10.1186/s12957-021-02367-3

Comprehensive analysis of angiogenesis subtype of squamous cell carcinoma
Cited by: 3
Author(s): Fanglu Qin, Sheng-hua Lin, Kun Deng, Junqi Qin, Zhanyu Xu, Liqiang Yuan, Jiangbo Wei, Yu Sun, Tiaozhan Zheng, Shikang Li
Software Mentions: 5
Published: about 5 years ago

10.1186/s12885-021-08390-7

Identification of prognostic markers for hepatocellular carcinoma based on the epithelial-mesenchymal transition-related gene BIRC5
Cited by: 13
Author(s): Rongzhong Xu, Lin Lei, Bo Zhang, Jian Wang, Fanchen Zhao, Xiaolin Liu, Yiping Li, Yan Li
Software Mentions: 5
Published: over 5 years ago

10.1038/srep31479

Pancreas-enriched miRNAs are altered in the circulation of subjects with diabetes: a pilot cross-sectional study
Cited by: 131
Author(s): Attila A. Seyhan, Yury O. Nunez Lopez, Hui Xie, Fanchao Yi, Clayton E. Mathews, Magdalena Pasarica, Richard E. Pratley
Software Mentions: 5
Published: about 10 years ago

10.1186/s12882-018-0944-z

Gene alterations in monocytes are pathogenic factors for immunoglobulin a nephropathy by bioinformatics analysis of microarray data
Cited by: 3
Author(s): Yingbo Guo, Weijie Gao, Danyang Wang, Weijing Liu, Zhongjie Liu
Software Mentions: 5
Published: about 8 years ago

10.7717/peerj.11422

The relationship between PLOD1 expression level and glioma prognosis investigated using public databases
Cited by: 5
Author(s): Lei Tian, Huandi Zhou, Guohui Wang, Wen Yan Wang, Yuehong Li, Xiaoying Xue
Software Mentions: 5
Published: over 5 years ago

10.1038/srep36055

Dual-species transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions
Cited by: 28
Author(s): Betty Hebecker, Sebastian Vlaic, Theresia Conrad, Michael Bauer, Sascha Brunke, Mario Kapitan, Jörg Linde, Bernhard Hube, Ilse D. Jacobsen
Software Mentions: 5
Published: almost 10 years ago

10.1038/srep31669

Organotypic culture in three dimensions prevents radiation-induced transformation in human lung epithelial cells
Cited by: 3
Author(s): Mariam El-Ashmawy, Melissa Coquelin, Krishna Luitel, Kimberly Batten, Jerry W. Shay
Software Mentions: 5
Published: about 10 years ago

10.1038/s41598-017-06355-0

Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity
Cited by: 5
Author(s): Prashanna Balaji Venkatasubramanian, Gamze Toydemir, Nicole de Wit, Edoardo Saccenti, Vítor A. P. Martins dos Santos, Peter van Baarlen, Jerry M. Wells, María Suárez-Diez, Jurriaan J. Mes
Software Mentions: 5
Published: about 9 years ago

10.1186/1471-2407-10-351

Characterization of the apoptotic response of human leukemia cells to organosulfur compounds
Cited by: 7
Author(s): Wendy Wei-Lynn Wong, Paul C. Boutros, Amanda R. Wasylishen, Kristal D. Guckert, Erin M. O’Brien, Rebecca E. Griffiths, Anna Martirosyan, Christina Bros, Igor Jurišica, Richard Francis Langler, Linda Z. Penn
Software Mentions: 5
Published: about 16 years ago

10.1038/srep29251

Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data
Cited by: 21
Author(s): Tin Nguyen, Diana Diaz, Rebecca Tagett, Sorin Drăghici
Software Mentions: 5
Published: about 10 years ago

10.1186/s13601-016-0105-z

Cow’s milk allergy in Dutch children: an epigenetic pilot survey
Cited by: 36
Author(s): Nicole C. M. Petrus, Peter Henneman, Andrea Venema, Adri N. Mul, Femke van Sinderen, Martin A. Haagmans, Olaf R.F. Mook, Raoul C. M. Hennekam, A. B. Sprikkelman, Marcel M.A.M. Mannens
Software Mentions: 5
Published: over 10 years ago

10.1038/s41598-017-07238-0

T2DiACoD: A Gene Atlas of Type 2 Diabetes Mellitus Associated Complex Disorders
Cited by: 32
Author(s): Jyoti Rani, Inna Mittal, Atreyi Pramanik, Namita Singh, Namita Dube, Smriti Sharma, Bhanwar Lal Puniya, Muthukurussi Varieth Raghunandanan, Ahmed Mobeen, Srinivasan Ramachandran
Software Mentions: 5
Published: about 9 years ago

10.1186/s13148-016-0266-6

DNA methylation and smoking in Korean adults: epigenome-wide association study
Cited by: 48
Author(s): Mi Kyeong Lee, Yoonki Hong, Sun‐Young Kim, Stephanie J. London, Woo Jin Kim
Software Mentions: 5
Published: almost 10 years ago

10.12688/wellcomeopenres.11253.2

A genomic atlas of human adrenal and gonad development
Cited by: 46
Author(s): Ignacio del Valle, Federica Buonocore, Andrew Duncan, Lin Lin, Martino Barenco, Rahul Parnaik, Sonia Shah, Michael Hubank, Dianne Gerrelli, John C. Achermann
Software Mentions: 5
Published: almost 9 years ago

10.1007/s00401-020-02228-5

Mosaic trisomy of chromosome 1q in human brain tissue associates with unilateral polymicrogyria, very early-onset focal epilepsy, and severe developmental delay
Cited by: 27
Author(s): Katja Kobow, Samir Jabari, Tom Pieper, Manfred Kudernatsch, Tilman Polster, Friedrich G. Woermann, Thilo Kalbhenn, Hajo M. Hamer, Karl Rössler, Angelika Mühlebner, Wim G.M. Spliet, Martha Feucht, Yanghao Hou, Damian Stichel, Andrey Korshunov, Felix Sahm, Roland Coras, Ingmar Blümcke, Andreas von Deimling
Software Mentions: 5
Published: almost 6 years ago

10.1038/srep21911

Transcriptional profiling of human smooth muscle cells infected with gingipain and fimbriae mutants of Porphyromonas gingivalis
Cited by: 6
Author(s): Boxi Zhang, Allan Sirsjö, Hazem Khalaf, Torbjörn Bengtsson
Software Mentions: 5
Published: over 10 years ago

10.3892/mmr.2014.3006

Analysis of the protein-protein interaction networks of differentially expressed genes in pulmonary embolism
Cited by: 5
Author(s): Hao Wang, Chen Wang, Lei Zhang, Yinghua Lu, Qianglin Duan, Zhu Gong, Aibin Liang, Haoming Song, Lemin Wang
Software Mentions: 5
Published: almost 12 years ago

10.1038/s41597-020-0527-2

Transcriptome data of temporal and cingulate cortex in the Rett syndrome brain
Cited by: 6
Author(s): Kimberly A. Aldinger, Andrew E. Timms, James W. MacDonald, Hanna K. McNamara, Jennifer Herstein, Theo K. Bammler, Oleg V. Evgrafov, James A. Knowles, Pat Levitt
Software Mentions: 5
Published: over 6 years ago

10.3389/fcell.2021.641987

Timing Does Matter: Nerve-Mediated HDAC1 Paces the Temporal Expression of Morphogenic Genes During Axolotl Limb Regeneration
Cited by: 3
Author(s): Mu-Hui Wang, Chih‐Cheng Hsu, Cheng‐Hsun Wu, Ling-Ling Chiou, Yi-Tzang Tsai, Hsuan-Shu Lee, Shau-Ping Lin
Software Mentions: 5
Published: over 5 years ago

10.1038/sdata.2018.136

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

10.1007/s10456-021-09788-4

The endosomal RIN2/Rab5C machinery prevents VEGFR2 degradation to control gene expression and tip cell identity during angiogenesis
Cited by: 20
Author(s): Lanette Kempers, Yuki Wakayama, Ivo van der Bijl, Charita Furumaya, Iris M. De Cuyper, Aldo Jongejan, Marije Kat, Anne-Marieke D. van Stalborch, Antonius L. van Boxtel, Marvin Hubert, Dirk Geerts, Jaap D. van Buul, Dirk de Korte, Wiebke Herzog, Coert Margadant
Software Mentions: 5
Published: over 5 years ago

10.18632/aging.103721

Gene expression-based clinical predictions in lung adenocarcinoma
Cited by: 3
Author(s): Yanlu Xiong, Jie Lei, Jinbo Zhao, Yangbo Feng, Tianyun Qiao, Yongsheng Zhou, Tao Jiang, Han Ye
Software Mentions: 5
Published: about 6 years ago

10.1186/s41016-021-00235-3

The increasing expression of GPX7 related to the malignant clinical features leading to poor prognosis of glioma patients
Cited by: 5
Author(s): Jiawei Yao, Xin Chen, Zhendong Liu, Ruotian Zhang, Cheng Zhang, Quan Yang, Penglei Yao, Qiuyi Jiang, Jianing Wu, Shen Zhao
Software Mentions: 5
Published: over 5 years ago

10.1186/s12885-020-07493-x

Identification of ALDH3A2 as a novel prognostic biomarker in gastric adenocarcinoma using integrated bioinformatics analysis
Cited by: 24
Author(s): Zhenhua Yin, Danni Wu, Jianping Shi, Xiao‐Hong Wei, Nuyun Jin, Xiaolan Lu, Xiaohan Ren
Software Mentions: 5
Published: almost 6 years ago

10.1186/s10020-021-00343-x

Long non-coding RNA profile study identifies a metabolism-related signature for colorectal cancer
Cited by: 19
Author(s): Yongqu Lu, Wendong Wang, Zhenzhen Liu, Junren Ma, Xin Zhou, Wei Fu
Software Mentions: 5
Published: about 5 years ago

10.1186/s12920-021-00905-2

Bioinformatic analysis reveals an exosomal miRNA-mRNA network in colorectal cancer
Cited by: 17
Author(s): Jun Ma, Peilong Wang, Lei Huang, Jianxia Qiao, Jianhong Li
Software Mentions: 5
Published: over 5 years ago

10.1016/j.cels.2021.05.005

A time-resolved proteomic and prognostic map of COVID-19
Cited by: 106
Author(s): Vadim Demichev, Pinkus Tober‐Lau, Oliver Lemke, Tatiana Nazarenko, Charlotte Thibeault, Harry J. Whitwell, Annika Röhl, Anja Freiwald, Łukasz Szyrwiel, Daniela Ludwig, Clara Correia‐Melo, Simran Kaur Aulakh, Elisa T Helbig, Paula Stubbemann, Lena J Lippert, Nana‐Maria Grüning, Oleg Blyuss, Spyros Vernardis, Matthew White, Christoph B. Messner, Michael Joannidis, Thomas Sonnweber, Sebastian Klein, Alex Pizzini, Yvonne Wohlfarter, Sabina Sahanic, Richard Hilbe, Benedikt Schaefer, Sonja Wagner, Mirja Mittermaier, Felix Machleidt, Carmen García, Christoph Ruwwe‐Glösenkamp, Tilman Lingscheid, Laure Bosquillon de Jarcy, Miriam Stegemann, Moritz Pfeiffer, Linda Jürgens, Sophy Denker, Daniel Zickler, Philipp Enghard, Aleksej Zelezniak, Archie Campbell, Caroline Hayward, David J. Porteous, Riccardo E. Marioni, Alexander Uhrig, Holger Müller-Redetzky, Heinz Zoller, Judith Löffler‐Ragg
Software Mentions: 5
Published: about 5 years ago

10.1038/s41422-018-0128-1

A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesis
Cited by: 46
Author(s): Marcos Morgan, Yuka Kabayama, Christian Much, Ivayla Ivanova, Monica Di Giacomo, Tatsiana Auchynnikava, Jack Monahan, Dimitrios Vitsios, Lina Vasiliauskaitė, Stefano Comazzetto, Juri Rappsilber, Robin C. Allshire, Bo T. Porse, Anton J. Enright, Dónal O’Carroll
Software Mentions: 5
Published: over 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

10.1186/s12920-019-0596-2

Transcriptome analysis identified a novel 3-LncRNA regulatory network of transthyretin attenuating glucose induced hRECs dysfunction in diabetic retinopathy
Cited by: 14
Author(s): Jun Shao, Yunbin Zhang, Guangming Fan, Yu Xin, Yong Yao
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41388-021-02005-y

Intron retention-induced neoantigen load correlates with unfavorable prognosis in multiple myeloma
Cited by: 19
Author(s): Chuanpeng Dong, Annamaria Cesarano, Giuseppe Bombaci, Jill L. Reiter, Christina Y. Yu, Yue Wang, Zhaoyang Jiang, Mohammad Abu Zaid, Kun Huang, Xiongbin Lu, Brian A Walker, Fabiana Perna, Yunlong Liu
Software Mentions: 5
Published: about 5 years ago

10.1073/pnas.1822046116

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

10.3390/proteomes8030015

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform
Cited by: 9
Author(s): Subina Mehta, Caleb Easterly, Ray Sajulga, Robert Millikin, Andrea Argentini, Ignacio Eguinoa, Lennart Martens, Michael R. Shortreed, Lloyd M. Smith, Thomas McGowan, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik Jagtap
Software Mentions: 5
Published: about 6 years ago

10.1155/2020/6937475

A New Prognostic Risk Model Based on PPAR Pathway-Related Genes in Kidney Renal Clear Cell Carcinoma
Cited by: 18
Author(s): Yingkun Xu, Xiunan Li, Yaling Han, Zilong Wang, Chenglin Han, Ningke Ruan, Jianyi Li, Xiao Yu, Qinghua Xia, Guangzhen Wu
Software Mentions: 5
Published: almost 6 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

10.1186/1471-2164-13-351

The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon
Cited by: 38
Author(s): Kusum Sharma, Nicholas Gillum, J Lomax Boyd, Amy K. Schmid
Software Mentions: 5
Published: about 14 years ago

10.1152/ajpendo.00473.2013

Brown and white adipose tissues: intrinsic differences in gene expression and response to cold exposure in mice
Cited by: 289
Author(s): Meritxell Rosell, Myrsini Kaforou, Andrea Frontini, Anthony Okolo, Yi‐Wah Chan, Evanthia Nikolopoulou, Steven Millership, Matthew Fenech, David A. MacIntyre, J. Turner, Jonathan D. Moore, E. K. Blackburn, William J. Gullick, Saverio Cinti, Giovanni Montana, Malcolm G. Parker, Mark Christian
Software Mentions: 5
Published: over 12 years ago

10.3389/fcell.2021.723721

Identification of the Immune-Related Genes in Tumor Microenvironment That Associated With the Recurrence of Head and Neck Squamous Cell Carcinoma
Cited by: 6
Author(s): Chengcheng Liu, Wenwen Qi, Nianqiao Gong, Fenlu Zhu, Ran Xu, Zhaogang Teng, Fanxing Xu, Ya‐Zhen Qin, Mingqiu Zhao, Xiaoming Li, Ming Xia
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.ppat.1008869

Macrophage maturation from blood monocytes is altered in people with HIV, and is linked to serum lipid profiles and activation indices: A model for studying atherogenic mechanisms
Cited by: 16
Author(s): Emily Bowman, Cheryl M. Cameron, Brian Richardson, Milind V. Kulkarni, Janelle Gabriel, Morgan J. Cichon, Ken M. Riedl, Yousef Mustafa, Michael Cartwright, Brandon Snyder, Subha V. Raman, David A. Zidar, Susan L. Koletar, Martin P. Playford, Nehal N. Mehta, Scott F. Sieg, Michael L. Freeman, Michael M. Lederman, Mark J. Cameron, Nicholas T. Funderburg
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.ppat.1008477

Immunosuppressive FK506 treatment leads to more frequent EBV-associated lymphoproliferative disease in humanized mice
Cited by: 15
Author(s): Nicole Caduff, Donal McHugh, Anita Murer, Patrick C. Rämer, Ana Raykova, Vanessa Landtwing, Lisa Rieble, Christian W. Keller, Michael Prummer, Laurent Hoffmann, Janice K. P. Lam, Aks Chiang, Friedrich Raulf, Tarik Azzi, Christoph Berger, Tina Rubic-Schneider, Elisabetta Traggiai, Jan D. Lünemann, Michael Kammüller, Christian Münz
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-017-1285-0

Chromosome contacts in activated T cells identify autoimmune disease candidate genes
Cited by: 66
Author(s): Oliver S. Burren, Arcadio Rubio Garćıa, Biola M. Javierre, Daniel B. Rainbow, Jonathan Cairns, Nicholas Cooper, John Lambourne, Ellen Schofield, Xaquín Castro Dopico, Ricardo C. Ferreira, Richard M. R. Coulson, Frances Burden, Sophia Rowlston, Kate Downes, Steven W. Wingett, Mattia Frontini, Willem H. Ouwehand, Peter Fraser, Mikhail Spivakov, John A. Todd, Linda S. Wicker, Antony J. Cutler, Chris Wallace
Software Mentions: 5
Published: about 9 years ago

10.1186/s12920-020-0670-9

Comparison of DNA methylation profiles from saliva in Coeliac disease and non-coeliac disease individuals
Cited by: 9
Author(s): Nerissa L. Hearn, Christine L Chiu, Joanne M. Lind
Software Mentions: 5
Published: over 6 years ago

10.1186/s12931-019-1085-z

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

10.1186/s13059-015-0863-2

IL-4 orchestrates STAT6-mediated DNA demethylation leading to dendritic cell differentiation
Cited by: 89
Author(s): Roser Vento‐Tormo, Carlos Company, Javier Rodríguez-Ubreva, Lorenzo de la Rica, José Urquiza, Biola M. Javierre, Radhakrishnan Sabarinathan, Ana Luque, Manel Esteller, Josep M. Aran, Damiana Álvarez-Errico, Esteban Ballestar
Software Mentions: 5
Published: over 10 years ago

10.1038/srep20533

Gene regulatory network inference using fused LASSO on multiple data sets
Cited by: 114
Author(s): Nooshin Omranian, Jeanne M. O. Eloundou-Mbebi, Bernd Mueller‐Roeber, Zoran Nikoloski
Software Mentions: 5
Published: over 10 years ago

10.1186/s13059-015-0844-5

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
Cited by: 1,843
Author(s): Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian H. Gersuk, Alex K. Shalek, Chloe K. Slichter, Hannah W. Miller, M. Juliana McElrath, Martin Prlic, Peter S. Linsley, Raphaël Gottardo
Software Mentions: 5
Published: almost 11 years ago

10.1186/s12885-016-2178-4

Genetic and cellular studies highlight that A Disintegrin and Metalloproteinase 19 is a protective biomarker in human prostate cancer
Cited by: 13
Author(s): Gerard F. Hoyne, Caoline Rudnicka, Qing‐Xiang Amy Sang, Mark D. Roycik, Sarah Howarth, Peter J. Leedman, Markus P. Schlaich, Patrick A. Candy, Vance B. Matthews
Software Mentions: 5
Published: over 10 years ago

10.3390/ijerph16040524

Age-Related Differences in miRNA Expression in Mexican-American Newborns and Children
Cited by: 6
Author(s): Karen Huen, Daneida Lizárraga, Katherine Kogut, Brenda Eskenazi, Nina Holland
Software Mentions: 5
Published: over 7 years ago

10.1186/s12885-021-07928-z

Integrated bioinformatic analysis identifies UBE2Q1 as a potential prognostic marker for high grade serous ovarian cancer
Cited by: 8
Author(s): Rachel Topno, I.K. Singh, Manoj Kumar, Pallavi Agarwal
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-015-0597-1

Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis
Cited by: 127
Author(s): Julieta L. Mateos, Pedro Madrigal, Kazuhiko Tsuda, Vimal Rawat, René Richter, Maida Romera-Branchat, Fabio Fornara, Korbinian Schneeberger, Paweł Krajewski, George Coupland
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pmed.1003229

Maternal dysglycaemia, changes in the infant’s epigenome modified with a diet and physical activity intervention in pregnancy: Secondary analysis of a randomised control trial
Cited by: 52
Author(s): Elie Antoun, Negusse Tadesse Kitaba, Philip Titcombe, Kathryn V. Dalrymple, Emma Garratt, Sheila J. Barton, Robert Murray, Paul Seed, Joanna D. Holbrook, Michael S. Kobor, David T.S. Lin, Julia L. MacIsaac, Graham C. Burdge, Sara L. White, Lucilla Poston, Keith M. Godfrey, Karen A. Lillycrop
Software Mentions: 5
Published: almost 6 years ago

10.3389/fcell.2021.633607

Development and Validation of a Hypoxia-Associated Prognostic Signature Related to Osteosarcoma Metastasis and Immune Infiltration
Cited by: 35
Author(s): Yucheng Fu, Qiyuan Bao, Zhuochao Liu, Guoyu He, Junxiang Wen, Qi Liu, Yanguang Xu, Zhijian Jin, Weibin Zhang
Software Mentions: 5
Published: over 5 years ago

10.1186/1741-7007-7-70

Genetical genomic determinants of alcohol consumption in rats and humans
Cited by: 136
Author(s): Boris Tabakoff, Laura Saba, Morton P. Printz, Pam Flodman, Colin A. Hodgkinson, David Goldman, George F. Koob, H. G. Richardson, Katerina Kechris, Richard L. Bell, Norbert Hübner, Matthias Heinig, Michal Pravenec, Jonathan Mangion, Lucie Legault, M Dongier, Katherine M. Conigrave, John B. Whitfield, John B. Saunders, Bridget F. Grant, Paula L. Hoffman
Software Mentions: 5
Published: almost 17 years ago

10.3389/fonc.2014.00251

Hidden Treasures in “Ancient” Microarrays: Gene-Expression Portrays Biology and Potential Resistance Pathways of Major Lung Cancer Subtypes and Normal Tissue
Cited by: 14
Author(s): Konstantinos Kerkentzes, Vincenzo Lagani, Ioannis Tsamardinos, Mogens Vyberg, Oluf Dimitri Røe
Software Mentions: 5
Published: almost 12 years ago

10.1186/s13059-014-0494-z

Genomic mapping of the MHC transactivator CIITA using an integrated ChIP-seq and genetical genomics approach
Cited by: 31
Author(s): Daniel Wong, Wanseon Lee, Peter Humburg, Seiko Makino, Evelyn Lau, Vivek Naranbhai, Benjamin P. Fairfax, Kenneth Chan, Katharine Plant, Julian C. Knight
Software Mentions: 5
Published: almost 12 years ago

10.1186/1471-2105-14-165

Separate-channel analysis of two-channel microarrays: recovering inter-spot information
Cited by: 28
Author(s): Gordon K. Smyth, Naomi Altman
Software Mentions: 5
Published: over 13 years ago

10.1186/s13059-015-0605-5

5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer
Cited by: 61
Author(s): Santiago Uribe-Lewis, Rory Stark, Thomas Carroll, Mark J. Dunning, Martin Bachman, Yoko Itō, Lovorka Stojic, Silvia Halim, Sarah L. Vowler, Andy G. Lynch, Benjamin Delatte, Eric James de Bony, Laurence Colin, Matthieu Defrance, Felix Krueger, Ana Luísa Silva, Rogier ten Hoopen, Ashraf E.K. Ibrahim, François Fuks, Adele Murrell
Software Mentions: 5
Published: over 11 years ago

10.1186/gb-2007-8-9-r190

DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data
Cited by: 29
Author(s): Michael Watson, Juliet Dukes, Abu-Bakr Abu-Median, Donald P. King, Paul Britton
Software Mentions: 5
Published: over 19 years ago

10.1186/s13058-019-1230-0

Elacestrant (RAD1901) exhibits anti-tumor activity in multiple ER+ breast cancer models resistant to CDK4/6 inhibitors
Cited by: 44
Author(s): Hemang Patel, Nianjun Tao, Kyung Min Lee, Mariela Huerta, Heike Arlt, Tara Mullarkey, Steven Troy, Carlos L. Arteaga, Teeru Bihani
Software Mentions: 5
Published: almost 7 years ago

10.1177/1759091419843393

Global Brain Transcriptome Analysis of a <i>Tpp1</i> Neuronal Ceroid Lipofuscinoses Mouse Model
Cited by: 11
Author(s): Miriam S. Domowicz, Wen-Ching Chan, Patricia Claudio-Vázquez, Judith Henry, Christopher B. Ware, Jorge Andrade, Glyn Dawson, Nancy B. Schwartz
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0240943

Three-gene prognostic biomarkers for seminoma identified by weighted gene co-expression network analysis
Cited by: 2
Author(s): Hualin Chen, Gang Chen, Yang Pan, Xiaoxiang Jin
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0041066

Transcriptional Response of Peripheral Blood Mononuclear Cells from Cattle Infected with Mycobacterium bovis
Cited by: 25
Author(s): Federico Carlos Blanco, Marcelo Soria, María Verónica Bianco, Fabiana Bigi
Software Mentions: 5
Published: about 14 years ago

10.1371/journal.pone.0038365

Detection of Simultaneous Group Effects in MicroRNA Expression and Related Target Gene Sets
Cited by: 21
Author(s): Stephan Artmann, Klaus Jung, Annalen Bleckmann, Tim Beißbarth
Software Mentions: 5
Published: over 14 years ago

10.3390/genes12060876

High SGO2 Expression Predicts Poor Overall Survival: A Potential Therapeutic Target for Hepatocellular Carcinoma
Cited by: 3
Author(s): Min Deng, Shaohua Li, Jie Mei, Wenping Lin, Jingwen Zou, Wei Wei, Rong Guo
Software Mentions: 5
Published: over 5 years ago

10.1186/s13041-020-00603-7

Ocular hypertension suppresses homeostatic gene expression in optic nerve head microglia of DBA/2 J mice
Cited by: 28
Author(s): James R. Tribble, Jeffrey M. Harder, Pete A. Williams, Simon W. M. John
Software Mentions: 5
Published: over 6 years ago

10.1186/s12263-021-00692-6

Transcriptomic changes in peripheral blood mononuclear cells with weight loss: systematic literature review and primary data synthesis
Cited by: 7
Author(s): Kaitlin Day, Aimee L. Dordevic, Helen Truby, Melissa C. Southey, Susan L. Coort, Chiara Murgia
Software Mentions: 5
Published: about 5 years ago

10.3390/v13081540

Multi-Tissue Transcriptomic-Informed In Silico Investigation of Drugs for the Treatment of Dengue Fever Disease
Cited by: 1
Author(s): Beatríz Sierra, Ana C. Magalhães, Daniel Lemos Soares, Bruno Cavadas, Ana B. Pérez, Mayling Álvarez, Eglys Aguirre, Claudia Bracho, Luı́sa Pereira, María G. Guzmán
Software Mentions: 5
Published: about 5 years ago

10.1186/s13058-017-0814-9

DCYTB is a predictor of outcome in breast cancer that functions via iron-independent mechanisms
Cited by: 28
Author(s): David J. Lemler, Miranda L. Lynch, Lia Tesfay, Zhiyong Deng, Bibbin T. Paul, Xiaohong Wang, Poornima Hegde, David H. Manz, Suzy V. Torti, Frank M. Torti
Software Mentions: 5
Published: over 9 years ago

10.1186/1471-2164-14-725

Positively correlated miRNA-mRNA regulatory networks in mouse frontal cortex during early stages of alcohol dependence
Cited by: 113
Author(s): Yury O. Nunez, Jay Truitt, Giorgio Gorini, Olga N. Ponomareva, Yuri A. Blednov, R. Adron Harris
Software Mentions: 5
Published: almost 13 years ago

10.1186/s12864-020-07228-z

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

10.18632/aging.202801

The construction and analysis of a ferroptosis-related gene prognostic signature for pancreatic cancer
Cited by: 26
Author(s): Pei-Cheng Jiang, Feng Yang, Caifeng Zou, Tianyuan Bao, Mengmeng Wu, Dongqin Yang, Shurui Bu
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-015-0708-8

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment
Cited by: 13
Author(s): Anwesha Bohler, Lars Eijssen, Martijn P. van Iersel, C. René Leemans, Egon Willighagen, Martina Kutmon, Magali Jaillard, Chris T. Evelo
Software Mentions: 5
Published: about 11 years ago

10.3390/genes11080868

Identification of circRNA-lncRNA-miRNA-mRNA Competitive Endogenous RNA Network as Novel Prognostic Markers for Acute Myeloid Leukemia
Cited by: 52
Author(s): Yuanrong Cheng, Yangfeng Su, Shoubi Wang, Yurun Liu, Lin Jin, Qi Wan, Ying Liu, Chaoyang Li, Xuan Sang, Yang Liu, Chang Liu, Zhichong Wang
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-015-1787-7

Identification and functional analysis of early gene expression induced by circadian light-resetting in Drosophila
Cited by: 20
Author(s): Adeolu B. Adewoye, Charalambos P. Kyriacou, Eran Tauber
Software Mentions: 5
Published: about 11 years ago

10.1007/s00401-019-02074-0

White matter DNA methylation profiling reveals deregulation of HIP1, LMAN2, MOBP, and other loci in multiple system atrophy
Cited by: 42
Author(s): Conceição Bettencourt, Sandrine C. Foti, Yasuo Miki, Juan A. Botía, A. K. Chatterjee, Thomas T. Warner, Tamás Révész, Tammaryn Lashley, R. Balázs, Emmanuelle Viré, Janice L. Holton
Software Mentions: 5
Published: about 7 years ago

10.1186/s13059-015-0781-3

Do count-based differential expression methods perform poorly when genes are expressed in only one condition?
Cited by: 5
Author(s): Xiaobei Zhou, Mark D. Robinson
Software Mentions: 5
Published: almost 11 years ago

10.7150/ijms.49449

Identification and Validation of Six Autophagy-related Long Non-coding RNAs as Prognostic Signature in Colorectal Cancer
Cited by: 19
Author(s): Lin Cheng, Tong Han, Zheyu Zhang, Pan Yi, Chunhu Zhang, Sifang Zhang, Weijun Peng
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0050253

Analysis of Gene Expression Data from Non-Small Cell Lung Carcinoma Cell Lines Reveals Distinct Sub-Classes from Those Identified at the Phenotype Level
Cited by: 2
Author(s): Andrew R. Dalby, Ibrahim Emam, Raimo Franke
Software Mentions: 5
Published: almost 14 years ago

10.1371/journal.pgen.1008611

A non-canonical RNAi pathway controls virulence and genome stability in Mucorales
Cited by: 17
Author(s): Carlos Pérez-Arques, María Isabel Navarro-Mendoza, Laura Murcia, Eusebio Navarro, Victoriano Garre
Software Mentions: 5
Published: about 6 years ago

10.3389/fpls.2018.01256

Comparative Transcriptomic Analysis of Two Actinorhizal Plants and the Legume Medicagotruncatula Supports the Homology of Root Nodule Symbioses and Is Congruent With a Two-Step Process of Evolution in the Nitrogen-Fixing Clade of Angiosperms
Cited by: 14
Author(s): Kai Battenberg, Daniel Potter, Christine A. Tabuloc, Joanna C. Chiu, Alison M. Berry
Software Mentions: 5
Published: almost 8 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: almost 6 years ago

10.3389/fgene.2020.00505

Analysis of Circular RNA-Related Competing Endogenous RNA Identifies the Immune-Related Risk Signature for Colorectal Cancer
Cited by: 16
Author(s): Wei Song, Jun Ren, Chuntao Wang, Yuhang Ge, Tao Fu
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2020.595361

Identification of Hub Prognosis-Associated Oxidative Stress Genes in Pancreatic Cancer Using Integrated Bioinformatics Analysis
Cited by: 8
Author(s): Xin Qiu, Qin-Han Hou, Qiuyue Shi, Haixing Jiang, Shanyu Qin
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2021.653209

Exploring the Imbalance of Periodontitis Immune System From the Cellular to Molecular Level
Cited by: 11
Author(s): Long-Fei He, Lijuan Liu, Ti Li, Deshu Zhuang, Jiayin Dai, Bo Wang, Liangjia Bi
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.707713

Identification of Candidate Blood mRNA Biomarkers in Intracerebral Hemorrhage Using Integrated Microarray and Weighted Gene Co-expression Network Analysis
Cited by: 3
Author(s): Feng Jin, Lei Li, Yuehan Hao, Ling Tang, Yuye Wang, Zhiyi He
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2015.00169

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

10.3389/fgene.2021.707299

Esophageal Cancer Associated Immune Genes as Biomarkers for Predicting Outcome in Upper Gastrointestinal Tumors
Cited by: 9
Author(s): Chuanhui Zhu, Qianqian Xia, Bin Gu, Mengjing Cui, Xing Zhang, Wenjing Yan, Dan Meng, Siyuan Shen, Shuqian Xie, Xueliang Li, Hua Jin, Shizhi Wang
Software Mentions: 5
Published: about 5 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: almost 7 years ago

10.3389/fgene.2021.722803

Identification of Potential Biomarkers for Psoriasis by DNA Methylation and Gene Expression Datasets
Cited by: 9
Author(s): Yong Liu, Shengnan Cui, Jiayi Sun, Xin Yan, Dongran Han
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2020.579709

Potential of Immune-Related Genes as Biomarkers for Diagnosis and Subtype Classification of Preeclampsia
Cited by: 8
Author(s): Ying Wang, Zhen Li, Guanhua Song, Jun Wang
Software Mentions: 5
Published: almost 6 years ago

10.3389/fgene.2021.622683

Bioinformatics Analysis Identifies Molecular Markers Regulating Development and Progression of Endometriosis and Potential Therapeutic Drugs
Cited by: 7
Author(s): Ying Peng, Cheng Peng, Fang Zheng, Gang Chen
Software Mentions: 5
Published: about 5 years ago

10.1172/jci.insight.142680

Exhausted-like CD8+ T cell phenotypes linked to C-peptide preservation in alefacept-treated T1D subjects
Cited by: 33
Author(s): Kirsten E. Diggins, Elisavet Serti, Virginia S. Muir, Mario G. Rosasco, Tingting Lü, Elisa Balmas, Gerald T. Nepom, S. Alice Long, Peter S. Linsley
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.619821

Comprehensive Profiling Reveals Distinct Microenvironment and Metabolism Characterization of Lung Adenocarcinoma
Cited by: 3
Author(s): Li Chang, Chen Tian, Yangyang Liu, Jinyan Liang, Yue Zeng, Qifan Yang, Yuting Liu, Di Wu, Jingjing Wu, Juanjuan Wang, Kai Zhang, Fei Gu, Yue Hu, Li Liu
Software Mentions: 5
Published: over 5 years ago

10.3389/fmolb.2020.566491

Four Immune-Related Long Non-coding RNAs for Prognosis Prediction in Patients With Hepatocellular Carcinoma
Cited by: 15
Author(s): Muqi Li, Minni Liang, Tian Lan, Xiwen Wu, Wenlin Xie, Tielong Wang, Z Chen, Shunli Shen, Baogang Peng
Software Mentions: 5
Published: almost 6 years ago

10.3389/fmolb.2021.670666

Identification of a Gene Set Correlated With Immune Status in Ovarian Cancer by Transcriptome-Wide Data Mining
Cited by: 8
Author(s): Lili Fan, Lei Han, Yu Lin, Zhengwei Zhou, Guang Shu, Zhipeng Yan, Haotian Chen, Tianxiang Zhang, Gang Yin
Software Mentions: 5
Published: about 5 years ago

10.3389/fmolb.2021.689037

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

10.7554/eLife.07295

Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100
Cited by: 179
Author(s): Shouan Liu, Barbara Kracher, J. Ziegler, Rainer P. Birkenbihl, Imre E. Somssich
Software Mentions: 5
Published: over 11 years ago

10.1534/g3.117.300125

Interchromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen
Cited by: 4
Author(s): Priyanka Surana, Ruo Xu, Greg Fuerst, Antony V. E. Chapman, Dan Nettleton, Roger P. Wise
Software Mentions: 5
Published: almost 9 years ago

10.3389/fnins.2021.620899

Integrated miRNA-Seq and mRNA-Seq Study to Identify miRNAs Associated With Alzheimer’s Disease Using Post-mortem Brain Tissue Samples
Cited by: 21
Author(s): Qingqin Li, Diana Cai
Software Mentions: 5
Published: over 5 years ago

10.3389/fnins.2018.00136

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