: 23
Author(s): Ishita Mukherjee, Sudipto Roy, Saikat Chakrabarti
Software Mentions: 2
Published: over 7 years ago

10.1186/s13046-020-01757-x

The molecular and gene/miRNA expression profiles of radioiodine resistant papillary thyroid cancer
Cited by: 21
Author(s): Carla Colombo, Emanuela Minna, Chiara Gargiuli, Marina Muzza, Matteo Dugo, Loris De Cecco, Gabriele Pogliaghi, Delfina Tosi, Gaetano Bulfamante, Angela Greco, Laura Fugazzola, Maria Grazia Borrello
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.ppat.1008468

Human papillomavirus E7 binds Oct4 and regulates its activity in HPV-associated cervical cancers
Cited by: 13
Author(s): Theofano Panayiotou, Stella Michael, Apostolos Zaravinos, Ece Demirag, Charis Achilleos, Katerina Strati
Software Mentions: 2
Published: over 6 years ago

10.1186/s12935-020-01271-2

Identification of immune-related biomarkers associated with tumorigenesis and prognosis in cutaneous melanoma patients
Cited by: 40
Author(s): Biao Huang, Wei Han, Zu-Feng Sheng, Ge Shen
Software Mentions: 2
Published: over 6 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776