bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1111/jcmm.16419

Circular RNA circANAPC2 mediates the impairment of endochondral ossification by miR‐874‐3p/SMAD3 signalling pathway in idiopathic short stature
Cited by: 12
Author(s): Xijuan Liu, Du Zhi, Xuan Yao, Tianle Sheng, Jinghong Yuan, Jingyu Jia
Software Mentions: 2
Published: over 5 years ago

10.1111/jcmm.16402

Integrated study of miR‐215 promoting breast cancer cell apoptosis by targeting RAD54B
Cited by: 8
Author(s): Mingyuan Wang, Jingnan Liao, Chang Tan, Hong Zhou, Jinjin Wang, Kangkai Wang, Yiming Li, Wei Wu
Software Mentions: 2
Published: over 5 years ago

10.1111/jcmm.16494

Construction of an immune‐related LncRNA signature with prognostic significance for bladder cancer
Cited by: 15
Author(s): Wenjie Luo, Xi Tian, Wenhao Xu, Yuanyuan Qu, Wenkai Zhu, Jie Wu, Chao Ma, Hai-Liang Zhang, Dingwei Ye, Yiping Zhu
Software Mentions: 2
Published: over 5 years ago

10.1111/jcmm.16439

Fructose‐1,6‐bisphosphatase aggravates oxidative stress‐induced apoptosis in asthma by suppressing the Nrf2 pathway
Cited by: 9
Author(s): Jiapeng Hu, Jia Wang, Chunlu Li, Yunxiao Shang
Software Mentions: 2
Published: over 5 years ago

10.1111/jcmm.16612

MiR‐193b deregulation is associated with Parkinson's disease
Cited by: 13
Author(s): Masoud Baghi, Elaheh Yadegari, Mohsen Rostamian Delavar, Maryam Peymani, Mazdak Ganjalikhani‐Hakemi, Mehri Salari, Mohammad Hossein Nasr-Esfahani, Timothy L. Megraw, Kamran Ghaedi
Software Mentions: 2
Published: over 5 years ago

10.1002/jcp.27049

Intratumor lactate levels reflect HER2 addiction status in HER2‐positive breast cancer
Cited by: 29
Author(s): Lorenzo Castagnoli, Egidio Iorio, Matteo Dugo, Ada Koschorke, Simona Faraci, Rossella Canese, Patrizia Casalini, Patrizia Nanni, Claudio Vernieri, Massimo Di Nicola, Daniele Morelli, Elda Tagliabue, Serenella M. Pupa
Software Mentions: 2
Published: about 8 years ago

10.1002/jcp.29067

Identification of hub genes and construction of transcriptional regulatory network for the progression of colon adenocarcinoma hub genes and TF regulatory network of colon adenocarcinoma
Cited by: 23
Author(s): Shuxun Wei, Jinshui Chen, Yu Fang Huang, Qiang Sun, Haolu Wang, Xiaowen Liang, Zhiqian Hu, Xinxing Li
Software Mentions: 2
Published: almost 7 years ago

10.1186/1758-2946-5-30

Drug repositioning: a machine-learning approach through data integration
Cited by: 255
Author(s): Francesco Napolitano, Yan Zhao, Vânia M. Moreira, Roberto Tagliaferri, Juha Kere, Mauro D’Amato, Dario Greco
Software Mentions: 2
Published: about 13 years ago

10.1111/jcpp.12740

Longitudinal epigenetic predictors of amygdala:hippocampus volume ratio
Cited by: 26
Author(s): Esther Walton, Charlotte A.M. Cecil, Matthew Suderman, Jingyu Liu, Jessica A. Turner, Vince D. Calhoun, Stefan Ehrlich, Caroline L Relton, Edward D. Barker
Software Mentions: 2
Published: over 9 years ago

10.1210/clinem/dgab072

Differential Mitochondrial Gene Expression in Adipose Tissue Following Weight Loss Induced by Diet or Bariatric Surgery
Cited by: 12
Author(s): Birgitta W. van der Kolk, Maheswary Muniandy, Dorota Kaminska, Marcus Alvarez, Arthur Ko, Min‐Hua Zong, Armand Valsesia, Dominique Langin, Maija Vaittinen, Mirva Pääkkönen, Riikka Jokinen, Sanna Kaye, Sini Heinonen, Kirsi A. Virtanen, Daniel P. Andersson, Ville Männistö, Wim H. M. Saris, Arne Astrup, Mikael Rydén, Ellen E. Blaak, Päivi Pajukanta, Jussi Pihlajamäki, Kirsi H. Pietiläinen
Software Mentions: 2
Published: over 5 years ago

10.1172/JCI124725

microRNA-142–mediated repression of phosphodiesterase 3B critically regulates peripheral immune tolerance
Cited by: 38
Author(s): Nelomi Anandagoda, Joanna Willis, Arnulf Hertweck, Luke B. Roberts, Ian Jackson, M. Refik Gökmen, Richard G. Jenner, Jane K. Howard, Graham M. Lord
Software Mentions: 2
Published: over 7 years ago

10.1172/JCI86924

Extracellular matrix proteomics identifies molecular signature of symptomatic carotid plaques
Cited by: 108
Author(s): Sarah R. Langley, Karin Willeit, Athanasios Didangelos, Ljubica Matic, Philipp Skroblin, Javier Barallobre-Barreiro, Mariette Lengquist, Gregor Rungger, Alexander Kapustin, Ludmilla Kedenko, Chris Molenaar, Ruifang Lu, Temo Barwari, Gonca Suna, Xiaoke Yin, Bernhard Iglseder, Bernhard Paulweber, Peter Willeit, Joseph Shalhoub, Gérard Pasterkamp, Alun H. Davies, Claudia Monaco, Ulf Hedin, Catherine M. Shanahan, Johann Willeit, Stefan Kiechl, Manuel Mayr
Software Mentions: 2
Published: over 9 years ago

10.1172/JCI134132

Orally bioavailable CDK9/2 inhibitor shows mechanism-based therapeutic potential in MYCN-driven neuroblastoma
Cited by: 38
Author(s): Evon Poon, Tong Liang, Yann Jamin, Susanne Walz, Colin Kwok, Anne Hakkert, Karen Barker, Zuzanna Urban, Khin Thway, Rhamy Zeid, Albert Hallsworth, Gary Box, Marli E. Ebus, Marco P. Licciardello, Yordan Sbirkov, Glori Lazaro, Elizabeth Calton, Barbara Martins Da Costa, Melanie Valenti, Alexis de Haven Brandon, Hannah Webber, Nicolas Tardif, Gilberto S. Almeida, Rossitza Christova, Gunther Boysen, Mark W. Richards, Giuseppe Barone, Anthony M. Ford, Richard Bayliss, Paul A. Clarke, Johann S. de Bono, Nathanael S. Gray, Julian Blagg, Simon P. Robinson, Suzanne A. Eccles, Daniella Zheleva, James E. Bradner, Jan J. Molenaar, Igor Vivanco, Martin Eilers, Paul Workman, Charles Y. Lin, Louis Chesler
Software Mentions: 2
Published: almost 6 years ago

10.1002/jcla.23428

Hsa_circ_0023642 promotes proliferation, invasion, and migration of gastric cancer by sponging microRNA‐223
Cited by: 6
Author(s): Yi Zhang, Lei Xia, Jing Wu, Xinyu Xu, Gang Li
Software Mentions: 2
Published: about 6 years ago

10.3390/jcm7110419

Unique MicroRNA and mRNA Interactions in EGFR-Mutated Lung Adenocarcinoma
Cited by: 13
Author(s): Sophia Subat, Kentaro Inamura, Hironori Ninomiya, Hiroko Nagano, Sakae Okumura
Software Mentions: 2
Published: almost 8 years ago

10.3390/jcm8111772

A CTC-Cluster-Specific Signature Derived from OMICS Analysis of Patient-Derived Xenograft Tumors Predicts Outcomes in Basal-Like Breast Cancer
Cited by: 35
Author(s): Hariprasad Thangavel, Carmine De Angelis, Suhas Vasaikar, Raksha Bhat, Mohit Kumar Jolly, Chandandeep Nagi, Chad J. Creighton, Ken Chen, Lacey E. Dobrolecki, Jason T. George, Tanya Kumar, Noor Mazin Abdulkareem, Sufeng Mao, Agostina Nardone, Mothaffar F. Rimawi, C. Kent Osborne, Michael T. Lewis, Herbert Levine, Bing Zhang, Rachel Schiff, Mario Giuliano, Meghana V. Trivedi
Software Mentions: 2
Published: almost 7 years ago

10.3390/jcm9051338

Genome-Wide Analysis of the DNA Methylation Profile Identifies the Fragile Histidine Triad (FHIT) Gene as a New Promising Biomarker of Crohn’s Disease
Cited by: 8
Author(s): Tae-Oh Kim, Dong Il Park, Yu Han, Keunsoo Kang, Sae-Gwang Park, Hae Ryoun Park, Joo Mi Yi
Software Mentions: 2
Published: over 6 years ago

10.3390/jcm10122680

Methylation Status of Corticotropin-Releasing Factor (CRF) Receptor Genes in Colorectal Cancer
Cited by: 8
Author(s): Μαρία Παναγοπούλου, Antonia Cheretaki, Makrina Karaglani, Ioanna Balgkouranidou, Eirini Biziota, Kyriakos Amarantidis, Nikolaos Xenidis, Stylianos Kakolyris, Stavroula Baritaki, Εkaterini Chatzaki
Software Mentions: 2
Published: over 5 years ago

10.1155/2020/4178639

Identification of Susceptibility Modules and Genes for Cardiovascular Disease in Diabetic Patients Using WGCNA Analysis
Cited by: 41
Author(s): Weiwei Liang, Fangfang Sun, Yingxin Zhao, Peng-Fei Shan, Han-Yu Lou
Software Mentions: 2
Published: over 6 years ago

10.1093/jxb/erv285

TheIDA/IDA-LIKEandPIP/PIP-LIKEgene families inArabidopsis: phylogenetic relationship, expression patterns, and transcriptional effect of the PIPL3 peptide
Cited by: 64
Author(s): Ane Kjersti Vie, Javad Najafi, Bin Liu, Per Winge, Melinka A. Butenko, Karina S. Hornslien, Robert P. Kumpf, Reidunn B. Aalen, Atle M. Bones, Tore Brembu
Software Mentions: 2
Published: over 11 years ago

10.1093/jxb/erv516

Kresoxim-methyl primesMedicago truncatulaplants against abiotic stress factors via altered reactive oxygen and nitrogen species signalling leading to downstream transcriptional and metabolic readjustment
Cited by: 28
Author(s): Panagiota Filippou, Chrystalla Antoniou, Toshihiro Obata, Katrien Van Der Kelen, Vaggelis Harokopos, Loukas Kanetis, Vassilis Aidinis, Frank Van Breusegem, Alisdair R. Fernie, Vasileios Fotopoulos
Software Mentions: 2
Published: over 10 years ago

10.1093/jxb/erw350

The build-up of osmotic stress responses within the growing root apex using kinematics and RNA-sequencing
Cited by: 12
Author(s): Mathilde Royer, David Cohen, Nathalie Aubry, Vera Vendramin, Simone Scalabrin, Federica Cattonaro, Marie‐Béatrice Bogeat‐Triboulot, Irène Hummel
Software Mentions: 2
Published: almost 10 years ago

10.1093/jxb/erx168

The IDA-LIKE peptides IDL6 and IDL7 are negative modulators of stress responses in Arabidopsis thaliana
Cited by: 28
Author(s): Ane Kjersti Vie, Javad Najafi, Per Winge, Ester Cattan, Michael Wrzaczek, Jaakko Kangasjärvi, Gad Miller, Tore Brembu, Atle M. Bones
Software Mentions: 2
Published: over 9 years ago

10.1093/jxb/erx254

Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana
Cited by: 43
Author(s): Pavel Cherenkov, Daria D. Novikova, N. A. Omelyanchuk, Victor G. Levitsky, Ivo Große, Dolf Weijers, В. В. Миронова
Software Mentions: 2
Published: about 9 years ago

10.1093/jxb/erw474

Nod factors potentiate auxin signaling for transcriptional regulation and lateral root formation inMedicago truncatula
Cited by: 15
Author(s): Violaine Herrbach, Ximena Chirinos, David Rodrı́guez-Lázaro, Kokoévi Agbévénou, Rémy Vincent, Stéphanie Pateyron, Stéphanie Huguet, Sandrine Balzergue, Asher Pasha, Nicholas J. Provart, Clare Gough, Sandra Bensmihen
Software Mentions: 2
Published: over 9 years ago

10.1093/jxb/eraa099

Transcriptional analysis of arogenate dehydratase genes identifies a link between phenylalanine biosynthesis and lignin biosynthesis
Cited by: 9
Author(s): Jorge El-Azaz, Fernando De la Torre, María Belén Pascual, Sandrine Debille, Francis Canlet, Luc Harvengt, Jean-François Trontin, Concepción Ávila
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1000604

Lethal Influenza Virus Infection in Macaques Is Associated with Early Dysregulation of Inflammatory Related Genes
Cited by: 197
Author(s): Cristian Cillóniz, Kyoko Shinya, Xinxia Peng, Marcus J. Korth, Sean Proll, Lauri Aicher, Victoria S. Carter, Jean Chang, Darwyn Kobasa, Friedericke Feldmann, James E. Strong, Heinz Feldmann, Yoshihiro Kawaoka, Michael G. Katze
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.ppat.1002315

Severe Acute Respiratory Syndrome Coronavirus Envelope Protein Regulates Cell Stress Response and Apoptosis
Cited by: 175
Author(s): Marta L. DeDiego, José L. Nieto-Torres, Jose M. Jiménez-Guardeño, José Ángel Regla-Nava, Enrique Álvarez, Juan Carlos Oliveros, Jincun Zhao, Craig Fett, Stanley Perlman, Luis Enjuanes
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.ppat.1004079

Exposure-Dependent Control of Malaria-Induced Inflammation in Children
Cited by: 135
Author(s): Sílvia Portugal, Jacqueline Moebius, Jeff Skinner, Safiatou Doumbo, Didier Doumtabé, Younoussou Koné, Seydou Dia, Kishore Kanakabandi, Daniel E. Sturdevant, Kimmo Virtaneva, Stephen F. Porcella, Shanping Li, Ogobara K. Doumbo, Kassoum Kayentao, Aissata Ongoïba, Boubacar Traoré, Peter D. Crompton
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.ppat.1004662

Prion Infections and Anti-PrP Antibodies Trigger Converging Neurotoxic Pathways
Cited by: 74
Author(s): U. Herrmann, Tiziana Sonati, Jeppe Falsig, Regina Reimann, Paolo Dametto, Tracy O’Connor, Bei Li, Agnes Lau, Simone Hornemann, Silvia Sorce, Uli Wagner, Despina Sanoudou, Adriano Aguzzi
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.ppat.1005263

Interferon-γ Inhibits Ebola Virus Infection
Cited by: 69
Author(s): Bethany A. Rhein, Linda S. Powers, Kai J. Rogers, Manu Anantpadma, Brajesh K. Singh, Yoshio Sakurai, Thomas B. Bair, Catherine L. Miller-Hunt, Patrick L. Sinn, Robert A. Davey, Martha M. Monick, Wendy Maury
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.ppat.1005936

Combined Activity of DCL2 and DCL3 Is Crucial in the Defense against Potato Spindle Tuber Viroid
Cited by: 49
Author(s): Κωνσταντίνα Κατσαρού, Eleni Mavrothalassiti, Wannes Dermauw, Thomas Van Leeuwen, Kriton Kalantidis
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.ppat.1006576

Malaria-induced interferon-γ drives the expansion of Tbethi atypical memory B cells
Cited by: 122
Author(s): Nyamekye Obeng-Adjei, Sílvia Portugal, Prasida Holla, Shanping Li, Hyung Sun Sohn, Abhijit A. Ambegaonkar, Jeff Skinner, Georgina Bowyer, Ogobara K. Doumbo, Boubacar Traoré, Susan K. Pierce, Peter D. Crompton
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.ppat.1006788

Lower temperatures reduce type I interferon activity and promote alphaviral arthritis
Cited by: 34
Author(s): Natalie A. Prow, Bing Tang, Joy Gardner, Thuy T. Le, Adam Taylor, Yee Suan Poo, Eri Nakayama, Thiago Dominguez Crespo Hirata, Helder I. Nakaya, Andrii Slonchak, Pamela Mukhopadhyay, Suresh Mahalingam, Wayne A. Schroder, William B. Klimstra, Andreas Suhrbier
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.ppat.1006871

Liver macrophage-associated inflammation correlates with SIV burden and is substantially reduced following cART
Cited by: 18
Author(s): Bridget S. Fisher, Richard Green, Rachel Brown, Matthew P. Wood, Tiffany Hensley-McBain, Cole Fisher, Jean Chang, Andrew D. Miller, William J. Bosche, Jeffrey D. Lifson, Maud Mavigner, Charlene Miller, Michael Gale, Guido Silvestri, Ann Chahroudi, Nichole R. Klatt, Donald L. Sodora
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.ppat.1007276

Cellular sheddases are induced by Merkel cell polyomavirus small tumour antigen to mediate cell dissociation and invasiveness
Cited by: 24
Author(s): Nnenna Nwogu, James R. Boyne, Samuel J. Dobson, Krzysztof Poterlowicz, G. Eric Blair, Andrew Macdonald, Jamel Mankouri, Adrian Whitehouse
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.ppat.1007298

Microvesicles from malaria-infected red blood cells activate natural killer cells via MDA5 pathway
Cited by: 48
Author(s): Weijian Ye, Marvin Chew, Jue Hou, Fritz Lai, Stije J. Leopold, Hooi Linn Loo, Aniruddha Ghose, A. K. Dutta, Yi‐Ping Phoebe Chen, Eng Eong Ooi, Nicholas J. White, Arjen M. Dondorp, Peter R. Preiser, Jianzhu Chen
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.ppat.1007528

Antagonistic paralogs control a switch between growth and pathogen resistance in C. elegans
Cited by: 62
Author(s): Kirthi C. Reddy, Tal Dror, Ryan Underwood, Guled A. Osman, Corrina R. Elder, Christopher A. Desjardins, Christina A. Cuomo, Michalis Barkoulas, Emily R. Troemel
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007684

The TLR4 adaptor TRAM controls the phagocytosis of Gram-negative bacteria by interacting with the Rab11-family interacting protein 2
Cited by: 26
Author(s): Astrid Skjesol, Mariya Yurchenko, Korbinian Bösl, Caroline S. Gravastrand, Kaja Elisabeth Nilsen, Lene Melsæther Grøvdal, Federica Agliano, Francesco Patanè, Germana Lentini, Hera Kim, Giuseppe Teti, A. Sharma, Richard K. Kandasamy, Bjørnar Sporsheim, Kristian K. Starheim, Douglas T. Golenbock, Harald Stenmark, Mary W. McCaffrey, Terje Espevik, Harald Husebye
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007748

CD8+ T cells retain protective functions despite sustained inhibitory receptor expression during Epstein-Barr virus infection in vivo
Cited by: 42
Author(s): Bithi Chatterjee, Yun Deng, Angelika Holler, Nicolás Gonzalo Núñez, Tarik Azzi, Liliana Danusia Vanoaica, Anne Müller, Hana Zdimerova, Olga Antsiferova, Andrea Zbinden, Riccarda Capaul, Johannes H. Dreyer, David Nadal, Burkhard Becher, Mark D. Robinson, Hans J. Stauss, Christian Münz
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007841

DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes
Cited by: 37
Author(s): Taylor M. Nye, Kristin M. Jacob, Elena K. Holley, Juan M Nevarez, Suzanne Dawid, Lyle A. Simmons, Michael Watson
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007880

Systems analysis of subjects acutely infected with the Chikungunya virus
Cited by: 26
Author(s): Alessandra Soares‐Schanoski, Natália Baptista Cruz, Luíza Antunes de Castro-Jorge, Roberto Gameiro de Carvalho, Cliomar Alves dos Santos, Nancy da Rós, Ursula de Oliveira, Danuza Duarte Costa, Cecília Luiza Simões Santos, Marielton dos Passos Cunha, Maria Leonor S. Oliveira, Juliana Cardoso Alves, Regina Adalva de Lucena Couto Océa, Danielle Rodrigues Ribeiro, André Nicolau Aquime Gonçalves, Patrícia Gonzalez-Dias, Andreas Suhrbier, Paolo Marinho de Andrade Zanotto, Inácio L.M. Junqueira-de-Azevedo, Dario S. Zamboni, Roque Pacheco de Almeida, Paulo Lee Ho, Jorge Kalil, Milton Yutaka Nishiyama-Jr, Helder I. Nakaya
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1007960

Dafachronic acid promotes larval development in Haemonchus contortus by modulating dauer signalling and lipid metabolism
Cited by: 31
Author(s): Guangxu Ma, Tao Wang, Pasi K. Korhonen, Neil D. Young, Shuai Nie, Ching‐Seng Ang, Nicholas A. Williamson, Gavin E. Reid, Robin B. Gasser
Software Mentions: 2
Published: about 7 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

10.1155/2020/6527564

The Role of Peroxisome Proliferator-Activated Receptors (PPARs) in Pan-Cancer
Cited by: 12
Author(s): Runzhi Huang, Jiaqi Zhang, Mingxiao Li, Penghui Yan, Huabin Yin, Suna Zhai, Xiaolong Zhu, Peng Hu, Jiaxin Zhang, Ling Huang, Man Li, Zehui Sun, Tong Meng, Daoke Yang, Zongqiang Huang
Software Mentions: 2
Published: almost 6 years ago

10.1073/pnas.2000943117

Macrophage metabolic reprogramming presents a therapeutic target in lupus nephritis
Cited by: 70
Author(s): Chenzhi Jing, Tomas Castro‐Dopico, Nathan Richoz, Zewen Kelvin Tuong, John R. Ferdinand, Laurence S.C. Lok, Kevin Loudon, Gemma D. Banham, Rebeccah J. Mathews, M Zaeem Cader, Susan F. Fitzpatrick, Kathleen R. Bashant, Mariana J. Kaplan, Arthur Kaser, Randall S. Johnson, Michael P. Murphy, Richard M. Siegel, Menna R. Clatworthy
Software Mentions: 2
Published: over 6 years ago

10.1073/pnas.2008762117

Single-nucleus transcriptome analysis reveals dysregulation of angiogenic endothelial cells and neuroprotective glia in Alzheimer’s disease
Cited by: 200
Author(s): Shun‐Fat Lau, Han Cao, Amy Kit Yu Fu, Nancy Y. Ip
Software Mentions: 2
Published: almost 6 years ago

10.1002/pros.23222

Accumulation of Palmitoylcarnitine and Its Effect on Pro‐Inflammatory Pathways and Calcium Influx in Prostate Cancer
Cited by: 21
Author(s): Ala'a Al‐Bakheit, Μαρία Τράκα, Shikha Saha, Richard Mithen, Antonietta Melchini
Software Mentions: 2
Published: about 10 years ago

10.3390/proteomes8030025

Serum Glycoproteomic Alterations in Patients with Diabetic Retinopathy
Cited by: 3
Author(s): Ashok Sharma, James Shell Cox, Joshua Glass, Tae Jin Lee, Sai Karthik Kodeboyina, Wenbo Zhi, Lane Ulrich, Zachary L. Lukowski, Shruti Sharma
Software Mentions: 2
Published: about 6 years ago

10.1098/rsos.160033

Domestication and tameness: brain gene expression in red junglefowl selected for less fear of humans suggests effects on reproduction and immunology
Cited by: 24
Author(s): Johan Bélteky, Beatrix Agnvall, Martin Johnsson, I. A. Wright, Per Jensen
Software Mentions: 2
Published: about 10 years ago

10.1186/1748-717X-9-111

Integrating microRNA and mRNA expression profiles in response to radiation-induced injury in rat lung
Cited by: 27
Author(s): Ling Xie, Jundong Zhou, Shuyu Zhang, Qing Chen, Renchun Lai, Wei‐Qun Ding, Chuanjun Song, Xingjun Meng, Jinchang Wu
Software Mentions: 2
Published: over 12 years ago

10.1186/s13014-018-1129-4

Molecular signature of response to preoperative radiotherapy in locally advanced breast cancer
Cited by: 14
Author(s): Miljana Tanić, Ana Krivokuća, Milena Čavić, Jasmina Mladenović, Vesna Plešinac Karapandžić, Stephan Beck, Siniša Radulović, Snežana Šušnjar, Radmila Janković
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13014-020-01620-5

Transcriptome network of the papillary thyroid carcinoma radiation marker CLIP2
Cited by: 1
Author(s): Martin Selmansberger, Agata Michna, Herbert Braselmann, Ines Höfig, Kenji Schorpp, Peter Weber, Nataša Anastasov, Horst Zitzelsberger, Julia Heß, Kristian Unger
Software Mentions: 2
Published: about 6 years ago

10.1016/j.redox.2019.101165

Mitochondria in precision medicine; linking bioenergetics and metabolomics in platelets
Cited by: 31
Author(s): Balu K. Chacko, M. R. Smith, Michelle S. Johnson, Gloria A. Benavides, Matilda Lillian Culp, Jyotsna Pilli, Sruti Shiva, Karan Uppal, Young‐Mi Go, Dean P. Jones, Victor Darley‐Usmar
Software Mentions: 2
Published: over 7 years ago

10.1186/s12958-017-0273-2

Differentiating mouse embryonic stem cells express markers of human endometrium
Cited by: 13
Author(s): Parveen Parasar, Caitlin R. Sacha, Nicholas Ng, E. R. McGuirk, Sireesha Chinthala, Pınar Özcan, J. Suzanne Lindsey, Sophia Salas, Marc R. Laufer, Stacey A. Missmer, Raymond M. Anchan
Software Mentions: 2
Published: about 9 years ago

10.1186/s12958-021-00706-3

Identification of key pathways and genes in polycystic ovary syndrome via integrated bioinformatics analysis and prediction of small therapeutic molecules
Cited by: 14
Author(s): Praveen Devarbhavi, Lata Telang, Basavaraj Vastrad, Anandkumar Tengli, Chanabasayya Vastrad, Iranna Kotturshetti
Software Mentions: 2
Published: over 5 years ago

10.1186/s12958-021-00778-1

Construction of lncRNA-related competing endogenous RNA network and identification of hub genes in recurrent implantation failure
Cited by: 8
Author(s): Jialyu Huang, Ning Song, Leizhen Xia, Lifeng Tian, Jun Tan, Qianqian Chen, Jing Zhu, Qiongfang Wu
Software Mentions: 2
Published: about 5 years ago

10.21203/rs.3.rs-784784/v1

Upper airway gene expression reveals a more robust innate and adaptive immune response to SARS-CoV-2 in children compared with older adults
Cited by: 2
Author(s): Eran Mick, Alexandra Tsitsiklis, Natasha Spottiswoode, Saharai Caldera, Paula Hayakawa Serpa, Angela M. Detweiler, Norma Neff, Angela Oliveira Pisco, Lucy M Li, Hanna Retallack, Kalani Ratnasiri, Kayla Williamson, Victoria Soesanto, Eric A F Simões, Amy Kistler, Brandie D. Wagner, Joseph L. DeRisi, Lilliam Ambroggio, Peter M. Mourani, Charles Langelier
Software Mentions: 2
Published: about 5 years ago

10.1186/s12931-016-0346-3

Gene-expression profiles in lung adenocarcinomas related to chronic wood smoke or tobacco exposure
Cited by: 15
Author(s): Alette Ortega-Gómez, Claudia Rangel‐Escareño, Camilo Molina-Romero, Eleazar Omar Macedo-Pérez, Alejandro Avilés‐Salas, Alejandra Lara-García, Gerardo J. Alanis-Funes, Rubén Rodríguez‐Bautista, Alfredo Hidalgo-Miranda, Óscar Arrieta
Software Mentions: 2
Published: over 10 years ago

10.1186/s12931-020-1317-2

Cigarette smoke and electronic cigarettes differentially activate bronchial epithelial cells
Cited by: 33
Author(s): Christian Herr, Κωνσταντίνος Τσίτουρας, Julia Niederstraßer, Christina Backes, Christoph Beißwenger, Lü Dong, Loïc Guillot, Andreas Keller, Robert Bals
Software Mentions: 2
Published: over 6 years ago

10.1186/s12931-020-01336-w

Heme metabolism genes Downregulated in COPD Cachexia
Cited by: 3
Author(s): A.C. Wilson, Preeti Lakshman Kumar, Sool Lee, Margaret M. Parker, Itika Arora, Jarrett Morrow, Emiel F.M. Wouters, Richard Casaburi, Stephen I. Rennard, David A. Lomas, Àlvar Agustí, Ruth Tal‐Singer, Mark T. Dransfield, James M. Wells, Surya P. Bhatt, George R. Washko, Victor J. Thannickal, Hemant K. Tiwari, Craig P. Hersh, Peter J. Castaldi, Edwin K. Silverman, Merry-Lynn McDonald
Software Mentions: 2
Published: over 6 years ago

10.1186/1742-4690-9-5

Relationships of PBMC microRNA expression, plasma viral load, and CD4+ T-cell count in HIV-1-infected elite suppressors and viremic patients
Cited by: 135
Author(s): Kenneth W. Witwer, Amy P. Watson, Joel N. Blankson, Janice E. Clements
Software Mentions: 2
Published: over 14 years ago

10.1093/rheumatology/key101

Widespread epigenomic, transcriptomic and proteomic differences between hip osteophytic and articular chondrocytes in osteoarthritis
Cited by: 19
Author(s): Julia Steinberg, Brooks Ra, Lorraine Southam, Sahir Bhatnagar, Roumeliotis Ti, Konstantinos Hatzikotoulas, Eleni Zengini, Wilkinson Jm, Jyoti S. Choudhary, Andrew W. McCaskie, Eleftheria Zeggini
Software Mentions: 2
Published: over 8 years ago

10.1016/j.xpro.2020.100219

Mapping protein networks in yeast mitochondria using proximity-dependent biotin identification coupled to proteomics
Cited by: 1
Author(s): Roger Salvatori, Wasim Aftab, Ignasi Forné, Axel Imhof, Martin Ott, Abeer Prakash Singh
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.schres.2019.05.011

Differential gene expression analysis in blood of first episode psychosis patients
Cited by: 23
Author(s): Daniel J. Leirer, Conrad Iyegbe, Marta Di Forti, Hamel Patel, Elena Carra, Sara Fraietta, Marco Colizzi, Valeria Mondelli, Diego Quattrone, John Lally, Olesya Ajnakina, Sang Hyuck Lee, Charles Curtis, Gerome Breen, Carmine Pariante, Katherine J. Aitchison, Paola Dazzan, Robin M. Murray, Richard Dobson, Stephen Newhouse
Software Mentions: 2
Published: about 7 years ago

10.1126/sciadv.aau8389

RUNX represses Pmp22 to drive neurofibromagenesis
Cited by: 10
Author(s): Ashley Hall, Kwangmin Choi, Wei Liu, Jonathan Rose, Chuntao Zhao, Yanan Yu, Youjin Na, Yuqi Cai, Robert A. Coover, Yi Wen Lin, Eva Dombi, Miok Kim, Ditsa Levanon, Yoram Groner, Elisa Boscolo, Dao Pan, P. Paul Liu, Qi Lu, Nancy Ratner, Gang Huang, Jianqiang Wu
Software Mentions: 2
Published: over 7 years ago

10.1126/sciadv.aba8196

A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells
Cited by: 8
Author(s): José Maria Moreira Dias, Zhanna Alekseenko, Ashwini Jeggari, Marcelo Boareto, Jannik Vollmer, M. N. Kozhevnikova, Hui Wang, Michael P. Matise, Andrey Alexeyenko, Dagmar Iber, Johan Ericson
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41597-019-0216-1

Multiomics analysis of tolerant interaction of potato with potato virus Y
Cited by: 11
Author(s): Tjaša Stare, Živa Ramšak, Maja Križnik, Kristina Gruden
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41597-020-0456-0

DNA methylation of chronic lymphocytic leukemia with differential response to chemotherapy
Cited by: 5
Author(s): Deyan Yordanov Yosifov, Johannes Bloehdorn, Hartmut Döhner, Peter Lichter, Stephan Stilgenbauer, Daniel Mertens
Software Mentions: 2
Published: over 6 years ago

10.1038/srep04954

Human leukocyte telomere length is associated with DNA methylation levels in multiple subtelomeric and imprinted loci
Cited by: 86
Author(s): Jessica L. Buxton, Matthew Suderman, Jane J. Pappas, Nada Borghol, Wendy L. McArdle, Alexandra I. F. Blakemore, Clyde Hertzman, Christine Power, Moshe Szyf, Marcus Pembrey
Software Mentions: 2
Published: over 12 years ago

10.1038/srep10775

Relationship between differentially expressed mRNA and mRNA-protein correlations in a xenograft model system
Cited by: 381
Author(s): Antonis Koussounadis, Simon P. Langdon, In Hwa Um, David J. Harrison, V. Anne Smith
Software Mentions: 2
Published: over 11 years ago

10.1038/srep12995

Identifying miRNA/mRNA negative regulation pairs in colorectal cancer
Cited by: 35
Author(s): Xile Zhou, Xiao Xu, Jinhai Wang, Jie Lin, Wenbin Chen
Software Mentions: 2
Published: about 11 years ago

10.1038/srep14392

Expression profile of a Caenorhabditis elegans model of adult neuronal ceroid lipofuscinosis reveals down regulation of ubiquitin E3 ligase components
Cited by: 7
Author(s): Hannah V. McCue, Xi Chen, Jeff W. Barclay, Alan Morgan, Robert D. Burgoyne
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep16882

Mycobacterial infection induces a specific human innate immune response
Cited by: 53
Author(s): John Blischak, Ludovic Tailleux, Amy Mitrano, Luis B. Barreiro, Yoav Gilad
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep20318

Human oral isolate Lactobacillus fermentum AGR1487 induces a pro-inflammatory response in germ-free rat colons
Cited by: 15
Author(s): Rachel C. Anderson, Dulantha Ulluwishewa, Wayne Young, Leigh Ryan, Gemma Henderson, Marjolein Meijerink, Eva Maier, Jerry M. Wells, Nicole C. Roy
Software Mentions: 2
Published: over 10 years ago

10.1038/srep20127

Hepatic circadian clock oscillators and nuclear receptors integrate microbiome-derived signals
Cited by: 87
Author(s): Alexandra Montagner, Agata Korecka, Arnaud Polizzi, Yannick Lippi, Yuna Blum, Cécile Canlet, Marie Tremblay-Franco, Amandine Gautier‐Stein, Rémy Burcelin, Yi-Chun Yen, H. Shawn Je, Maha Al-Asmakh, Gilles Mithieux, Velmurugesan Arulampalam, Sandrine Lagarrigue, Hervé Guillou, Sven Pettersson, Walter Wahli
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-019-45151-w

Locally advanced rectal cancer transcriptomic-based secretome analysis reveals novel biomarkers useful to identify patients according to neoadjuvant chemoradiotherapy response
Cited by: 12
Author(s): Luísa Matos do Canto, Sarah Santiloni Cury, Mateus Camargo Barros-Filho, Bruna Elisa Catin Kupper, Maria D. Begnami, Cristovam Scapulatempo‐Neto, Robson Francisco Carvalho, Fábio Albuquerque Marchi, Dorte Aalund Olsen, Jonna Skov Madsen, Birgitte Mayland Havelund, Samuel Aguiar, Sílvia Regina Rogatto
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-45371-0

Effect of heritable symbionts on maternally-derived embryo transcripts
Cited by: 4
Author(s): Mariana Mateos, Nadisha O. Silva, Paulino Ramirez, Victor M. Higareda‐Alvear, Rodolfo Aramayo, James Erickson
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-46331-4

Anti-inflammatory nutrition with high protein attenuates cardiac and skeletal muscle alterations in a pulmonary arterial hypertension model
Cited by: 9
Author(s): Paulien Vinke, T. Scott Bowen, Mark V. Boekschoten, Renger F. Witkamp, Volker Adams, Klaske van Norren
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-46440-0

Regulation of stomatal opening and histone modification by photoperiod in Arabidopsis thaliana
Cited by: 16
Author(s): Saya Aoki, Shigeo Toh, Norihito Nakamichi, Yuji Hayashi, Yin Wang, Takamasa Suzuki, Hiroyuki Tsuji, Toshinori Kinoshita
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-48167-4

Allelic Imbalance of Recurrently Mutated Genes in Acute Myeloid Leukaemia
Cited by: 9
Author(s): Aarif M.N. Batcha, Stefanos A. Bamopoulos, Paul Kerbs, Ashwini Kumar, Vindi Jurinović, Maja Rothenberg‐Thurley, Bianka Ksienzyk, Julia Philippou‐Massier, Stefan Krebs, Helmut Blum, Stephanie Schneider, Nikola P. Konstandin, Stefan K. Bohlander, Caroline A. Heckman, Mika Kontro, Wolfgang Hiddemann, Karsten Spiekermann, Jan Braess, Klaus H. Metzeler, Philipp A. Greif, Ulrich Mansmann, Tobias Herold
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-49648-2

Cigarette smoke alters the transcriptome of non-involved lung tissue in lung adenocarcinoma patients
Cited by: 14
Author(s): Giulia Pintarelli, Sara Noci, Davide Maspero, Angela Pettinicchio, Matteo Dugo, Loris De Cecco, Matteo Incarbone, Davide Tosi, Luigi Santambrogio, Tommaso A. Dragani, Francesca Colombo
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-50547-9

CD98hc (SLC3A2) sustains amino acid and nucleotide availability for cell cycle progression
Cited by: 26
Author(s): Sara Cano-Crespo, Josep Chillarón, Alexandra Junza, Gonzalo Fernández-Miranda, Judit García, Christine Polte, Laura Rodríguez de la Ballina, Zoya Ignatova, Óscar Yanes, António Zorzano, Camille Stephan‐Otto Attolini, Manuel Palacı́n
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-51054-7

Crosstalk between protein N-glycosylation and lipid metabolism in Saccharomyces cerevisiae
Cited by: 13
Author(s): Antonisamy William James, Chidambaram Ravi, Malathi Srinivasan, Vasanthi Nachiappan
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-51578-y

EV-associated miRNAs from pleural lavage as potential diagnostic biomarkers in lung cancer
Cited by: 27
Author(s): Berta Roman‐Canal, Cristian P. Moiola, Sònia Gatius, Sarah Bonnin, Maria Ruiz‐Miró, Esperanza González, Amaia Ojanguren, José Luis Recuero Díaz, Antonio Gil‐Moreno, Juan Manuel Falcón‐Pérez, Julia Ponomarenko, José M. Porcel, Xavier Matías‐Guiu, Eva Colás
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-52388-y

Comparison of whole blood and spleen transcriptional signatures over the course of an experimental malaria infection
Cited by: 5
Author(s): Carlos Talavera-López, Yaw Bediako, Jing-wen Lin, John Joseph Valletta, Mario Recker, Jean Langhorne
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-54358-w

The integrative knowledge base for miRNA-mRNA expression in colorectal cancer
Cited by: 16
Author(s): Daša Jevšinek Skok, Nina Hauptman, Emanuela Boštjančič, Nina Zidar
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-56367-1

Characterization of a five-microRNA signature as a prognostic biomarker for esophageal squamous cell carcinoma
Cited by: 13
Author(s): Jun Yu, Ming Zhu, Min Lv, Xiaoliu Wu, Xiaomei Zhang, Yuanying Zhang, Jintian Li, Qin Zhang
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-57076-5

The ETS transcription factor ETV5 is a target of activated ALK in neuroblastoma contributing to increased tumour aggressiveness
Cited by: 19
Author(s): Liselot Mus, Irina Lambertz, Shana Claeys, Candy Kumps, Wouter Van Loocke, Christophe Van Neste, Ganesh Umapathy, Marica Vaapil, Christoph Bartenhagen, Geneviève Laureys, Olivier De Wever, Daniel Bexell, Matthias Fischer, Bengt Hållberg, Johannes H. Schulte, Bram De Wilde, Kaat Durinck, Geertrui Denecker, Katleen De Preter, Frank Speleman
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-57451-7

Identification, functional prediction, and key lncRNA verification of cold stress-related lncRNAs in rats liver
Cited by: 13
Author(s): Hong Ji, Chunyang Niu, Xuelong Zhan, Jing Xu, Shuai Lian, Bin Xu, Jiang Guo, Zhen Li, Huanmin Yang, Shize Li, Li Ma
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-56339-5

PulmonDB: a curated lung disease gene expression database
Cited by: 11
Author(s): Ana B. Villaseñor-Altamirano, Marco Moretto, M. Maldonado, Alejandra Zayas-Del Moral, Adrián Munguía-Reyes, Yair Romero, Jair Santiago García-Sotelo, L. A. Aguilar, Oscar Aldana-Assad, Kristof Engelen, Moisés Selman, Julio Collado‐Vides, Yalbi I. Balderas-Martínez, Alejandra Medina-Rivera
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-57495-9

Manatee: detection and quantification of small non-coding RNAs from next-generation sequencing data
Cited by: 16
Author(s): Joanna E. Handzlik, Spyros Tastsoglou, Ioannis S. Vlachos, Artemis G. Hatzigeorgiou
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-57691-7

A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules
Cited by: 26
Author(s): Natasha L. Patel-Murray, Miriam Adam, Nhan Huynh, Brook T. Wassie, Pamela Milani, Ernest Fraenkel
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-57924-9

Likelihood contrasts: a machine learning algorithm for binary classification of longitudinal data
Cited by: 4
Author(s): Рику Клен, Markku Karhunen, Laura L. Elo
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-56877-y

Sox2 controls Schwann cell self-organization through fibronectin fibrillogenesis
Cited by: 19
Author(s): Elen Torres-Mejía, Dietrich Trümbach, Charlotte Kleeberger, Ulf Dornseifer, Tanja Orschmann, Theresa Bäcker, Jara Kerstin Brenke, Kamyar Hadian, Wolfgang Wurst, Hernán López‐Schier, Sabrina C. Desbordes
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-58923-6

The Golgi Glycoprotein MGAT4D is an Intrinsic Protector of Testicular Germ Cells From Mild Heat Stress
Cited by: 8
Author(s): Ayodélé Akintayo, Meng Liang, Boris Bartholdy, Frank Batista, Jennifer Aguilan, Jillian Prendergast, Afsana Sabrin, Subha Sundaram, Pamela Stanley
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-59186-x

Target prediction and validation of microRNAs expressed from FSHR and aromatase genes in human ovarian granulosa cells
Cited by: 16
Author(s): Ilmatar Rooda, Kati Hensen, Birgitta Kaselt, Sergo Kasvandik, Martin Pook, Ants Kurg, Andres Salumets, Agne Velthut-Meikas
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-59259-x

Downregulation of peripheral PTGS2/COX-2 in response to valproate treatment in patients with epilepsy
Cited by: 20
Author(s): Chitra Rawat, Rintu Kutum, Samiksha Kukal, Ankit Srivastava, Ujjwal Ranjan Dahiya, Suman Kushwaha, Sangeeta Sharma, Debasis Dash, Luciano Saso, Achal K. Srivastava, Ritushree Kukreti
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-60480-x

High WBP5 expression correlates with elevation of HOX genes levels and is associated with inferior survival in patients with acute myeloid leukaemia
Cited by: 8
Author(s): Carl Ward, Pierre Cauchy, Paloma García, Jonathan Frampton, Miguel A. Esteban, Giacomo Volpe
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-61016-z

Gene regulatory network analysis with drug sensitivity reveals synergistic effects of combinatory chemotherapy in gastric cancer
Cited by: 6
Author(s): Jeong Hoon Lee, Yu Rang Park, Min-A Jung, Sun Gyo Lim
Software Mentions: 2
Published: over 6 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776