bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1051/bmdcn/2019090427

The RNA degradation pathway is involved in PPARα-modulated anti-oral tumorigenesis
Cited by: 13
Author(s): Nen Chung Chang, Yiping Huang
Software Mentions: 1
Published: about 7 years ago

The sugar composition of the fibre in selected plant foods modulates weaning infants’ gut microbiome composition and fermentation metabolites in vitro
Cited by: 9
Author(s): Shanthi G. Parkar, Jovyn K. T. Frost, Douglas Rosendale, Halina Stoklosinski, Carel M. H. Jobsis, Duncan I. Hedderley, Pramod K. Gopal
Software Mentions: 1
Published: over 5 years ago

10.1155/2019/7149296

miRNA and mRNA Integration Network Construction Reveals Novel Key Regulators in Left-Sided and Right-Sided Colon Adenocarcinoma
Cited by: 15
Author(s): Likun Yang, Li Lin, Jing Ma, Shimin Yang, Chao Zou, Xiaozhou Yu
Software Mentions: 1
Published: over 7 years ago

10.1186/s13046-021-01875-0

A preliminary study of micro-RNAs as minimally invasive biomarkers for the diagnosis of prostate cancer patients
Cited by: 16
Author(s): Simona Giglio, Cosimo De Nunzio, Roberto Cirombella, Antonella Stoppacciaro, Omar Faruq, Stefano Volinia, Gustavo Baldassarre, Andrea Tubaro, Hideshi Ishii, Carlo M. Croce, Andrea Vecchione
Software Mentions: 1
Published: over 5 years ago

10.1002/art.40545

Functional Characterization of the Osteoarthritis Genetic Risk Residing at ALDH1A2 Identifies rs12915901 as a Key Target Variant
Cited by: 41
Author(s): Colin Shepherd, Dongxing Zhu, Andrew Skelton, Jennifer Combe, Harrison Threadgold, Longji Zhu, Tonia L. Vincent, Paul Stuart, Louise N. Reynard, John Loughlin
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-021-89288-z

Biomechanical regulation of breast cancer metastasis and progression
Cited by: 10
Author(s): Adrianne Spencer, Andrew D. Sligar, Daniel Chavarria, Jason Lee, Darshil Choksi, Nikita P. Patil, HooWon Lee, Austin Veith, William J. Riley, Shubh Desai, Ali Abbaspour, Rohan Singeetham, Aaron Baker
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.24903

Ceramide species are elevated in human breast cancer and are associated with less aggressiveness
Cited by: 71
Author(s): Kazuki Moro, Tsutomu Kawaguchi, Junko Tsuchida, Emmanuel Gabriel, Qianya Qi, Li Yan, Toshifumi Wakai, Kazuaki Takabe, Masayuki Nagahashi
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-021-89170-y

Single-cell transcriptome profiling of buffelgrass (Cenchrus ciliaris) eggs unveils apomictic parthenogenesis signatures
Cited by: 5
Author(s): Yuji Ke, Maricel Podio, Joann A. Conner, Peggy Ozias‐Akins
Software Mentions: 1
Published: over 5 years ago

10.1155/2017/4585213

MicroRNA Mediating Networks in Granulosa Cells Associated with Ovarian Follicular Development
Cited by: 9
Author(s): Bao-Yun Zhang, Long Chen, Guangde Feng, Xu Wei, Ke Zhang, Mingxing Chu, Pingqing Wang
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13075-019-1988-6

Cartilage endoplasmic reticulum stress may influence the onset but not the progression of experimental osteoarthritis
Cited by: 12
Author(s): Louise H. W. Kung, Lorna Mullan, Jamie Soul, Ping Wang, Kazutoshi Mori, John F. Bateman, Michael D. Briggs, Raymond P. Boot-Handford
Software Mentions: 1
Published: about 7 years ago

10.1186/s12974-020-01774-9

Transcriptomic profiling of microglia and astrocytes throughout aging
Cited by: 87
Author(s): Jie Pan, Nana Ma, Bo Yu, Wei Zhang, Jun Wan
Software Mentions: 1
Published: over 6 years ago

10.1186/s12974-016-0648-x

Circulating microRNAs as biomarkers for rituximab therapy, in neuromyelitis optica (NMO)
Cited by: 27
Author(s): Adi Vaknin‐Dembinsky, Hanna Charbit, Livnat Brill, Oded Abramsky, Devorah Gur‐Wahnon, Iddo Z. Ben‐Dov, Iris Lavon
Software Mentions: 1
Published: over 10 years ago

10.18632/oncotarget.27575

Distinct pattern of one-carbon metabolism, a nutrient-sensitive pathway, in invasive breast cancer: A metabolomic study
Cited by: 2
Author(s): Jailma Rodrigues dos Santos, Dan Linetzky Waitzberg, Ismael Dale Cotrim Guerreiro da Silva, Tharcísio Citrângulo Tortelli, Luciana Rodrigues Carvalho Barros, Gisele André Baptista Canuto, Andréa Tedesco Faccio, Lydia F. Yamaguchi, Massuo Jorge Kato, Marina Franco Maggi Tavares, Ana Cristina Utrillas Martínez, Ângela Flávia Logullo, Raquel Susana Torrinhas, Graziela Rosa Ravacci
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-021-89853-6

Accelerating cryoprotectant diffusion kinetics improves cryopreservation of pancreatic islets
Cited by: 8
Author(s): Nikola Doležalová, Anja V. Gruszczyk, Kerry Barkan, John Gamble, Sam G Galvin, Till Moreth, Kevin O’Holleran, Krishnaa Mahbubani, Jackie Higgins, Fiona M. Gribble, Frank Reimann, Jakub Surmacki, Simon Andrews, John Casey, Francesco Pampaloni, Michael P. Murphy, Graham Ladds, Nigel K.H. Slater, Kourosh Saeb‐Parsy
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-90148-z

Whole transcriptome RNA-seq reveals key regulatory factors involved in type 2 diabetes pathology in peripheral fat of Asian Indians
Cited by: 7
Author(s): Aditya Saxena, Navneet Mathur, Prabhat Tiwari, Sandeep Kumar Mathur
Software Mentions: 1
Published: over 5 years ago

10.1155/2021/6681925

Identification of Critical Genes and lncRNAs in Osteolysis after Total Hip Arthroplasty and Osteoarthritis by RNA Sequencing
Cited by: 2
Author(s): Guang Yang, Kai Tang, Qiao Li, Yixin Li, Shui Sun
Software Mentions: 1
Published: over 5 years ago

10.1186/s13075-017-1378-x

Identification of differential co-expressed gene networks in early rheumatoid arthritis achieving sustained drug-free remission after treatment with a tocilizumab-based or methotrexate-based strategy
Cited by: 17
Author(s): Xavier M Teitsma, Johannes W. G. Jacobs, Michal Mokrý, Michelle E A Borm, Attila Pethö‐Schramm, Jacob M van Laar, J. W. J. Bijlsma, Floris P. J. G. Lafeber
Software Mentions: 1
Published: over 9 years ago

10.1155/2021/8890176

Transcriptomic Analyses Reveal Gene Expression Profiles and Networks in Nasopharyngeal Carcinoma
Cited by: 3
Author(s): Yuwen Zhou, Weiqiang Yang, Xueshuang Mei, Hongyi Hu
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-021-90467-1

PET-CT and RNA sequencing reveal novel targets for acupuncture-induced lowering of blood pressure in spontaneously hypertensive rats
Cited by: 1
Author(s): Jing Li, Chong Peng, Dongjian Lai, Yajing Fang, Daihong Luo, Zunming Zhou, Chenyun Li, Xinsheng Lai
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-021-90515-w

Identification of BHLHE40 expression in peripheral blood mononuclear cells as a novel biomarker for diagnosis and prognosis of hepatocellular carcinoma
Cited by: 4
Author(s): Pattapon Kunadirek, Chaiyaboot Ariyachet, Supachaya Sriphoosanaphan, Nutcha Pinjaroen, Pongserath Sirichindakul, Intawat Nookaew, Natthaya Chuaypen, Pisit Tangkijvanich
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.25048

Transcriptome analysis reveals a long non-coding RNA signature to improve biochemical recurrence prediction in prostate cancer
Cited by: 7
Author(s): Jiu Hua Xu, Yujia Lan, Fulong Yu, Shiwei Zhu, Jianrong Ran, Jiali Zhu, Hongyi Zhang, Lili Li, Shujun Cheng, Yun Xiao, Xia Li
Software Mentions: 1
Published: over 8 years ago

10.1155/2019/2365416

Identification of mRNAs Related to Tibial Cartilage Development of Yorkshire Piglets
Cited by: 1
Author(s): Shuaifei Feng, Xiaoyong Du, Chao Wang, Dengdeng Ye, Guanjun Ma, Shuhong Zhao, Haiyan Wang, Xiangdong Liu
Software Mentions: 1
Published: about 7 years ago

10.1155/2020/5762932

Transcriptome Analysis Reveals the Negative Effect of 16 T High Static Magnetic Field on Osteoclastogenesis of RAW264.7 Cells
Cited by: 3
Author(s): Ting Huyan, Hourong Peng, Suna Cai, Qi Li, Di Dong, Zhouqi Yang, Peng Shang
Software Mentions: 1
Published: over 6 years ago

10.1155/2021/9958745

The Potential Genes Mediate the Pathogenicity of Allogeneic CD4+T Cell in aGVHD Mouse Model
Cited by: 2
Author(s): Zhengyu Yu, Chenchen Qin, Min Cao, Xiaoya He, Hanyun Ren, Huihui Liu
Software Mentions: 1
Published: over 5 years ago

10.1007/s00204-018-2256-2

Comparison of base-line and chemical-induced transcriptomic responses in HepaRG and RPTEC/TERT1 cells using TempO-Seq
Cited by: 36
Author(s): Alice Limonciel, Gamze Ates, Giada Carta, Anja Wilmes, Manfred Watzele, Peter J. Shepard, Harper VanSteenhouse, Bruce Seligmann, Joanne M. Yeakley, Bob van de Water, Mathieu Vinken, Paul Jennings
Software Mentions: 1
Published: over 8 years ago

10.1155/2019/2951427

Transcriptome Analysis Reveals the Effect of Long Intergenic Noncoding RNAs on Pig Muscle Growth and Fat Deposition
Cited by: 9
Author(s): Guoting Chen, Xiangdong Cheng, Gaoli Shi, Cheng Zou, Lin Chen, Jingxuan Li, Mengxun Li, Fang Cui, Changchun Li
Software Mentions: 1
Published: over 7 years ago

10.1007/s00204-020-02835-x

Valproic acid promotes mitochondrial dysfunction in primary human hepatocytes in vitro; impact of C/EBPα-controlled gene expression
Cited by: 8
Author(s): Florian Caiment, Jarno E J Wolters, Evelyn Smit, Yannick Schrooders, Jos Kleinjans, Twan van den Beucken
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-021-90633-5

Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh
Cited by: 8
Author(s): Jifang Zhang, Jian Zhao, Qunyun Tan, Xiaojun Qiu, Shuqi Mei
Software Mentions: 1
Published: over 5 years ago

10.1155/2020/2043785

Extraction and Hypolipidemic Activity of Low Molecular Weight Polysaccharides Isolated from Rosa Laevigata Fruits
Cited by: 6
Author(s): Xuejiao Zhang, Hu Y, Chenzhong Jin, Weiguo Wu
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-021-90672-y

Rootstock effects on scion gene expression in maritime pine
Cited by: 10
Author(s): Miriam López‐Hinojosa, Nuria de María, M. Ángeles Guevara, María Dolores Vélez, José Antonio Cabezas, Luis Manuel Díaz, José Antonio Mancha, Alberto Pizarro, Lorenzo Federico Manjarrez, Carmen Collada, Carmen Dı́az-Sala, M T Cervera Goy
Software Mentions: 1
Published: over 5 years ago

10.3390/biology10090875

Intersex Plays a Role in Microbial Homeostasis in the Brown Planthopper
Cited by: 1
Author(s): Hou‐Hong Zhang, Hanjing Li, Yuxuan Ye, Ji-Chong Zhuo, Chuan-Xi Zhang
Software Mentions: 1
Published: about 5 years ago

10.3390/biology10090867

The Genetic Network of Forkhead Gene Family in Development of Brown Planthoppers
Cited by: 3
Author(s): Haiyan Lin, Cheng-Qi Zhu, Hou‐Hong Zhang, Zhicheng Shen, Chuan-Xi Zhang, Yuxuan Ye
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-91269-1

Identifying molecular pathways and candidate genes associated with knob traits by transcriptome analysis in the goose (Anser cygnoides)
Cited by: 3
Author(s): Wangyang Ji, li E Hou, Xi Yuan, Tiantian Gu, ZhuoYu Chen, Yu Zhang, Yang Zhang, Guohong Chen, Qi Xu, Wenming Zhao
Software Mentions: 1
Published: over 5 years ago

10.3390/biology10080753

Identification of Riptortus pedestris Salivary Proteins and Their Roles in Inducing Plant Defenses
Cited by: 7
Author(s): Hai‐Jian Huang, Xiaotian Yan, Zhongyan Wei, Yi-Zhe Wang, Jianping Chen, Junmin Li, Zongtao Sun, Chuan‐Xi Zhang
Software Mentions: 1
Published: over 5 years ago

10.3390/biology9070153

A First Insight into North American Plant Pathogenic Fungi Armillaria sinapina Transcriptome
Cited by: 6
Author(s): Narimene Fradj, Nicolas de Montigny, Natacha Mérindol, Fatima Awwad, Yacine Boumghar, Hugo Germain, Isabel Desgagné‐Penix
Software Mentions: 1
Published: over 6 years ago

10.1186/s12974-019-1600-7

Profiling the microRNA signature of the peripheral sensory ganglia in experimental autoimmune encephalomyelitis (EAE)
Cited by: 8
Author(s): Timothy N. Friedman, Muhammad Saad Yousuf, Ana Catuneanu, Mansi Desai, Camille A. Juźwik, Alyson E. Fournier, Bradley J. Kerr
Software Mentions: 1
Published: about 7 years ago

10.1128/AEM.00483-18

Enrichment of Clinically Relevant Organisms in Spontaneous Preterm-Delivered Placentas and Reagent Contamination across All Clinical Groups in a Large Pregnancy Cohort in the United Kingdom
Cited by: 60
Author(s): Lydia J. Leon, Ronan Doyle, Ernest Diez Benavente, Taane G. Clark, Nigel Klein, Philip Stanier, Gudrun E. Moore
Software Mentions: 1
Published: over 8 years ago

10.3390/biology10050440

Integrated Signals of Jasmonates, Sugars, Cytokinins and Auxin Influence the Initial Growth of the Second Buds of Chrysanthemum after Decapitation
Cited by: 9
Author(s): Daojin Sun, Luyao Zhang, Qi Yu, Jiali Zhang, Peiling Li, Yu Zhang, Xiangzhuo Xing, Lian Ding, Weimin Fang, Fadi Chen, Aiping Song
Software Mentions: 1
Published: over 5 years ago

10.1128/AEM.02634-16

Interactions of Freshwater Cyanobacteria with Bacterial Antagonists
Cited by: 26
Author(s): Omneya Ahmed Osman, Sara Beier, Manfred Grabherr, Stefan Bertilsson
Software Mentions: 1
Published: over 9 years ago

10.1186/s13293-021-00387-y

Sexual dimorphism of monocyte transcriptome in individuals with chronic low-grade inflammation
Cited by: 10
Author(s): Jisun So, Albert Tai, Alice H. Lichtenstein, Dayong Wu, Stefania Lamon‐Fava
Software Mentions: 1
Published: over 5 years ago

10.1186/s13293-020-00305-8

Transcriptional analysis of the multiple Sry genes and developmental program at the onset of testis differentiation in the rat
Cited by: 5
Author(s): Jeremy W. Prokop, Surya B. Chhetri, J. Edward Van Veen, Xuqi Chen, Adam Underwood, Katie Uhl, Melinda R. Dwinell, Aron M. Geurts, Stephanie M. Correa, Arthur P. Arnold
Software Mentions: 1
Published: over 6 years ago

10.1242/bio.030254

Re-evaluating functional landscape of the cardiovascular system during development
Cited by: 6
Author(s): Norio Takada, Madoka Omae, Fumihiko Sagawa, C. Neil, Satsuki Endo, Satoshi Kozawa, Thomas N. Sato
Software Mentions: 1
Published: almost 10 years ago

10.1242/bio.046474

Combinatorial genetic replenishments in myocardial and outflow tract tissues restore heart function in tnnt2 mutant zebrafish
Cited by: 5
Author(s): Lian Liu, Fei Fei, Ranran Zhang, Fang Wu, Qian Yang, Feng Wang, Song Sun, Hui Zhao, Qiang Li, Lei Wang, Youhua Wang, Yonghao Gui, Xu Wang
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13287-021-02419-1

High-efficiency c-Myc-mediated induction of functional hepatoblasts from the human umbilical cord mesenchymal stem cells
Cited by: 3
Author(s): Jie Deng, Kai Luo, Pengchao Xu, Qingyuan Jiang, Yuan Wang, Yao Yuxia, Xiaolei Chen, Fuyi Cheng, Dan Xie, Hongxin Deng
Software Mentions: 1
Published: over 5 years ago

10.18632/oncotarget.25535

Extensive screening of microRNA populations identifies hsa-miR-375 and hsa-miR-133a-3p as selective markers for human rectal and colon cancer
Cited by: 16
Author(s): David C. Weber, Laurence Amar, Daniel Gödde, Christian Prinz
Software Mentions: 1
Published: over 8 years ago

10.1186/s13287-021-02486-4

Bone marrow mesenchymal stem cells derived from juvenile macaques reversed ovarian ageing in elderly macaques
Cited by: 7
Author(s): Chuan Tian, Jie He, Yuanyuan An, Zailing Yang, Donghai Yan, Hang Pan, Guanke Lv, Ye Li, Yanying Wang, Yu-Kun Yang, Gaohong Zhu, Zhisong He, Xiaoyan Zhu, Xinghua Pan
Software Mentions: 1
Published: about 5 years ago

10.1186/s13287-021-02560-x

Human Wharton's jelly-derived mesenchymal stem cells alleviate concanavalin A-induced fulminant hepatitis by repressing NF-κB signaling and glycolysis
Cited by: 8
Author(s): Longfa Pan, Chang Liu, Qiuli Liu, Yanli Li, Cong Du, Xinmei Kang, Shuai Dong, Zhuowei Zhou, Huaxin Chen, Xiaowei Liang, Jiajie Chu, Yan Xu, Qi Zhang
Software Mentions: 1
Published: about 5 years ago

10.1242/bio.049684

Neuronal upregulation of Prospero protein is driven by alternative mRNA polyadenylation and Syncrip-mediated mRNA stabilisation
Cited by: 13
Author(s): Tamsin J Samuels, Yoav Arava, Aino I Järvelin, Francesca Robertson, Young Seok Lee, Yang Lu, Ching-Po Yang, Tzumin Lee, David Ish‐Horowicz, Ilan Davis
Software Mentions: 1
Published: almost 7 years ago

10.1155/2020/1634270

High Throughput Approaches to Unravel the Mechanism of Action of a New Vanadium-Based Compound against Trypanosoma cruzi
Cited by: 13
Author(s): M. Florencia Mosquillo, Pablo Smircich, Analı́a Lima, Sérgio Alexandre Gehrke, Gonzalo Scalese, Ignacio Machado, Dinorah Gambino, Beatríz Garat, Leticia Pérez-Díaz
Software Mentions: 1
Published: over 6 years ago

10.1093/bioinformatics/bty998

TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators
Cited by: 0
Author(s): Asa Thibodeau, Dong-Guk Shin
Software Mentions: 1
Published: almost 8 years ago

10.1128/AEM.02312-19

Competitive Exclusion Is a Major Bioprotective Mechanism of Lactobacilli against Fungal Spoilage in Fermented Milk Products
Cited by: 45
Author(s): Solvej Siedler, Martin Holm Rau, Susanne Bidstrup, Justin M. Vento, Stina D. Aunsbjerg, Elleke Fenna Bosma, Laura Mikél McNair, Chase L. Beisel, Ana Rute Neves
Software Mentions: 1
Published: over 6 years ago

10.1002/stem.2919

Histone Acetyltransferase KAT2A Stabilizes Pluripotency with Control of Transcriptional Heterogeneity
Cited by: 35
Author(s): Naomi Moris, Shlomit Edri, Denis Seyres, Rashmi Kulkarni, Ana Filipa Domingues, Tina Balayo, Mattia Frontini, Cristina Pina
Software Mentions: 1
Published: about 8 years ago

10.18632/aging.202971

LncRNAs induce oxidative stress and spermatogenesis by regulating endoplasmic reticulum genes and pathways
Cited by: 13
Author(s): Tie-Cheng Sun, Yi Zhang, Kun Yu, Li Yao, Haiyang Yu, Shan-Jie Zhou, Yapeng Wang, Shoulong Deng, Li Tian
Software Mentions: 1
Published: over 5 years ago

10.1093/bioinformatics/bty553

An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets
Cited by: 10
Author(s): Florian Schmidt, Markus List, Engin Cukuroglu, Sebastian Köhler, Jonathan Göke, Marcel H. Schulz
Software Mentions: 1
Published: about 8 years ago

10.1155/2019/8195614

Oxygen Regulates Human Pluripotent Stem Cell Metabolic Flux
Cited by: 20
Author(s): Jarmon G. Lees, Timothy S. Cliff, Amanda Gammilonghi, James G. Ryall, Stephen Dalton, David K. Gardner, Alexandra J Harvey
Software Mentions: 1
Published: over 7 years ago

10.1155/2019/8475389

MEK Inhibition Targets Cancer Stem Cells and Impedes Migration of Pancreatic Cancer CellsIn VitroandIn Vivo
Cited by: 11
Author(s): Karolin Walter, Kanishka Tiwary, Marija Trajkovic‐Arsic, Ana Hidalgo-Sastre, Laura Dierichs, Sven T. Liffers, Jiangning Gu, Johann Gout, Lucas Schulte, Jan Münch, Thomas Seufferlein, Bruno Sáinz, Jens T. Siveke, Eva Rodriguez-Aznar, Patrick Hermann
Software Mentions: 1
Published: over 7 years ago

10.1128/AEM.02151-19

DNA Stable-Isotope Probing Delineates Carbon Flows from Rice Residues into Soil Microbial Communities Depending on Fertilization
Cited by: 29
Author(s): Yali Kong, Yakov Kuzyakov, Yang Ruan, Junwei Zhang, Tingting Wang, Min Wang, Shiwei Guo, Qirong Shen, Ning Ling
Software Mentions: 1
Published: over 6 years ago

10.1093/aobpla/plab043

Transcriptome profiling of two rice genotypes under mild field drought stress during grain-filling stage
Cited by: 17
Author(s): Yuya Liang, Rodante E. Tabien, Lee Tarpley, Abdul Razack Mohammed, Endang M. Septiningsih
Software Mentions: 1
Published: over 5 years ago

10.1155/2019/7630894

Circular RNA hsa_circRNA_0007334 is Predicted to Promote MMP7 and COL1A1 Expression by Functioning as a miRNA Sponge in Pancreatic Ductal Adenocarcinoma
Cited by: 50
Author(s): Jinghui Yang, Xianling Cong, Mingchun Ren, Hongyan Sun, Tao Liu, Gaoyang Chen, Qingyu Wang, Zhaoyan Li, Shan Yu, Qiwei Yang
Software Mentions: 1
Published: over 7 years ago

10.1155/2021/5522723

Pluripotency-State-Dependent Role of Dax1 in Embryonic Stem Cells Self-Renewal
Cited by: 2
Author(s): Jianjun He, Yuda Cheng, Yan Ruan, Jiali Wang, Yanping Tian, Jiaqi Wang, Fengsheng Wang, Chen Zhang, Yixiao Xu, Lianlian Liu, Meng Yu, Jiangjun Wang, Binyu Zhao, Yue Zhang, Yi Yang, Gaoke Liu, Wei Wu, Ping He, Jiaxiang Xiong, He Huang, Junlei Zhang, Rui Jian
Software Mentions: 1
Published: over 5 years ago

10.1155/2021/9041423

Intestinal Organoids in Colitis Research: Focusing on Variability and Cryopreservation
Cited by: 1
Author(s): Talke F. zur Bruegge, Andrea Liese, Sören Donath, Stefan Kalies, Maike Kosanke, Oliver Dittrich–Breiholz, Sandra Czech, Verena N. Bauer, André Bleich, Manuela Büettner
Software Mentions: 1
Published: about 5 years ago

10.1186/s40478-019-0775-6

TERT expression is susceptible to BRAF and ETS-factor inhibition in BRAFV600E/TERT promoter double-mutated glioma
Cited by: 25
Author(s): Lisa Gabler, Daniela Lötsch, Dominik Kirchhofer, Sushilla van Schoonhoven, Hannah Maren Schmidt, Lisa Mayr, Christine Pirker, Katharina Neumayer, Carina Dinhof, Lucia Kastler, Amedeo A. Azizi, Christian Dorfer, Thomas Czech, Christine Haberler, Andreas Peyrl, Rajiv Kumar, Irene Slavc, Sabine Spiegl-Kreinecker, Johannes Gojo, Walter Berger
Software Mentions: 1
Published: over 7 years ago

10.1002/sctm.19-0286

Propagation of human prostate tissue from induced pluripotent stem cells
Cited by: 22
Author(s): Anastasia C. Hepburn, Emma L. Curry, Mohammad Moad, R.E. Steele, Omar E. Franco, Laura Wilson, Parmveer Singh, Adriana Buskin, Susan E. Crawford, Luke Gaughan, Ian G. Mills, Simon W. Hayward, Craig Robson, Rakesh Heer
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2019.02074

The Transcription Unit Architecture of Streptomyces lividans TK24
Cited by: 23
Author(s): Yong Jae Lee, Namil Lee, Yu‐Jin Jeong, Soonkyu Hwang, Woori Kim, Suhyung Cho, Bernhard Ø. Palsson, Byung-Kwan Cho
Software Mentions: 1
Published: about 7 years ago

10.1093/aobpla/plaa041

Transcriptome analysis in osmo-primed tomato seeds with enhanced longevity by heat shock treatment
Cited by: 2
Author(s): Thiago Barbosa Batista, Geysson Javier Fernández, Edvaldo Aparecido Amaral da Silva, Júlio Maia, Edvaldo Aparecido Amaral da Silva
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2021.664598

Genomic and Transcriptomic Investigation of the Physiological Response of the Methylotroph Bacillus methanolicus to 5-Aminovalerate
Cited by: 3
Author(s): Carsten Haupka, Luciana Fernandes de Brito, Tobias Busche, Daniel Wibberg, Volker F. Wendisch
Software Mentions: 1
Published: over 5 years ago

10.1016/j.bioflm.2019.100002

Interkingdom interactions on the denture surface: Implications for oral hygiene
Cited by: 13
Author(s): Christopher Delaney, Lindsay E. O’Donnell, Ryan Kean, Leighann Sherry, Jason L. Brown, Gareth Calvert, Christopher J. Nile, Laura J. Cross, David J. Bradshaw, Bernd W. Brandt, Douglas Robertson, Gordon Ramage
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2020.00744

Genomic and Transcriptomic Study for Screening Genes Involved in the Limonene Biotransformation of Penicillium digitatum DSM 62840
Cited by: 10
Author(s): Lulu Zhang, Wen Huang, Yingying Zhang, Gang Fan, Jin He, Jianmin Ren, Zhi Li, Xiao Li, Siyi Pan
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2016.00175

Understanding the Role of the Master Regulator XYR1 in Trichoderma reesei by Global Transcriptional Analysis
Cited by: 60
Author(s): Lílian dos Santos Castro, Renato Graciano de Paula, Amanda Cristina Campos Antoniêto, Gabriela Félix Persinoti, Rafael Silva‐Rocha, Roberto do Nascimento Silva
Software Mentions: 1
Published: over 10 years ago

10.3389/fmicb.2020.532447

Impact of Ocean Warming and Acidification on Symbiosis Establishment and Gene Expression Profiles in Recruits of Reef Coral Acropora intermedia
Cited by: 10
Author(s): Yuhan Sun, Lei Jiang, Sanqiang Gong, Ming Guo, Xiangcheng Yuan, Guowei Zhou, Xinming Lei, Yuyang Zhang, Tao Yuan, Lian Ji, Pei‐Yuan Qian, Hui Huang
Software Mentions: 1
Published: about 6 years ago

10.1007/s00122-021-03938-4

A mutation in LacDWARF1 results in a GA-deficient dwarf phenotype in sponge gourd (Luffa acutangula)
Cited by: 4
Author(s): Gangjun Zhao, Caixia Luo, Jianxun Luo, Junxing Li, Hao Gong, Xiujue Zheng, Xiaoxi Liu, Junhui Guo, Lingyan Zhou, Haibin Wu
Software Mentions: 1
Published: over 5 years ago

10.1016/j.bbadis.2018.03.021

SURF1 knockout cloned pigs: Early onset of a severe lethal phenotype
Cited by: 22
Author(s): Corinne Quadalti, Dario Brunetti, Irina Lagutina, Roberto Duchi, Andrea Perota, Giovanna Lazzari, Raffaele Cerutti, Ivano Di Meo, Mark A. Johnson, Emanuela Bottani, Paola Crociara, Cristiano Corona, Silvia Grifoni, Valeria Tiranti, Erika Fernández-Vizarra, Alan J. Robinson, Carlo Viscomi, Cristina Casalone, Massimo Zeviani, Cesare Galli
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2019.02769

Physiology and Transcriptional Analysis of (p)ppGpp-Related Regulatory Effects in Corynebacterium glutamicum
Cited by: 7
Author(s): Matthias Ruwe, Marcus Persicke, Tobias Busche, Benjamin Müller, Joern Kalinowski
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2020.590325

A Cross-Sectional Study of Dairy Cattle Metagenomes Reveals Increased Antimicrobial Resistance in Animals Farmed in a Heavy Metal Contaminated Environment
Cited by: 12
Author(s): Natália Carrillo Gaeta, Emily Bean, Asha M. Miles, Daniel Ubriaco Oliveira Gonçalves de Carvalho, Mario Augusto Reyes Alemán, Jeferson Silva Carvalho, Lílian Gregory, Erika Ganda
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2016.01592

A Sample-to-Sequence Protocol for Genus Targeted Transcriptomic Profiling: Application to Marine Synechococcus
Cited by: 1
Author(s): Frances Diana Pitt, Andrew Millard, Martin Ostrowski, Suat Dervish, Sophie Mazard, Ian T. Paulsen, Mikhail V. Zubkov, David J. Scanlan
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2020.604485

More Than a Methanotroph: A Broader Substrate Spectrum for Methylacidiphilum fumariolicum SolV
Cited by: 18
Author(s): Nunzia Picone, Sepehr S. Mohammadi, Annemiek C. Waajen, Theo A. van Alen, Mike S. M. Jetten, Arjan Pol, Huub J. M. Op den Camp
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2017.02114

Analysis of Microbiome Data in the Presence of Excess Zeros
Cited by: 191
Author(s): Abhishek Kaul, Siddhartha Mandal, Ori Davidov, Shyamal D. Peddada
Software Mentions: 1
Published: about 9 years ago

10.1016/j.bbrep.2021.101038

Analysis of differentially expressed genes responsible for the suppressive effect of anisomycin on cell proliferation of DLD-1 cells
Cited by: 3
Author(s): Hironori Ushijima, Rina Monzaki, Mika Funakoshi
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2018.00366

The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial
Cited by: 68
Author(s): Shumeng Kou, Gilles Vincent, Emmanuel González, Frédéric E. Pitre, Michel Labrecque, Nicholas J. B. Brereton
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2020.591926

GapB Is Involved in Biofilm Formation Dependent on LrgAB but Not the SinI/R System in Bacillus cereus 0-9
Cited by: 6
Author(s): Juanmei Zhang, Meng Li, Yubing Zhang, Lidan Sang, Qing Liu, Linlin Zhao, Fengying Liu, Gang Wang
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2020.536865

Quorum Sensing System Affects the Plant Growth Promotion Traits of Serratia fonticola GS2
Cited by: 14
Author(s): Byung Kwon Jung, Jerald Conrad Ibal, Huy Quang Pham, Min‐Chul Kim, Gun-Seok Park, Sung-Jun Hong, Hyung Woo Jo, Chang Eon Park, Seung-Dae Choi, Young Hun Jung, Setu Bazie Tagele, Jae‐Ho Shin
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2020.02022

Amphotericin B Specifically Induces the Two-Component System LnrJK: Development of a Novel Whole-Cell Biosensor for the Detection of Amphotericin-Like Polyenes
Cited by: 11
Author(s): Ainhoa Revilla-Guarinos, Franziska Dürr, Philipp F. Popp, Michaela Döring, Thorsten Mascher
Software Mentions: 1
Published: about 6 years ago

10.1186/s12917-020-02395-3

Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis
Cited by: 3
Author(s): Chinatsu Mukai, Eun‐Ju Choi, Kelly L. Sams, Elena Zu Klampen, Lynne J. Anguish, Brooke A. Marks, Edward J. Rice, Wen‐Zhao Zhong, Lauren A Choate, Shao Pei Chou, Yukinari Kato, Andrew D. Miller, Charles G. Danko, Scott A. Coonrod
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2021.557180

Distinct Changes Occur in the Human Breast Milk Microbiome Between Early and Established Lactation in Breastfeeding Guatemalan Mothers
Cited by: 21
Author(s): Emmanuel González, Nicholas J. B. Brereton, Chen Li, Lilian Lopez Leyva, Noel W. Solomons, Luis B. Agellon, Marilyn Scott, Kristine G. Koski
Software Mentions: 1
Published: almost 6 years ago

10.7150/thno.43744

Discrete functional and mechanistic roles of chromodomain Y-like 2 (CDYL2) transcript variants in breast cancer growth and metastasis
Cited by: 13
Author(s): Lifeng Yang, Fan Yang, Fanglin Zhang, Yifan Xie, Zhixiang Hu, Shenglin Huang, Zhimin Shao, Da‐Qiang Li
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2021.628269

Burkholderiaceae Are Key Acetate Assimilators During Complete Denitrification in Acidic Cryoturbated Peat Circles of the Arctic Tundra
Cited by: 23
Author(s): Stefanie A. Hetz, Marcus A. Horn
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2018.02251

Comparative Time-Scale Gene Expression Analysis Highlights the Infection Processes of Two Amoebophrya Strains
Cited by: 10
Author(s): Sarah Farhat, Isabelle Florent, Benjamin Noël, Ehsan Kayal, Corinne Da Silva, Estelle Bigeard, Adriana Alberti, Karine Labadie, Erwan Corre, Jean‐Marc Aury, Stéphane Rombauts, Patrick Wincker, Laure Guillou, Betina M. Porcel
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2018.01602

Genetically Obese Human Gut Microbiota Induces Liver Steatosis in Germ-Free Mice Fed on Normal Diet
Cited by: 36
Author(s): Ruirui Wang, Hui Li, Xin Yang, Xinhe Xue, Liman Deng, Jian Shen, Menghui Zhang, Liping Zhao, Chenhong Zhang
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2018.01795

Genomic and Functional Characterization of Environmental Strains of SDS-Degrading Pseudomonas spp., Providing a Source of New Sulfatases
Cited by: 14
Author(s): Ewa M. Furmanczyk, Leszek Lipiński, Andrzej Dziembowski, Adam Sobczak
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2019.02829

A Similar Secretome Disturbance as a Hallmark of Non-pathogenic Botrytis cinerea ATMT-Mutants?
Cited by: 15
Author(s): Amélie de Vallée, Pascal Bally, Christophe Bruel, Lucie Chandat, Mathias Choquer, Cindy Dieryckx, Jean-William Dupuy, Sophie Kaiser, Marie‐Pascale Latorse, Elise Loisel, Géraldine Mey, Georges Morgant, Christine Rascle, Julia Schumacher, Adeline Simon, Eytham Souibgui, Muriel Viaud, François Villalba, Nathalie Poussereau
Software Mentions: 1
Published: almost 7 years ago

10.7150/thno.43894

Interleukin-22 drives a metabolic adaptive reprogramming to maintain mitochondrial fitness and treat liver injury
Cited by: 15
Author(s): Wei Chen, Wenjing Zai, Jiajun Fan, Xuyao Zhang, Xian Zeng, Jingyun Luan, Yichen Wang, Yilan Shen, Ziyu Wang, Shixuan Dai, Fang Si, Zhen Zhao, Dianwen Ju
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2021.718487

Resource Allocation During the Transition to Diazotrophy in Klebsiella oxytoca
Cited by: 5
Author(s): Christopher Waite, Anya Lindström Battle, Mark H. Bennett, Matthew Carey, Chun K Hong, Ioly Kotta‐Loizou, Martin Buck, Julia Schumacher
Software Mentions: 1
Published: over 5 years ago

10.3390/antiox10091435

Comparative Transcriptome Analysis of the Expression of Antioxidant and Immunity Genes in the Spleen of a Cyanidin 3-O-Glucoside-Treated Alzheimer’s Mouse Model
Cited by: 11
Author(s): Varun Jaiswal, Miey Park, Hae‐Jeung Lee
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2020.556064

Transcriptomic and Phenotypic Analysis of a spoIIE Mutant in Clostridium beijerinckii
Cited by: 7
Author(s): Mamou Diallo, Nicolas Kint, Marc Monot, Florent Collas, Isabelle Martin‐Verstraete, John van der Oost, S.W.M. Kengen, Ana M. López-Contreras
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2018.02558

Mechanistic Insights Into the Cross-Feeding of Ruminococcus gnavus and Ruminococcus bromii on Host and Dietary Carbohydrates
Cited by: 99
Author(s): Emmanuelle H. Crost, Gwénaëlle Le Gall, Jenny A. Laverde-Gomez, Indrani Mukhopadhya, Harry J. Flint, Nathalie Juge
Software Mentions: 1
Published: about 8 years ago

10.3389/fmicb.2018.03201

Early Response of Sulfolobus acidocaldarius to Nutrient Limitation
Cited by: 18
Author(s): Lisa Franziska Bischof, M. Florencia Haurat, Lena Hoffmann, Andreas Albersmeier, Jacqueline Wolf, Astrid Neu, Trong Khoa Pham, Stefan P. Albaum, Tobias Jakobi, Stefan Schouten, Meina Neumann‐Schaal, Phillip C. Wright, Jörn Kalinowski, Bettina Siebers, Sonja Albers
Software Mentions: 1
Published: almost 8 years ago

10.3389/fmicb.2020.01617

Diversity of Cellulase-Producing Filamentous Fungi From Tibet and Transcriptomic Analysis of a Superior Cellulase Producer Trichoderma harzianum LZ117
Cited by: 18
Author(s): Jiaxiang Li, Fei Zhang, Dan-Dan Jiang, Jun Li, Feng-Lou Wang, Zhang Zhang, Wei Wang, Xin‐Qing Zhao
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2020.00151

The Epipeptide YydF Intrinsically Triggers the Cell Envelope Stress Response of Bacillus subtilis and Causes Severe Membrane Perturbations
Cited by: 26
Author(s): Philipp F. Popp, Alhosna Benjdia, Henrik Strahl, Olivier Berteau, Thorsten Mascher
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2017.01811

Transcriptomic Analysis of the Adaptation of Listeria monocytogenes to Lagoon and Soil Matrices Associated with a Piggery Environment: Comparison of Expression Profiles
Cited by: 16
Author(s): Anne-Laure Vivant, Jérémy Desneux, Anne‐Marie Pourcher, Pascal Piveteau
Software Mentions: 1
Published: about 9 years ago

10.3389/fmicb.2017.02489

Physiological and Pathological Transcriptional Activation of Endogenous Retroelements Assessed by RNA-Sequencing of B Lymphocytes
Cited by: 29
Author(s): Jan Attig, George R. Young, Jonathan P. Stoye, George Kassiotis
Software Mentions: 1
Published: almost 9 years ago

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Papers Mentioning DESeq2 9,583