bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-93128-5

Introducing the novel Cytoscape app TimeNexus to analyze time-series data using temporal MultiLayer Networks (tMLNs)
Cited by: 5
Author(s): Michaël Pierrelée, Ana Reynders, Fabrice Lopez, Aziz Moqrich, Laurent Tichit, Bianca Habermann
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-92489-1

Identification of potential microRNAs and KEGG pathways in denervation muscle atrophy based on meta-analysis
Cited by: 2
Author(s): Xinyi Gu, Bo Jin, Zhidan Qi, Xiaofeng Yin
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-90982-1

Analysis of the role of Purα in the pathogenesis of Alzheimer's disease based on RNA-seq and ChIP-seq
Cited by: 4
Author(s): Xiaoguang Shi, Shuanglai Ren, Bingying Zhang, Shanshan Guo, Wenxin He, Chengmin Yuan, Xiaofan Yang, Kevin Ig-lzevbekhai, Tao Sun, Qinwen Wang, Jianqi Cui
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-89948-0

The chemical defensome of five model teleost fish
Cited by: 15
Author(s): Marta Eide, Xiaokang Zhang, Odd André Karlsen, Jeffrey Goldstone, John J. Stegeman, Inge Jonassen, Anders Goksøyr
Software Mentions: 1
Published: about 5 years ago

10.7554/eLife.40969

Chromatin mapping identifies BasR, a key regulator of bacteria-triggered production of fungal secondary metabolites
Cited by: 41
Author(s): Juliane Fischer, Sebastian Müller, Tina Netzker, Nils Jäger, Agnieszka Gacek‐Matthews, Kirstin Scherlach, Maria C. Stroe, María García‐Altares, Francesco Pezzini, Hanno Schoeler, Michael Reichelt, Jonathan Gershenzon, Mario K. C. Krespach, Ekaterina Shelest, Volker Schroeckh, Vito Valiante, Thorsten Heinzel, Christian Hertweck, Joseph Strauss, Axel A. Brakhage
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-021-88874-5

ATHB2 is a negative regulator of germination in Arabidopsis thaliana seeds
Cited by: 3
Author(s): Rocío Soledad Tognacca, Monica Carabelli, Giorgio Morelli, Ida Ruberti, Javier Francisco Botto
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-87991-5

Genome-wide identification, evolutionary relationship and expression analysis of AGO, DCL and RDR family genes in tea
Cited by: 9
Author(s): Debasish B. Krishnatreya, Pooja Moni Baruah, Bhaskar Dowarah, Soni Chowrasia, Tapan Kumar Mondal, Niraj Agarwala
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.52613

Cell-type diversity and regionalized gene expression in the planarian intestine
Cited by: 31
Author(s): David J. Forsthoefel, Nicholas Cejda, Umair W Khan, Phillip A. Newmark
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-021-86465-y

Powerful p-value combination methods to detect incomplete association
Cited by: 25
Author(s): Susan A. Yoon, Bukyung Baik, Taesung Park, Dougu Nam
Software Mentions: 1
Published: over 5 years ago

10.1128/JVI.01873-15

Epstein-Barr Viruses (EBVs) Deficient in EBV-Encoded RNAs Have Higher Levels of Latent Membrane Protein 2 RNA Expression in Lymphoblastoid Cell Lines and Efficiently Establish Persistent Infections in Humanized Mice
Cited by: 19
Author(s): Goran Gregorovic, Elizabeth A. Boulden, Rachel Bosshard, Claudio Elgueta Karstegl, Rebecca L. Skalsky, Bryan R. Cullen, Cornelia Gujer, Patrick C. Rämer, Christian Münz, Paul J. Farrell
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-021-85886-z

Comparative transcriptome analysis during developmental stages of direct somatic embryogenesis in Tilia amurensis Rupr
Cited by: 9
Author(s): Hyein Kang, Chae-Bin Lee, Sae-Hyuk Kwon, Jimin Park, Kyu-Suk Kang, Donghwan Shim
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-85480-3

Transcriptional regulation of dosage compensation in Carica papaya
Cited by: 4
Author(s): Juan Liu, Jennifer Han, Anupma Sharma, Ching Man Wai, Ray Ming, Qingyi Yu
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.63938

Volatile DMNT directly protects plants against Plutella xylostella by disrupting the peritrophic matrix barrier in insect midgut
Cited by: 21
Author(s): Chen Chen, Hongyi Chen, Shenghong Huang, Tao‐Shan Jiang, Chuanhong Wang, Zhen Tao, Chen He, Qingfeng Tang, Peijin Li
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-85394-0

Differential normal skin transcriptomic response in total body irradiated mice exposed to scattered versus scanned proton beams
Cited by: 4
Author(s): Alexandre Leduc, Samia Chaouni, Frédéric Pouzoulet, Ludovic De Marzi, Frédérique Mégnin-Chanet, Erwan Corre, Dinu Stefan, Jean‐Louis Habrand, François Sichel, Carine Laurent
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-42025-z

Transcriptomic analysis reveals differences in the regulation of amino acid metabolism in asexual and sexual planarians
Cited by: 11
Author(s): Kiyono Sekii, Shunta Yorimoto, Hikaru Okamoto, Nanna Nagao, Takanobu Maezawa, Yasuhisa Matsui, Katsushi Yamaguchi, Ryo Furukawa, Shuji Shigenobu, Kazuya Kobayashi
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.22054

Transcriptome analysis illuminates the nature of the intracellular interaction in a vertebrate-algal symbiosis
Cited by: 40
Author(s): John A. Burns, Huanjia Zhang, Elizabeth M. Hill, Eun-Soo Kim, Ryan Kerney
Software Mentions: 1
Published: over 9 years ago

10.7150/jca.47902

Clinical significance of long non-coding RNA DUXAP8 and its protein coding genes in hepatocellular carcinoma
Cited by: 10
Author(s): Xiangkun Wang, Xiwen Liao, Rui Huang, Jianlu Huang, Zijun Chen, Xin Zhou, Chengkun Yang, Chuangye Han, Guangzhi Zhu, Tao Peng
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-42010-6

A Network-guided Association Mapping Approach from DNA Methylation to Disease
Cited by: 16
Author(s): Yandan Lin, De-Shuang Huang
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.05462

Dosage compensation can buffer copy-number variation in wild yeast
Cited by: 106
Author(s): James Hose, Chris Mun Yong, Maria Sardi, Zhishi Wang, Michael A. Newton, Audrey P. Gasch
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-019-40227-z

Transcriptome analysis of the curry tree (Bergera koenigii L., Rutaceae) during leaf development
Cited by: 2
Author(s): Vikram S. Shivakumar, Gabriel Johnson, Elizabeth A. Zimmer
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-39852-5

Suppression of glioblastoma by a drug cocktail reprogramming tumor cells into neuronal like cells
Cited by: 19
Author(s): Lei Gao, Shichao Huang, Hong Zhang, Wei Hua, Shunmei Xin, Lin Cheng, Wuqiang Guan, Yongchun Yu, Ying Mao, Gang Pei
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-39100-w

Early responses given distinct tactics to infection of Peronophythora litchii in susceptible and resistant litchi cultivar
Cited by: 10
Author(s): Jun Sun, Liangjing Cao, L Huanling, Wenbin Guo, Shujun Wang, Fang Li, Xuefeng Zou, Jiabao Wang
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-39273-4

A RNA sequencing-based six-gene signature for survival prediction in patients with glioblastoma
Cited by: 41
Author(s): Shuguang Zuo, Xinhong Zhang, Liping Wang
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.38675

Changes to social feeding behaviors are not sufficient for fitness gains of the Caenorhabditis elegans N2 reference strain
Cited by: 31
Author(s): Yuehui Zhao, Lijiang Long, Wen Xu, Richard F. Campbell, Edward Large, Joshua S. Greene, Patrick T. McGrath
Software Mentions: 1
Published: almost 8 years ago

10.3390/insects12030209

Antennal Transcriptome Analysis and Identification of Candidate Chemosensory Genes of the Harlequin Ladybird Beetle, Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae)
Cited by: 11
Author(s): Gabriele Rondoni, Alessandro Roman, Camille Meslin, Nicolas Montagné, Eric Conti, Emmanuelle Jacquin‐Joly
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-38628-1

Metabolic adaptation of adherent-invasive Escherichia coli to exposure to bile salts
Cited by: 38
Author(s): Julien Delmas, Lucie Gibold, Tiphanie Faïs, Sylvine Batista, Martin Leremboure, Clara Sinel, Emilie Vazeille, Vincent Cattoir, Anthony Buisson, Nicolas Barnich, Guillaume Dalmasso, Richard Bonnet
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-38368-8

Higher abundance of enterovirus A species in the gut of children with islet autoimmunity
Cited by: 31
Author(s): Ki Wook Kim, Jessica L. Horton, Chi Nam Ignatius Pang, Komal Jain, Preston Leung, Sonia R Isaacs, Rowena A. Bull, Fabio Luciani, Marc R. Wilkins, Jacki Catteau, W. Ian Lipkin, William D. Rawlinson, Thomas Briese, Maria E. Craig
Software Mentions: 1
Published: over 7 years ago

10.7150/jca.37267

Overexpression of DUSP6 enhances chemotherapy-resistance of ovarian epithelial cancer by regulating the ERK signaling pathway
Cited by: 17
Author(s): Yan Gao, Hui Li, Qing Han, Yuan Li, Tongxia Wang, Cuiyu Huang, Youdong Mao, Xi Wang, Qun Zhang, Tian Jing, David M. Irwin, Tan H, Hongyan Guo
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.63502

Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection
Cited by: 88
Author(s): Anastasia A. Minervina, Ekaterina A. Komech, Aleksei Titov, Meriem Bensouda Koraichi, Elisa Rosati, Ilgar Z. Mamedov, André Franke, Grigory A. Efimov, Dmitriy M. Chudakov, Thierry Mora, Aleksandra M. Walczak, Yuri B Lebedev, Mikhail V. Pogorelyy
Software Mentions: 1
Published: over 5 years ago

10.1186/s12967-020-02639-8

Plasma exosome-derived microRNAs expression profiling and bioinformatics analysis under cross-talk between increased low-density lipoprotein cholesterol level and ATP-sensitive potassium channels variant rs1799858
Cited by: 7
Author(s): Cheng Liu, Yanxian Lai, Songsong Ying, Junfang Zhan, Yan Shen
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-37755-5

Reference assembly and gene expression analysis of Apostichopus japonicus larval development
Cited by: 9
Author(s): Alexey V. Boyko, Alexander S. Girich, М. Г. Елисейкина, С. И. Масленников, Igor Yu. Dolmatov
Software Mentions: 1
Published: over 7 years ago

10.7150/jca.33157

Establishment and Characterization of a CTC Cell Line from Peripheral Blood of Breast Cancer Patient
Cited by: 19
Author(s): Pan Zhao, Weiping Zhou, Chang Liu, Huirong Zhang, Zhiqiang Cheng, Weiqing Wu, Kaisheng Liu, Hong Hu, Caineng Zhong, Yayuan Zhang, Dongxian Zhou, Feiyuan Liu, Yong Dai, Jianhong Wang, Chang Zou
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.9181

RNA sequencing-based analysis of gallbladder cancer reveals the importance of the liver X receptor and lipid metabolism in gallbladder cancer
Cited by: 11
Author(s): Mingxin Zuo, Asif Rashid, Ying Wang, Apurva Jain, Donghui Li, Anu Behari, Vinay K. Kapoor, Eugene J. Koay, Ping Chang, Jean Nicholas Vauthey, Yanan Li, Jaime A. Espinoza, Juan Carlos Roa, Milind Javle
Software Mentions: 1
Published: over 10 years ago

10.18632/oncotarget.9297

Characterization of the novel indolylmaleimides' PDA-66 and PDA-377 effect on canine lymphoma cells
Cited by: 8
Author(s): Wen Li, Julia Beck, Laura Schmidt, Catrin Roolf, Anahit Pews‐Davtyan, Barbara C. Rütgen, Sabine E. Hammer, Saskia Willenbrock, Anett Sekora, Arndt Rolfs, Matthias Beller, Bertram Brenig, Ingo Nolte, Christian Junghanß, Ekkehard Schütz, Hugo Murua Escobar
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-018-37609-0

Genetic regulatory mechanisms in human osteoclasts suggest a role for the STMP1 and DCSTAMP genes in Paget’s disease of bone
Cited by: 20
Author(s): Benjamin H. Mullin, Kun Zhu, Suzanne J. Brown, Shelby Mullin, Jennifer Tickner, Nathan J. Pavlos, Frank Dudbridge, Jiake Xu, John P. Walsh, Scott G. Wilson
Software Mentions: 1
Published: over 7 years ago

10.3390/insects11110816

Chemosensory-Related Gene Family Members of the Horn Fly, Haematobia irritans irritans (Diptera: Muscidae), Identified by Transcriptome Analysis
Cited by: 5
Author(s): Pia U. Olafson, Christopher Saski
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.9779

Chemotherapy-related cachexia is associated with mitochondrial depletion and the activation of ERK1/2 and p38 MAPKs
Cited by: 131
Author(s): Rafael Barreto, David L. Waning, Hongyu Gao, Yunlong Liu, Teresa A. Zimmers, Andrea Bonetto
Software Mentions: 1
Published: about 10 years ago

10.1186/s12929-018-0477-6

Differential genome-wide profiling of alternative polyadenylation sites in nasopharyngeal carcinoma by high-throughput sequencing
Cited by: 7
Author(s): Ya Xu, Ying Qing Li, Na Liu, Qiuming He, Xin Tang, Xin Wen, Xiao Yang, Ying Sun, Ling TANG
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-37763-5

Leukocyte expression profiles reveal gene sets with prognostic value for seizure-free outcome following stereotactic laser amygdalohippocampotomy
Cited by: 2
Author(s): Ryan Sprissler, Robert W. Bina, Willard S. Kasoff, Marlys H. Witte, Michael Bernas, C. Walter, David M. Labiner, Branden Lau, Michael F. Hammer, Martin E. Weinand
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.10216

Desmoglein 2 promotes vasculogenic mimicry in melanoma and is associated with poor clinical outcome
Cited by: 36
Author(s): Lih Y. Tan, Chris Mintoff, M. Zahied Johan, Brenton Ebert, Clare G. Fedele, You Fang Zhang, Pacman Szeto, Karen E. Sheppard, Grant A. McArthur, Erwin Foster‐Smith, Andrew Ruszkiewicz, Michael P. Brown, Claudine S. Bonder, Mark Shackleton, Lisa M. Ebert
Software Mentions: 1
Published: about 10 years ago

10.18632/oncotarget.10333

Dual tumor suppressing and promoting function of Notch1 signaling in human prostate cancer
Cited by: 24
Author(s): Karine Lefort, Paola Ostano, Maurizia Mello-Grand, Valérie Calpini, Maria Scatolini, Antonella Farsetti, G. Paolo Dotto, Giovanna Chiorino
Software Mentions: 1
Published: about 10 years ago

10.1186/s12967-018-1739-5

NovelmiRNA-25 inhibits AMPD2 in peripheral blood mononuclear cells of patients with systemic lupus erythematosus and represents a promising novel biomarker
Cited by: 26
Author(s): Gangqiang Guo, Huijing Wang, Xinyu Shi, Lele Ye, Kai Wu, Kuan‐Yu Lin, Sisi Ye, Baoqing Li, Huidi Zhang, Qiaoai Lin, Shuang Ye, Xiangyang Xue, Chaosheng Chen
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-37422-9

Virulence Characteristics and an Action Mode of Antibiotic Resistance in Multidrug-Resistant Pseudomonas aeruginosa
Cited by: 51
Author(s): Won Ju Hwang, Sang Sun Yoon
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.10729

Ago-RIP-Seq identifies Polycomb repressive complex I member CBX7 as a major target of miR-375 in prostate cancer progression
Cited by: 32
Author(s): Julia M. A. Pickl, Diana Tichy, Vladimir Kuryshev, Yanis Tolstov, Michael Falkenstein, Julia Schüler, Daniel Reidenbach, Agnes Hotz‐Wagenblatt, Glen Kristiansen, Wilfried Roth, Boris Hadaschik, Markus Hohenfellner, Stefan Duensing, Doreen Heckmann, Holger Sültmann
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-018-35891-6

De novo assembly of Agave sisalana transcriptome in response to drought stress provides insight into the tolerance mechanisms
Cited by: 34
Author(s): Muhammad Sarwar, Zarnab Ahmad, Bushra Rashid, Sahar Hassan, Per L. Gregersen, Maria De la O. Leyva, István Nagy, Torben Asp, Tayyab Husnain
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-36726-0

Piwi-interacting RNA (piRNA) expression patterns in pearl oyster (Pinctada fucata) somatic tissues
Cited by: 17
Author(s): Songqian Huang, Yūki Ichikawa, Yoji Igarashi, Kazutoshi Yoshitake, Shigeharu Kinoshita, Fumito Omori, Kaoru Maeyama, Kiyohito Nagai, Shugo Watabe, Shuichi Asakawa
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-37177-3

The Metabolic Response to a Low Amino Acid Diet is Independent of Diet-Induced Shifts in the Composition of the Gut Microbiome
Cited by: 15
Author(s): Heidi H. Pak, Nicole E. Cummings, Cara L Green, Jacqueline A. Brinkman, Deyang Yu, Jay L. Tomasiewicz, Shany E. Yang, Colin Boyle, Elizabeth N. Konon, Irene M. Ong, Dudley W. Lamming
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.10239

Prognostic significance of PLIN1 expression in human breast cancer
Cited by: 33
Author(s): Cefan Zhou, Ming Wang, Li Zhou, Yi Zhang, Weiyong Liu, Wenying Qin, Rong He, Lu Yang, Yefu Wang, Xing-Zhen Chen, Jingfeng Tang
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-018-36376-2

Transcriptome analysis of Aeromonas hydrophila infected hybrid sturgeon (Huso dauricus×Acipenser schrenckii)
Cited by: 20
Author(s): Nan Jiang, Yuding Fan, Yong Zhou, Weiling Wang, Jie Ma, Lingbing Zeng
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.12841

Serum exosomal miR-4772-3p is a predictor of tumor recurrence in stage II and III colon cancer
Cited by: 89
Author(s): Chang Liu, Cathy Eng, Jianjun Shen, Yue Lu, Yoko Takata, Amir Mehdizadeh, George J. Chang, Miguel A. Rodrı́guez-Bigas, Yanan Li, Ping Chang, Yiming Mao, Manal M. Hassan, Fangyu Wang, Donghui Li
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41598-018-35531-z

The presence of extracellular microRNAs in the media of cultured Drosophila cells
Cited by: 14
Author(s): Stijn Van den Brande, M. J. M. Gijbels, Niels Wynant, Dulce Santos, Lina Mingels, Yannick Gansemans, Filip Van Nieuwerburgh, Jozef Vanden Broeck
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-34575-5

Transcriptomic changes with increasing algal symbiont reveal the detailed process underlying establishment of coral-algal symbiosis
Cited by: 38
Author(s): Ikuko Yuyama, Masakazu Ishikawa, Masahiro Nozawa, Masa‐aki Yoshida, Kazuho Ikeo
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-34333-7

Comparative cochlear transcriptomics of echolocating bats provides new insights into different nervous activities of CF bat species
Cited by: 7
Author(s): Hui Wang, Hanbo Zhao, Xiaobin Huang, Keping Sun, Feng Jiang
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.13857

Induction of hypoxia and necrosis in multicellular tumor spheroids is associated with resistance to chemotherapy treatment
Cited by: 143
Author(s): Silvio Däster, Nunzia Amatruda, Diego Calabrese, Robert Ivánek, Eleonora Turrini, Raoul A. Droeser, Paul Zajac, Carmela Fimognari, Giulio C. Spagnoli, Giovanna Iezzi, Valentina Mele, Manuele Giuseppe Muraro
Software Mentions: 1
Published: over 9 years ago

10.18632/oncotarget.13936

A childhood acute lymphoblastic leukemia-specific lncRNA implicated in prednisolone resistance, cell proliferation, and migration
Cited by: 33
Author(s): Manon Ouimet, Simon Drouin, Mathieu Lajoie, Maxime Caron, Pascal St-Onge, Romain Gioia, Chantal Richer, Daniel Sinnett
Software Mentions: 1
Published: over 9 years ago

10.1016/j.jbc.2021.101156

Iron loading induces cholesterol synthesis and sensitizes endothelial cells to TNFα-mediated apoptosis
Cited by: 9
Author(s): Allison L. Fisher, Daniel N. Srole, Nicolaos Palaskas, David Meriwether, Srinivasa T. Reddy, Tomas Ganz, Elizabeta Nemeth
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-018-34256-3

Genome-wide RNA-seq analysis indicates that the DAG1 transcription factor promotes hypocotyl elongation acting on ABA, ethylene and auxin signaling
Cited by: 13
Author(s): Riccardo Lorrai, Francesco Gandolfi, Alessandra Boccaccini, Veronica Ruta, Marco Possenti, Anna Tramontano, Paolo Costantino, Rosalba Lepore, Paola Vittorioso
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.11938

Ex vivo miRNome analysis in Ptch1+/− cerebellum granule cells reveals a subset of miRNAs involved in radiation-induced medulloblastoma
Cited by: 12
Author(s): Barbara Tanno, Gabriele Babini, Simona Leonardi, Paola Giardullo, Ilaria De Stefano, Emanuela Pasquali, A. Ottolenghi, Michael J. Atkinson, Anna Saran, Mariateresa Mancuso
Software Mentions: 1
Published: almost 10 years ago

10.3390/insects10080245

Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection
Cited by: 30
Author(s): Dafu Chen, Huazhi Chen, Yuguang Du, Dingding Zhou, Suxia Geng, Haipeng Wang, Jieqi Wan, Chuan Xiong, Yusheng Zheng, Rui Guo
Software Mentions: 1
Published: about 7 years ago

10.1186/s12967-018-1637-x

Molecular network-based identification of competing endogenous RNAs and mRNA signatures that predict survival in prostate cancer
Cited by: 36
Author(s): Ning Xu, Yupeng Wu, Hubin Yin, Xue-Yi Xue, Xin Gou
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.15027

Comparative transcriptomic analysis of mice liver treated with different AMPK activators in a mice model of atherosclerosis
Cited by: 6
Author(s): Ang Ma, Dongmei Wang, Yuanyuan An, Wei Fang, Haibo Zhu
Software Mentions: 1
Published: over 9 years ago

10.18632/oncotarget.15161

Comprehensive investigation of a novel differentially expressed lncRNA expression profile signature to assess the survival of patients with colorectal adenocarcinoma
Cited by: 82
Author(s): Jiang‐Hui Zeng, Liang Liang, Rong‐Quan He, Rongjiang Tang, Xiujun Cai, Junqiang Chen, Dan Luo, Gang Chen
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-33899-6

Small non-coding RNA landscape of extracellular vesicles from human stem cells
Cited by: 50
Author(s): Sippy Kaur, Ahmed G. Abu-Shahba, Riku O. Paananen, Heidi Hongisto, Hanna Hiidenmaa, Heli Skottman, Riitta Seppänen‐Kaijansinkko, Bettina Mannerström
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.15190

Harnessing RNA sequencing for global, unbiased evaluation of two new adjuvants for dendritic-cell immunotherapy
Cited by: 11
Author(s): Till S.M. Mathan, Johannes Textor, Annette E. Sköld, Inge Reinieren-Beeren, Tom van Oorschot, Mareke Brüning, Carl G. Figdor, Sonja I. Buschow, Ghaith Bakdash, I. Jolanda M. de Vries
Software Mentions: 1
Published: over 9 years ago

10.1186/s12967-021-02857-8

Identifying the functions of two biomarkers in human oligodendrocyte progenitor cell development
Cited by: 4
Author(s): Huixia Zhou, HE Ya, Zhaoyan Wang, Qian Wang, Caiyan Hu, Xiaohua Wang, Shan Lu, Ké Li, Ye Yang, Zuo Luan
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-33597-3

Comparative transcriptomic analysis reveals common molecular factors responsive to heat and drought stress in Agrostis stolonifera
Cited by: 30
Author(s): Yi Xu, Bingru Huang
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-33100-y

Caloric restriction promotes functional changes involving short-chain fatty acid biosynthesis in the rat gut microbiota
Cited by: 49
Author(s): Alessandro Tanca, Marcello Abbondio, Antonio Palomba, Cristina Fraumene, Fabio Marongiu, Mauro Serra, Daniela Pagnozzi, Ezio Laconi, Sergio Uzzau
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-31719-5

Changes in circRNA expression profiles related to the antagonistic effects of Escherichia coli F17 in lamb spleens
Cited by: 9
Author(s): Chengyan Jin, Jianjun Bao, Yue Wang, Wei-Hao Chen, Shuangxia Zou, Tianyi Wu, Lihong Wang, Xiaoyang Lv, Wen Gao, Buzhong Wang, Guoqiang Zhu, Guojun Dai, Dongfang Shi, Wei Sun
Software Mentions: 1
Published: almost 8 years ago

10.1016/j.jbc.2021.100403

Targeting primary and metastatic uveal melanoma with a G protein inhibitor
Cited by: 20
Author(s): Michael D. Onken, Carol M. Makepeace, Kevin M. Kaltenbronn, Joelle Choi, Leonel F. Hernandez‐Aya, Katherine N. Weilbaecher, Kisha Piggott, P. Kumar Rao, Carla M. Yuede, Alethia J. Dixon, Patrick Osei‐Owusu, John A. Cooper, Kendall J. Blumer
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-31592-2

Expression profiling of ubiquitin-related genes in LKB1 mutant lung adenocarcinoma
Cited by: 3
Author(s): Guanghui Wang, Fenglong Bie, Xiao Qu, Xudong Yang, Shaorui Liu, Yu Wang, Can Huang, Kai Wang, Jiajun Du
Software Mentions: 1
Published: almost 8 years ago

10.18632/oncotarget.15947

UBE2T knockdown inhibits gastric cancer progression
Cited by: 46
Author(s): Changjiang Luo, Yunyi Yao, Zeyuan Yu, Huinian Zhou, Ling‐Yun Guo, Junqiang Zhang, Hongtai Cao, Genyuan Zhang, Yumin Li, Jiao Zhang
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-30262-7

Identification of candidate UDP-glycosyltransferases involved in protopanaxadiol-type ginsenoside biosynthesis in Panax ginseng
Cited by: 35
Author(s): Kyo Bin Kang, Murukarthick Jayakodi, Yun Sun Lee, Van Binh Nguyen, Hyun-Seung Park, Hyun Jo Koo, Ik‐Young Choi, Dae Hyun Kim, You Jin Chung, Byeol Ryu, Dong Hoon Lee, Sang Hyun Sung, Tae-Jin Yang
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-30147-9

Comparative transcriptomics provides insight into the molecular basis of species diversification of section Trigonopedia (Cypripedium) on the Qinghai-Tibetan Plateau
Cited by: 8
Author(s): Yanyan Guo, Yongqiang Zhang, Guoqiang Zhang, Laiqiang Huang, Zhong‐Jian Liu
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-29662-6

An integrative omics approach to unravel toxicity mechanisms of environmental chemicals: effects of a formulated herbicide
Cited by: 22
Author(s): Tiago Simões, Sara C. Novais, Tiago Natal-da-Luz, Bart Devreese, Tjalf de Boer, Dick Roelofs, José Paulo Sousa, Nico M. van Straalen, Marco F.L. Lemos
Software Mentions: 1
Published: about 8 years ago

10.1074/jbc.RA120.015877

Elongin A associates with actively transcribed genes and modulates enhancer RNA levels with limited impact on transcription elongation rate in vivo
Cited by: 13
Author(s): M. Behfar Ardehali, Manashree Damle, Carlos Perea-Resa, Michael D. Blower, Robert E. Kingston
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.17321

Inhibition of stress-inducible HSP70 impairs mitochondrial proteostasis and function
Cited by: 31
Author(s): Julia I-Ju Leu, Thibaut Barnoud, Gao Zhang, Tian Tian, Zhi Wei, Meenhard Herlyn, Maureen E. Murphy, Donna L. George
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-28916-7

An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets
Cited by: 41
Author(s): Pablo Ivan Pereira Ramos, Darío Augusto Fernández Do Porto, Esteban Lanzarotti, Ezequiel Sosa, Germán Burguener, Agustín Pardo, Cecília C. Klein, Marie‐France Sagot, Ana Tereza Ribeiro de Vasconcelos, Ana Cristina Gales, Marcelo A. Martí, Adrián Turjanski, Marisa Fabiana Nicolás
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-018-28297-x

Pirfenidone decreases mesothelioma cell proliferation and migration via inhibition of ERK and AKT and regulates mesothelioma tumor microenvironment in vivo
Cited by: 31
Author(s): Chang Li, Veronika Rezov, Emmi I. Joensuu, Ville Vartiainen, Mikko Rönty, Miao Yin, Marjukka Myllärniemi, Katri Koli
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.17506

A five-long non-coding RNA signature to improve prognosis prediction of clear cell renal cell carcinoma
Cited by: 27
Author(s): Da Shi, Qinghua Qu, Qimeng Chang, Yilin Wang, Yan Gui, Dong Dong
Software Mentions: 1
Published: over 9 years ago

10.18632/oncotarget.18833

The molecular characterization of porcine egg precursor cells
Cited by: 10
Author(s): Te-Sha Tsai, Jacqueline L. Johnson, Yvonne A.R. White, Justin C. St. John
Software Mentions: 1
Published: about 9 years ago

10.18632/oncotarget.18234

Cell lines generated from a chronic lymphocytic leukemia mouse model exhibit constitutive Btk and Akt signaling
Cited by: 17
Author(s): Simar Pal Singh, Saravanan Y. Pillai, Marjolein J. W. de Bruijn, Ralph Stadhouders, Odilia B. J. Corneth, Henk-Jan van den Ham, Alice F. Muggen, Wilfred F. J. van IJcken, Erik Slinger, Annemieke Kuil, Marcel Spaargaren, Arnon P. Kater, Anton W. Langerak
Software Mentions: 1
Published: about 9 years ago

10.18632/oncotarget.19532

Integration of genomic, transcriptomic and functional profiles of aggressive osteosarcomas across multiple species
Cited by: 12
Author(s): Lara E. Davis, Sophia Jeng, Matthew N. Svalina, Elaine Huang, Janét Pittsenbarger, Emma L. Cantor, Noah Berlow, Bernard Séguin, Atiya Mansoor, Shannon K. McWeeney, Charles Keller
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-018-27527-6

Presymptomatic change in microRNAs modulates Tau pathology
Cited by: 6
Author(s): Salil Sharma, Inès Khadimallah, Adam Williamson Corya, Yousuf Ali, Xi Rao, Yunlong Liu, Hui Lü
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.18279

LncRNA-SVUGP2 suppresses progression of hepatocellular carcinoma
Cited by: 18
Author(s): Jiangfeng Hu, Chenlin Song, Bensong Duan, Xiaoyan Zhang, Dongliang Li, Liang Zhu, Hengjun Gao
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-018-27628-2

Molecular chaperoning helps safeguarding mitochondrial integrity and motor functions in the Sahara silver ant Cataglyphis bombycina
Cited by: 12
Author(s): Quentin Willot, Patrick Mardulyn, Matthieu Defrance, Cyril Gueydan, Serge Aron
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.21087

Identification of glycerol-3-phosphate dehydrogenase 1 as a tumour suppressor in human breast cancer
Cited by: 28
Author(s): Cefan Zhou, Jing Yu, Ming Wang, Jing Yang, Hui Xiong, Huang Huang, Dongli Wu, Shiyu Hu, Yefu Wang, Xing-Zhen Chen, Jingfeng Tang
Software Mentions: 1
Published: almost 9 years ago

10.1074/jbc.M116.733733

miR-30 Family Controls Proliferation and Differentiation of Intestinal Epithelial Cell Models by Directing a Broad Gene Expression Program That Includes SOX9 and the Ubiquitin Ligase Pathway
Cited by: 33
Author(s): Bailey C. E. Peck, John Sincavage, Sydney Feinstein, Amanda T. Mah, James G. Simmons, P. Kay Lund, Praveen Sethupathy
Software Mentions: 1
Published: about 10 years ago

10.1186/s12967-019-2032-y

Prognosis of clear cell renal cell carcinoma (ccRCC) based on a six-lncRNA-based risk score: an investigation based on RNA-sequencing data
Cited by: 31
Author(s): Jiang‐Hui Zeng, Wei Lü, Liang Liang, Gang Chen, Huihua Lan, Xiu-Yun Liang, Xu Zhu
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-26738-1

Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells
Cited by: 18
Author(s): Agnes P. Chan, Yongwook Choi, Lauren Brinkac, R. Krishnakumar, Jessica DePew, Maria Kim, Mary Hinkle, Emil Lesho, Derrick E. Fouts
Software Mentions: 1
Published: about 8 years ago

10.1093/jac/dkaa296

A genome-wide analysis of Escherichia coli responses to fosfomycin using TraDIS-Xpress reveals novel roles for phosphonate degradation and phosphate transport systems
Cited by: 13
Author(s): A. Keith Turner, Muhammad Yasir, Sarah Bastkowski, Andrea Telatin, Andrew J. Page, Ian G. Charles, Mark A. Webber
Software Mentions: 1
Published: about 6 years ago

10.18632/oncotarget.23290

Comprehensive transcriptional landscape of porcine cardiac and skeletal muscles reveals differences of aging
Cited by: 32
Author(s): Jianning Chen, Qin Zou, Daojun Lv, Yingying Wei, Muhammad Ali Raza, Chen Yan, Peilin Li, Xiaoyu Xi, Huaming Xu, Anxiang Wen, Li Zhu, Guoqing Tang, Mingzhou Li, Anan Jiang, Yihui Liu, Yuhua Fu, Yanzhi Jiang, Xuewei Li
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-24999-4

A Meloidogyne incognita effector MiISE5 suppresses programmed cell death to promote parasitism in host plant
Cited by: 18
Author(s): Qianqian Shi, Zhenchuan Mao, Xi Zhang, Xiaoping Zhang, Yunsheng Wang, Jian Ling, Runmao Lin, Denghui Li, Xincong Kang, Wenxian Sun, Bingyan Xie
Software Mentions: 1
Published: over 8 years ago

10.1186/s40104-017-0202-4

Evaluation of fatty acid metabolism and innate immunity interactions between commercial broiler, F1 layer × broiler cross and commercial layer strains selected for different growth potentials
Cited by: 8
Author(s): Nicky‐Lee Willson, R. E. A. Forder, Rick Tearle, G. S. Nattrass, Robert J. Hughes, P. I. Hynd
Software Mentions: 1
Published: almost 9 years ago

10.18632/oncotarget.23534

Analysis of the circular RNA transcriptome in endometrial cancer
Cited by: 49
Author(s): Bei Jun Chen, Frances L. Byrne, Konii Takenaka, Susan C. Modesitt, Ellen M. Olzomer, James D. Mills, Rhonda Farrell, Kyle L. Hoehn, Michael Janitz
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-25516-3

Additional mitochondrial DNA influences the interactions between the nuclear and mitochondrial genomes in a bovine embryo model of nuclear transfer
Cited by: 18
Author(s): Kanokwan Srirattana, Justin C. St. John
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.24260

ALK is a critical regulator of the MYC-signaling axis in ALK positive lung cancer
Cited by: 21
Author(s): Amanda B. Pilling, Jihye Kim, Adriana Estrada-Bernal, Qiong Zhou, Anh‐Tuan Le, Katherine R. Singleton, Lynn E. Heasley, Aik Choon Tan, James DeGregori, Robert C. Doebele
Software Mentions: 1
Published: over 8 years ago

10.1016/j.jaci.2016.05.031

Tumor progression locus 2 reduces severe allergic airway inflammation by inhibiting Ccl24 production in dendritic cells
Cited by: 9
Author(s): Yashaswini Kannan, Yanda Li, Stephanie M. Coomes, Isobel Okoye, Victoria S. Pelly, Srividya Sriskantharajah, Eva Gückel, Lauren M. Webb, Stephanie Czieso, Nikolay P. Nikolov, Andrew S. MacDonald, Steven C. Ley, Mark S. Wilson
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-25103-6

Whole-transcriptome analysis of atrophic ovaries in broody chickens reveals regulatory pathways associated with proliferation and apoptosis
Cited by: 35
Author(s): Lingbin Liu, Qihai Xiao, Elizabeth R. Gilbert, Zhifu Cui, Xiaoling Zhao, Yan Wang, Huadong Yin, Diyan Li, Haihan Zhang, Qing Zhu
Software Mentions: 1
Published: over 8 years ago

10.1186/s12967-019-1987-z

Frequent genetic aberrations in the cell cycle related genes in mucosal melanoma indicate the potential for targeted therapy
Cited by: 18
Author(s): Lina Xu, Zhiyuan Cheng, Chuanliang Cui, Xiaowen Wu, Huan Yu, Jun Guo, Yan Kong
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-018-25611-5

Ca2+ imaging and gene expression profiling of Lonicera Confusa in response to calcium-rich environment
Cited by: 10
Author(s): Wenwen Jin, Yan Long, Chunhua Fu, Libin Zhang, Jun Xiang, Baoshan Wang, Maoteng Li
Software Mentions: 1
Published: over 8 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568