bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1172/jci.insight.143023

Shifting osteogenesis in vascular calcification
Cited by: 11
Author(s): Jiayi Yao, Xinhui Wu, Xuguang Qiao, Daoqin Zhang, Li Zhang, Jocelyn Ma, Xinjiang Cai, Kristina I. Boström, Yucheng Yao
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms19103170

De Novo Transcriptome Sequencing Analysis of Goose (Anser anser) Embryonic Skin and the Identification of Genes Related to Feather Follicle Morphogenesis at Three Stages of Development
Cited by: 15
Author(s): Chang Liu, Cornelius Tlotliso Sello, Yanbo Sun, Yifang Zhou, Hongtao Lu, Yuanyuan Sui, Jingtao Hu, Chi Xu, Yue Sun, Jing Liu, Shengyi Li, Yiming Zhang, Kaiyan Zhang
Software Mentions: 1
Published: almost 8 years ago

10.3390/ijms19103180

iTRAQ-Based Proteomic Analysis of Ogura-CMS Cabbage and Its Maintainer Line
Cited by: 12
Author(s): Fengqing Han, Xiaoli Zhang, Limei Yang, Mu Zhuang, Yangyong Zhang, Zhansheng Li, Zhiyuan Fang, Honghao Lv
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0145507

Inhibition of Hedgehog-Signaling Driven Genes in Prostate Cancer Cells by Sutherlandia frutescens Extract
Cited by: 6
Author(s): Yuan Lu, Nicholas J.E. Starkey, Lei W, Jilong Li, Jianlin Cheng, William R. Folk, Dennis B. Lubahn
Software Mentions: 1
Published: over 10 years ago

10.1099/mic.0.000579

Haem-iron plays a key role in the regulation of the Ess/type VII secretion system of Staphylococcus aureus RN6390
Cited by: 15
Author(s): Maria Guillermina Casabona, Holger Kneuper, Daniela Alferes De Lima, Catriona P. Harkins, Martin Zoltner, Erik Hjerde, Matthew T. G. Holden, Tracy Palmer
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-021-83074-7

Small RNAs and their targets are associated with the transgenerational effects of water-deficit stress in durum wheat
Cited by: 13
Author(s): Haipei Liu, Amanda J. Able, Jason A. Able
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0187052

Insight into cordycepin biosynthesis of Cordyceps militaris: Comparison between a liquid surface culture and a submerged culture through transcriptomic analysis
Cited by: 22
Author(s): Ahmad Suparmin, Tatsuya Kato, Hideo Dohra, Enoch Y. Park
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0175197

Bacterial biofilm under flow: First a physical struggle to stay, then a matter of breathing
Cited by: 80
Author(s): Philippe Thomen, Jérôme Robert, Amaury Monmeyran, Anne-Florence Bitbol, Carine Douarche, Nelly Henry
Software Mentions: 1
Published: over 9 years ago

10.1021/acs.jafc.1c00130

1H NMR Metabolomics and Full-Length RNA-Seq Reveal Effects of Acylated and Nonacylated Anthocyanins on Hepatic Metabolites and Gene Expression in Zucker Diabetic Fatty Rats
Cited by: 8
Author(s): Kang Chen, Xuetao Wei, Raghunath Pariyani, Maaria Kortesniemi, Yumei Zhang, Baoru Yang
Software Mentions: 1
Published: over 5 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/s41420-021-00440-0

Dysregulation of miR-23b-5p promotes cell proliferation via targeting FOXM1 in hepatocellular carcinoma
Cited by: 9
Author(s): Xiaopei Yang, Shuguang Yang, Jun Song, Wenjie Yang, Jicheng Yang, Feng Zhang, Jianhua Rao
Software Mentions: 1
Published: over 5 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: about 9 years ago

10.1038/s41598-021-82848-3

A transcriptomic view to wounding response in young Scots pine stems
Cited by: 9
Author(s): Kean‐Jin Lim, Tanja Paasela, Anni Harju, Martti Venäläinen, Lars Paulín, Petri Auvinen, Katri Kärkkäinen, Teemu H. Teeri
Software Mentions: 1
Published: over 5 years ago

10.1111/pbi.13058

Os<scp>ACL</scp>‐A2 negatively regulates cell death and disease resistance in rice
Cited by: 43
Author(s): Banpu Ruan, Zhihua Hua, Juan Zhao, Bin Zhang, Deyong Ren, Chaolei Liu, Shenglong Yang, Anpeng Zhang, Hongzhen Jiang, Haiping Yu, Jiang Hu, Li Zhu, Guang Chen, Lan Shen, Guojun Dong, Guangheng Zhang, Dali Zeng, Longbiao Guo, Qian Qian, Zhenyu Gao
Software Mentions: 1
Published: over 7 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

10.1038/s41419-019-2027-x

Circ-Spidr enhances axon regeneration after peripheral nerve injury
Cited by: 22
Author(s): Susu Mao, Tao Huang, Yuanyuan Chen, Longxiang Shen, Shuoshuo Zhou, Shanshan Zhang, Bin Yu
Software Mentions: 1
Published: almost 7 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

10.3390/ijms19113412

Transcriptomic Analysis of Betula halophila in Response to Salt Stress
Cited by: 17
Author(s): Fenjuan Shao, Lisha Zhang, Iain W. Wilson, Deyou Qiu
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-021-83835-4

Lysosome repositioning as an autophagy escape mechanism by Mycobacterium tuberculosis Beijing strain
Cited by: 12
Author(s): Thanida Laopanupong, Pinidphon Prombutara, Phongthon Kanjanasirirat, Salisa Benjaskulluecha, Atsadang Boonmee, Tanapat Palaga, Stéphane Méresse, Jiraporn Paha, Tegar Adriansyah Putra Siregar, Tanawadee Khumpanied, Suparerk Borwornpinyo, Angkana Chaiprasert, Pongsak Utaisincharoen, Marisa Ponpuak
Software Mentions: 1
Published: over 5 years ago

10.1016/j.mec.2021.e00184

Transport engineering for improving the production and secretion of valuable alkaloids in Escherichia coli
Cited by: 8
Author(s): Yasuyuki Yamada, Miya Urui, Hidehiro Oki, Kai Inoue, Haruyuki Matsui, Yoshito Ikeda, Akira Nakagawa, Fumihiko Sato, Hiromichi Minami, Nobukazu Shitan
Software Mentions: 1
Published: almost 5 years ago

10.1111/pbi.12960

Transgenic creeping bentgrass overexpressing Osa‐miR393a exhibits altered plant development and improved multiple stress tolerance
Cited by: 63
Author(s): Junlong Zhao, Shuangrong Yuan, Man Zhou, Nannan Yuan, Zhigang Li, Qian Hu, Frank Bethea, Haibo Liu, Shigui Li, Hong Luo
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

10.1016/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/s41598-021-84355-x

The role of gut microbiota and amino metabolism in the effects of improvement of islet β-cell function after modified jejunoileal bypass
Cited by: 9
Author(s): Cai Tan, Zhihua Zheng, Xiaogang Wan, Jiaqing Cao, Ran Wei, Jinyuan Duan
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms19123735

Comparative Transcriptome Analysis between a Resistant and a Susceptible Wild Tomato Accession in Response to Phytophthora parasitica
Cited by: 25
Author(s): Zunaira Afzal Naveed, Gul Shad Ali
Software Mentions: 1
Published: almost 8 years ago

10.1155/2021/5584099

Transcriptomic Analysis Exploring the Molecular Mechanisms of Hanchuan Zupa Granules in Alleviating Asthma in Rat
Cited by: 2
Author(s): Hai-Long Yin, Yanbo Fan, Dandan Mu, Fei Song, Fang Tian, Qiang Yin
Software Mentions: 1
Published: about 5 years ago

10.3390/nu10111721

The Effect of Dietary Mushroom Agaricus bisporus on Intestinal Microbiota Composition and Host Immunological Function
Cited by: 25
Author(s): Gloria Solano‐Aguilar, Saebyeol Jang, Sukla Lakshman, Richi Gupta, Ethiopia Beshah, Masoumeh Sikaroodi, Bryan T. Vinyard, Aleksey Molokin, Patrick M. Gillevet, Joseph F. Urban
Software Mentions: 1
Published: almost 8 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

10.1186/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/s41598-021-84402-7

Absence of X-chromosome dosage compensation in the primordial germ cells of Drosophila embryos
Cited by: 3
Author(s): Ryoma Ota, Makoto Hayashi, Shumpei Morita, Hideharu Miura, Satoru Kobayashi
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-84519-9

Comparative transcriptome profiles of large and small bodied large-scale loaches cultivated in paddy fields
Cited by: 3
Author(s): Liulan Zhao, Kuo He, Qing Xiao, Qiao Li, Wei Luo, Jie Luo, Hongmei Fu, Jiayao Li, Xugan Wu, Jun Du, Quan Gong, Xun Wang
Software Mentions: 1
Published: over 5 years ago

10.1111/pbi.12754

Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth
Cited by: 40
Author(s): Qiang Lu, Fenjuan Shao, Colleen MacMillan, Iain W. Wilson, Karen Van der Merwe, Steven G. Hussey, Alexander Andrew Myburg, Xiaomei Dong, Deyou Qiu
Software Mentions: 1
Published: about 9 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

10.1038/s41419-018-0705-8

Jnk2 deficiency increases the rate of glaucomatous neurodegeneration in ocular hypertensive DBA/2J mice
Cited by: 16
Author(s): Jeffrey M Harder, Pete A. Williams, Ileana Soto, Nicole E. Foxworth, Kimberly A. Fernandes, Nelson F. Freeburg, Richard T. Libby, Simon W. M. John
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms20030539

Global Transcriptional Insights of Pollen-Pistil Interactions Commencing Self-Incompatibility and Fertilization in Tea [Camellia sinensis (L.) O. Kuntze]
Cited by: 29
Author(s): Romit Seth, Abhishek Bhandawat, Rajni Parmar, Pradeep Singh, Sanjay Kumar, Ram Kumar Sharma
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms20040944

Insights into Body Size Evolution: A Comparative Transcriptome Study on Three Species of Asian Sisoridae Catfish
Cited by: 3
Author(s): Weixing Jiang, Yicheng Guo, Kuo-Pin Yang, Qiong Shi, Jing Yang
Software Mentions: 1
Published: over 7 years ago

10.1111/pbi.12913

Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat
Cited by: 27
Author(s): Elodie Rey, Michaël Abrouk, Gabriel Keeble‐Gagnère, Miroslava Karafiátová, Jan Vrána, Sandrine Balzergue, Ludivine Soubigou‐Taconnat, Véronique Brunaud, Marie‐Laure Martin‐Magniette, Takashi R. Endo, Jan Bartoš, R. Appels, Jaroslav Doležel
Software Mentions: 1
Published: over 8 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

10.3390/ijms16010840

Identification of Retinopathy of Prematurity Related miRNAs in Hyperoxia-Induced Neonatal Rats by Deep Sequencing
Cited by: 12
Author(s): Ran Zhao, Lijuan Qian, Li Jiang
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0148311

Genome-Wide Analysis of Acute Endurance Exercise-Induced Translational Regulation in Mouse Skeletal Muscle
Cited by: 14
Author(s): Hideki Sako, Keigo Yada, Katsuhiko Suzuki
Software Mentions: 1
Published: over 10 years ago

10.1186/s13072-018-0241-x

Physiological effects of KDM5C on neural crest migration and eye formation during vertebrate development
Cited by: 17
Author(s): Youni Kim, Youngeun Jeong, Kujin Kwon, Tayaba Ismail, Hyun-Kyung Lee, Chowon Kim, Jeen‐Woo Park, Oh Nam Kwon, Beom‐Sik Kang, Dong‐Seok Lee, Tae Joo Park, Taejoon Kwon, Hyun‐Shik Lee
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0176155

Mercury-induced epigenetic transgenerational inheritance of abnormal neurobehavior is correlated with sperm epimutations in zebrafish
Cited by: 94
Author(s): Michael J. Carvan, Thomas Achankunju Kalluvila, Rebekah Klingler, Jeremy K. Larson, Matthew Christopher Pickens, Francisco X. Mora-Zamorano, Victoria P. Connaughton, Ingrid Sadler‐Riggleman, Daniel Beck, Michael K. Skinner
Software Mentions: 1
Published: over 9 years ago

10.1038/s41396-020-00797-7

Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta
Cited by: 14
Author(s): Gust Bilcke, Koen Van Den Berge, Sam De Decker, Eli Bonneure, Nicole Poulsen, Petra Bulánková, Cristina Maria Osuna-Cruz, Jack Dickenson, Koen Sabbe, Georg Pohnert, Klaas Vandepoele, Sven Mangelinckx, Lieven De Veylder, Wim Vyverman
Software Mentions: 1
Published: almost 6 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

10.1186/s40168-020-00812-1

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures.
Cited by: 1
Author(s): Nathan D. Olson, M. S. Binoj Kumar, Shan Li, Domenick J. Braccia, Stephanie Hao, Winston Timp, Marc Salit, O. Colin Stine, Héctor Corrada Bravo
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0172700

Metabolic activity, urease production, antibiotic resistance and virulence in dual species biofilms of Staphylococcus epidermidis and Staphylococcus aureus
Cited by: 20
Author(s): Ilse Vandecandelaere, Filip Van Nieuwerburgh, Dieter Deforce, Tom Coenye
Software Mentions: 1
Published: over 9 years ago

10.1038/s41396-019-0393-0

Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide
Cited by: 101
Author(s): Zahra F. Islam, Paul R. F. Cordero, Joanna Feng, Ya-Jou Chen, Sean K. Bay, Thanavit Jirapanjawat, Roslyn M. Gleadow, Carlo R. Carere, Matthew B. Stott, Eleonora Chiri, Chris Greening
Software Mentions: 1
Published: over 7 years ago

10.1007/s00425-020-03424-z

The identification of differentially expressed genes in male and female gametophytes of simple thalloid liverwort Pellia endiviifolia sp. B using an RNA-seq approach
Cited by: 3
Author(s): Izabela Sierocka, Sylwia Alaba, Artur Jarmołowski, Wojciech M. Karłowski, Zofia Szweykowska-Kulińska
Software Mentions: 1
Published: about 6 years ago

10.1038/s41396-017-0034-4

Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise
Cited by: 27
Author(s): Songjun Hou, Mario López‐Pérez, Ulrike Pfreundt, Natalia Belkin, Kurt Stüber, Bruno Huettel, Richard Reinhardt, Ilana Berman‐Frank, Francisco Rodrı́guez-Valera, Wolfgang R. Hess
Software Mentions: 1
Published: over 8 years ago

10.3389/fonc.2021.614925

The Human Cytomegalovirus US31 Gene Predicts Favorable Survival and Regulates the Tumor Microenvironment in Gastric Cancer
Cited by: 2
Author(s): Sisi Ye, Yuanbo Hu, Chenbin Chen, Sian Chen, Xinya Tong, Huanbo Zhu, Bo Deng, Xianjing Hu, Xia Sun, Xiao Chen, Xinyu Shi, Ruihong Gu, Wangkai Xie, Gangqiang Guo, Dong Xing, Xian Shen, Xiangyang Xue, Shurong Shen
Software Mentions: 1
Published: over 5 years ago

10.7150/jca.46084

UXT antisense RNA 1 sever as a novel prognostic long non-coding RNA in early stage pancreatic ductal adenocarcinoma patients after receiving pancreaticoduodenectomy
Cited by: 1
Author(s): Xiwen Liao, Rui Huang, Xiangkun Wang, Ketuan Huang, Chengkun Yang, Xin Zhou, Chuangye Han, Hao Su, Xinping Ye, Kang Liu, Guangzhi Zhu, Tao Peng
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms20061411

Map-Based Cloning, Phylogenetic, and Microsynteny Analyses of ZmMs20 Gene Regulating Male Fertility in Maize
Cited by: 22
Author(s): Yan Bo Wang, Dongcheng Liu, Youhui Tian, Wu Shu, Xianghai An, Zhenying Dong, Simiao Zhang, Jianxi Bao, Ziwen Li, Jinping Li, Xiangyuan Wan
Software Mentions: 1
Published: over 7 years ago

10.1038/s41396-017-0005-9

Deciphering the nature of the coral–Chromera association
Cited by: 31
Author(s): Amin R. Mohamed, Vivian R. Cumbo, Saki Harii, Chuya Shinzato, Cheong Xin Chan, Mark A. Ragan, Nori Satoh, Eldon E. Ball, David J. Miller
Software Mentions: 1
Published: over 8 years ago

10.1038/ismej.2017.18

Chance and necessity in the genome evolution of endosymbiotic bacteria of insects
Cited by: 27
Author(s): Beatriz Sabater-Muñoz, Christina Toft, David Alvarez‐Ponce, Mario A. Fares
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0151816

CsoR Is Essential for Maintaining Copper Homeostasis in Mycobacterium tuberculosis
Cited by: 33
Author(s): Sarah A. Marcus, Sarah W. Sidiropoulos, Howard Steinberg, Adel M. Talaat
Software Mentions: 1
Published: over 10 years ago

10.1002/mbo3.899

Shared and unique microbes between Small hive beetles (Aethina tumida) and their honey bee hosts
Cited by: 9
Author(s): Qiang Huang, Dawn Lopez, Jay D. Evans
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms20081906

Comparative Transcriptomic Studies on a Cadmium Hyperaccumulator Viola baoshanensis and Its Non-Tolerant Counterpart V. inconspicua
Cited by: 19
Author(s): Haoyue Shu, Jun Zhang, Fuye Liu, Chao Bian, Jie-Liang Liang, Jiaqi Liang, Weihe Liang, Zhiliang Caleb Lin, Wen‐Sheng Shu, Jintian Li, Qiong Shi, Bin Liao
Software Mentions: 1
Published: over 7 years ago

10.14814/phy2.14344

Transcriptomic profiles reveal differences between the right and left ventricle in normoxia and hypoxia
Cited by: 9
Author(s): Matthew W. Gorr, Krishna Sriram, Amy M. Chinn, Abinaya Muthusamy, Paul A. Insel
Software Mentions: 1
Published: over 6 years ago

10.1111/jcmm.14048

MCLPMDA: A novel method for miRNA-disease association prediction based on matrix completion and label propagation
Cited by: 50
Author(s): Shengsheng Yu, Cheng Liang, Qiu Xiao, Guanghui Li, Pingjian Ding, Jiawei Luo
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13072-015-0013-9

Modelling the conditional regulatory activity of methylated and bivalent promoters
Cited by: 7
Author(s): David Budden, Daniel Hurley, Edmund J. Crampin
Software Mentions: 1
Published: about 11 years ago

10.1111/jcmm.14567

MicroRNA‐transcriptome networks in whole blood and monocytes of women undergoing preterm labour
Cited by: 12
Author(s): Alison G. Paquette, Oksana Shynlova, Xiaogang Wu, Mark Kibschull, Kai Wang, Nathan D. Price, Stephen J. Lye
Software Mentions: 1
Published: about 7 years ago

10.1111/jcmm.14627

Long non‐coding RNA LINC01225 promotes proliferation, invasion and migration of gastric cancer via Wnt/β‐catenin signalling pathway
Cited by: 13
Author(s): Ying Xü, Guohua Zhang, Chen Zou, Wenliang Qi, Zhigang Gong, Guoliang Zhang, Guansheng Ma, Wenbo Zhang, Pengcheng Jiang
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0178717

The Ebola virus VP35 protein binds viral immunostimulatory and host RNAs identified through deep sequencing
Cited by: 17
Author(s): Kari A. Dilley, Alexander A. Voorhies, Priya Luthra, Vinita Puri, Timothy B. Stockwell, Hernán Lorenzi, Christopher F. Basler, Reed S. Shabman
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0192610

De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform
Cited by: 18
Author(s): Dan Hou, Linchun Shi, Mengmeng Yang, Jiong Li, Shuang Zhou, Hongxiao Zhang, Huawei Xu
Software Mentions: 1
Published: over 8 years ago

10.1111/jcmm.14719

Systematic construction and validation of an immune prognostic model for lung adenocarcinoma
Cited by: 43
Author(s): Chenghan Luo, Mengyuan Lei, Yixia Zhang, Qian Zhang, Lifeng Li, Jingyao Lian, Shasha Li, Liping Wang, Guofu Pi
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41396-020-0718-z

Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms
Cited by: 12
Author(s): Rebecca E. Cooper, Carl‐Eric Wegner, Stefan Kügler, Remington X. Poulin, Nico Ueberschaar, Jens D. Wurlitzer, Daniel Stettin, Thomas Wichard, Georg Pohnert, Kirsten Küsel
Software Mentions: 1
Published: about 6 years ago

10.14814/phy2.12473

The effect of acute and long-term physical activity on extracellular matrix and serglycin in human skeletal muscle
Cited by: 43
Author(s): Marit Hjorth, Frode Norheim, Astri Jeanette Meen, Shirin Pourteymour, Sindre Lee, Torgeir Holen, Jørgen Jensen, Kåre I. Birkeland, Vladimir Martinov, Torgrim M. Langleite, Kristin Eckardt, Christian A. Drevon, Svein Olav Kolset
Software Mentions: 1
Published: about 11 years ago

10.1111/jcmm.15090

Hedgehog signalling mediates drug resistance through targeting TAP1 in hepatocellular carcinoma
Cited by: 22
Author(s): Xiaotian Zhou, Jia Ding, Hui‐Yan Li, Jie‐Liang Zuo, Shengyang Ge, Hongyan Jia, Jian Wu
Software Mentions: 1
Published: over 6 years ago

10.1111/jcmm.15161

LncRNA ADAMTS9‐AS2 suppresses the proliferation of gastric cancer cells and the tumorigenicity of cancer stem cells through regulating SPOP
Cited by: 18
Author(s): Feiran Wang, Chong Tang, Dong Xu, Yijie Tang, Yasu Jiang, Xuesong Gao, Jiacheng Xu
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms20092349

An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Differential Regulation of Carbon and Nitrogen Metabolism in Response to Nitrogen Availability
Cited by: 66
Author(s): Xin Wei, Lina Zhang, Wenzhong Zhang, Jiping Gao, Jun Yi, Xiaoxi Zhen, Ziang Li, Zhao Ying, Chengcheng Peng, Chen Zhao
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0166920

Expression and Regulation of PIWIL-Proteins and PIWI-Interacting RNAs in Rheumatoid Arthritis
Cited by: 21
Author(s): Lenka Pleštilová, Michel Neidhart, Giancarlo Russo, Mojca Frank-Bertoncelj, Caroline Ospelt, Adrian Ciurea, Christoph Kolling, Renate E. Gay, Beat A. Michel, Jiří Vencovský, Steffen Gay, Astrid Jüngel
Software Mentions: 1
Published: almost 10 years ago

10.3390/ijms20092360

OsbZIP81, A Homologue of Arabidopsis VIP1, May Positively Regulate JA Levels by Directly Targetting the Genes in JA Signaling and Metabolism Pathway in Rice
Cited by: 22
Author(s): Defang Liu, Shaopeng Shi, Hao Zhang, Wentao Xiong, Meizhong Luo
Software Mentions: 1
Published: over 7 years ago

10.14814/phy2.14289

Prostaglandin D2signaling is not involved in the recovery of rat hind limb tendons from injury
Cited by: 3
Author(s): Dylan C. Sarver, Kristoffer B. Sugg, Jeffrey R Talarek, Jacob B. Swanson, David J. Oliver, Aaron C. Hinken, Henning F. Kramer, Christopher L. Mendias
Software Mentions: 1
Published: almost 7 years ago

10.1111/jcmm.15242

Characterization of the prognostic values and response to immunotherapy/chemotherapy of Krüppel‐like factors in prostate cancer
Cited by: 20
Author(s): Jialin Meng, Xiaofan Lu, Yu Jie Zhou, Meng Zhang, Lei Gao, Shenglin Gao, Fangrong Yan, Chaozhao Liang
Software Mentions: 1
Published: over 6 years ago

10.1111/jcmm.15244

Analysis of deep sequencing exosome‐microRNA expression profile derived from CP‐II reveals potential role of gga‐miRNA‐451 in inflammation
Cited by: 12
Author(s): Yabo Zhao, Yali Fu, Meiling Zou, Yingfei Sun, Xun Yin, Liangjie Niu, Yanzhang Gong, Xiuli Peng
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms21124252

Micro-Transcriptome Analysis Reveals Immune-Related MicroRNA Regulatory Networks of Paralichthys olivaceus Induced by Vibrio anguillarum Infection
Cited by: 11
Author(s): Xianhui Ning, Li Sun
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0221444

Proteome-transcriptome alignment of molecular portraits achieved by self-contained gene set analysis: Consensus colon cancer subtypes case study
Cited by: 0
Author(s): Galina Glazko, Boris Zybailov, Frank Emmert‐Streib, Ancha Baranova, Yasir Rahmatallah
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0237189

Herpes simplex virus infection, Acyclovir and IVIG treatment all independently cause gut dysbiosis
Cited by: 6
Author(s): Chandran Ramakrishna, Stacee Mendonca, Paul Ruegger, Jane Hannah Kim, James Borneman, Edouard M. Cantin
Software Mentions: 1
Published: about 6 years ago

10.7150/ijbs.55559

Generation of VEGF knock-in Cashmere goat via the CRISPR/Cas9 system
Cited by: 12
Author(s): Xiao Hu, Hao Fei, Xiaocong Li, Zhiyuan Xun, Yuan Gao, Bo Ren, Ming Cang, Hao Liang, Dongjun Liu
Software Mentions: 1
Published: over 5 years ago

10.7150/ijbs.63430

CCNB2/SASP/Cathepsin B & PGE2 Axis Induce Cell Senescence Mediated Malignant Transformation
Cited by: 5
Author(s): Ying Wang, Hanbing Zhang, Minglei Wang, Jing He, Hui Guo, Lihua Li, Jie Wang
Software Mentions: 1
Published: over 5 years ago

10.7150/ijbs.57871

Characteristics of the PI3K/AKT and MAPK/ERK pathways involved in the maintenance of self-renewal in lung cancer stem-like cells
Cited by: 14
Author(s): Jingyuan Li, Yunlong Wang, Dan Xie, Pei Qin, Xue Wan, H. Rosie Xing, Ting Ye
Software Mentions: 1
Published: over 5 years ago

10.7150/ijbs.59581

The effect of mitochondrial transplantation therapy from different gender on inhibiting cell proliferation of malignant melanoma
Cited by: 8
Author(s): Zhenyao Yu, Yixue Hou, Wei Zhou, Zizhen Zhao, Zesheng Liu, Ailing Fu
Software Mentions: 1
Published: over 5 years ago

10.7150/ijbs.62471

Rutin attenuates Sorafenib-induced Chemoresistance and Autophagy in Hepatocellular Carcinoma by regulating BANCR/miRNA-590-5P/OLR1 Axis
Cited by: 28
Author(s): Meng Zhou, Gan Zhang, Jun Hu, Yanzhi Zhu, Haoming Lan, Xianfeng Shen, Yi Lv, Lei Huang
Software Mentions: 1
Published: over 5 years ago

10.7150/ijbs.36412

Circular RNA profiling identified an abundant circular RNA circTMTC1 that inhibits chicken skeletal muscle satellite cell differentiation by sponging miR-128-3p
Cited by: 56
Author(s): Xiaoxu Shen, Zihao Liu, Xinao Cao, Haorong He, Shunshun Han, Yuqi Chen, Can Cui, Jing Zhao, Diyan Li, Yan Wang, Qing Zhu, Huadong Yin
Software Mentions: 1
Published: over 7 years ago

10.1111/jcmm.16381

Theragnostic chromosomal rearrangements in treatment‐naive pancreatic ductal adenocarcinomas obtained via endoscopic ultrasound
Cited by: 0
Author(s): Stephen J. Murphy, Michael J. Levy, James B. Smadbeck, Giannoula Karagouga, Alexa McCune, Frances Harris, Julia Udell, Sarah H. Johnson, Sarah E. Kerr, John C. Cheville, Benjamin R. Kipp, George Vasmatzis, Ferga C. Gleeson
Software Mentions: 1
Published: over 5 years ago

10.7150/ijbs.58916

Circular RNA circBCBM1 promotes breast cancer brain metastasis by modulating miR-125a/BRD4 axis
Cited by: 27
Author(s): Bo Fu, Wei Liu, Congshan Zhu, Peng Li, Li Wang, Pan Li, Ké Li, Peiying Cai, Min Meng, Yiting Wang, Anqi Zhang, Wenqiang Tang, Meng An
Software Mentions: 1
Published: over 5 years ago

10.1186/s40168-020-00888-9

Gut microbiome composition differences among breeds impact feed efficiency in swine
Cited by: 91
Author(s): Matteo Bergamaschi, Francesco Tiezzi, Jeremy Howard, Yongjun Huang, Kent Gray, Constantino Schillebeeckx, Nathan P. McNulty, Christian Maltecca
Software Mentions: 1
Published: about 6 years ago

10.1111/jcmm.16760

The subtype‐specific molecular function of SPDEF in breast cancer and insights into prognostic significance
Cited by: 4
Author(s): Ting Ye, Jingyuan Li, June Feng, Jinglan Guo, Xue Wan, Dan Xie, Jinbo Liu
Software Mentions: 1
Published: about 5 years ago

10.1186/s13046-018-0833-0

Overexpression of the Kininogen-1 inhibits proliferation and induces apoptosis of glioma cells
Cited by: 41
Author(s): Jinfang Xu, Jun Fang, Zhonghao Cheng, Longlong Fan, Weiwei Hu, Feng Zhou, Hong Shen
Software Mentions: 1
Published: about 8 years ago

10.1111/jcmm.16700

LncRNA PVT1 promotes the progression of ovarian cancer by activating TGF‐β pathway via miR‐148a‐3p/AGO1 axis
Cited by: 13
Author(s): Yuxian Wu, Wenqian Gu, Xiao Han, Zhendong Jin
Software Mentions: 1
Published: about 5 years ago

10.1038/s41420-019-0152-z

The whole transcriptome and proteome changes in the early stage of myocardial infarction
Cited by: 15
Author(s): Yanfei Li, Cuiping Wang, Tingting Li, Linlin Ma, Fangzhou Fan, Yueling Jin, Junwei Shen
Software Mentions: 1
Published: over 7 years ago

10.1111/jcmm.16825

MicroRNA‐205‐5p targets E2F1 to promote autophagy and inhibit pulmonary fibrosis in silicosis through impairing SKP2‐mediated Beclin1 ubiquitination
Cited by: 7
Author(s): Qian Qin, Qinghua Ma, Bin Wang, Qingqiang Qian, Changsong Zhao, Feng Fang, Xiaona Dong
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0157173

Insights into Sexual Precocity of Female Oriental River Prawn Macrobrachium nipponense through Transcriptome Analysis
Cited by: 13
Author(s): Hongxia Jiang, Xilian Li, Yuhang Sun, Fujun Hou, Yufei Zhang, Fēi Li, Zhenxin Gu, Xiaolin Liu
Software Mentions: 1
Published: about 10 years ago

10.1002/mbo3.836

Metabolic comparison of aerial and submerged mycelia formed in the liquid surface culture of Cordyceps militaris
Cited by: 14
Author(s): Ahmad Suparmin, Tatsuya Kato, Hiroyuki Takemoto, Enoch Y. Park
Software Mentions: 1
Published: over 7 years ago

10.3389/fnins.2020.00181

Prdx1 Reduces Intracerebral Hemorrhage-Induced Brain Injury via Targeting Inflammation- and Apoptosis-Related mRNA Stability
Cited by: 14
Author(s): Guoqiang Yang, Jiacheng Huang, Junjie Yuan, Zhang Qin, Chang‐Xiong Gong, Qiong Chen, Qiang Xie, Lin Xie, Ru Chen, Zhongming Qiu, Kai Zhou, Rui Xu, Guohui Jiang, Xiao‐Yi Xiong, Qingwu Yang
Software Mentions: 1
Published: over 6 years ago

10.14814/phy2.12750

RNA-sequencing of WFS1-deficient pancreatic islets
Cited by: 17
Author(s): Marilin Ivask, Alison Hugill, Sulev Kõks
Software Mentions: 1
Published: over 10 years ago

10.1186/s13046-019-1315-8

Long non-coding RNA LUCAT1/miR-5582-3p/TCF7L2 axis regulates breast cancer stemness via Wnt/β-catenin pathway
Cited by: 93
Author(s): Aiping Zheng, Xinyue Song, Lin Zhang, Lin Zhao, Xiaoyun Mao, Minjie Wei, Feng Jin
Software Mentions: 1
Published: about 7 years ago

10.1096/fj.201701558R

Macrophage‐derived extracellular vesicles mediate smooth muscle hyperplasia: role of altered miRNA cargo in response to HIV infection and substance abuse
Cited by: 45
Author(s): Himanshu Sharma, Mahendran Chinnappan, Stuti Agarwal, Pranjali Dalvi, Sumedha Gunewardena, Amy O’Brien-Ladner, Navneet K. Dhillon
Software Mentions: 1
Published: over 8 years ago

10.1289/ehp.1408188

Effects of the Endocrine-Disrupting Chemical DDT on Self-Renewal and Differentiation of Human Mesenchymal Stem Cells
Cited by: 53
Author(s): Amy L. Strong, Zhenzhen Shi, Michael J. Strong, David F. Miller, Douglas B. Rusch, Aaron Buechlein, Erik K. Flemington, John A. McLachlan, Kenneth P. Nephew, Matthew E. Burow, Bruce A. Bunnell
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0089158

Normalization of RNA-Sequencing Data from Samples with Varying mRNA Levels
Cited by: 45
Author(s): Håvard Aanes, Cecilia Lanny Winata, Lars Fredrik Moen, Oľga Østrup, Sinnakaruppan Mathavan, Philippe Collas, Torbjørn Rognes, Peter Alestrøm
Software Mentions: 1
Published: over 12 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568