bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/srep43062

Targeted RP9 ablation and mutagenesis in mouse photoreceptor cells by CRISPR-Cas9
Cited by: 16
Author(s): Ji‐Neng Lv, Gao-Hui Zhou, Xuejiao Chen, Hui Chen, Kun Wu, Lan Xiang, Xin‐Lan Lei, Xiao Zhang, Ronghan Wu, Zi‐Bing Jin
Software Mentions: 1
Published: over 9 years ago

10.1038/srep43023

Identification of novel cancer therapeutic targets using a designed and pooled shRNA library screen
Cited by: 32
Author(s): David J. Oliver, Hao Jiang, Piaomu Liu, Alexander V. Gasparian, Ellen Gardiner, Samuel Lee, Adrián Zenteno, Lillian O. Perinskaya, Mengqian Chen, Phillip Buckhaults, Eugenia V. Broude, Michael D. Wyatt, Homayoun Valafar, Edsel A. Peña, Michael Shtutman
Software Mentions: 1
Published: over 9 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/fimmu.2020.01240

Neonatal Diet Impacts Circulatory miRNA Profile in a Porcine Model
Cited by: 4
Author(s): Laura E. Carr, Anne K. Bowlin, Ahmed A. Elolimy, Stephanie D. Byrum, Charity L. Washam, Christopher E. Randolph, Stewart L. MacLeod, Laxmi Yeruva
Software Mentions: 1
Published: about 6 years ago

10.1038/srep45295

Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum
Cited by: 41
Author(s): Pradeep Singh, Gagandeep Singh, Abhishek Bhandawat, Gopal Singh, Rajni Parmar, Romit Seth, Ram Kumar Sharma
Software Mentions: 1
Published: over 9 years ago

10.3389/fimmu.2020.01602

Systemic Sclerosis Perturbs the Architecture of the Immunome
Cited by: 10
Author(s): Bhairav Paleja, Andrea Low, Pavanish Kumar, Suzan Saidin, Ahmad Lajam, Sharifah Nur Hazirah, Camillus Chua, Lai Li Yun, Salvatore Albani
Software Mentions: 1
Published: about 6 years ago

10.3390/microorganisms9071408

Identification of Resistance Determinants for a Promising Antileishmanial Oxaborole Series
Cited by: 8
Author(s): Magali Van den Kerkhof, Philippe Leprohon, Dorien Mabille, Sarah Hendrickx, L.B. Tulloch, Richard J. Wall, Susan Wyllie, Eric Chatelain, Charles E. Mowbray, Stéphanie Braillard, Marc Ouellette, Louis Maes, Guy Caljon
Software Mentions: 1
Published: about 5 years ago

10.3389/fimmu.2019.02888

Mycobacterium abscessus—Bronchial Epithelial Cells Cross-Talk Through Type I Interferon Signaling
Cited by: 15
Author(s): Chongxu Zhang, Huda Asif, Gregory E. Holt, Anthony J. Griswold, Michael Campos, P.A. Bejarano, Nevis Fregien, Mehdi Mirsaeidi
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2020.592569

Helpless Priming Sends CD8+ T Cells on the Road to Exhaustion
Cited by: 23
Author(s): Julia Busselaar, Sun Tian, Hans van Eenennaam, Jannie Borst
Software Mentions: 1
Published: almost 6 years ago

10.3389/fimmu.2016.00670

Regulation of Marginal Zone B-Cell Differentiation by MicroRNA-146a
Cited by: 22
Author(s): Jennifer K. King, Nolan Ung, May Paing, Jorge R. Contreras, Michael O. Alberti, Thilini R. Fernando, Kelvin Zhang, Matteo Pellegrini, Dinesh S. Rao
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms20143582

In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma
Cited by: 12
Author(s): Rajesh Kumar, Sumeet Patiyal, Vinod Kumar, Gandharva Nagpal, Gajendra P. S. Raghava
Software Mentions: 1
Published: about 7 years ago

10.1186/s12934-020-01503-0

Effect of overexpression of SNF1 on the transcriptional and metabolic landscape of baker’s yeast under freezing stress
Cited by: 10
Author(s): Meng Kai Lü, Yang Xu, Xue Lin, Huan-Yuan Jiang, Xiaoping Hu, Sixin Liu
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-64288-7

Transcriptome profile analysis of two Vicia faba cultivars with contrasting salinity tolerance during seed germination
Cited by: 19
Author(s): Fangwen Yang, Hongwei Chen, Changyan Liu, Li Li, Liangjun Liu, Xuesong Han, Zhengjie Wan, Aihua Sha
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2021.729776

The Molecular Mechanism of Multiple Organ Dysfunction and Targeted Intervention of COVID-19 Based on Time-Order Transcriptomic Analysis
Cited by: 15
Author(s): Miao Zou, Xiaoyun Su, Luoying Wang, Xingcheng Yi, Yue Qiu, Xirui Yin, Xuan Zhou, Xinhui Niu, Liuli Wang, Manman Su
Software Mentions: 1
Published: about 5 years ago

10.3389/fimmu.2021.688294

Macrophage Polarization Modulated by Porcine Circovirus Type 2 Facilitates Bacterial Coinfection
Cited by: 6
Author(s): Wen Zhang, Zhendong Fu, Hongyan Yin, Qin Han, Wenhui Fan, Fangkun Wang, Yue Shang
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-64022-3

Transcriptome profiling reveals insertional mutagenesis suppressed the expression of candidate pathogenicity genes in honeybee fungal pathogen, Ascosphaera apis
Cited by: 3
Author(s): Awraris Getachew, Tessema Aynalem Abejew, Jiangli Wu, Jin Xu, Yu Hou, Jian Tan, Peng-Jie Wu, Yan Tu, Weipeng Kang, Zheng Wang, Shufa Xu
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-64890-9

Transcriptomic evidence that insulin signalling pathway regulates the ageing of subterranean termite castes
Cited by: 13
Author(s): Haroon, Xiaoming Ma, Yuxin Li, Hongxin Zhang, Qing Liu, Xiaoqing Su, Lianxi Xing
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2021.703632

A Biological Circuit Involving Mef2c, Mef2d, and Hdac9 Controls the Immunosuppressive Functions of CD4+Foxp3+ T-Regulatory Cells
Cited by: 4
Author(s): Eros Di Giorgio, Liqing Wang, Yan Xiong, Lanette M Christensen, Tatiana Akimova, Rongxiang Han, Arabinda Samanta, Matteo Trevisanut, Claudio Brancolini, Ulf H. Beier, Wayne W. Hancock
Software Mentions: 1
Published: about 5 years ago

10.1186/s12934-021-01603-5

Site-directed mutagenesis of the quorum-sensing transcriptional regulator SinR affects the biosynthesis of menaquinone in Bacillus subtilis
Cited by: 10
Author(s): Jiang Wu, Wei Li, Su Zhao, Qian Senhe, Wang Zhou, Mengjie Zhou, Wenchao Hu, Jian Wang, Liu-xiu Hu, Yan Liu, Zhenglian Xue
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms20174117

Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado (Persea americana)
Cited by: 17
Author(s): Yu Ge, Zhihao Cheng, Xiongyuan Si, Wei Ma, Lin Tan, Xiaoping Zang, Bin Wu, Zining Xu, Nan Wang, Zhaoxi Zhou, Xiao Lin, Xiangshu Dong, Rulin Zhan
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-020-65536-6

Opposite Roles of the JMJD1A Interaction Partners MDFI and MDFIC in Colorectal Cancer
Cited by: 16
Author(s): Shushan Yuan, Yongming Li, Sangphil Oh, Bin Zhang, Willard M. Freeman, Sook Shin, Ralf Janknecht
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2020.02191

Human Chondrocyte Activation by Toxins From Premolis semirufa, an Amazon Rainforest Moth Caterpillar: Identifying an Osteoarthritis Signature
Cited by: 4
Author(s): Isadora Maria Villas-Boas, Giselle Pidde, Flávio Lichtenstein, Ana Tung Ching Ching, Inácio L.M. Junqueira-de-Azevedo, Carlos DeOcesano-Pereira, Carlos Eduardo Madureira Trufen, Ana Marisa Chudzinski‐Tavassi, Kátia L.P. Morais, Denise V. Tambourgi
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-66469-w

Transcriptomic study in women with trisomy 21 identifies a possible role of the GTPases of the immunity-associated proteins (GIMAP) in the protection of breast cancer
Cited by: 13
Author(s): André Mégarbané, David Piquemal, Anne-Sophie Rebillat, Samantha Stora, Fabien Pierrat, Roman Bruno, Florian Noguier, Clotilde Mircher, Aimé Ravel, Marie Vilaire-Meunier, Sophie Durand, Gérard Lefranc
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-66500-0

Transcriptome analyses suggest that changes in fungal endophyte lifestyle could be involved in grapevine bud necrosis
Cited by: 13
Author(s): Thales Henrique Cherubino Ribeiro, Christiane Noronha Fernandes-Brum, C. R. de Souza, Frédérico Alcântara Novelli Dias, Osmar de Almeida-Junior, Murilo de Albuquerque Regina, Kellen Kauanne Pimenta de Oliveira, Gabriel Lasmar dos Reis, Larissa Maia de Oliveira, Fernanda de Paula Fernandes, Laurent Torregrosa, Jorge Teodoro de Souza, Antônio Chalfun-Júnior
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-66675-6

Transcriptome profiling of the flowering transition in saffron (Crocus sativus L.)
Cited by: 23
Author(s): Jing Hu, Yuping Liu, Xiaohui Tang, Huajing Rao, Chaoxiang Ren, Chen Jiang, Qinghua Wu, Yi Jiang, Fuchang Geng, Jin Pei
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-66021-w

Functional shell matrix proteins tentatively identified by asymmetric snail shell morphology
Cited by: 11
Author(s): Akito Ishikawa, Keisuke Shimizu, Yukinobu Isowa, Takeshi Takeuchi, Rongjun Zhao, Keiji Kito, Manabu Fujie, Noriyuki Satoh, Kazuhiko Endo
Software Mentions: 1
Published: about 6 years ago

10.3389/fimmu.2020.01064

Different Exosomal microRNA Profile in Aquaporin-4 Antibody Positive Neuromyelitis Optica Spectrum Disorders
Cited by: 7
Author(s): Chen Chen, Yunting Wu, Miaochang Li, Chun-Ping Chu, Yipeng Zhao, Xiaobo Sun, Yuge Wang, Chunxin Liu, Haotian Wu, Xiaonan Zhong, Allan G. Kermode, Lisheng Peng
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-64257-0

Core Binding Factors are essential for ovulation, luteinization, and female fertility in mice
Cited by: 10
Author(s): Somang Lee-Thacker, Hayce Jeon, Yohan Choi, Ichiro Taniuchi, Takeshi Takarada, Yukio Yoneda, Che Myong Ko, Misung Jo
Software Mentions: 1
Published: about 6 years ago

10.3389/fimmu.2021.722500

Transcriptional Changes in Pulmonary Phagocyte Subsets Dictate the Outcome Following Interaction With The Fungal Pathogen Cryptococcus neoformans
Cited by: 4
Author(s): Ashlee Hawkins, Brenden F. Determann, Benjamin N. Nelson, Karen L. Wozniak
Software Mentions: 1
Published: almost 5 years ago

10.3389/fgene.2021.698983

Comparative Transcriptomic Analysis Reveals the Immunosuppressive Targets of Mesalazine in Dextran Sulfate Sodium-Induced Ulcerative Colitis
Cited by: 1
Author(s): Rong Li, Lin Cheng, Qi Wang, Liming Zhou
Software Mentions: 1
Published: about 5 years ago

10.3389/fgene.2021.635599

Comparative Small RNA Profiling and Functional Exploration on Wheat With High- and Low-Cadmium Accumulation
Cited by: 6
Author(s): Yuqing Liu, Xudong Wang, Leyi Yuan, Yuxiang Liu, Tong Shen, Yunhua Zhang
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms20194933

Transforming Growth Factor-β1 Selectively Recruits microRNAs to the RNA-Induced Silencing Complex and Degrades CFTR mRNA under Permissive Conditions in Human Bronchial Epithelial Cells
Cited by: 13
Author(s): Nilay Mitash, Fangping Mu, Joshua E Donovan, Michael M. Myerburg, Sarangarajan Ranganathan, Catherine M. Greene, Agnieszka Swiatecka‐Urban
Software Mentions: 1
Published: almost 7 years ago

10.3389/fgene.2021.667877

Leveraging Methylation Alterations to Discover Potential Causal Genes Associated With the Survival Risk of Cervical Cancer in TCGA Through a Two-Stage Inference Approach
Cited by: 7
Author(s): Jinhui Zhang, Haojie Lu, Shuo Zhang, Ting Wang, Huashuo Zhao, Fengjun Guan, Ping Zeng
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2020.617872

Transcriptome Analyses Identify an RNA Binding Protein Related Prognostic Model for Clear Cell Renal Cell Carcinoma
Cited by: 8
Author(s): Yue Wu, Wa Xian, Huan Feng, Bintao Hu, Bo Liu, Yang Luan, Yajun Ruan, Xiaohui Liu, Zhuo Liu, Shaogang Wang, Jihong Liu, Tao Wang
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2021.607238

The TP53-Related Signature Predicts Immune Cell Infiltration, Therapeutic Response, and Prognosis in Patients With Esophageal Carcinoma
Cited by: 7
Author(s): Hongpan Zhang, Zheng Huang, Yangguang Song, Zhihao Yang, Qi Shi, Kaige Wang, Zhiyu Zhang, Zheng Lv, Xiaobin Cui, Feng Li
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-67476-7

Co-expression based cancer staging and application
Cited by: 7
Author(s): Xiangchun Yu, Sha Cao, Yi Zhou, Zhezhou Yu, Ying Xu
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-67635-w

Genomics and transcriptomics analysis reveals the mechanism of isobutanol tolerance of a laboratory evolved Lactococcus lactis strain
Cited by: 7
Author(s): Jaya Gupta, Sagar Thapa, Madhulika Verma, Ritu Som, Kakali Mukherjee
Software Mentions: 1
Published: about 6 years ago

10.3389/fgene.2021.674856

LncRNA SOX2-OT/miR-30d-5p/PDK1 Regulates PD-L1 Checkpoint Through the mTOR Signaling Pathway to Promote Non-small Cell Lung Cancer Progression and Immune Escape
Cited by: 14
Author(s): Zhoumiao Chen, Zhao Chun-hua, Shaohua Xu, Qiang Zhang
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-66387-x

Combined PLT and NE to predict the prognosis of patients with locally advanced cervical cancer
Cited by: 5
Author(s): Han Wang, Wen-Ming Chen, Yong-Heng Zhou, Jianping Shi, Yongzhen Huang, Wenjie Wang
Software Mentions: 1
Published: about 6 years ago

10.3389/fgene.2020.00273

HSD17B4, ACAA1, and PXMP4 in Peroxisome Pathway Are Down-Regulated and Have Clinical Significance in Non-small Cell Lung Cancer
Cited by: 12
Author(s): Xiuzhi Zhang, Hongmei Yang, Jinzhong Zhang, Fenglan Gao, Liping Dai
Software Mentions: 1
Published: over 6 years ago

10.1111/1751-7915.13440

Integrated transcriptomic and secretomic approaches reveal critical pathogenicity factors in Pseudofabraea citricarpa inciting citrus target spot
Cited by: 6
Author(s): Yang Yong, Anfei Fang, Yang Yu, Chaowei Bi, Changyong Zhou
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-68339-x

Transcriptional and in silico analyses of MIF cytokine and TLR signalling interplay in the LPS inflammatory response of Ciona robusta
Cited by: 9
Author(s): Vincenzo Arizza, Angela Bonura, Laura La Paglia, Alfonso Urso, Annalisa Pinsino, Aiti Vizzini
Software Mentions: 1
Published: about 6 years ago

10.3389/fgene.2019.00409

Dynamic Transcriptome Analysis Reveals Potential Long Non-coding RNAs Governing Postnatal Pineal Development in Pig
Cited by: 8
Author(s): Yalan Yang, Rong Zhou, Wentong Li, Ying Liu, Yanmin Zhang, Ai Hong, Hua Li, Kui Li
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms20205172

Novel Pituitary Actions of Epidermal Growth Factor: Receptor Specificity and Signal Transduction for UTS1, EGR1, and MMP13 Regulation by EGF
Cited by: 5
Author(s): Qiongyao Hu, Shaohua Xu, Ya Cheng, Jingyi Jia, Lingling Zhou, Guangfu Hu
Software Mentions: 1
Published: almost 7 years ago

10.3389/fgene.2016.00191

Epigenetic DNA Methylation Profiling with MSRE: A Quantitative NGS Approach Using a Parkinson's Disease Test Case
Cited by: 9
Author(s): Adam G. Marsh, Matthew T. Cottrell, Morton F. Goldman
Software Mentions: 1
Published: almost 10 years ago

10.3389/fgene.2020.577000

Exploration of Sorafenib Influences on Gene Expression of Hepatocellular Carcinoma
Cited by: 0
Author(s): Huancheng Wang, Jia Liu
Software Mentions: 1
Published: almost 6 years ago

10.1128/CVI.00027-17

Novel Mechanisms Revealed in the Trachea Transcriptome of Resistant and Susceptible Chicken Lines following Infection with Newcastle Disease Virus
Cited by: 46
Author(s): Melissa S. Deist, Rodrigo A. Gallardo, David Bunn, T. Ross Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 1
Published: over 9 years ago

10.1002/ctm2.314

A 12‐genus bacterial signature identifies a group of severe autistic children with differential sensory behavior and brain structures
Cited by: 3
Author(s): Kai Shi, Lingli Zhang, Juehua Yu, Zilin Chen, Senying Lai, Xingzhong Zhao, Wei‐Guang Li, Qiang Luo, Wei Lin, Jianfeng Feng, Peer Bork, Xing‐Ming Zhao, Fēi Li
Software Mentions: 1
Published: over 5 years ago

10.1002/ctm2.147

STXBP6, reciprocally regulated with autophagy, reduces triple negative breast cancer aggressiveness
Cited by: 3
Author(s): Govinda Lenka, Jingxuan Shan, Najeeb Halabi, Sirin W. J. Abuaqel, Neha Goswami, Frank Schmidt, Shaza B. Zaghlool, Atilio Reyes Romero, Subramanian Mahadevan, Salha Boujassoum, Issam Al‐Bozom, Salah Gehani, Noor Al Khori, Davide Bedognetti, Karsten Suhre, Xiaojing Ma, Alexander Dömling, Arash Rafii, Lotfi Chouchane
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms20205069

Renal Artery Stenosis Alters Gene Expression in Swine Scattered Tubular-Like Cells
Cited by: 7
Author(s): Arash Aghajani Nargesi, Xiang Yang Zhu, Yuanhang Liu, Hui Tang, Kyra L. Jordan, Lilach O. Lerman, Alfonso Eirin
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13601-017-0163-x

Abstracts from the 11th Symposium on Experimental Rhinology and Immunology of the Nose (SERIN 2017)
Cited by: 0
Author(s): Ibon Eguiluz Gracia, Carmen Rondón, Paloma Campo, A. Prieto, Lina Mayorga, Luisa Galindo, A. Criado Molina, Miguel Blanca, Marı́a José Torres, Taiyo Morikawa, Ayumi Fukuoka, Kazunobu Matsushita, Shigeharu Fujieda, Tomohiro Yoshimoto, Naruhito Iwasaki, Tamar Smulders, Danielle van Egmond, Kees van Drunen, Marc van der Schee, Achim G. Beule, Margot Berings, A. Jult, Hanne Vermeulen, Natalie De Ruyck, Lara Derycke, Hakan Uçar, P. Ghekiere, Robin Temmerman, John Ellis, Claus Bachert, Bart Lambrecht, Mélissa Dullaers, Philippe Gevaert, Stefania Arasi, Serena Perna, Yvonne Resch, Christian Lupinek, Kuan-Wei Chen, Susanne Vrtala, Rudolf Valenta, Paolo Maria Matricardi, Ivânia Gonçalves, Tiago Jacinto, Rita Amaral, Ana Margarida Pereira, Luís Araújo, Mariana Couto, João Almeida Fonseca, Pär Stjärne, Ranbir Kaulsay, Wolfgang Pohl, Maria Carmen Plaza, Ana Maria Prieto, Cristobalina Mayorga, M. Herknerova, Tengchin Wang, Chiejun Wu, Jonathan Kilimajer, Laura Pujols, Jordi Roca‐Ferrer, Borja Callejas, Mireya Fuentes, M Pérez-González, Isam Alobid, Antonio Valero, César Picado, Ruth Murray, Joaquim Mullol, Brecht Steelant, Katleen Martens, Guy E. Boeckxstaens, Sven Seys, Peter Hellings, Timothy C. Biggs, Stephen M. Hayes, Philip G. Harries, Sylvia L.F. Pender, Rami J. Salib, Jean Kim, Hyun Sil Lee, Livije Kalogjera, Nada Vrkić, Anita Topić, Dejan Tomljenović, Tomislav Gregurić, P Radovanović, R. Jund, Pascal Haimerl, Adam Chaker, Yvonne Schober, Sonja Schindela, Andreas Nockher, Carsten B. Schmidt‐Weber, Julia Esser–von Bieren, Pascal Ickrath, Norbert Kleinsasser, Niklas Beyersdorf, Xiangdong Ding, Rudolf Hagen, Stephan Hackenberg, Daniela Cangiano, Francesco Cinetto, Giuseppe Brescia, Gino Marioni, Claudia Zanotti, Franco Schiavon, Roberto Padoan, Ilaria Caputo, Raffaella Neri, Carlo Agostini, Ji Heui Kim, Yong Ju Jang, Ji Youn Lim, Sung Hee Kim, Е. Л. Савлевич, Leonid Gaganov, Maria Kochnova, V.V. Egorov, Jie Shen Fok, Tanzeela Hanif, Jutta Renkonen, Sakari Joenväärä, Matti Kankainen, Mika Mäkelä, Paula Kauppi, Anna Pelkonen, Pirkko Mattila, Risto Renkonen, Sanna Toppila‐Salmi, Gabriële Holtappels, Bart Lambrecht, Natalia Blanca‐López, Miguel Gonzalez-Visiedo, Raquel Jurado, Gabriela Cantó
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-020-69434-9

Comparative transcriptome analysis of Sclerotinia sclerotiorum revealed its response mechanisms to the biological control agent, Bacillus amyloliquefaciens
Cited by: 18
Author(s): Xiaoxiang Yang, Lei Zhang, Yunjia Xiang, Lei Du, Xiaoqin Huang, Yong Liu
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-67760-6

A cluster of metabolism-related genes predict prognosis and progression of clear cell renal cell carcinoma
Cited by: 21
Author(s): Mei Liu, Qiufeng Pan, Ruihai Xiao, Yi Yu, Wenbao Lu, Longwang Wang
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-68637-4

Cellular, mitochondrial and molecular alterations associate with early left ventricular diastolic dysfunction in a porcine model of diabetic metabolic derangement
Cited by: 14
Author(s): Ilkka Heinonen, Oana Sorop, Bas M. van Dalen, Rob C I Wüst, Jens van de Wouw, Vincent J. de Beer, Yanti Octavia, Richard van Duin, Youri Hoogstrate, Lau Blonden, Milla Alkio, Katja Anttila, Andrew Stubbs, Jolanda van der Velden, Daphne Merkus, Dirk J. Duncker
Software Mentions: 1
Published: about 6 years ago

10.3390/microorganisms8020278

Differential Potential of Phytophthora capsici Resistance Mechanisms to the Fungicide Metalaxyl in Peppers
Cited by: 12
Author(s): Weiyan Wang, Xiao Liu, Tao Han, Kunyuan Li, Yang Qu, Zhimou Gao
Software Mentions: 1
Published: over 6 years ago

10.1186/s13148-018-0561-5

T cell epigenetic remodeling and accelerated epigenetic aging are linked to long-term immune alterations in childhood cancer survivors
Cited by: 27
Author(s): Sara K. Daniel, Vibe Nylander, Lars R. Ingerslev, Ling Zhong, Odile Fabre, Briana K. Clifford, Karen Johnston, Richard J. Cohn, Romain Barrès, David Simar
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-020-70484-2

Construct a circRNA/miRNA/mRNA regulatory network to explore potential pathogenesis and therapy options of clear cell renal cell carcinoma
Cited by: 50
Author(s): Shengjie Bai, Yinying Wu, Yanli Yan, Shuai Shao, Jiangzhou Zhang, Jiaxin Liu, Baojun Hui, Rui Li, Hailin Ma, Xiaozhi Zhang, Juan Ren
Software Mentions: 1
Published: about 6 years ago

10.3390/microorganisms8030314

Molecular Mechanisms Underpinning Aggregation in Acidiphilium sp. C61 Isolated from Iron-Rich Pelagic Aggregates
Cited by: 4
Author(s): Qianqian Li, Rebecca E. Cooper, Carl‐Eric Wegner, Kirsten Küsel
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms20235893

An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Root Growth Regulation Mechanisms in Response to Nitrogen Availability
Cited by: 39
Author(s): Xin Wei, Lina Zhang, Wenzhong Zhang, Jiping Gao, Jun Yi, Xiaoxi Zhen, Min Du, Yanze Zhao, Liqiang Chen
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-020-70932-z

Elucidation of resistance signaling and identification of powdery mildew resistant mapping loci (ClaPMR2) during watermelon-Podosphaera xanthii interaction using RNA-Seq and whole-genome resequencing approach
Cited by: 6
Author(s): Mihir Mandal, Haktan Suren, Chandrasekar S. Kousik
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-71050-6

RNA-Seq analysis of differentially expressed genes of Staphylococcus epidermidis isolated from postoperative endophthalmitis and the healthy conjunctiva
Cited by: 3
Author(s): Qing Liu, Nan Chen, Huabo Chen, Yusen Huang
Software Mentions: 1
Published: about 6 years ago

10.1186/s13148-018-0446-7

Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots
Cited by: 76
Author(s): Lars R. Ingerslev, Ida Donkin, Odile Fabre, Soetkin Versteyhe, Mie Mechta, Pattarawan Pattamaprapanont, Bent Ole Gram Mortensen, Nikolaj T. Krarup, Romain Barrès
Software Mentions: 1
Published: over 8 years ago

10.1161/CIRCULATIONAHA.115.021019

Smooth Muscle Enriched Long Noncoding RNA ( SMILR ) Regulates Cell Proliferation
Cited by: 178
Author(s): Margaret D. Ballantyne, Karine Pinel, Rachel Dakin, Alex Vesey, Louise A Diver, Ruth M. Mackenzie, Raquel García, Paul Welsh, Naveed Sattar, Graham Hamilton, Nikhil Joshi, Marc R Dweck, Joseph M. Miano, Martin W. McBride, David E. Newby, Robert McDonald, Andrew H. Baker
Software Mentions: 1
Published: over 10 years ago

10.3390/microorganisms9081626

Genetic Responses of Metabolically Active Limnospira indica Strain PCC 8005 Exposed to γ-Radiation during Its Lifecycle
Cited by: 1
Author(s): Anu Yadav, Laurens Maertens, Tim Meese, Filip Van Nieuwerburgh, Mohamed Mysara, Natalie Leys, Ann Cuypers, Paul Janssen
Software Mentions: 1
Published: about 5 years ago

10.1080/19336950.2020.1859248

Trigeminal neuropathic pain is alleviated by inhibition of Cav3.3 T-type calcium channels in mice
Cited by: 17
Author(s): Marena A. Montera, Aleyah E. Goins, Leos Cmarko, Norbert Weiss, Karin N. Westlund, Sascha R.A. Alles
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-72117-0

A central role for the transcriptional regulator VtlR in small RNA-mediated gene regulation in Agrobacterium tumefaciens
Cited by: 9
Author(s): James A. Budnick, Lauren M. Sheehan, Miranda. J. Ginder, Kevin C. Failor, Julia. M. Perkowski, John. F. Pinto, Kirsten A. Kohl, Lin Kang, Pawel Michalak, Li Luo, Jason E. Heindl, Clayton C. Caswell
Software Mentions: 1
Published: almost 6 years ago

10.3390/cells9122582

Leucine Supplementation Decreases HDAC4 Expression and Nuclear Localization in Skeletal Muscle Fiber of Rats Submitted to Hindlimb Immobilization
Cited by: 3
Author(s): Paula Ketilly Nascimento Alves, André Cruz, William J. Silva, Siegfried Labeit, Anselmo Sigari Moriscot
Software Mentions: 1
Published: almost 6 years ago

10.3390/cells9040794

Circulating Small Noncoding RNAs Have Specific Expression Patterns in Plasma and Extracellular Vesicles in Myelodysplastic Syndromes and Are Predictive of Patient Outcome
Cited by: 25
Author(s): Andrea Hruštincová, Zdeněk Krejčík, David Kundrát, Katarína Szikszai, Monika Beličková, Pavla Pecherková, Jǐŕı Kléma, Jitka Veselá, Monika Hruba, Jaroslav Čermák, Tereza Hrdinova, Matyáš Krijt, J Válka, Anna Jonášová, Michaela Dostálová Merkerová
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-72448-y

Proteasomal degradation of polycomb-group protein CBX6 confers MMP-2 expression essential for mesothelioma invasion
Cited by: 6
Author(s): Katsuya Sakai, Takumi Nishiuchi, Shoichiro Tange, Yoshinori Suzuki, Seiji Yano, Minoru Terashima, Takeshi Suzuki, Kunio Matsumoto
Software Mentions: 1
Published: almost 6 years ago

10.3390/cells9010256

Agonist Antibody Converts Stem Cells into Migrating Brown Adipocyte-Like Cells in Heart
Cited by: 4
Author(s): Kyung Ho Han, Britni M. Arlian, Chih-Wei Lin, Hyun Yong Jin, Geun‐Hyung Kang, Sahmin Lee, Peter Chang-Whan Lee, Richard A. Lerner
Software Mentions: 1
Published: over 6 years ago

10.3390/cells10092174

Retinoic Acid Receptors and the Control of Positional Information in the Regenerating Axolotl Limb
Cited by: 3
Author(s): Trey Polvadore, Malcolm Maden
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-74049-1

De novo transcriptome analysis of the critically endangered alpine Himalayan herb Nardostachys jatamansi reveals the biosynthesis pathway genes of tissue-specific secondary metabolites
Cited by: 8
Author(s): Nisha Dhiman, Anil Kumar, Dinesh Kumar, Amita Bhattacharya
Software Mentions: 1
Published: almost 6 years ago

10.1007/s00408-019-00257-w

Growth Hormone-Releasing Hormone Receptor Antagonist Modulates Lung Inflammation and Fibrosis due to Bleomycin
Cited by: 29
Author(s): Chongxu Zhang, Renzhi Cai, Aaron Lazerson, Gaëtan J.-R. Delcroix, Medhi Wangpaichitr, Mehdi Mirsaeidi, Anthony J. Griswold, Andrew V. Schally, Robert M. Jackson
Software Mentions: 1
Published: about 7 years ago

10.3390/cells8111400

Identification of a Diagnostic Set of Endomyocardial Biopsy microRNAs for Acute Cellular Rejection Diagnostics in Patients after Heart Transplantation Using Next-Generation Sequencing
Cited by: 11
Author(s): Tereza Nováková, Táňa Macháčková, Jan Novák, Petr Hude, Július Godava, Víta Žampachová, Jan Oppelt, Filip Zlámal, Petr Němec, Helena Bedáňová, Ondřej Slabý, Julie Bienertová-Vašků, Lenka Špinarová, Jan Krejčí
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-020-74789-0

Metabolomic and transcriptomic analyses reveal the regulation of pigmentation in the purple variety of Dendrobium officinale
Cited by: 23
Author(s): Xinqiao Zhan, Jufeng Qi, Bin Zhou, Bizeng Mao
Software Mentions: 1
Published: almost 6 years ago

10.3390/cells10071762

Viral MicroRNAs Encoded by Nucleocapsid Gene of SARS-CoV-2 Are Detected during Infection, and Targeting Metabolic Pathways in Host Cells
Cited by: 27
Author(s): Fei Meng, Gilman Kit-Hang Siu, Bobo Wing-Yee Mok, Jiahong Sun, Kitty S. C. Fung, Jimmy Yiu-Wing Lam, Nonthaphat Kent Wong, Lealem Gedefaw, Shuai Luo, Thomas M. H. Lee, Shea Ping Yip, Chien‐Ling Huang
Software Mentions: 1
Published: about 5 years ago

10.1016/j.cels.2017.08.013

Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer
Cited by: 90
Author(s): Emanuel Gonçalvès, Athanassios Fragoulis, Luz Garcia‐Alonso, Thorsten Cramer, Julio Sáez-Rodríguez, Pedro Beltrão
Software Mentions: 1
Published: almost 9 years ago

10.3390/microorganisms9030652

In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexus aggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat
Cited by: 11
Author(s): Shigeru Kawai, Joval N. Martinez, Mads Lichtenberg, Erik Trampe, Michael Kühl, Marcus Tank, Shin Haruta, Arisa Nishihara, Satoshi Hanada, Vera Thiel
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-73164-3

Assessing the prognostic value of stemness-related genes in breast cancer patients
Cited by: 5
Author(s): Wenjie Wang, Han Wang, Meng-Sen Wang, Yongzhen Huang, Yuan Ma, Jie Qi, Jianping Shi, Wei Li
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-75537-0

Enhanced FGFR3 activity in postmitotic principal neurons during brain development results in cortical dysplasia and axonal tract abnormality
Cited by: 5
Author(s): Jui-Yen Huang, Bruna Baumgarten Krebs, Marisha Lynn Miskus, May Lin Russell, Eamonn Patrick Duffy, Jason Michael Graf, Hui-Chen Lu
Software Mentions: 1
Published: almost 6 years ago

10.1016/j.celrep.2021.109449

Chemical interplay and complementary adaptative strategies toggle bacterial antagonism and co-existence
Cited by: 24
Author(s): Carlos Molina‐Santiago, David Vela‐Corcía, Daniel Petras, Luis Díaz-Martínez, Alicia Isabel Pérez-Lorente, Sara Sopeña-Torres, J. R. A. Pearson, Andrés Mauricio Caraballo‐Rodríguez, Pieter C. Dorrestein, Antonio de Vicente, Diego Romero
Software Mentions: 1
Published: about 5 years ago

10.1111/cpr.12932

BCL2 enhances survival of porcine pluripotent stem cells through promoting FGFR2
Cited by: 11
Author(s): Zhenshuo Zhu, Qin Pan, Wenxu Zhao, Xiaolong Wu, Shuai Yu, Qiaoyan Shen, Juqing Zhang, Wei Y, Sha Peng, Na Li, Shiqiang Zhang, Anmin Lei
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41423-020-0500-1

Inhibition of CCL2 by bindarit alleviates diabetes-associated periodontitis by suppressing inflammatory monocyte infiltration and altering macrophage properties
Cited by: 27
Author(s): Zhen Shen, Shuhong Kuang, Min Zhang, Xin Huang, Jiayao Chen, Meiliang Guan, Wei Qin, Hockin H.K. Xu, Lin Zhao
Software Mentions: 1
Published: about 6 years ago

10.1016/j.jcmgh.2018.09.005

Enhancer of Zeste Homologue 2 Inhibition Attenuates TGF-β Dependent Hepatic Stellate Cell Activation and Liver Fibrosis
Cited by: 48
Author(s): Rosa Martín-Mateos, Thiago M. de Assuncao, Juan Pablo Arab, Nidhi Jalan‐Sakrikar, Usman Yaqoob, Thomas Greuter, Vikas Verma, Angela Mathison, Sheng Cao, Gwen Lomberk, Philippe Maury, Raúl Urrutia, Robert C. Huebert, Vijay H. Shah
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-76171-6

Characterization of transcriptional response of Lactobacillus plantarum under acidic conditions provides insight into bacterial adaptation in fermentative environments
Cited by: 6
Author(s): Sera Jung, Jong Hee Lee
Software Mentions: 1
Published: almost 6 years ago

10.3390/microorganisms7120634

Transcriptomic Analysis of Viable but Non-Culturable Escherichia coli O157:H7 Formation Induced by Low Temperature
Cited by: 16
Author(s): Junliang Zhong, Xihong Zhao
Software Mentions: 1
Published: almost 7 years ago

10.1186/s11658-021-00256-x

Relationship between miR-378c and YY1 expression in patients with gastric cancer and the clinicopathological features
Cited by: 11
Author(s): Lei Zhang, Lei Zou, Peng Sun
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms21010159

Transcriptome Response to Drought, Rehydration and Re-Dehydration in Potato
Cited by: 47
Author(s): Yongkun Chen, Canhui Li, Jing Yi, Yang Yu, Chunxia Lei, Ming Gong
Software Mentions: 1
Published: over 6 years ago

10.1016/j.chom.2017.09.006

Epithelial-Cell-Derived Phospholipase A 2 Group 1B Is an Endogenous Anthelmintic
Cited by: 36
Author(s): Lewis J. Entwistle, Victoria S. Pelly, Stephanie M. Coomes, Yashaswini Kannan, Jimena Perez-Lloret, Stephanie Czieso, Mariana Silva dos Santos, James I. MacRae, Lucy M. Collinson, Abdul Karim Sesay, Nikolay P. Nikolov, Amina Metidji, Helena Helmby, David Y. Hui, Mark S. Wilson
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41420-021-00465-5

MDM2 inhibitor APG-115 exerts potent antitumor activity and synergizes with standard-of-care agents in preclinical acute myeloid leukemia models
Cited by: 19
Author(s): Douglas D. Fang, Qiuqiong Tang, Ying Kong, Rong Tao, Qixin Wang, Na Li, Fang Xu, Jiaxing Gu, Dengkun Xiong, Yan Yin, Jing Deng, Dajun Yang, Yifan Zhai
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0158711

Transition of an Anaerobic Escherichia coli Culture to Aerobiosis: Balancing mRNA and Protein Levels in a Demand-Directed Dynamic Flux Balance Analysis
Cited by: 14
Author(s): Joachim von Wulffen, RecogNice-Team, Oliver Sawodny, Ronny Feuer
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-020-74594-9

Involvement of neutrophils in machineries underlying the rupture of intracranial aneurysms in rats
Cited by: 19
Author(s): Mika Kushamae, Haruka Miyata, Makoto Shirai, Kampei Shimizu, Mieko Oka, Hirokazu Koseki, Yu Abekura, Isao Ono, Kazuhiko Nozaki, Tohru Mizutani, Tomohiro Aoki
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0073783

Inducible Knockdown of Plasmodium Gene Expression Using the glmS Ribozyme
Cited by: 190
Author(s): Parichat Prommana, Chairat Uthaipibull, Chayaphat Wongsombat, Sumalee Kamchonwongpaisan, Yongyuth Yuthavong, Ellen Knuepfer, Anthony A. Holder, Philip Shaw
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0174892

Changes in circulating microRNA levels can be identified as early as day 8 of pregnancy in cattle
Cited by: 29
Author(s): Jason Ioannidis, F.X. Donadeu
Software Mentions: 1
Published: over 9 years ago

10.3390/microorganisms9051065

Deletion of the PA4427-PA4431 Operon of Pseudomonas aeruginosa PAO1 Increased Antibiotics Resistance and Reduced Virulence and Pathogenicity by Affecting Quorum Sensing and Iron Uptake
Cited by: 1
Author(s): Liuhong Shen, Lang Gao, Mengjiao Yang, Jian Zhang, Yulu Wang, Yongdong Feng, Liping Wang, Shiwei Wang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0182866

IFNAR2-dependent gene expression profile induced by IFN-α in Pteropus alecto bat cells and impact of IFNAR2 knockout on virus infection
Cited by: 25
Author(s): Qian Zhang, Leiping Zeng, Peng Zhou, Aaron T. Irving, Shang Li, Shi Z, Lin‐Fa Wang
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-020-77177-w

Transcriptome analyses reveals the dynamic nature of oil accumulation during seed development of Plukenetia volubilis L.
Cited by: 6
Author(s): Lu Guo, Zhihua Wu, Peng Yan, Xiuhua Shang, Yi Xie, R. J. Arnold
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-77598-7

Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding
Cited by: 7
Author(s): Selisha A. Sooklal, Phelelani T. Mpangase, Mihai-Silviu Tomescu, Shaun Aron, Scott Hazelhurst, Robert H. Archer, Karl Rumbold
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0214526

Bacterial translocation in acute lymphocytic leukemia
Cited by: 7
Author(s): Yajing Song, Péter Gyarmati
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0022953

Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows
Cited by: 42
Author(s): Stefan Siebert, Mark D. Robinson, Sophia C. Tintori, Freya Goetz, Rebecca R. Helm, Stephen A. Smith, Nathan C. Shaner, Steven H. D. Haddock, Casey W. Dunn
Software Mentions: 1
Published: about 15 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568