bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1038/s41392-021-00575-7

RNA-induced liquid phase separation of SARS-CoV-2 nucleocapsid protein facilitates NF-κB hyper-activation and inflammation
Cited by: 74
Author(s): Yiming Wu, Ling Ma, Sihui Cai, Zhen Zhuang, Zhiyao Zhao, Shouheng Jin, Weidong Xie, Lingli Zhou, Lei Zhang, Jincun Zhao, Jun Cui
Software Mentions: 1
Published: over 5 years ago

10.1007/s13258-021-01076-1

Overlapping and non-overlapping roles of the class-I histone deacetylase-1 corepressors LET-418, SIN-3, and SPR-1 in Caenorhabditis elegans embryonic development
Cited by: 2
Author(s): Yukihiko Kubota, Yuto Ohnishi, Tasuku Hamasaki, Gen Yasui, Natsumi Ota, Hiromu Kitagawa, Arashi Esaki, Muhamad Fahmi, Masahiro Ito
Software Mentions: 1
Published: over 5 years ago

10.1186/s12964-019-0444-1

Induction of LEF1 by MYC activates the WNT pathway and maintains cell proliferation
Cited by: 42
Author(s): Yi Hao, M. Carmen Lafita-Navarro, Lauren G. Zacharias, Nofit Borenstein‐Auerbach, Min Kim, Spencer Barnes, Jiwoong Kim, Jerry W. Shay, Ralph J. DeBerardinis, Maralice Conacci‐Sorrell
Software Mentions: 1
Published: about 7 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

10.1186/s12964-018-0234-1

High co-expression of the SDF1/CXCR4 axis in hepatocarcinoma cells is regulated by AnnexinA7 in vitro and in vivo
Cited by: 10
Author(s): Jingwen Wang, Yühong Huang, Jun Zhang, Boyi Xing, Wei Xuan, Honghai Wang, He Huang, Jiayu Yang, Jianwu Tang
Software Mentions: 1
Published: over 8 years ago

10.1186/s12263-019-0630-1

High-throughput sequencing of small RNAs and analysis of differentially expressed microRNAs associated with high-fat diet-induced hepatic insulin resistance in mice
Cited by: 13
Author(s): Xue Zhao, Chen Zhao, Zengyuan Zhou, Yuzheng Li, Yuan‐Yuan Wang, Zihao Zhou, Huimin Lu, Chongde Sun, Xia Chu
Software Mentions: 1
Published: over 7 years ago

10.1111/eva.13162

The molecular mechanisms that determine different degrees of polyphagy in the Bemisia tabaci species complex
Cited by: 11
Author(s): Osnat Malka, Ester Feldmesser, Sharon van Brunschot, Diego Santos-García, Wenfeng Han, Susan Seal, John Colvin, Shai Morin
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41392-021-00716-y

Decreased inhibition of exosomal miRNAs on SARS-CoV-2 replication underlies poor outcomes in elderly people and diabetic patients
Cited by: 40
Author(s): Han Li, Xiao Zhu, Xiaming Jiang, Jingwei Guo, Zheng Fu, Zhen Zhou, Ping Yang, Hongyuan Guo, Xu Guo, Gaoli Liang, Ping Zeng, Gengfu Xiao, Jie Ma, Xin Yin, Leike Zhang, Chao Yan, Chenyu Zhang
Software Mentions: 1
Published: over 5 years ago

10.1590/1678-4685-GMB-2019-0255

Transcriptomics analysis of Psidium cattleyanum Sabine (Myrtaceae) unveil potential genes involved in fruit pigmentation
Cited by: 8
Author(s): Nicole Moreira Vetö, Frank Guzmán, Franceli Rodrigues Kulcheski, Ana Lúcia Anversa Segatto, Maria Eduarda G Lacerda, Rogério Margis, Andreia Carina Turchetto‐Zolet
Software Mentions: 1
Published: almost 7 years ago

10.7554/eLife.58213

IL18 signaling promotes homing of mature Tregs into the thymus
Cited by: 21
Author(s): Cristina Peligero-Cruz, Tal Givony, Arnau Sebé-Pedrós, Jan Dobeš, Noam Kadouri, Shir Nevo, Francesco Roncato, Ronen Alon, Yael Goldfarb, Jakub Abramson
Software Mentions: 1
Published: over 6 years ago

10.1590/1678-4685-GMB-2019-0373

Gene expression evaluation of antioxidant enzymes in patients with hepatocellular carcinoma: RT-qPCR and bioinformatic analyses
Cited by: 7
Author(s): Andressa de Freitas Alves, Ana Carolina de Moura, Huander Felipe Andreolla, Ana Beatriz Gorini da Veiga, Marilu Fiegenbaum, Márcia Giovenardi, Silvana Almeida
Software Mentions: 1
Published: almost 6 years ago

10.3390/microorganisms7080261

Assessing Transcriptional Responses to Light by the Dinoflagellate Symbiodinium
Cited by: 6
Author(s): Bahareh Zaheri, Steve Dagenais-Bellefeuille, Bo Song, David Morse
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0152792

Identifying Cancer Subtypes from miRNA-TF-mRNA Regulatory Networks and Expression Data
Cited by: 57
Author(s): Taosheng Xu, Thuc Duy Le, Lin Liu, Rujing Wang, Bingyu Sun, Jiuyong Li
Software Mentions: 1
Published: over 10 years ago

10.3390/cells10071656

Altered Cytokine Response of Human Brain Endothelial Cells after Stimulation with Malaria Patient Plasma
Cited by: 3
Author(s): Michaela Raacke, Amy Kerr, Michael Dörpinghaus, Jana Brehmer, Yifan Wu, Stephan Lorenzen, Christine Fink, Thomas Jacobs, Thomas Roeder, Julie Sellau, Anna Bachmann, Nahla Galal Metwally, Iris Bruchhaus
Software Mentions: 1
Published: over 5 years ago

10.1097/HS9.0000000000000514

Gene Expression Profiling Predicts Sensitivity of Chronic Lymphocytic Leukemia Cells to Dasatinib
Cited by: 0
Author(s): Tamara J. Blätte, Marcin M. Machnicki, Eliza Głodkowska-Mrówka, Anna Dolnik, Marta Karp, Agnieszka Karczmarczyk, Krzysztof Giannopoulos, Lars Bullinger, Tomasz Stokłosa
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13395-021-00273-6

The pan HDAC inhibitor Givinostat improves muscle function and histological parameters in two Duchenne muscular dystrophy murine models expressing different haplotypes of the LTBP4 gene
Cited by: 13
Author(s): Simonetta Andrea Licandro, Luca Crippa, Roberta Pomarico, Rita Perego, Gianluca Fossati, Flavio Leoni, Christian Steinkühler
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22147557

A Complex Network of Sigma Factors and sRNA StsR Regulates Stress Responses in R. sphaeroides
Cited by: 1
Author(s): Katrin M. H. Eisenhardt, Bernhardt Remes, Julian Grützner, Daniel-Timon Spanka, Andreas Jäger, Gabriele Klug
Software Mentions: 1
Published: over 5 years ago

10.1186/s41065-020-00153-x

Comparative transcriptomic analysis of the tea plant (Camellia sinensis) reveals key genes involved in pistil deletion
Cited by: 2
Author(s): Yufei Liu, Dan Pang, Yaping Tian, Youyong Li, Hong-Yan Jiang, Yanxia Sun, Lifei Xia, Linbo Chen
Software Mentions: 1
Published: about 6 years ago

10.1186/s41065-021-00188-8

Identification and characterization of miRNAs associated with sterile flower buds in the tea plant based on small RNA sequencing
Cited by: 4
Author(s): Hao Qu, Yue Liu, Hong-Yan Jiang, Yuanyuan Liu, Weixi Song, Linbo Chen
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2021.643497

The Expression Profiles of mRNAs and lncRNAs in Buffalo Muscle Stem Cells Driving Myogenic Differentiation
Cited by: 4
Author(s): Ruimen Zhang, Jinling Wang, Zhengzhong Xiao, Chao-Xia Zou, Qiang An, Hui Li, Xiaoqing Zhou, Zhuyue Wu, Deshun Shi, Yanfei Deng, Sufang Yang, Yanfei Wei
Software Mentions: 1
Published: over 5 years ago

10.1038/s41438-019-0206-7

Effective genome editing and identification of a regiospecific gallic acid 4-O-glycosyltransferase in pomegranate (Punica granatum L.)
Cited by: 28
Author(s): Liming Chang, Sheng Wu, Li Tian
Software Mentions: 1
Published: about 7 years ago

10.3390/nu12061586

Effect of a Multispecies Probiotic on Intestinal and Skin Colonization by Multidrug-Resistant Gram-Negative Bacteria in Patients in a Long-Term Care Facility: A Pilot Study
Cited by: 2
Author(s): Ines Zollner‐Schwetz, Monika Scarpatetti, Gerhard Pichler, Christian Pux, Ingeborg Klymiuk, Slave Trajanoski, Robert Krause
Software Mentions: 1
Published: over 6 years ago

10.1016/j.stemcr.2019.03.006

Pathological ASXL1 Mutations and Protein Variants Impair Neural Crest Development
Cited by: 15
Author(s): Friederike Matheus, Ejona Rusha, Rizwan Rehimi, Lena Molitor, Anna Pertek, Miha Modic, Regina Feederle, Andrew Flatley, Elisabeth Kremmer, Arie Geerlof, Valentyna M. Rishko, Álvaro Rada-Iglesias, Micha Drukker
Software Mentions: 1
Published: over 7 years ago

10.1096/fj.201701098R

Analysis of chromatin accessibility in decidualizing human endometrial stromal cells
Cited by: 28
Author(s): Pavle Vrljicak, Emma S. Lucas, Lauren Lansdowne, Raffaella Lucciola, Joanne Muter, Nigel P. Dyer, Jan J. Brosens, Sascha Ott
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41438-020-00455-1

Chromosome-scale genome assembly provides insights into the evolution and flavor synthesis of passion fruit (Passiflora edulis Sims)
Cited by: 52
Author(s): Zhiqiang Xia, Dongmei Huang, Shengkui Zhang, Wenquan Wang, Funing Ma, Bin Wu, Yi Xu, Biao Xu, Di Chen, Meiling Zou, Hongtao Xu, Xiaojin Zhou, Rulin Zhan, Santai Song
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

10.1371/journal.pone.0238380

Transcriptional and immunohistological assessment of immune infiltration in pancreatic cancer
Cited by: 8
Author(s): Brady Bernard, Venkatesh Rajamanickam, Christopher Dubay, Brian D. Piening, Emilio Alonso, Zeljka Jutric, Ephraim Tang, Pippa Newell, Paul Hansen, Terry R. Medler, Andrew Gunderson, Kristina H. Young, Carlo Bifulco, Joanna Pucliowska, Marka R. Crittenden, Michael Gough
Software Mentions: 1
Published: about 6 years ago

10.3390/biomedicines9080949

Evaluation of β-Catenin Inhibition of Axitinib and Nitazoxanide in Human Monocyte-Derived Dendritic Cells
Cited by: 1
Author(s): Waqas Azeem, Ragnhild Maukon Bakke, Benjamin Gabriel, Silke Appel, Anne Margrete Øyan, Karl‐Henning Kalland
Software Mentions: 1
Published: over 5 years ago

10.1038/s41438-021-00576-1

DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.)
Cited by: 10
Author(s): Ling Yin, Zhendong Zhu, Liangjun Huang, Xuan Luo, Yun Li, Chaowen Xiao, Jin Yang, Jisheng Wang, Qiong Zou, Lanrong Tao, Zeming Kang, Rong Tang, Maolin Wang, Shaohong Fu
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms9091864

Vaginal Microbiota of the Sexually Transmitted Infections Caused by Chlamydia trachomatis and Trichomonas vaginalis in Women with Vaginitis in Taiwan
Cited by: 12
Author(s): Shu-Fang Chiu, Po-Jung Huang, Wei-Hung Cheng, Ching-Yun Huang, Lichieh Julie Chu, Chi-Ching Lee, Hsin‐Chung Lin, Lih‐Chyang Chen, Wei‐Ning Lin, Chang‐Huei Tsao, Petrus Tang, Yuan-Ming Yeh, Kuo‐Yang Huang
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0220365

Transcriptomic differences noted in Glaesserella parasuis between growth in broth and on agar
Cited by: 2
Author(s): Samantha J. Hau, Kathy T. Mou, Darrell O. Bayles, Susan L. Brockmeier
Software Mentions: 1
Published: over 7 years ago

10.1038/s41438-020-0262-z

Lipidomic and transcriptomic analysis reveals reallocation of carbon flux from cuticular wax into plastid membrane lipids in a glossy “Newhall” navel orange mutant
Cited by: 20
Author(s): Hu Wan, Hongbo Liu, Jingyu Zhang, Yi Lyu, Zhuoran Li, Yuan He, Xiaoliang Zhang, Xiuxin Deng, Yariv Brotman, Alisdair R. Fernie, Yunjiang Cheng, Weiwei Wen
Software Mentions: 1
Published: over 6 years ago

10.1016/j.stemcr.2020.05.003

Pro-maturational Effects of Human iPSC-Derived Cortical Astrocytes upon iPSC-Derived Cortical Neurons
Cited by: 38
Author(s): Anne Hedegaard, Jimena Monzón‐Sandoval, Sarah E. Newey, Emma Whiteley, Caleb Webber, Colin J. Akerman
Software Mentions: 1
Published: over 6 years ago

10.3390/microorganisms9010199

Fecal Microbiota Transplant from Human to Mice Gives Insights into the Role of the Gut Microbiota in Non-Alcoholic Fatty Liver Disease (NAFLD)
Cited by: 28
Author(s): Sebastian D. Burz, Magali Monnoye, Catherine Philippe, William Farin, Vlad Ratziu, Francesco Strozzi, Jean‐Michel Paillarse, Laurent Chêne, Hervé M. Blottière, Philippe Gérard
Software Mentions: 1
Published: almost 6 years ago

10.3390/nu13061837

Foxtail Millet Improves Blood Glucose Metabolism in Diabetic Rats through PI3K/AKT and NF-κB Signaling Pathways Mediated by Gut Microbiota
Cited by: 25
Author(s): Xin Ren, Linxuan Wang, Zenglong Chen, Dianzhi Hou, Yong Xue, Xianmin Diao, Qun Shen
Software Mentions: 1
Published: over 5 years ago

10.1111/eva.13129

Comparison of anadromous and landlocked Atlantic salmon genomes reveals signatures of parallel and relaxed selection across the Northern Hemisphere
Cited by: 11
Author(s): Erik Kjærner-Semb, Rolf B. Edvardsen, Fernando Ayllón, Petra Vogelsang, Tomasz Furmanek, Carl-Johan Rubin, А. Е. Веселов, Tom Ole Nilsen, Stephen D. McCormick, Craig R. Primmer, Anna Wargelius
Software Mentions: 1
Published: about 6 years ago

10.1038/s41438-020-00366-1

The GAMYB-like gene SlMYB33 mediates flowering and pollen development in tomato
Cited by: 28
Author(s): Yan Zhang, Bo Zhang, Yang Tao, Jie Zhang, Bin Liu, Xiangqiang Zhan, Yan Liang
Software Mentions: 1
Published: about 6 years ago

10.1016/j.stemcr.2021.07.021

Generation of pancreatic progenitors from human pluripotent stem cells by small molecules
Cited by: 14
Author(s): Yuqian Jiang, Chuanxin Chen, Lauren N. Randolph, Songtao Ye, Xin Zhang, Xiaoping Bao, Xiaojun Lian
Software Mentions: 1
Published: about 5 years ago

10.1016/j.scr.2020.101931

Hypermethylation and reduced expression of Gtl2, Rian and Mirg at the Dlk1-Dio3 imprinted locus as a marker for poor developmental potential of mouse embryonic stem cells
Cited by: 2
Author(s): Maria Schacker, Ying Cheng, Mélanie Eckersley-Maslin, Richard Michael Snaith, William H. Colledge
Software Mentions: 1
Published: about 6 years ago

10.1186/s13287-019-1155-7

Platelet-rich plasma improves therapeutic effects of menstrual blood-derived stromal cells in rat model of intrauterine adhesion
Cited by: 65
Author(s): Siwen Zhang, Pingping Li, Zhengwei Yuan, Jichun Tan
Software Mentions: 1
Published: over 7 years ago

10.1038/s41438-021-00518-x

A gene that underwent adaptive evolution, LAC2 (LACCASE), in Populus euphratica improves drought tolerance by improving water transport capacity
Cited by: 20
Author(s): Zhimin Niu, Guiting Li, Hongbo Hu, Jiaojiao Lv, Qiwei Zheng, Jianquan Liu, Dongshi Wan
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2020.594933

NETO2 Is Deregulated in Breast, Prostate, and Colorectal Cancer and Participates in Cellular Signaling
Cited by: 6
Author(s): Maria S. Fedorova, Anastasiya V. Snezhkina, Anastasiya V. Lipatova, Vladislav Pavlov, Anastasiya A. Kobelyatskaya, Zulfiya G. Guvatova, Elena A. Pudova, М. В. Савватеева, Irina A. Ishina, Т. Б. Демидова, Н. Н. Волченко, Trofimov D.Yu. Trofimov, Г. Т. Сухих, George S. Krasnov, Anna V. Kudryavtseva
Software Mentions: 1
Published: almost 6 years ago

10.1002/2211-5463.13132

Dkk1 inhibits malignant transformation induced by Bmi1 via the β‐catenin signaling axis in WB‐F344 oval cells
Cited by: 2
Author(s): Jinjun Ye, Le Xin, Jidong Liu, Tao Tang, Xiaoyong Bao, Yukuang Yan
Software Mentions: 1
Published: over 5 years ago

10.1186/s13287-019-1306-x

lncRNA-mRNA expression profiles and functional networks of mesenchymal stromal cells involved in monocyte regulation
Cited by: 5
Author(s): Ming Li, Zhongyu Xie, Zhaopeng Cai, Fang Su, Guoyan Zheng, Jinteng Li, Shan Wang, Shuizhong Cen, Wenjie Liu, Simin Tang, Guiwen Ye, Zhaofeng Li, Rujia Mi, Yiqian Pan, Peng Wang, Yanfeng Wu, Huiyong Shen
Software Mentions: 1
Published: over 7 years ago

10.3390/cells10020467

Identification of Accessible Hepatic Gene Signatures for Interindividual Variations in Nutrigenomic Response to Dietary Supplementation of Omega-3 Fatty Acids
Cited by: 2
Author(s): Yu Shi, Ping Li, Cuiping Jiang, Yi Chen, Yonghe Ma, Nikhil Gupta, Xiangbo Ruan, Haiming Cao
Software Mentions: 1
Published: over 5 years ago

10.1038/s41438-020-00451-5

Lignin provides mechanical support to herbaceous peony (Paeonia lactiflora Pall.) stems
Cited by: 26
Author(s): Daqiu Zhao, Yuting Luan, Xing Xia, Wanliang Shi, Yuhan Tang, Jun Tao
Software Mentions: 1
Published: almost 6 years ago

10.1002/2211-5463.13019

Methylthioadenosine (MTA) boosts cell‐specific productivities of Chinese hamster ovary cultures: dosage effects on proliferation, cell cycle and gene expression
Cited by: 2
Author(s): Natascha Verhagen, Julia Zieringer, Ralf Takors
Software Mentions: 1
Published: about 6 years ago

10.1128/mBio.01606-21

A New Model Trypanosomatid, Novymonas esmeraldas : Genomic Perception of Its “ Candidatus Pandoraea novymonadis” Endosymbiont
Cited by: 6
Author(s): Alexandra Zakharova, Andreu Saura, Anzhelika Butenko, Lucie Podešvová, Sandra Warmusová, Alexei Y. Kostygov, Anna Nenarokova, Julius Lukeš, Frederik Opperdoes, Vyacheslav Yurchenko
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22147473

Global Transcriptional Analyses of the Wnt-Induced Development of Neural Stem Cells from Human Pluripotent Stem Cells
Cited by: 5
Author(s): Bingchun Liu, Fang-Yuan Liu, Xinyue Gao, Yang-Lin Chen, Qiao-Qiao Meng, Yongli Song, Xihe Li, Siqin Bao
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms9061232

The Fungal Effector Mlp37347 Alters Plasmodesmata Fluxes and Enhances Susceptibility to Pathogen
Cited by: 7
Author(s): Saifur Rahman, Mst Hur Madina, Mélodie B. Plourde, Karen Cristine Gonçalves dos Santos, Xiaoqiang Huang, Yang Zhang, Jean‐François Laliberté, Hugo Germain
Software Mentions: 1
Published: over 5 years ago

10.1038/s41438-021-00520-3

The histone variant Sl_H2A.Z regulates carotenoid biosynthesis and gene expression during tomato fruit ripening
Cited by: 13
Author(s): Xuedong Yang, Xuelian Zhang, Youxin Yang, Hui Zhang, Weimin Zhu, Wen-Feng Nie
Software Mentions: 1
Published: over 5 years ago

10.1002/2211-5463.13076

Gene expression profile of human follicle dermal papilla cells in response to Camellia japonica phytoplacenta extract
Cited by: 3
Author(s): Won Kyong Cho, Hyein Kim, Seung Hye Paek, Sooyun Kim, Hyo Hyun Seo, Jihyeok Song, Ok Hwa Lee, Jiae Min, Sang Jun Lee, Yeonhwa Jo, Hoseong Choi, Jeong Hun Lee, Sang Hyun Moh
Software Mentions: 1
Published: almost 6 years ago

10.1128/mBio.01416-21

CdrS Is a Global Transcriptional Regulator Influencing Cell Division in Haloferax volcanii
Cited by: 12
Author(s): Yan Liao, Verena Vogel, Sabine Hauber, Jürgen Bartel, Omer S. Alkhnbashi, Sandra Maaß, Thandi S. Schwarz, Rolf Backofen, Dörte Becher, Iain G. Duggin, Anita Marchfelder
Software Mentions: 1
Published: about 5 years ago

10.1038/s41438-019-0231-6

The ability to manipulate ROS metabolism in pepper may affect aphid virulence
Cited by: 8
Author(s): Mengjing Sun, Roeland E. Voorrips, Martijn van Kaauwen, Richard G. F. Visser, Ben Vosman
Software Mentions: 1
Published: almost 7 years ago

10.3390/microorganisms9030468

The Two-Component System 09 Regulates Pneumococcal Carbohydrate Metabolism and Capsule Expression
Cited by: 7
Author(s): Stephanie Hirschmann, Alejandro Gómez-Mejía, Ulrike Mäder, Julia Karsunke, Dominik Driesch, Manfred Rohde, Susanne Häußler, Gerhard Burchhardt, Sven Hammerschmidt
Software Mentions: 1
Published: over 5 years ago

10.1038/s41438-021-00588-x

Dynamic changes in transposable element and gene methylation in mulberry (Morus notabilis) in response to Botrytis cinerea
Cited by: 15
Author(s): Youchao Xin, Bi Ma, Qiwei Zeng, Wenmin He, Meiling Qin, Ningjia He
Software Mentions: 1
Published: over 5 years ago

10.1128/mSphere.00030-15

A Three-Dimensional Cell Culture Model To Study Enterovirus Infection of Polarized Intestinal Epithelial Cells
Cited by: 34
Author(s): Coyne Drummond, Cheryl A. Nickerson, Carolyn B. Coyne
Software Mentions: 1
Published: over 10 years ago

10.3390/microorganisms9081590

Oligosaccharide Metabolism and Lipoteichoic Acid Production in Lactobacillus gasseri and Lactobacillus paragasseri
Cited by: 6
Author(s): Takeshi Shiraishi, Shintaro Maeno, Sayoko Kishi, Tadashi Fujii, Hiroki Tanno, Katsuaki Hirano, Takumi Tochio, Yasuhiro Tanizawa, Masanori Arita, Shinichi Yokota, Akihito Endo
Software Mentions: 1
Published: over 5 years ago

10.1111/eva.12487

Transcriptional mechanisms underlying life-history responses to climate change in the three-spined stickleback
Cited by: 22
Author(s): Sin‐Yeon Kim, María M. Costa, Anna Esteve‐Codina, Alberto Velando
Software Mentions: 1
Published: over 9 years ago

10.1038/s41438-020-00387-w

Depicting the battle between nectarine and Monilinia laxa: the fruit developmental stage dictates the effectiveness of the host defenses and the pathogen’s infection strategies
Cited by: 21
Author(s): Marta Balsells-Llauradó, Christian J. Silva, J. Usall, Núria Vall‐llaura, Sandra Serrano-Prieto, Neus Teixidó, Saskia D Mesquida-Pesci, Antonieta De Cal, Bárbara Blanco-Ulate, Rosário Torres
Software Mentions: 1
Published: about 6 years ago

10.1016/j.ibror.2018.06.001

The transcriptome of the rat subfornical organ is altered in response to early postnatal overnutrition
Cited by: 7
Author(s): Colleen S. Peterson, Shuo Huang, Samantha A. Lee, Alastair V. Ferguson, Mark Fry
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0143161

Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide
Cited by: 25
Author(s): Amanda E. Hargrove, Thomas F. Martínez, Alissa A. Hare, Alexis A. Kurmis, John W. Phillips, Sudha Sud, Kenneth J. Pienta, Peter B. Dervan
Software Mentions: 1
Published: almost 11 years ago

10.1098/rsob.200246

Temperature modulates immune gene expression in mosquitoes during arbovirus infection
Cited by: 18
Author(s): B. M. C. Randika Wimalasiri-Yapa, Roberto A. Barrero, Liesel Stassen, Louise M. Hafner, Elizabeth A. McGraw, Alyssa T. Pyke, Cassie C. Jansen, Andreas Suhrbier, Laith Yakob, Wenbiao Hu, Gregor J. Devine, Francesca D. Frentiu
Software Mentions: 1
Published: almost 6 years ago

10.1002/iid3.366

Transcriptomic analysis reveals novel mechanisms of SARS‐CoV‐2 infection in human lung cells
Cited by: 12
Author(s): Shaomin Yang, Songbin Wu, Zhijian Yu, Jia-Bin Huang, X.Y. Zhong, Xiao Dong Liu, Hua Zhu, Lizu Xiao, Qi Deng, Wuping Sun
Software Mentions: 1
Published: about 6 years ago

10.1128/mSphere.00769-20

A Trypanosoma brucei ORFeome-Based Gain-of-Function Library Identifies Genes That Promote Survival during Melarsoprol Treatment
Cited by: 10
Author(s): McKenzie Carter, Stephanie Gomez, Sam Gritz, Stephen Larson, Eugenia Silva-Herzog, Hee-Sook Kim, Danae Schulz, Galadriel Hovel-Miner
Software Mentions: 1
Published: about 6 years ago

10.1186/s13578-021-00536-1

Neuregulin 1/ErbB4 signaling contributes to the anti-epileptic effects of the ketogenic diet
Cited by: 6
Author(s): Jin Wang, Jie Huang, Yuanquan Li, Shan Yao, Chunqing Wu, Ying Wáng, Feng Gao, Min-Dong Xu, Guobin Huang, Changqin Zhao, Jiahui Wu, Yun-Long Zhang, Renjie Jiao, Zihao Deng, Wei Jie, Huibin Li, Aiguo Xuan, Xiangdong Sun
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms22157874

Investigating LMNA-Related Dilated Cardiomyopathy Using Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes
Cited by: 7
Author(s): Yuval Shemer, Lucy N. Mekies, Ronen Ben Jehuda, Polina Baskin, Rita Shulman, Binyamin Eisen, D. Regev, Eloisa Arbustini, Brenda Gerull, Mihaela Gherghiceanu, Eyal Gottlieb, Michael Arad
Software Mentions: 1
Published: over 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

10.1016/j.immuni.2018.06.012

PD-1 Controls Follicular T Helper Cell Positioning and Function
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Author(s): Jingwen Shi, Shiyue Hou, Qian Fang, Xin Liu, Xiaolong Liu, Hai Qi
Software Mentions: 1
Published: over 8 years ago

10.3390/microorganisms7110567

Transcriptome Analysis of Choke Stroma and Asymptomatic Inflorescence Tissues Reveals Changes in Gene Expression in Both Epichloë festucae and Its Host Plant Festuca rubra subsp. rubra
Cited by: 6
Author(s): Ruying Wang, Bruce B. Clarke, Faith C. Belanger
Software Mentions: 1
Published: almost 7 years ago

10.1016/j.immuni.2019.01.009

Chemokine Receptor Redundancy and Specificity Are Context Dependent
Cited by: 83
Author(s): Douglas P. Dyer, Laura Medina-Ruiz, Robin Bartolini, Fabian Schuette, Catherine E. Hughes, Kenneth Pallas, Francesca Vidler, Megan K. L. MacLeod, Christopher J. Kelly, Kit Ming Lee, Christopher A.H. Hansell, Gerard J. Graham
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0230266

Comparison of transcriptomes from two chemosensory organs in four decapod crustaceans reveals hundreds of candidate chemoreceptor proteins
Cited by: 35
Author(s): Mihika T. Kozma, Hanh Ngo-Vu, YW Wong, Neal S. Shukla, Shrikant Pawar, Adriano Senatore, Manfred Schmidt, Charles D. Derby
Software Mentions: 1
Published: over 6 years ago

10.1016/j.immuni.2019.05.004

The Intestine Harbors Functionally Distinct Homeostatic Tissue-Resident and Inflammatory Th17 Cells
Cited by: 202
Author(s): Sara Omenetti, Claudio Bussi, Amina Metidji, Andrea Iseppon, Sunjae Lee, Mauro Tolaini, Ying Liu, Gavin Kelly, Probir Chakravarty, Saeed Shoaie, Maximiliano G. Gutiérrez, Brigitta Stockinger
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0199083

Role of the tomato TAGL1 gene in regulating fruit metabolites elucidated using RNA sequence and metabolomics analyses
Cited by: 13
Author(s): Xiaodan Zhao, Xinyu Yuan, Sha Chen, Lanhuan Meng, Daqi Fu
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pntd.0007052

Genomic instability at the locus of sterol C24-methyltransferase promotes amphotericin B resistance in Leishmania parasites
Cited by: 38
Author(s): Andrew W. Pountain, Stefan Weidt, Clément Regnault, Paul A. Bates, Anne M. Donachie, Nicholas J. Dickens, Michael P. Barrett
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pntd.0006835

Stress susceptibility in Trypanosoma brucei lacking the RNA-binding protein ZC3H30
Cited by: 9
Author(s): Chaitali Chakraborty, Christine Clayton
Software Mentions: 1
Published: about 8 years ago

10.4049/immunohorizons.1900099

The Taste Receptor TAS1R3 Regulates Small Intestinal Tuft Cell Homeostasis
Cited by: 42
Author(s): Michael R. Howitt, Ying Cao, Matthew B Gologorsky, Jessica A. Li, Adam L. Haber, Moshe Biton, Jessica Lang, Monia Michaud, Aviv Regev, Wendy S. Garrett
Software Mentions: 1
Published: almost 7 years ago

10.1093/femsec/fiy095

Cold adaptation and replicable microbial community development during long-term low-temperature anaerobic digestion treatment of synthetic sewage
Cited by: 25
Author(s): Ciara Keating, Dermot Hughes, Thérèse Mahony, Denise Cysneiros, Umer Zeeshan Ijaz, Colette Smith, Vincent O'Flaherty
Software Mentions: 1
Published: over 8 years ago

10.3389/fgene.2020.00449

A Panel of Plasma Exosomal miRNAs as Potential Biomarkers for Differential Diagnosis of Thyroid Nodules
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Author(s): Meihua Liang, Su Jeong Yu, Shuli Tang, Lu Bai, Jianan Cheng, Yuanlong Gu, Shuang Li, Xin Zheng, Lian Duan, Liang Wang, Yanqiao Zhang, Xiaoyi Huang
Software Mentions: 1
Published: over 6 years ago

10.1128/mSphere.01093-20

A 39-Amino-Acid C-Terminal Truncation of GDV1 Disrupts Sexual Commitment in Plasmodium falciparum
Cited by: 12
Author(s): Marta Tibúrcio, Eva Hitz, Igor Niederwieser, Gavin Kelly, Heledd Davies, Christian Doerig, Oliver Billker, Till S. Voss, Moritz Treeck
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2021.617059

Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways
Cited by: 29
Author(s): Maxim Sorokin, Nicolas Borisov, Denis Kuzmin, Alexander Gudkov, Marianna Zolotovskaia, Andrew Garazha, Anton Buzdin
Software Mentions: 1
Published: almost 6 years ago

10.1128/IAI.00866-16

The Rhomboid Protease GlpG Promotes the Persistence of Extraintestinal Pathogenic Escherichia coli within the Gut
Cited by: 18
Author(s): Colin W. Russell, Amanda C Richards, Alexander S. Chang, Matthew Mulvey
Software Mentions: 1
Published: over 9 years ago

10.1128/IAI.01423-15

Genes Required for the Fitness of Salmonella enterica Serovar Typhimurium during Infection of Immunodeficient gp91 −/− phox Mice
Cited by: 22
Author(s): A. Grant, Olusegun Oshota, Roy R. Chaudhuri, Matthew Mayho, Sarah Peters, Simon Clare, Duncan J. Maskell, Pietro Mastroeni
Software Mentions: 1
Published: over 10 years ago

10.1128/mSphere.00443-21

Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility
Cited by: 9
Author(s): Anand V. Sastry, Nicholas Dillon, Amitesh Anand, Saugat Poudel, Ying Hefner, Sibei Xu, Richard Szubin, Adam M. Feist, Victor Nizet, Jaehyung Kim
Software Mentions: 1
Published: about 5 years ago

10.1128/IAI.00661-18

Characterization of Host Responses during Pseudomonas aeruginosa Acute Infection in the Lungs and Blood and after Treatment with the Synthetic Immunomodulatory Peptide IDR-1002
Cited by: 15
Author(s): Kelli Wuerth, Ahwon Lee, Reza Falsafi, Erin E. Gill, Robert E. W. Hancock
Software Mentions: 1
Published: almost 8 years ago

10.1098/rsob.200182

Genetic regulation and heritability of miRNA and mRNA expression link to phosphorus utilization and gut microbiome
Cited by: 4
Author(s): Siriluck Ponsuksili, Michael Oster, Henry Reyer, Frieder Hadlich, Nares Trakooljul, M. Rodehutscord, Amélia Camarinha‐Silva, Jörn Bennewitz, Klaus Wimmers
Software Mentions: 1
Published: almost 6 years ago

10.3390/biom11050677

Unravelling the Molecular Mechanisms Underlying the Protective Effect of Lactate on the High-Pressure Resistance of Listeria monocytogenes
Cited by: 5
Author(s): Cristina Serra-Castelló, Ilario Ferrocino, Anna Jofré, Luca Simone Cocolin, Sara Bover‐Cid, Kalliopi Rantsiou
Software Mentions: 1
Published: over 5 years ago

10.3390/cells10010069

New Insights into Plant Extracellular DNA. A Study in Soybean Root Extracellular Trap
Cited by: 9
Author(s): Marie Chambard, Carole Plasson, Céline Derambure, Sophie Coutant, Isabelle Tournier, Benjamin Lefranc, Jérôme Leprince, Marie‐Christine Kiefer‐Meyer, Azeddine Driouich, Marie-Laure Follet-Gueye, Isabelle Boulogne
Software Mentions: 1
Published: almost 6 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/insects11020139

Transcriptomic Analysis of the Brown Planthopper, Nilaparvata lugens, at Different Stages after Metarhizium anisopliae Challenge
Cited by: 5
Author(s): Yifan Peng, Jifeng Tang, Jiaqin Xie
Software Mentions: 1
Published: over 6 years ago

10.1186/s12987-021-00255-2

Reduction in pericyte coverage leads to blood–brain barrier dysfunction via endothelial transcytosis following chronic cerebral hypoperfusion
Cited by: 32
Author(s): Zhengyu Sun, Chenhao Gao, Dandan Gao, Ruihua Sun, Wei Li, Feng‐Yu Wang, Yanliang Wang, Huixia Cao, Guoyu Zhou, Jiewen Zhang, Junkui Shang
Software Mentions: 1
Published: over 5 years ago

10.3390/insects11030171

Transcriptome Analyses of Diaphorina citri Midgut Responses to Candidatus Liberibacter Asiaticus Infection
Cited by: 28
Author(s): Hai‐Zhong Yu, Ning‐Yan Li, Xiang-Dong Zeng, Jian-Chun Song, Yu Xj, Huanan Su, Ci-Xiang Chen, Long Yi, Zhanjun Lu
Software Mentions: 1
Published: over 6 years ago

10.1155/2021/6637513

Transcriptome Profiling of Human Follicle Dermal Papilla Cells in response to Porphyra-334 Treatment by RNA-Seq
Cited by: 6
Author(s): Su Yeon Kim, Won Kyong Cho, Hyein Kim, Seung Hye Paek, Sung Joo Jang, Yeonhwa Jo, Hoseong Choi, Jeong Hun Lee, Sang Hyun Moh
Software Mentions: 1
Published: almost 6 years ago

10.3390/insects12030237

Regulation of Juvenile Hormone on Summer Diapause of Geleruca daurica and Its Pathway Analysis
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Author(s): Hong-Yue Ma, Yanyan Li, Ling Li, Yao Tan, Bao-Ping Pang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pntd.0008709

Mycolactone induces cell death by SETD1B-dependent degradation of glutathione
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Author(s): Birgit Förster, Caroline Demangel, Thorsten Thye
Software Mentions: 1
Published: about 6 years ago

10.3390/biom11091395

A Set of 17 microRNAs Common for Brain and Cerebrospinal Fluid Differentiates Primary Central Nervous System Lymphoma from Non-Malignant Brain Tumors
Cited by: 3
Author(s): Maria Sromek, Grzegorz Rymkiewicz, Agnieszka Paziewska, Lukasz Szafron, Maria Kulecka, Michalina Zajdel, Mariusz Kulińczak, Michalina Dąbrowska, Aneta Bałabas, Zbigniew Bystydzieński, Magdalena Chechlińska, Jan Konrad Siwicki
Software Mentions: 1
Published: about 5 years ago

10.3390/insects12080661

Identification and Expression Profile of Chemosensory Genes in the Small Hive Beetle Aethina tumida
Cited by: 8
Author(s): Lixian Wu, Xin Zhai, Liangbin Li, Qiang Li, Fang Liu, Hongxia Zhao
Software Mentions: 1
Published: over 5 years ago

10.3390/insects12080736

Transcriptome Analysis of Hormone-and Cuticle-Related Genes in the Development Process of Deutonymph in Tetranychus urticae
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Author(s): Gang Li, Xinyao Gu, Shun‐Hua Gui, Jianjun Guo, Tian‐Ci Yi, Dao‐Chao Jin
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22157899

Human Placental Transcriptome Reveals Critical Alterations in Inflammation and Energy Metabolism with Fetal Sex Differences in Spontaneous Preterm Birth
Cited by: 23
Author(s): Yu‐Chin Lien, Zhe Zhang, Yi C, Erzsébet Polyák, Laura Sillers, Marni J. Falk, Harry Ischiropoulos, Samuel Parry, Rebecca A. Simmons
Software Mentions: 1
Published: over 5 years ago

10.1128/mSystems.00024-16

Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre
Cited by: 283
Author(s): Jessica A. Bryant, Tara M. Clemente, Donn A. Viviani, Allison A. Fong, Kimberley Anh Thomas, Paul F. Kemp, David M. Karl, Angelicque E. White, Edward F. DeLong
Software Mentions: 1
Published: over 10 years ago

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

Bonuses:

Papers Mentioning DESeq2 9,583