bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1016/j.xcrm.2020.100039

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

10.18632/aging.102185

Prognostic value of long non-coding RNA signatures in bladder cancer
Cited by: 30
Author(s): Anbang He, Shiming He, Peng Ding, Yonghao Zhan, Yifan Li, Zhicong Chen, Yanqing Gong, Xuesong Li, Liqun Zhou
Software Mentions: 5
Published: about 7 years ago

10.1093/gigascience/giab067

Association of female reproductive tract microbiota with egg production in layer chickens
Cited by: 5
Author(s): Yuan Su, Shilin Tian, Diyan Li, Wei Zhu, Tao Wang, Suchismita Mishra, Ranlei Wei, Zhongxian Xu, Mengnan He, Xiaoling Zhao, Huadong Yin, Xiaolan Fan, Bo Zeng, Mingyao Yang, Deying Yang, Qingyong Ni, Yan Li, Mingwang Zhang, Qing Zhu, Mingzhou Li
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13075-015-0544-2

Transcriptome analysis of ageing in uninjured human Achilles tendon
Cited by: 61
Author(s): Mandy J. Peffers, Yongxiang Fang, Kathleen Cheung, Tim Koh Jia Wei, Peter Clegg, Helen L. Birch
Software Mentions: 5
Published: over 11 years ago

10.1186/s13045-020-01005-x

RNA sequencing: new technologies and applications in cancer research
Cited by: 187
Author(s): Mingye Hong, Shuangping Tao, Ling Zhang, Li-Ting Diao, Xuanmei Huang, Shaohui Huang, Shu‐Juan Xie, Zhilong Xiao, Hua Zhang
Software Mentions: 5
Published: over 5 years ago

10.1007/s12072-019-09962-3

Identification and validation of a prognostic four-genes signature for hepatocellular carcinoma: integrated ceRNA network analysis
Cited by: 41
Author(s): Yongcong Yan, Yaobin Lu, Kai Mao, Mengyu Zhang, Haohan Liu, Qicun Zhou, Jianhong Lin, Jianlong Zhang, Jie Wang, Zhiyu Xiao
Software Mentions: 5
Published: about 7 years ago

10.1016/j.celrep.2018.10.072

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

10.1093/gigascience/giaa125

Localized effect of treated wastewater effluent on the resistome of an urban watershed
Cited by: 17
Author(s): Christopher N Thornton, Windy Tanner, James VanDerslice, William J. Brazelton
Software Mentions: 5
Published: almost 6 years ago

10.7717/peerj.10462

Development and clinical validation of a 3-miRNA signature to predict prognosis of gastric cancer
Cited by: 8
Author(s): Wenqian Qi, Qian Zhang
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-017-4380-4

Resistant and susceptible chicken lines show distinctive responses to Newcastle disease virus infection in the lung transcriptome
Cited by: 36
Author(s): Melissa S. Deist, Rodrigo A. Gallardo, David Bunn, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 5
Published: over 8 years ago

10.1093/gigascience/giy117

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

10.1155/2021/8880585

Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells
Cited by: 3
Author(s): Szabolcs Éliás, Angelika Schmidt, David Green, Jesper Tegnér
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.27014

Regulation of life span by the gut microbiota in the short-lived African turquoise killifish
Cited by: 262
Author(s): Patrick M. Smith, David Willemsen, Miriam Popkes, Franziska Metge, Edson Gandiwa, Martin Reichard, Dario Riccardo Valenzano
Software Mentions: 5
Published: almost 9 years ago

10.1128/AEM.02992-18

Characterizing the Key Agents in a Disease-Suppressed Soil Managed by Reductive Soil Disinfestation
Cited by: 33
Author(s): Liang Liang Liu, Xinqi Huang, Jun Zhao, Jinbo Zhang, Zucong Cai
Software Mentions: 5
Published: over 7 years ago

10.1186/s12885-021-08362-x

Differential chromatin accessibility landscape of gain-of-function mutant p53 tumours
Cited by: 2
Author(s): Bhavya Dhaka, Radhakrishnan Sabarinathan
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-018-5411-5

Bacterial and viral pathogen-associated molecular patterns induce divergent early transcriptomic landscapes in a bovine macrophage cell line
Cited by: 6
Author(s): Felix N. Toka, Kiera Dunaway, Felicia Smaltz, Lidia Szulc-Dąbrowska, Jenny Drnevich, Matylda Barbara Mielcarska, Magdalena Bossowska-Nowicka, Matthias Schweizer
Software Mentions: 5
Published: over 7 years ago

10.3389/fendo.2021.632060

Isolating the Role of Corticosterone in the Hypothalamic-Pituitary-Gonadal Transcriptomic Stress Response
Cited by: 8
Author(s): Suzanne H. Austin, Rayna M. Harris, April M. Booth, Andrew S. Lang, Victoria S. Farrar, Jesse S. Krause, Tyler A. Hallman, Matthew D. MacManes, Rebecca M. Calisi
Software Mentions: 5
Published: about 5 years ago

10.1038/s41421-020-00214-5

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

10.1186/s12864-016-2386-y

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics
Cited by: 103
Author(s): Viktor Jönsson, Tobias Österlund, Olle Nerman, Erik Kristiansson
Software Mentions: 5
Published: over 10 years ago

10.3390/ijms22010382

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

10.1186/s13073-017-0492-3

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists
Cited by: 63
Author(s): Xun Zhu, Thomas Wolfgruber, Austin Tasato, Cédric Arisdakessian, David Garmire, Lana X. Garmire
Software Mentions: 5
Published: over 8 years ago

10.3390/ijms22042046

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

10.1186/s13073-020-00760-3

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

10.7717/peerj.3817

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
Cited by: 208
Author(s): Simon Roux, Joanne B. Emerson, Emiley A. Eloe‐Fadrosh, Matthew B. Sullivan
Software Mentions: 5
Published: almost 9 years ago

10.1093/gbe/evab145

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

10.1093/gbe/evab110

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

10.1186/s13059-021-02464-2

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

10.7717/peerj.1782

H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups
Cited by: 24
Author(s): Sarah Piché‐Choquette, Julien Tremblay, Susannah G. Tringe, Philippe Constant
Software Mentions: 5
Published: over 10 years ago

10.1186/s12859-019-2697-5

GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display
Cited by: 5
Author(s): Karl Stamm, Aoy Tomita‐Mitchell, Serdar Bozdag
Software Mentions: 5
Published: over 7 years ago

10.3390/ijms221810006

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

10.7717/peerj.10818

Cytochrome P450 monooxygenase genes in the wild silkworm, Bombyx mandarina
Cited by: 5
Author(s): Linrong Wan, Zhou Anlian, Wen‐Fu Xiao, Bangxing Zou, Yaming Jiang, Jing Xiao, Cao Deng, Youhong Zhang, Mengjia Liu
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.576

Error estimates for the analysis of differential expression from RNA-seq count data
Cited by: 39
Author(s): Conrad J. Burden, Sumaira Qureshi, Susan R. Wilson
Software Mentions: 5
Published: almost 12 years ago

10.1186/s13059-020-02048-6

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

10.3389/fmicb.2017.00398

Transcriptomics Indicates Active and Passive Metronidazole Resistance Mechanisms in Three Seminal Giardia Lines
Cited by: 30
Author(s): Brendan R E Ansell, Louise Baker, Samantha J. Emery, Malcolm J. McConville, Staffan G. Svärd, Robin B. Gasser, Aaron R. Jex
Software Mentions: 5
Published: over 9 years ago

10.1186/s12864-015-2040-0

Plasmodium parasites mount an arrest response to dihydroartemisinin, as revealed by whole transcriptome shotgun sequencing (RNA-seq) and microarray study
Cited by: 27
Author(s): Philip Shaw, Sastra Chaotheing, Pavita Kaewprommal, Jittima Piriyapongsa, Chayaphat Wongsombat, Nattida Suwannakitti, Pongpisid Koonyosying, Chairat Uthaipibull, Yongyuth Yuthavong, Sumalee Kamchonwongpaisan
Software Mentions: 5
Published: almost 11 years ago

10.1186/s13073-016-0315-y

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

10.1186/s12864-018-4987-0

PdumBase: a transcriptome database and research tool for Platynereis dumerilii and early development of other metazoans
Cited by: 16
Author(s): Hsien-Chao Chou, Natalia Acevedo-Luna, Julie A. Kuhlman, Stephan Schneider
Software Mentions: 5
Published: about 8 years ago

10.1186/s12864-021-07849-y

Genome-wide identification and characterization of caffeoyl-coenzyme A O-methyltransferase genes related to the Fusarium head blight response in wheat
Cited by: 7
Author(s): Guang Yang, Wenqiu Pan, Ruoyu Zhang, Yan Pan, Qifan Guo, Weining Song, Wenbin Zheng, Xiaojun Nie
Software Mentions: 5
Published: about 5 years ago

10.1093/gbe/evz150

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

10.1371/journal.pone.0184471

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

10.1186/1471-2164-14-230

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro
Cited by: 39
Author(s): Nicolas C. Nalpas, Stephen D. E. Park, David A. Magee, Maria Taraktsoglou, John A. Browne, Kevin M. Conlon, Kévin Rue-Albrecht, Kate E. Killick, Karsten Hokamp, Amanda J. Lohan, Brendan J. Loftus, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 5
Published: over 13 years ago

10.3389/fpls.2020.597589

Chloroplast Electron Chain, ROS Production, and Redox Homeostasis Are Modulated by COS-OGA Elicitation in Tomato (Solanum lycopersicum) Leaves
Cited by: 3
Author(s): Sophie Moreau, Géraldine van Aubel, Rekin’s Janky, Pierre Van Cutsem
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1005385

MoSET1 (Histone H3K4 Methyltransferase in Magnaporthe oryzae) Regulates Global Gene Expression during Infection-Related Morphogenesis
Cited by: 66
Author(s): Kieu T.M. Pham, Yushi Inoue, Vu Van Ba, Hanh Hieu Nguyen, Toru Nakayashiki, Kenichi Ikeda, Hitoshi Nakayashiki
Software Mentions: 5
Published: about 11 years ago

10.1186/s40478-019-0805-4

Profiling the unique protective properties of intracranial arterial endothelial cells
Cited by: 7
Author(s): Dorien Hermkens, Olga C.G. Stam, Nienke M. de Wit, Ruud D. Fontijn, Aldo Jongejan, Perry D. Moerland, Claire Mackaaij, Ingeborg S. E. Waas, M. J. A. P. Daemen, Helga E. de Vries
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0227303

Transcriptome analysis of Actinidia chinensis in response to Botryosphaeria dothidea infection
Cited by: 8
Author(s): Yuanxiu Wang, Guihong Xiong, Zhe He, Mingfeng Yan, M. Q. Zou, Junxi Jiang
Software Mentions: 5
Published: over 6 years ago

10.1186/s13073-016-0348-2

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

10.1186/s12859-018-2122-5

IntEREst: intron-exon retention estimator
Cited by: 18
Author(s): Ali Oghabian, Dario Greco, Mikko J. Frilander
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pgen.1006222

KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans
Cited by: 68
Author(s): Agnieszka Gacek‐Matthews, Harald Berger, Takahiko Sasaki, Kathrin Wittstein, Clemens Gruber, Zachary A. Lewis, Joseph Strauss
Software Mentions: 5
Published: almost 10 years ago

10.3389/fmicb.2020.00360

Time-Course RNAseq Reveals Exserohilum turcicum Effectors and Pathogenicity Determinants
Cited by: 16
Author(s): Maria Petronella Human, David Kenneth Berger, Bridget Genevieve Crampton
Software Mentions: 5
Published: over 6 years ago

10.3389/fmicb.2020.00582

Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes
Cited by: 12
Author(s): Sainur Samad, Hyo‐Jung Lee, Sławek Cerbin, Marion Meima-Franke, Paul L. E. Bodelier
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1007431

Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development
Cited by: 18
Author(s): Timothy M. Johanson, Hannah D. Coughlan, Aaron T. L. Lun, Naiara G. Bediaga, Gaetano Naselli, Alexandra L. Garnham, Leonard C. Harrison, Rhys S. Allan
Software Mentions: 5
Published: about 8 years ago

10.1186/s13073-017-0432-2

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

10.1186/s12864-019-5801-3

Identification of key genes and molecular mechanisms associated with low egg production of broiler breeder hens in ad libitum
Cited by: 15
Author(s): Zehui Wei, Pengcheng Li, Sijia Huang, Purevsuren Lkhagvagarav, Mengqi Zhu, C. Liang, Caixia Jia
Software Mentions: 5
Published: about 7 years ago

10.3389/fpls.2020.00132

Developmental Analysis of Mimulus Seed Transcriptomes Reveals Functional Gene Expression Clusters and Four Imprinted, Endosperm-Expressed Genes
Cited by: 9
Author(s): Miguel A. Flores‐Vergara, Elen Oneal, Mário Costa, Gonzalo H. Villarino, Caitlyn Roberts, María Angels de Luis Balaguer, Sı́lvia Coimbra, John H. Willis, Robert G. Franks
Software Mentions: 5
Published: over 6 years ago

10.18632/aging.102697

Identification of a nomogram based on long non-coding RNA to improve prognosis prediction of esophageal squamous cell carcinoma
Cited by: 45
Author(s): Wenli Li, Jun Li, Hetong Zhao
Software Mentions: 5
Published: over 6 years ago

10.1186/s12859-020-3416-y

Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes
Cited by: 12
Author(s): Michelle L. Treiber, Diana H. Taft, Ian F Korf, David A. Mills, Danielle G. Lemay
Software Mentions: 5
Published: over 6 years ago

10.1038/s41438-021-00529-8

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

10.1371/journal.pgen.1007981

Disruption of the Caenorhabditis elegans Integrator complex triggers a non-conventional transcriptional mechanism beyond snRNA genes
Cited by: 29
Author(s): Eva Gómez-Orte, Beatriz Sáenz-Narciso, Angelina Zheleva, Begoña Ezcurra, María de Toro, Rosa López, Irene Gastaca, Hilde Nilsen, María P. Sacristán, Ralf Schnabel, Juan Cabello
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-020-07313-3

The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation
Cited by: 7
Author(s): Longsheng Xing, Yu X, Xi Qiao, Cong Huang, Qiang Wu, Yang Ni, Jiao Guo, Wan‐Xue Liu, Wei Fan, Fang‐Hao Wan, Wanqiang Qian
Software Mentions: 5
Published: over 5 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

10.1371/journal.pone.0119027

Comparative Transcriptome Analysis of Anthurium “Albama” and Its Anthocyanin-Loss Mutant
Cited by: 17
Author(s): Zhiying Li, Jiabin Wang, Xuequan Zhang, Li Xu
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0153932

Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis
Cited by: 24
Author(s): Randy J. Hempel, John P. Bannantine, Judith R. Stabel
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0252685

Expanded transcriptomic view of strawberry fruit ripening through meta-analysis
Cited by: 0
Author(s): Gibum Yi, Hosub Shin, Kyeonglim Min, Eun Jin Lee
Software Mentions: 5
Published: about 5 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: over 5 years ago

10.1016/j.ajhg.2021.04.024

Bi-allelic loss-of-function variants in BCAS3 cause a syndromic neurodevelopmental disorder
Cited by: 6
Author(s): Holger Hengel, Shabab B. Hannan, Sarah Dyack, Sara MacKay, Ulrich Schatz, Martin Fleger, Andreas Kurringer, Ghassan Balousha, Zaïd Ghanim, Fowzan S. Alkuraya, Hamad Alzaidan, Hessa S. Alsaif, Tadahiro Mitani, Sevcan Tuğ Bozdoğan, Davut Pehlivan, James R. Lupski, Joseph J Gleeson, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Elliott H. Sherr, Kendall C. Parks, Emanuela Argilli, Amber Begtrup, Hamid Galehdari, Osama Balousha, Gholamreza Shariati, Neda Mazaheri, Reza Azizi Malamiri, Alistair T. Pagnamenta, Helen Kingston, Siddharth Banka, Adam Jackson, Mathew Osmond, Angelika Rieß, Tobias B. Haack, Thomas Nägele, Stefanie Schuster, Stefan Hauser, Jakob Admard, Nicolas Casadei, Ana Velić, Boris Maček, Stephan Ossowski, Henry Houlden, Reza Maroofian, Lüdger Schöls
Software Mentions: 5
Published: about 5 years ago

10.1016/j.isci.2020.101249

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

10.3389/fmicb.2021.705712

Dual Transcriptomic Analyses Unveil Host–Pathogen Interactions Between Salmonella enterica Serovar Enteritidis and Laying Ducks (Anas platyrhynchos)
Cited by: 1
Author(s): Yu Zhang, Lina Song, Li-e Hou, Zhen Cao, Wanwipa Vongsangnak, Guoqiang Zhu, Qi Xu, Guohong Chen
Software Mentions: 5
Published: about 5 years ago

10.1186/s12974-021-02154-7

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

10.1186/s12864-017-3810-7

The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species
Cited by: 27
Author(s): Ezra Lencer, Wesley C. Warren, Richard G. Harrison, Amy R. McCune
Software Mentions: 5
Published: about 9 years ago

10.18632/aging.203422

Hedgehog dysregulation contributes to tissue-specific inflammaging of resident macrophages
Cited by: 8
Author(s): Mahamat Babagana, Kyu-Seon Oh, Sayantan Chakraborty, Alicja Pacholewska, Mohammad Aqdas, Myong-Hee Sung
Software Mentions: 5
Published: about 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

10.1038/s41597-020-0352-7

Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L.
Cited by: 69
Author(s): Won-Hee Kang, Young Mi Sim, Namjin Koo, Jae Do Nam, Junesung Lee, Nayoung Kim, Hakgi Jang, Yongmin Kim, Seon-In Yeom
Software Mentions: 5
Published: over 6 years ago

10.1186/s13195-020-00716-0

Prognosis prediction model for conversion from mild cognitive impairment to Alzheimer’s disease created by integrative analysis of multi-omics data
Cited by: 27
Author(s): Daichi Shigemizu, Shintaro Akiyama, Sayuri Higaki, Toshiyuki Sugimoto, Takashi Sakurai, Keith A. Boroevich, Alok Sharma, Tatsuhiko Tsunoda, Takahiro Ochiya, Shumpei Niida, Kouichi Ozaki
Software Mentions: 5
Published: almost 6 years ago

10.1155/2013/481545

Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies
Cited by: 13
Author(s): Shanrong Zhao, Kurt Prenger, Lance Smith
Software Mentions: 5
Published: almost 13 years ago

10.3389/fimmu.2018.02406

Molecular Signature of Aluminum Hydroxide Adjuvant in Ovine PBMCs by Integrated mRNA and microRNA Transcriptome Sequencing
Cited by: 15
Author(s): Endika Varela-Martínez, Naiara Abendaño, Javier Asín, Maialen Sistiaga-Poveda, Marta Pérez, Ramsés Reina, D. de Andrés, Lluís Luján, Begoña M. Jugo
Software Mentions: 5
Published: almost 8 years ago

10.1111/acel.13320

BiT age: A transcriptome‐based aging clock near the theoretical limit of accuracy
Cited by: 45
Author(s): David Meyer, Björn Schumacher
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1006648

Adaptation of A-to-I RNA editing in Drosophila
Cited by: 56
Author(s): Yuange Duan, Shengqian Dou, Shiqi Luo, Hong Zhang, Jian Lü
Software Mentions: 5
Published: over 9 years ago

10.7717/peerj.11237

NGScloud2: optimized bioinformatic analysis using Amazon Web Services
Cited by: 4
Author(s): Fernando Mora‐Márquez, José Luis Vázquez-Poletti, Unai López de Heredia
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms22062901

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

10.1186/s13071-015-0772-y

Dynamic expression of miRNAs across immature and adult stages of the malaria mosquito Anopheles stephensi
Cited by: 26
Author(s): Shanu Jain, Vandita Rana, T. Adak, Sujatha Sunil, Raj K. Bhatnagar
Software Mentions: 5
Published: over 11 years ago

10.7554/eLife.51796

A MAC2-positive progenitor-like microglial population is resistant to CSF1R inhibition in adult mouse brain
Cited by: 44
Author(s): Lihong Zhan, Li Fan, Lay Kodama, Peter Sohn, Man Ying Wong, Gergey Alzaem Mousa, Yungui Zhou, Yaqiao Li, Li Gan
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pgen.1008420

Physiological and genomic evidence that selection on the transcription factor Epas1 has altered cardiovascular function in high-altitude deer mice
Cited by: 50
Author(s): Rena M. Schweizer, Jonathan P. Velotta, Catherine M. Ivy, Matthew R. Jones, Sarah M. Muir, Gideon S. Bradburd, Jay F. Storz, Graham R. Scott, Zachary A. Cheviron
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.33480

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes
Cited by: 86
Author(s): David A. Knowles, Courtney K Burrows, John Blischak, Kristen Patterson, Daniel J. Serie, Nadine Norton, Carole Ober, Jonathan K. Pritchard, Yoav Gilad
Software Mentions: 5
Published: over 8 years ago

10.1186/s12859-019-2969-0

Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models
Cited by: 24
Author(s): Marina Esteban-Medina, María Peña‐Chilet, Carlos Loucera, Joaquı́n Dopazo
Software Mentions: 5
Published: about 7 years ago

10.1186/s12863-018-0660-5

Skeletal muscle in aged mice reveals extensive transformation of muscle gene expression
Cited by: 45
Author(s): I‐Hsuan Lin, Junn-Liang Chang, Kate Hua, Wan-Chen Huang, Ming Hsu, Yifan Chen
Software Mentions: 5
Published: about 8 years ago

10.1007/s00442-019-04499-6

Resistance is futile: RNA-sequencing reveals differing responses to bat fungal pathogen in Nearctic Myotis lucifugus and Palearctic Myotis myotis
Cited by: 20
Author(s): Thomas M. Lilley, Jenni M. Prokkola, Anna Blomberg, Steve Paterson, Joseph S. Johnson, Gregory G. Turner, Tomáš Bartonička, Erik Bachorec, DeeAnn M. Reeder, Kenneth A. Field
Software Mentions: 5
Published: almost 7 years ago

10.3389/fcimb.2016.00136

The Transcriptome of Exophiala dermatitidis during Ex-vivo Skin Model Infection
Cited by: 22
Author(s): Caroline Poyntner, Barbara Blasi, Elsa Arcalís, Ursula Mirastschijski, Katja Sterflinger, Hakim Tafer
Software Mentions: 5
Published: almost 10 years ago

10.7717/peerj.9658

A prognostic gene model of immune cell infiltration in diffuse large B-cell lymphoma
Cited by: 9
Author(s): Hao Zhou, Chang Zheng, Desheng Huang
Software Mentions: 5
Published: about 6 years ago

10.3389/fgene.2021.570336

A Novel Immune-Related Prognostic Signature in Head and Neck Squamous Cell Carcinoma
Cited by: 10
Author(s): Yi Zhang, Ping Chen, Qiang Zhou, Hongyan Wang, Qingquan Hua, Jie Wang, Hongliang Zhong
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1007268

Activation of DAF-16/FOXO by reactive oxygen species contributes to longevity in long-lived mitochondrial mutants in Caenorhabditis elegans
Cited by: 106
Author(s): Megan M. Senchuk, Dylan J. Dues, Claire E. Schaar, Benjamin K. Johnson, Zachary Madaj, Megan J. Bowman, Mary E. Winn, Jeremy M. Van Raamsdonk
Software Mentions: 5
Published: over 8 years ago

10.1128/AEM.00338-19

Wood Modification by Furfuryl Alcohol Resulted in a Delayed Decomposition Response in Rhodonia ( Postia ) placenta
Cited by: 13
Author(s): Inger Skrede, Monica Hongrø Solbakken, Jaqueline Hess, Carl Gunnar Fossdal, Olav A. Hegnar, Gry Alfredsen
Software Mentions: 5
Published: about 7 years ago

10.1093/bioinformatics/btaa1009

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

10.1016/j.cell.2020.09.062

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

10.1016/j.cell.2019.05.047

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

10.1016/j.cell.2020.04.035

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

10.1016/j.cell.2016.09.006

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

10.1016/j.cell.2018.09.043

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

10.1007/s00395-021-00887-3

LncRNA LncHrt preserves cardiac metabolic homeostasis and heart function by modulating the LKB1-AMPK signaling pathway
Cited by: 24
Author(s): Ning Liu, Masaharu Kataoka, Yingchao Wang, Linbin Pu, Xiaoxuan Dong, Xuyang Fu, Feng Zhang, Feng Gao, Tian Liang, Jianqiu Pei, Changchen Xiao, Qiongzi Qiu, TingTing Hong, Qiming Chen, Jing Zhao, Long‐Guan Zhu, Junhua He, Xiaoyun Hu, Yu Nie, Wei Zhu, Hong Yu, Douglas B. Cowan, Xinyang Hu, Jianan Wang, Dazhi Wang, Jinghai Chen
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-86544-0

An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk
Cited by: 5
Author(s): Gabriel Jiménez-Domínguez, Patrice Ravel, Stéphan Jalaguier, Vincent Cavaillès, Jacques Colinge
Software Mentions: 5
Published: over 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568