bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.7150/ijbs.49243

Deciphering the genomic and lncRNA landscapes of aerobic glycolysis identifies potential therapeutic targets in pancreatic cancer
Cited by: 14
Author(s): Lili Zhu, Zheng Wu, Rongkun Li, Xin Xing, Yongsheng Jiang, Jun Li, Yahui Wang, Li-Peng Hu, Xu Wang, Weiting Qin, Yongwei Sun, Zhigang Zhang, Qin Yang, Shu‐Heng Jiang
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2020.01968

Cytoplasmic Citrate Flux Modulates the Immune Stimulatory NKG2D Ligand MICA in Cancer Cells
Cited by: 10
Author(s): Sofie Hedlund Møller, Maiken Mellergaard, Mikkel Madsen, Amaia Vergara Bermejo, Stine Dam Jepsen, Marie Haugsten Hansen, Rikke Illum Høgh, Blanca I. Aldana, Claus Desler, Lene Juel Rasmussen, Elahu G. Sustarsic, Zachary Gerhart-Hines, Evangelia Daskalaki, Craig E. Wheelock, Thomas K. Hiron, Dazhen Lin, Christopher A. O’Callaghan, Hans H. Wandall, Lars Ole Andresen, Søren Skov
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pgen.1004562

A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways
Cited by: 60
Author(s): Bode A. Olukolu, Guan‐Feng Wang, Vijay Vontimitta, Bala P. Venkata, Sandeep Marla, Jiabing Ji, Emma W. Gachomo, Kevin Chu, Adisu Negeri, Jacqueline Benson, Rebecca Nelson, Peter J. Bradbury, Dahlia M. Nielsen, James B. Holland, Peter Balint‐Kurti, Gurmukh S. Johal
Software Mentions: 3
Published: about 12 years ago

10.1016/j.ebiom.2018.02.017

Reciprocal modulation of mesenchymal stem cells and tumor cells promotes lung cancer metastasis
Cited by: 45
Author(s): Giulia Fregni, Mathieu Quinodoz, Emely Möller, Joanna A. Vuille, Sabine Galland, Carlo Fusco, Patricia Martin, Igor Letovanec, Paolo Provero, Carlo Rivolta, Nicolò Riggi, Ivan Stamenkovic
Software Mentions: 3
Published: over 8 years ago

10.1186/s13195-019-0558-0

APOE2 orchestrated differences in transcriptomic and lipidomic profiles of postmortem AD brain
Cited by: 36
Author(s): Iliya Lefterov, Cody M. Wolfe, Nicholas F. Fitz, Kyong Nyon Nam, Florent Letronne, Richard J. Biedrzycki, Julia Kofler, Xianlin Han, Jianing Wang, Jonathan Schug, Radosveta Koldamova
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-019-5763-5

Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006
Cited by: 27
Author(s): Rocío M. Gamez, Fernando Rodríguez, Newton Medeiros Vidal, Sandra Ramírez, Roberto Vera Alvarez, David Landsman, Leonardo Mariño-Ramírez
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-019-5525-4

Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon
Cited by: 22
Author(s): Amin R. Mohamed, Klara L. Verbyla, Hawlader Abdullah Al-Mamun, Sean McWilliam, Bradley S. Evans, Hilary King, Peter D. Kube, James W. Kijas
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2018.01344

Common Features of Regulatory T Cell Specialization During Th1 Responses
Cited by: 37
Author(s): Katharina Littringer, Claudia Moresi, Nikolas Rakebrandt, Xiaobei Zhou, Michelle Schorer, Tamas Dolowschiak, Florian Kirchner, Felix Rost, Christian W. Keller, Donal McHugh, Salomé LeibundGut‐Landmann, Mark D. Robinson, Nicole Joller
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pgen.1008934

A mega-analysis of expression quantitative trait loci in retinal tissue
Cited by: 20
Author(s): Tobias Strunz, Christina Kiel, Felix Graßmann, Rinki Ratnapriya, Madeline Kwicklis, Marcus Karlstetter, Sascha Fauser, Nicole Arend, Anand Swaroop, Thomas Langmann, Armin Wolf, Bernhard H. F. Weber
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13195-021-00810-x

Comorbidity between Alzheimer’s disease and major depression: a behavioural and transcriptomic characterization study in mice
Cited by: 15
Author(s): Ana Martín‐Sánchez, Janet Piñero, Lara Nonell, Magdalena Arnal, Elena M. Ribé, Alejo J. Nevado‐Holgado, Simon Lovestone, Ferrán Sanz, Laura I. Furlong, Olga Valverde
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-2363-5

Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients
Cited by: 41
Author(s): Roy G. Danzmann, Andrea L. Kocmarek, Joseph D. Norman, Caird E. Rexroad, Yniv Palti
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-019-56790-4

Fetal androgen exposure is a determinant of adult male metabolic health
Cited by: 16
Author(s): Katarzyna Siemienowicz, Panagiotis Filis, Sophie Shaw, Alex Douglas, Jessica Thomas, Sally Mulroy, Forbes Howie, Paul A. Fowler, W. Colin Duncan, Michael T. Rae
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1009465

Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination
Cited by: 21
Author(s): Sarah L. Whiteley, Clare E. Holleley, Susan Wagner, James Blackburn, Ira W. Deveson, Jennifer A. Marshall Graves, Arthur Georges
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1008591

The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter
Cited by: 13
Author(s): Selamawit Abi Woldemeskel, Allison K. Daitch, Laura Álvarez, Gaël Panis, Rilee Zeinert, Diego González, Erika Smith, Justine Collier, Peter Chien, Felipe Cava, Patrick H. Viollier, Erin D. Goley
Software Mentions: 3
Published: over 6 years ago

10.3389/fimmu.2020.595877

Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors
Cited by: 5
Author(s): Vladimir A. Veselovsky, Marina S. Dyachkova, Egor Menyailo, Polina S. Polyaeva, Evgenii I. Olekhnovich, Egor Shitikov, Dmitry Bespiatykh, Tatiana A. Semashko, Artem S. Kasianov, Elena N. Ilina, В Н Даниленко, Ksenia M. Klimina
Software Mentions: 3
Published: almost 6 years ago

10.3389/fimmu.2019.02484

Gut Antibody Deficiency in a Mouse Model of CVID Results in Spontaneous Development of a Gluten-Sensitive Enteropathy
Cited by: 18
Author(s): Ahmed Dawood Mohammed, M.A. Wadud Khan, Ioulia Chatzistamou, Douja Chamseddine, Katie N. Kang, Mason Perry, Reilly T. Enos, Angela Murphy, Gregorio Gomez, Ahmed Al-Adhami, Carole A. Oskeritzian, Amy Jolly, Yan Chang, Siying He, Zui Pan, Jason L. Kubinak
Software Mentions: 3
Published: almost 7 years ago

10.3389/fimmu.2021.611656

IL-12p40/IL-23p40 Blockade With Ustekinumab Decreases the Synovial Inflammatory Infiltrate Through Modulation of Multiple Signaling Pathways Including MAPK-ERK and Wnt
Cited by: 16
Author(s): Renée H Fiechter, Henriëtte M. de Jong, Leonieke J J van Mens, Inka A. Fluri, Sander W. Tas, Dominique Baeten, Nataliya Yeremenko, Marleen G H van de Sande
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1008768

Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum
Cited by: 30
Author(s): Eva L. Koch, Frédéric Guillaume
Software Mentions: 3
Published: over 6 years ago

10.1186/s13229-019-0285-1

RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulation
Cited by: 13
Author(s): Ayden Saffari, Matt Arno, Eric Nasser, Angelica Ronald, Chloe Wong, Leonard C Schalkwyk, Jonathan Mill, Frank Dudbridge, Emma L. Meaburn
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-018-4679-9

Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles
Cited by: 39
Author(s): Andrea Grilli, Rossella Bengalli, Eleonora Longhin, Laura Capasso, Maria Carla Proverbio, Mattia Forcato, Silvio Bicciato, Maurizio Gualtieri, Cristina Battaglia, Marina Camatini
Software Mentions: 3
Published: over 8 years ago

10.18632/aging.101578

High expression of the breast cancer susceptibility gene BRCA1 in long-lived termite kings
Cited by: 9
Author(s): Eisuke Tasaki, Yuki Mitaka, Tomonari Nozaki, Keiko Kobayashi, Kenji Matsuura, Yoshihito Iuchi
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12870-015-0627-x

Transcriptomic comparison of the self-pollinated and cross-pollinated flowers of Erigeron breviscapus to analyze candidate self-incompatibility-associated genes
Cited by: 19
Author(s): Wei Zhang, Wei Xiang, Meng Heng-lin, Chunhua Ma, Ni-Hao Jiang, Guanghui Zhang, Shengchao Yang
Software Mentions: 3
Published: almost 11 years ago

10.1038/s41598-019-55896-z

System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster
Cited by: 7
Author(s): Julia Bespyatykh, Egor Shitikov, Andrei Guliaev, Alexander Smolyakov, Ksenia M. Klimina, Vladimir A. Veselovsky, М В Малахова, Georgij Arapidi, Marine Dogonadze, Olga Manicheva, Dmitry Bespiatykh, Igor Mokrousov, Viacheslav Zhuravlev, Elena N. Ilina, Vadim M. Govorun
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-55132-8

Tissue-type plasminogen activator-primed human iPSC-derived neural progenitor cells promote motor recovery after severe spinal cord injury
Cited by: 7
Author(s): Yasuhiro Shiga, Akina Shiga, Pinar Mesci, HyoJun Kwon, Coralie Brifault, Jung Hyun Kim, Jacob Jeziorski, Chanond A. Nasamran, Seiji Ohtori, Alysson R. Muotri, Steven L. Gonias, W. Marie Campana
Software Mentions: 3
Published: over 6 years ago

10.1186/s12885-015-1955-9

The genomic and transcriptomic landscape of anaplastic thyroid cancer: implications for therapy
Cited by: 51
Author(s): Katayoon Kasaian, Sam M. Wiseman, Blair Walker, Jacqueline E. Schein, Yongjun Zhao, Martin Hirst, Richard A. Moore, Andrew J. Mungall, Marco A. Marra, Steven J.M. Jones
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1009650

DAF-18/PTEN inhibits germline zygotic gene activation during primordial germ cell quiescence
Cited by: 7
Author(s): Amanda L. Fry, Amy K. Webster, Julia Burnett, Rojin Chitrakar, L. Ryan Baugh, E. Jane Albert Hubbard
Software Mentions: 3
Published: about 5 years ago

10.1186/s13229-018-0219-3

Role of miR-146a in neural stem cell differentiation and neural lineage determination: relevance for neurodevelopmental disorders
Cited by: 57
Author(s): Lam Son Nguyen, Julien Fregeac, Christine Bôle‐Feysot, Nicolas Cagnard, Anand M. Iyer, Jasper J. Anink, Eleonora Aronica, Olivier Alibeu, Patrick Nitschké, Laurence Colleaux
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pgen.1009803

A biallelic SNIP1 Amish founder variant causes a recognizable neurodevelopmental disorder
Cited by: 4
Author(s): Zineb Ammous, Lettie E Rawlins, Hannah Jones, Joseph S Leslie, Olivia Wenger, Ethan M. Scott, Jim Deline, Tom Herr, R. J. Evans, Angela Scheid, Joanna Kennedy, Barry A. Chioza, Ryan M. Ames, Harold E. Cross, Erik G. Puffenberger, Lorna W. Harries, Emma L. Baple, Andrew H. Crosby
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12885-021-08539-4

A methylation-based nomogram for predicting survival in patients with lung adenocarcinoma
Cited by: 5
Author(s): Xuelong Wang, Bin Zhou, Yuxin Xia, Jianjun Zuo, Yanchao Liu, Xin Bi, Xiong Luo, Chengwei Zhang
Software Mentions: 3
Published: about 5 years ago

10.3389/fimmu.2017.00335

CD103+ CD8 T Cells in the Toxoplasma-Infected Brain Exhibit a Tissue-Resident Memory Transcriptional Profile
Cited by: 45
Author(s): Tyler Landrith, Suhas Sureshchandra, Andrea Rivera, Jessica Jang, Maham Rais, Meera G. Nair, Ilhem Messaoudi, Emma H. Wilson
Software Mentions: 3
Published: over 9 years ago

10.1186/s12987-020-00207-2

Advancing brain barriers RNA sequencing: guidelines from experimental design to publication
Cited by: 14
Author(s): David Francisco, Luca Marchetti, Sabela Rodríguez‐Lorenzo, Eduardo Frías-Anaya, Ricardo Figueiredo, Marjolein Heymanns, Maxime Culot, Ana Raquel Santa-Maria, Mária A. Deli, Raoul Freitas Vale Germano, Benoît Vanhollebeke, Nikolaos Kakogiannos, Monica Giannotta, Elisabetta Dejana, Amaia Dominguez-Belloso, Stefan Liebner, Markus Schuster, Harm‐Anton Klok, Marie Wiatr, Horst Schroten, Tobias Tenenbaum, Gijs Kooij, Peter Winter, Ignacio A. Romero, Helga E. de Vries, Britta Engelhardt, Rémy Bruggmann
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms22031252

Gene Expression Responses to Sequential Nutrient Deficiency Stresses in Soybean
Cited by: 7
Author(s): Jamie A. O’Rourke, Michelle A. Graham
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2019.02016

Continuous Developmental and Early Life Trichloroethylene Exposure Promoted DNA Methylation Alterations in Polycomb Protein Binding Sites in Effector/Memory CD4+ T Cells
Cited by: 10
Author(s): Stephanie D. Byrum, Charity L. Washam, John M. Patterson, Kanan K. Vyas, Kathleen M. Gilbert, Sarah J. Blossom
Software Mentions: 3
Published: about 7 years ago

10.3389/fimmu.2019.00120

Vaccine-Induced Protection Against Furunculosis Involves Pre-emptive Priming of Humoral Immunity in Arctic Charr
Cited by: 14
Author(s): Laura M. Braden, S. K. Whyte, Alyson Brown, Carter Van Iderstine, Corinne Letendre, David B. Groman, J. Lewis, Sara L. Purcell, Tiago S. Hori, Mark D. Fast
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1006477

Gene Expression Differences in Prostate Cancers between Young and Old Men
Cited by: 26
Author(s): Yuan-Chun Ding, Huiqing Wu, Charles Warden, Linda Steele, Xueli Liu, Maarten van Iterson, Xiwei Wu, Rebecca A. Nelson, Zheng Liu, Yate-Ching Yuan, Susan L. Neuhausen
Software Mentions: 3
Published: over 9 years ago

10.1155/2017/8027626

Transcriptome Analysis of Two Different Developmental Stages of <i>Paeonia lactiflora</i> Seeds
Cited by: 7
Author(s): Yong-Lei Ma, Jinqiu Cui, Xiujun Lu, Lijie Zhang, Zhijing Chen, Riwen Fei, Xiulan Sun
Software Mentions: 3
Published: over 9 years ago

10.3389/fnagi.2017.00064

Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease
Cited by: 9
Author(s): Francisco Altimiras, Barbara Uszczyńska-Ratajczak, Francisco Câmara, Anna Vlasova, Emilio Palumbo, Stephen Newhouse, Robert M. J. Deacon, Leandro A. E. Farias, Michael Hurley, David E. Loyola, Rodrigo A. Vásquez, Richard Dobson, Roderic Guigó, Patricia Cogram
Software Mentions: 3
Published: over 9 years ago

10.3389/fnagi.2019.00101

Transcriptional Dysregulation Study Reveals a Core Network Involving the Progression of Alzheimer's Disease
Cited by: 22
Author(s): Guofeng Meng, Hongkang Mei
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2020.00708

Transcriptome Profiling of Lung Innate Immune Responses Potentially Associated With the Pathogenesis of Acinetobacter baumannii Acute Lethal Pneumonia
Cited by: 10
Author(s): Xi Zeng, Hao Gu, Peng Li, Yang Yao, Ning Wang, Yun Shi, Quanming Zou
Software Mentions: 3
Published: over 6 years ago

10.3389/fimmu.2021.725323

Non-Coding RNAs in Human Breast Milk: A Systematic Review
Cited by: 29
Author(s): Lina Tingö, Emelie Ahlberg, Lars-Åke Johansson, Sindre Andre Pedersen, Konika Chawla, Pål Sætrom, Erika Cione, Melanie Rae Simpson
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-017-3743-1

Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python
Cited by: 30
Author(s): Audra L. Andrew, Blair W. Perry, Daren C. Card, Drew R. Schield, Robert P. Ruggiero, Suzanne E. McGaugh, Amit Choudhary, Stephen M. Secor, Todd A. Castoe
Software Mentions: 3
Published: over 9 years ago

10.18632/aging.104004

Integrated analysis of transcriptomic and metabolomic data demonstrates the significant role of pyruvate carboxylase in the progression of ovarian cancer
Cited by: 9
Author(s): Hongjing Shang, Jianfeng Zheng, Jinyi Tong
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12885-021-08634-6

Overexpression of UBE2C in esophageal squamous cell carcinoma tissues and molecular analysis
Cited by: 6
Author(s): Rong Li, Xing-Feng Pang, Zhi‐Guang Huang, Lihua Yang, Zhigang Peng, Jie Ma, Rong‐Quan He
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-54180-4

A framework for identification of on- and off-target transcriptional responses to drug treatment
Cited by: 23
Author(s): Yi Huang, Masaaki Furuno, Takahiro Arakawa, Satoshi Takizawa, Michiel de Hoon, Harukazu Suzuki, Erik Arner
Software Mentions: 3
Published: almost 7 years ago

10.3389/fimmu.2019.00280

Studies Into β-Glucan Recognition in Fish Suggests a Key Role for the C-Type Lectin Pathway
Cited by: 49
Author(s): Jules Petit, Erin C. Bailey, Robert T. Wheeler, Carlos Alberto Ferreira de Oliveira, Maria Forlenza, G.F. Wiegertjes
Software Mentions: 3
Published: over 7 years ago

10.18632/aging.202380

Diagnostic and prognostic values of AKR1C3 and AKR1D1 in hepatocellular carcinoma
Cited by: 8
Author(s): Pengfei Zhu, Ru Feng, Lei Xu, Ling Yuan, Zhicheng Du, Wenlong Zhai, Kunlun Chen
Software Mentions: 3
Published: over 5 years ago

10.1186/s12885-019-6327-4

Molecular subtyping improves prognostication of Stage 2 colorectal cancer
Cited by: 13
Author(s): Rachel Purcell, Sebastian Schmeier, Yee Chen Lau, John F. Pearson, F. A. Frizelle
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12885-021-08283-9

A novel treatment strategy for lapatinib resistance in a subset of HER2-amplified gastric cancer
Cited by: 8
Author(s): Gang Ning, Qihui Zhu, Wonyoung Kang, Hamin Lee, Leigh Maher, Yun Suhk Suh, Michael Michaud, Mayerlin Silva, Jee Young Kwon, Chengsheng Zhang, Charles Lee
Software Mentions: 3
Published: about 5 years ago

10.3389/fbioe.2020.611701

Efficient Production of Pyruvate Using Metabolically Engineered Lactococcus lactis
Cited by: 5
Author(s): Fan Suo, Jianming Liu, Jun Chen, Xuanji Li, Peter Ruhdal Jensen
Software Mentions: 3
Published: over 5 years ago

10.1186/s13229-020-0318-9

Transcriptomics of Gabra4 knockout mice reveals common NMDAR pathways underlying autism, memory, and epilepsy
Cited by: 19
Author(s): Cui-Xia Fan, Yue Gao, Guanmei Liang, Lang Huang, Jing Wang, Xiaoxue Yang, Yi‐Wu Shi, Ursula C. Dräger, Ming Zhong, Tianming Gao, Xinping Yang
Software Mentions: 3
Published: over 6 years ago

10.1186/s13229-019-0311-3

TSC patient-derived isogenic neural progenitor cells reveal altered early neurodevelopmental phenotypes and rapamycin-induced MNK-eIF4E signaling
Cited by: 27
Author(s): Pauline Martín, Vilas Wagh, Surya A. Reis, Serkan Erdin, Roberta L. Beauchamp, Ghalib Shaikh, Michael E. Talkowski, Elizabeth A. Thiele, Steven D. Sheridan, Stephen J. Haggarty, Vijaya Ramesh
Software Mentions: 3
Published: over 6 years ago

10.1093/ajcn/nqz012

Transcriptional changes in prostate of men on active surveillance after a 12-mo glucoraphanin-rich broccoli intervention—results from the Effect of Sulforaphane on prostate CAncer PrEvention (ESCAPE) randomized controlled trial
Cited by: 61
Author(s): Μαρία Τράκα, Antonietta Melchini, Jack Coode‐Bate, Omar Al Kadhi, Shikha Saha, Marianne Defernez, Perla Troncoso‐Rey, Helen Kibblewhite, Carmel M. O’Neill, Federico Bernuzzi, Laura Mythen, Jackie C. Hughes, Paul W. Needs, J. Dainty, George M. Savva, Robert Mills, Richard Y. Ball, Christopher S. Cooper, Richard Mithen
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2020.586658

Cardiac Regeneration and Tumor Growth—What Do They Have in Common?
Cited by: 1
Author(s): Severin Dicks, Lonny Jürgensen, Florian Leuschner, David Hassel, Geoffroy Andrieux, Melanie Boerries
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-52559-x

Transcriptomic Analysis of mRNA-lncRNA-miRNA Interactions in Hepatocellular Carcinoma
Cited by: 35
Author(s): Xia Tang, Delong Feng, Min Li, Jinxue Zhou, Xiaoyuan Li, Dachun Zhao, Bingtao Hao, Dewei Li, Keyue Ding
Software Mentions: 3
Published: almost 7 years ago

10.3389/fgene.2019.00408

Identification of Hub Genes Associated With Progression and Prognosis in Patients With Bladder Cancer
Cited by: 18
Author(s): Xin Yan, Xiaoping Li, Zixin Guo, Tong-Zu Liu, Sheng Li
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-52375-3

A New Strategy for Identifying Mechanisms of Drug-drug Interaction Using Transcriptome Analysis: Compound Kushen Injection as a Proof of Principle
Cited by: 4
Author(s): Hao Shen, Zhibo Qu, Yuka Harata-Lee, Jingang Cui, Thazin Nwe Aung, Wei Wang, R. Daniel Kortschak, David L. Adelson
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-016-2704-4

Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health
Cited by: 30
Author(s): Nikol Voutsina, Adrienne Payne, Robert D. Hancock, Graham J. J. Clarkson, Steve D. Rothwell, Mark A. Chapman, Gail Taylor
Software Mentions: 3
Published: over 10 years ago

10.3389/fcell.2020.00807

The Pathogenic Effects of Fusobacterium nucleatum on the Proliferation, Osteogenic Differentiation, and Transcriptome of Osteoblasts
Cited by: 8
Author(s): Hui Gao, Tianyong Sun, Fanghong Yang, Jiakan Yuan, Mei Yang, Wenyan Kang, Di Tang, Jun Zhang, Qiang Feng
Software Mentions: 3
Published: almost 6 years ago

10.1093/bioinformatics/btv425

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment
Cited by: 72
Author(s): Marek Gierliński, Christian Callebaut, Pietà Schofield, Nicholas J. Schurch, Alexander Sherstnev, Vijender Singh, Nicola Wrobel, Karim Gharbi, Gordon G. Simpson, Tom Owen-Hughes, Mark Blaxter, Geoffrey J. Barton
Software Mentions: 3
Published: about 11 years ago

10.1186/s12864-018-4651-8

Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry
Cited by: 11
Author(s): Yang Jin, Rolf Erik Olsen, Mari‐Ann Östensen, Gareth Benjamin Gillard, Sven Arild Korsvoll, Nina Santi, Arne B. Gjuvsland, Jon Olav Vik, Jacob Torgersen, Simen Rød Sandve, Yngvar Ôlsen
Software Mentions: 3
Published: over 8 years ago

10.1186/s12885-021-08229-1

Identification of NTRK3 as a potential prognostic biomarker associated with tumor mutation burden and immune infiltration in bladder cancer
Cited by: 13
Author(s): Zhao Zhang, Yizhi Yu, Pengfei Zhang, Guofeng Ma, Mingxin Zhang, Ye Liang, Wei Jiao, Haitao Niu
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2021.619857

Identification of Predictor Genes for Feed Efficiency in Beef Cattle by Applying Machine Learning Methods to Multi-Tissue Transcriptome Data
Cited by: 14
Author(s): Wei-Hao Chen, Pâmela Almeida Alexandre, Gabriela de Cássia Ribeiro, Heidge Fukumasu, Wei Sun, Antônio Reverter, Yutao Li
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2021.685494

Novel Functional Genes Involved in Transdifferentiation of Canine ADMSCs Into Insulin-Producing Cells, as Determined by Absolute Quantitative Transcriptome Sequencing Analysis
Cited by: 2
Author(s): Pengxiu Dai, Jiakai Li, Yijing Chen, Luwen Zhang, Xinke Zhang, Jinglu Wang, Guixiang Qi, Yihua Zhang
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2019.00916

An Integrated System Biology Approach Yields Drug Repositioning Candidates for the Treatment of Heart Failure
Cited by: 3
Author(s): Guodong Yang, Aiqun Ma, Zhaohui S. Qin
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-019-5556-x

Linear models enable powerful differential activity analysis in massively parallel reporter assays
Cited by: 272
Author(s): Leslie Myint, Dimitrios Avramopoulos, Loyal A. Goff, Kasper D. Hansen
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2019.01410

A Novel Method to Efficiently Highlight Nonlinearly Expressed Genes
Cited by: 3
Author(s): Qifei Wang, Haojian Zhang, Yuqing Liang, Huichuan Jiang, Siqiao Tan, Feng Luo, Zheming Yuan, Yuan Chen
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2021.743786

SOCS3 is Related to Cell Proliferation in Neuronal Tissue: An Integrated Analysis of Bioinformatics and Experiments
Cited by: 4
Author(s): Yeuni Yu, Soon Ki Sung, Chi Hyung Lee, Mihyang Ha, Junmo Kang, Eun Jung Kwon, Ji Wan Kang, Youngjoo Kim, Ga Hyun Kim, Hye Jin Heo, Hansong Lee, Tae Woo Kim, Yoonsung Lee, Kyungjae Myung, Chang‐Kyu Oh, Yun Hak Kim
Software Mentions: 3
Published: almost 5 years ago

10.1155/2020/6827057

Development of a Ten-lncRNA Signature Prognostic Model for Breast Cancer Survival: A Study with the TCGA Database
Cited by: 11
Author(s): Wenqing Zhou, Yongkui Pang, Yunmin Yao, Huiying Qiao
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pgen.1002962

A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals
Cited by: 119
Author(s): Frank W. Albert, Mehmet Somel, Miguel Carneiro, Ayinuer Aximu‐Petri, Michael Halbwax, Olaf Thalmann, José Antonio Blanco‐Aguiar, I. Z. Plyusnina, Lyudmila N. Trut, Rafael Villafuerte, Nuno Ferrand, Sylvia Kaiser, Per Jensen, Svante Pääbo
Software Mentions: 3
Published: almost 14 years ago

10.3389/fgene.2021.592135

Genome-Wide DNA Methylation and Hydroxymethylation Changes Revealed Epigenetic Regulation of Neuromodulation and Myelination in Yak Hypothalamus
Cited by: 2
Author(s): Zhixin Chai, Zhijuan Wu, Qiumei Ji, Jikun Wang, Jiabo Wang, Hui Wang, Chengfu Zhang, Jincheng Zhong, Jinwei Xin
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12885-017-3860-x

Gene expression, regulation of DEN and HBx induced HCC mice models and comparisons of tumor, para-tumor and normal tissues
Cited by: 18
Author(s): Qin Tang, Qi Wang, Qiong Zhang, Sheng‐Yan Lin, Yanhong Zhu, Xiangliang Yang, An‐Yuan Guo
Software Mentions: 3
Published: over 8 years ago

10.1186/s12885-017-3711-9

Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma
Cited by: 22
Author(s): Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong’echa, Ann M. Moormann, Jeffrey A. Bailey
Software Mentions: 3
Published: almost 9 years ago

10.3389/fcell.2021.727183

A Novel Pyroptosis-Associated Long Non-coding RNA Signature Predicts Prognosis and Tumor Immune Microenvironment of Patients With Breast Cancer
Cited by: 29
Author(s): Liqin Ping, Kaiming Zhang, Xueqi Ou, Xingsheng Qiu, Xia Xiao
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-50718-8

The role of extracellular matrix in mouse and human corneal neovascularization
Cited by: 19
Author(s): Marco Barbariga, F. Vallone, Ettore Mosca, Fabio Bignami, Cinzia Magagnotti, Phillippe Fonteyne, Federica Chiappori, Luciano Milanesi, Paolo Rama, Annapaola Andolfo, Giulio Ferrari
Software Mentions: 3
Published: almost 7 years ago

10.18632/aging.203425

ADAM15 correlates with prognosis, immune infiltration and apoptosis in hepatocellular carcinoma
Cited by: 9
Author(s): Jun Xu, Yong Guan, Yi Chao Zhang, Zhendong Qiu, Yu Zhou, Chen Chen, Jie-Ping Yu, Weixing Wang
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2019.00350

An Adaptive Multivariate Two-Sample Test With Application to Microbiome Differential Abundance Analysis
Cited by: 10
Author(s): Kalins Banerjee, Ni Zhao, A. Srinivasan, Lingzhou Xue, Steven D. Hicks, Frank A. Middleton, Rongling Wu, Xiang Zhan
Software Mentions: 3
Published: over 7 years ago

10.3390/biology10080726

Integrated Analysis of lncRNA and mRNA in Subcutaneous Adipose Tissue of Ningxiang Pig
Cited by: 7
Author(s): Yan Gong, Jun He, Biao Li, Yu Xiao, Qinghua Zeng, Kang Xu, Yehui Duan, Jun He, Haiming Ma
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2021.642227

Selecting Classification Methods for Small Samples of Next-Generation Sequencing Data
Cited by: 2
Author(s): Jiadi Zhu, Ziyang Yuan, Lianjie Shu, Wenhui Liao, Mingtao Zhao, Yan Zhou
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2020.583434

Human Fetal Scalp Dermal Papilla Enriched Genes and the Role of R-Spondin-1 in the Restoration of Hair Neogenesis in Adult Mouse Cells
Cited by: 9
Author(s): Elizabeth Weber, Yung-Chih Lai, Mingxing Lei, Ting‐Xin Jiang, Cheng‐Ming Chuong
Software Mentions: 3
Published: almost 6 years ago

10.3389/fcell.2020.603815

Genome-Wide Integrated Analysis Revealed Functions of lncRNA–miRNA–mRNA Interaction in Growth of Intermuscular Bones in Megalobrama amblycephala
Cited by: 14
Author(s): Yulong Chen, Shiming Wan, Qing Li, Xiaoru Dong, Jinghan Diao, Qing Liao, Guiying Wang, Zexia Gao
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2020.602493

The Identification of Plasma Exosomal miR-423-3p as a Potential Predictive Biomarker for Prostate Cancer Castration-Resistance Development by Plasma Exosomal miRNA Sequencing
Cited by: 29
Author(s): Tianyu Guo, Yang Wang, Jing Jia, Xueying Mao, Elżbieta Stankiewicz, Glenda Scandura, Edwina Burke, Lei Xu, Jacek Marzec, Caitlin R. Davies, Jiaying Lu, Prabhakar Rajan, Alistair Grey, K. H. Tipples, John Hines, Sakunthala C. Kudahetti, Tim Oliver, Thomas Powles, Constantine Alifrangis, Manish Kohli, Greg Shaw, Wen Wang, Na Feng, Jonathan Shamash, Daniel M. Berney, Liang Wang, Yong‐Jie Lu
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-3396-5

DEIVA: a web application for interactive visual analysis of differential gene expression profiles
Cited by: 37
Author(s): Jayson Harshbarger, Anton Kratz, Piero Carninci
Software Mentions: 3
Published: over 9 years ago

10.3389/fcell.2021.580834

Construction of circRNA-miRNA-mRNA Network for Exploring Underlying Mechanisms of Lubrication Disorder
Cited by: 2
Author(s): Shengnan Cong, Jinlong Li, Jingjing Zhang, Jingyi Feng, Aixia Zhang, Lianjun Pan, Jianhua Ma
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms21239198

Multi-Omics Analysis Provides Novel Insight into Immuno-Physiological Pathways and Development of Thermal Resistance in Rainbow Trout Exposed to Acute Thermal Stress
Cited by: 18
Author(s): HyeongJin Roh, Ahran Kim, Nameun Kim, Yoonhang Lee, Do-Hyung Kim
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2020.00520

Multi-Omic Approach to Identify Phenotypic Modifiers Underlying Cerebral Demyelination in X-Linked Adrenoleukodystrophy
Cited by: 11
Author(s): Phillip A. Richmond, Frans van der Kloet, Frédéric M. Vaz, David T.S. Lin, Anuli Uzozie, Emma Graham, Michael S. Kobor, Sara Mostafavi, Perry D. Moerland, Philipp F. Lange, Antoine H. C. van Kampen, Wyeth W. Wasserman, Marc Engelen, Stephan Kemp, Clara van Karnebeek
Software Mentions: 3
Published: about 6 years ago

10.3389/fcell.2021.663032

Phenotypically Anchored mRNA and miRNA Expression Profiling in Zebrafish Reveals Flame Retardant Chemical Toxicity Networks
Cited by: 6
Author(s): Subham Dasgupta, Cheryl L. Dunham, Lisa Truong, Michael T. Simonich, Christopher Sullivan, Robyn L Tanguay
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1006571

Enhancer of polycomb coordinates multiple signaling pathways to promote both cyst and germline stem cell differentiation in the Drosophila adult testis
Cited by: 25
Author(s): Lijuan Feng, Zhen Shi, Xin Chen
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms21228430

Complementary Transcriptome and Proteome Analyses Provide Insight into the Floral Transition in Bamboo (Dendrocalamus latiflorus Munro)
Cited by: 3
Author(s): Xiaoyan Wang, Yujiao Wang, Guoqian Yang, Lei Zhao, Xuemei Zhang, Li D, Zhenhua Guo
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12862-015-0316-2

Evidence that natural selection maintains genetic variation for sleep in Drosophila melanogaster
Cited by: 31
Author(s): Nicolas Svetec, Li Zhao, Perot Saelao, Joanna C. Chiu, David J. Begun
Software Mentions: 3
Published: over 11 years ago

10.1186/s12862-017-1074-0

Evidence of high-altitude adaptation in the glyptosternoid fish, Creteuchiloglanis macropterus from the Nujiang River obtained through transcriptome analysis
Cited by: 17
Author(s): Jingliang Kang, Xiuhui Ma, Shunping He
Software Mentions: 3
Published: almost 9 years ago

10.18632/aging.102393

Systematic identification of lncRNA-based prognostic biomarkers for glioblastoma
Cited by: 12
Author(s): Mingdong Li, Shengrong Long, Jinqu Hu, Zan Wang, Chao Geng, Shaowu Ou
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12862-016-0767-0

Close ecological relationship among species facilitated horizontal transfer of retrotransposons
Cited by: 11
Author(s): Xianzong Wang, Xiaolin Liu
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41598-019-50310-0

Comparative transcriptomics between species attributes reactogenicity pathways induced by the capsular group B meningococcal vaccine, 4CMenB, to the membrane-bound endotoxin of its outer membrane vesicle component
Cited by: 9
Author(s): Dylan Sheerin, Daniel O’Connor, Christina Dold, Elizabeth A. Clutterbuck, Moustafa Attar, Christine S. Rollier, Manish Sadarangani, Andrew J. Pollard
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-12-11

The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis
Cited by: 142
Author(s): Xuefeng Fang, Jae-Geun Yoon, Lisha Li, Wei Yu, Jiaofang Shao, Dasong Hua, Suiping Zheng, Leroy Hood, David R. Goodlett, Gregory Foltz, Biaoyang Lin
Software Mentions: 3
Published: over 15 years ago

10.3389/fcell.2021.615098

Transcriptome Analysis of Dnmt3l Knock-Out Mice Derived Multipotent Mesenchymal Stem/Stromal Cells During Osteogenic Differentiation
Cited by: 2
Author(s): Chih-Yi Yang, Rita Jui-Hsien Lu, Ming-Kang Lee, Felix Shih-Hsian Hsiao, Ya-Ping Yen, Chi‐Feng Cheng, Pu-Sheng Hsu, Yi-Tzang Tsai, Shih‐Kuo Chen, I-Hsuan Liu, Pao‐Yang Chen, Shau-Ping Lin
Software Mentions: 3
Published: over 5 years ago

10.1155/2020/9235101

Identification of Key Differentially Expressed Transcription Factors in Glioblastoma
Cited by: 8
Author(s): Gang Qin, Beiquan Hu, Xianfeng Li, Rongjie Li, Youshi Meng, Yimei Wang, Donghua Zou, Feng Wang
Software Mentions: 3
Published: about 6 years ago

10.1186/s12870-021-03124-0

The role of strigolactones in P deficiency induced transcriptional changes in tomato roots
Cited by: 17
Author(s): Yanting Wang, Hernando G. Suárez Duran, Jan C. van Haarst, Elio Schijlen, Carolien Ruyter-Spira, Marnix H. Medema, Lemeng Dong, Harro J. Bouwmeester
Software Mentions: 3
Published: about 5 years ago

10.3389/fendo.2018.00245

Drosophila Insulin-Like Peptides DILP2 and DILP5 Differentially Stimulate Cell Signaling and Glycogen Phosphorylase to Regulate Longevity
Cited by: 65
Author(s): Stephanie Post, Galina Karashchuk, John D. Wade, Waseem Sajid, Pierre De Meyts, Marc Tatar
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-019-50229-6

Model-based clustering for identifying disease-associated SNPs in case-control genome-wide association studies
Cited by: 8
Author(s): Yan Xu, Li Xing, Jessica Su, Xuekui Zhang, Weiliang Qiu
Software Mentions: 3
Published: almost 7 years ago

10.3389/fcell.2021.671211

Identification of ZNF26 as a Prognostic Biomarker in Colorectal Cancer by an Integrated Bioinformatic Analysis
Cited by: 2
Author(s): Jiaqi Liu, Yimin Li, Yaqi Gan, Qing Xiao, Ruotong Tian, Guang Shu, Gang Yin
Software Mentions: 3
Published: about 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568