bioconductor: edgeR | Projects | Ecosyste.ms: Papers

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

10.3389/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

10.3390/ijms19103083

Comprehensive Analysis of MicroRNA–Messenger RNA from White Yak Testis Reveals the Differentially Expressed Molecules Involved in Development and Reproduction
Cited by: 18
Author(s): Quanwei Zhang, Qi Wang, Yong Zhang, Cheng ShuRu, Junjie Hu, Youji Ma, Xingxu Zhao
Software Mentions: 1
Published: almost 8 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/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: almost 5 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

10.3389/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

10.3390/ijms19103170

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

10.3389/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

10.3390/ijms19103180

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

10.3389/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

10.3389/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

10.3390/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

10.3389/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: about 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/fonc.2019.00448

Integrated Bioinformatic Analysis of a Competing Endogenous RNA Network Reveals a Prognostic Signature in Endometrial Cancer
Cited by: 20
Author(s): Leilei Xia, Ye Wang, Meng Qi, Xiaoling Su, Jizi Shen, Jing Wang, Haiwei He, Biwei Wen, Caihong Zhang, Man Xu
Software Mentions: 1
Published: about 7 years ago

10.3389/fonc.2021.587548

A 15-Gene Signature and Prognostic Nomogram for Predicting Overall Survival in Non-Distant Metastatic Oral Tongue Squamous Cell Carcinoma
Cited by: 3
Author(s): Muyuan Liu, Litian Tong, Bin Liang, Xuhong Song, Lingzhu Xie, Hanwei Peng, Dongyang Huang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-51150-8

Depth-dependent transcriptomic response of diatoms during spring bloom in the western subarctic Pacific Ocean
Cited by: 4
Author(s): Shigekatsu Suzuki, Takafumi Kataoka, Tsuyoshi Watanabe, Haruyo Yamaguchi, Akira Kuwata, Masanobu Kawachi
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0124823

Variation in the Ovine Abomasal Lymph Node Transcriptome between Breeds Known to Differ in Resistance to the Gastrointestinal Nematode
Cited by: 15
Author(s): Albin Mostaque Ahmed, Barbara Good, J. P. Hanrahan, Paul A. McGettigan, John A. Browne, Orla M. Keane, Bojlul Bahar, Jai Prakash Mehta, Bryan Markey, Amanda J. Lohan, T. Sweeney
Software Mentions: 1
Published: over 11 years ago

10.3389/fonc.2021.687208

LINC00346 Sponges miR-30c-2-3p to Promote the Development of Lung Adenocarcinoma by Targeting MYBL2 and Regulating CELL CYCLE Signaling Pathway
Cited by: 10
Author(s): Qinying Xu, Zuo-Feng Xu, Kai Zhu, Jinlan Lin, Bo Ye
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pgen.1006772

Pheromone independent unisexual development in Cryptococcus neoformans
Cited by: 27
Author(s): Rachana Gyawali, Youbao Zhao, Jianfeng Lin, Yumeng Fan, Xinping Xu, Srijana Upadhyay, Xiaorong Lin
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0134419

Uncovering the Differential Molecular Basis of Adaptive Diversity in Three Echinochloa Leaf Transcriptomes
Cited by: 25
Author(s): Gyoungju Nah, Ji-Hoon Im, Jin-Won Kim, Hae-Rim Park, Min-Jung Yook, Tae-Jin Yang, Albert J. Fischer, Do-Soon Kim
Software Mentions: 1
Published: about 11 years ago

10.1038/s41598-019-52225-2

The Role and Therapeutic Potential of miRNAs in Colorectal Liver Metastasis
Cited by: 9
Author(s): Smiti Snigdha Sahu, Shatovisha Dey, Sarah C. Nabinger, Guanglong Jiang, Alison Bates, Hiromi Tanaka, Yunlong Liu, Janaiah Kota
Software Mentions: 1
Published: almost 7 years ago

10.3389/fonc.2021.699625

Circular RNA hsa_circ_0007507 May Serve as a Biomarker for the Diagnosis and Prognosis of Gastric Cancer
Cited by: 5
Author(s): Weiwei Zhang, Ming Zheng, Shan Kong, Xian Li, Shuting Meng, Xudong Wang, Feng Wang, Chenxue Tang, Shaoqing Ju
Software Mentions: 1
Published: almost 5 years ago

10.3389/fonc.2021.736620

A Phase II Trial of Adjuvant Durvalumab Following Trimodality Therapy for Locally Advanced Esophageal and Gastroesophageal Junction Adenocarcinoma: A Big Ten Cancer Research Consortium Study
Cited by: 20
Author(s): Hirva Mamdani, Bryan J. Schneider, Susan M. Perkins, Heather N. Burney, Pashtoon Murtaza Kasi, Laith Abushahin, Thomas J. Birdas, Kenneth A. Kesler, Tracy M. Watkins, Sunil Badve, Milan Radovich, Shadia I. Jalal
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0065424

Transcriptional Response of Honey Bee Larvae Infected with the Bacterial Pathogen Paenibacillus larvae
Cited by: 40
Author(s): Robert S. Cornman, Dawn Lopez, Jay D. Evans
Software Mentions: 1
Published: about 13 years ago

10.3389/fonc.2020.581985

Bioinformatic Analysis Identifies Potential Key Genes in the Pathogenesis of Melanoma
Cited by: 9
Author(s): Yanjie Han, Xinxin Li, Jiliang Yan, Chunyan Ma, Xin Wang, Hong Pan, Xiaoli Zheng, Zhen Zhang, Biao Gao, Xin‐Ying Ji
Software Mentions: 1
Published: almost 6 years ago

10.1155/2021/4754454

Propofol Suppresses Microglia Inflammation by Targeting TGM2/NF-κB Signaling
Cited by: 5
Author(s): Yuanyuan Hou, Xi Xiao, Wei Yu, Shijie Qi
Software Mentions: 1
Published: almost 5 years ago

10.3389/fonc.2021.626858

Genome-Wide Analyses of Prognostic and Therapeutic Alternative Splicing Signatures in Bladder Urothelial Carcinoma
Cited by: 1
Author(s): Zhongru Fan, Zhe Zhang, Chiyuan Piao, Zhuona Liu, Ze‐Shu Wang, Chuize Kong
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0062149

Genome-Wide Characterization of Transcriptional Patterns in High and Low Antibody Responders to Rubella Vaccination
Cited by: 29
Author(s): Iana H. Haralambieva, Ann L. Oberg, Inna G. Ovsyannikova, Richard B. Kennedy, Diane E. Grill, Sumit Middha, Brian M. Bot, Vivian W. Wang, Jeremy C. Smith, Robert M. Jacobson, Gregory A. Poland
Software Mentions: 1
Published: over 13 years ago

10.3389/fonc.2020.00850

CircCSPP1 Functions as a ceRNA to Promote Colorectal Carcinoma Cell EMT and Liver Metastasis by Upregulating COL1A1
Cited by: 19
Author(s): Qingyuan Wang, Li Shi, Kui Shi, Bo Yuan, Gang Cao, Chenchen Kong, Jun Fu, Zhongsong Man, Xu Li, Xuanfeng Zhang, Yifei Feng, Xinglu Jiang, Xinhui Zhang, Jun Yan, Xiaohu Wu, Yueming Sun
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-019-53717-x

Differentially Expressed Genes between Carrot Petaloid Cytoplasmic Male Sterile and Maintainer during Floral Development
Cited by: 9
Author(s): Bo Liu, C. Ou, Shumin Chen, Qiongwen Cao, Zhi‐Wei Zhao, Zengjian Miao, Xiaoping Kong, Feiyun Zhuang
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2019.00929

Transcriptome Analysis Reveals That Alfalfa Promotes Rumen Development Through Enhanced Metabolic Processes and Calcium Transduction in Hu Lambs
Cited by: 9
Author(s): Bin Yang, Hongwei Chen, Jiawen Cao, Bo He, Shanshan Wang, Yang Luo, Jiakun Wang
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0197404

Changes in mRNA/protein expression and signaling pathways in in vivo passaged mouse ovarian cancer cells
Cited by: 7
Author(s): Qingchun Cai, Qipeng Fan, Aaron Buechlein, David F. Miller, Kenneth P. Nephew, Sheng Liu, Jun Wan, Yan Xu
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0218574

Co-expression analysis reveals dysregulated miRNAs and miRNA-mRNA interactions in the development of contrast-induced acute kidney injury
Cited by: 9
Author(s): Zhiqing Wang, Weiwei Bao, X. Zou, Ping-Heng Tan, Hao Chen, Cancan Lai, Donglin Liu, Zhen Luo, Mingfang Huang
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0205881

Transcriptomic analysis reveals similarities in genetic activation of detoxification mechanisms resulting from imidacloprid and chlorothalonil exposure
Cited by: 18
Author(s): Justin Clements, Benjamin Sanchez‐Sedillo, Christopher A. Bradfield, Russell L. Groves
Software Mentions: 1
Published: almost 8 years ago

10.1155/2021/8846951

Construction of Potential Gene Expression and Regulation Networks in Prostate Cancer Using Bioinformatics Tools
Cited by: 4
Author(s): Heyu Liu, Lirong Li, Fan Yu, Yaping Lü, Changhong Zhu, Wei Xia
Software Mentions: 1
Published: almost 5 years ago

10.3389/fgene.2020.00494

Quantitative Estimation of Oxidative Stress in Cancer Tissue Cells Through Gene Expression Data Analyses
Cited by: 6
Author(s): Liyang Liu, Haining Cui, Ying Xu
Software Mentions: 1
Published: about 6 years ago

10.3390/nu10111721

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

10.3389/fgene.2020.00534

Novel Insights Into Triple-Negative Breast Cancer Prognosis by Comprehensive Characterization of Aberrant Alternative Splicing
Cited by: 8
Author(s): Shasha Gong, Zhijian Song, David Ethan Spezia-Lindner, Feilong Meng, Tingting Ruan, Guangzhi Ying, Changhong Lai, Qianqian Wu, Yong Liang
Software Mentions: 1
Published: about 6 years ago

10.3389/fgene.2020.00881

SlGID1a Is a Putative Candidate Gene for qtph1.1, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height
Cited by: 4
Author(s): Xiaolin Liu, Wencai Yang, Jing Wang, Ming Yang, Kai Wei, Xiaoyan Liu, Zhengkun Qiu, Tong van Giang, Xiaoxuan Wang, Yanmei Guo, Junming Li, Lei Liu, Jinshuai Shu, Yan Du, Zejun Huang
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0107608

Depletion of the RNA-Binding Protein RBP33 Results in Increased Expression of Silenced RNA Polymerase II Transcripts in Trypanosoma brucei
Cited by: 10
Author(s): Sandra M. Fernández‐Moya, Mark Carrington, Antonio M. Estévez
Software Mentions: 1
Published: almost 12 years ago

10.3389/fendo.2021.687586

Metabolic Syndrome Is Associated With Altered mRNA and miRNA Content in Human Circulating Extracellular Vesicles
Cited by: 3
Author(s): Yongxin Li, Yijun Meng, Xiangyang Zhu, André J. van Wijnen, Alfonso Eirin, Lilach O. Lerman
Software Mentions: 1
Published: about 5 years ago

10.3389/fendo.2016.00165

Muscle Contraction Induces Acute Hydroxymethylation of the Exercise-Responsive Gene Nr4a3
Cited by: 28
Author(s): Pattarawan Pattamaprapanont, Christian Garde, Odile Fabre, Romain Barrès
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-019-55954-6

TopControl: A Tool to Prioritize Candidate Disease-associated Genes based on Topological Network Features
Cited by: 7
Author(s): Maryam Nazarieh, Volkhard Helms
Software Mentions: 1
Published: over 6 years ago

10.3389/fendo.2018.00574

Leptin Selectively Regulates Nutrients Metabolism in Nile Tilapia Fed on High Carbohydrate or High Fat Diet
Cited by: 33
Author(s): Caizhi Liu, Anbang He, Lei Ning, Yuan Luo, Dongliang Li, Meiling Zhang, Liqiao Chen, Zhen‐Yu Du
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41389-018-0089-8

MicroRNA-transcription factor network analysis reveals miRNAs cooperatively suppress RORA in oral squamous cell carcinoma
Cited by: 28
Author(s): Xueqing Zheng, Kejing Wu, Shengjie Liao, Yifan Pan, Yanan Sun, Xinming Chen, Yi Zhang, Sun-Hui Xia, Yaying Hu, Jiali Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0034150

Differential Expression of miRNAs in Colorectal Cancer: Comparison of Paired Tumor Tissue and Adjacent Normal Mucosa Using High-Throughput Sequencing
Cited by: 141
Author(s): Julian Hamfjord, Astrid M. Stangeland, Timothy R. Hughes, Martina L. Skrede, Kjell Magne Tveit, Tone Ikdahl, Elin H. Kure
Software Mentions: 1
Published: over 14 years ago

10.1038/s41598-019-56150-2

Immunity-related genes and signaling pathways under hypoxic stresses in Haliotis diversicolor: a transcriptome analysis
Cited by: 9
Author(s): Yulong Sun, Xin Zhang, Yilei Wang, Robert W. Day, Huanming Yang, Ziping Zhang
Software Mentions: 1
Published: over 6 years ago

10.3389/fendo.2019.00553

Identification of a New Theca/Interstitial Cell-Specific Gene and Its Biological Role in Growth of Mouse Ovarian Follicles at the Gonadotropin-Independent Stage
Cited by: 6
Author(s): Masato Aoyama, Akira Shiraishi, Shin Matsubara, Kazuyuki Horie, Tomohiro Osugi, Toru Kawada, Keiko Yasuda, Honoo Satake
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0094352

MicroRNA Buffering and Altered Variance of Gene Expression in Response to Salmonella Infection
Cited by: 13
Author(s): Hua Bao, Arun Kommadath, Graham Plastow, Christopher K. Tuggle, Le Luo Guan, Paul Stothard
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0224765

Identifying resurrection genes through the differentially expressed genes between Selaginella tamariscina (Beauv.) spring and Selaginella moellendorffii Hieron under drought stress
Cited by: 12
Author(s): Wei Gu, Aqin Zhang, Hongmei Sun, Yuchen Gu, Chao Ji, Rong Tian, Jin‐Ao Duan
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pntd.0004929

The Effects of Ivermectin on Brugia malayi Females In Vitro: A Transcriptomic Approach
Cited by: 21
Author(s): Cristina Ballesteros, Lucienne Tritten, Maeghan O’Neill, Erica Burkman, Weam I. Zaky, Jianguo Xia, Andrew R. Moorhead, Steven A. Williams, Timothy G. Geary
Software Mentions: 1
Published: about 10 years ago

10.1038/s41598-019-56832-x

Dominant Role of the Gut Microbiota in Chemotherapy Induced Neuropathic Pain
Cited by: 59
Author(s): Chandran Ramakrishna, Jose Corleto, Paul Ruegger, Geoffrey D. Logan, Beth B. Peacock, Stacee Mendonca, Shanni Yamaki, Trinka W. Adamson, Richard W. Ermel, David D. McKemy, James Borneman, Edouard M. Cantin
Software Mentions: 1
Published: over 6 years ago

10.3389/fendo.2021.650625

Estrogen Receptor Beta Influences the Inflammatory p65 Cistrome in Colon Cancer Cells
Cited by: 1
Author(s): Rajitha Indukuri, Linnea Hases, Amena Archer, Cecilia Williams
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-56955-1

Transcriptomic changes during TGF-β-mediated differentiation of airway fibroblasts to myofibroblasts
Cited by: 37
Author(s): Erin J. Walker, Déborah Heydet, Timothy Veldre, Reena Ghildyal
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-56844-7

Construction of the gene regulatory network identifies MYC as a transcriptional regulator of SWI/SNF complex
Cited by: 6
Author(s): Srimari Srikanth, Srimathy Ramachandran, Suma Mohan
Software Mentions: 1
Published: over 6 years ago

10.1002/JLB.3A0120-001RRR

Monocytes differentiated into macrophages and dendritic cells in the presence of human IFN-λ3 or IFN-λ4 show distinct phenotypes
Cited by: 7
Author(s): Manjarika De, Anand Bhushan, Sreedhar Chinnaswamy
Software Mentions: 1
Published: over 5 years ago

10.3389/fendo.2021.743155

Identification of mRNA Prognostic Markers for TGCT by Integration of Co-Expression and CeRNA Network
Cited by: 3
Author(s): Fang Zhu, Zhizhong Liu, Qianyin Zhou, Jingyu Fan, Dai Zhou, Xing Liu, Hao Bo, Le Tang, Liqing Fan
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pgen.1002327

MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains
Cited by: 112
Author(s): Hai Hu, Songlin Guo, Xi Jiang, Yanyan Zheng, Ning Fu, Xiaoyu Zhang, Corinna Menzel, Hongyu Liang, Hongyi Yang, Min Zhao, Rong Zeng, Wei Chen, Svante Pääbo, Philipp Khaitovich
Software Mentions: 1
Published: almost 15 years ago

10.1038/s41598-019-57409-4

MicroRNA and mRNA interactions coordinate the immune response in non-lethal heat stressed Litopenaeus vannamei against AHPND-causing Vibrio parahaemolyticus
Cited by: 16
Author(s): Pakpoom Boonchuen, Benedict A. Maralit, Phattarunda Jaree, Anchalee Tassanakajon, Kunlaya Somboonwiwat
Software Mentions: 1
Published: over 6 years ago

10.3389/fncel.2020.566148

Pioglitazone Ameliorates Gentamicin Ototoxicity by Affecting the TLR and STAT Pathways in the Early Postnatal Organ of Corti
Cited by: 3
Author(s): Marijana Sekulic-Jablanovic, Matthew B. Wright, Vesna Petkovic, Daniel Bodmer
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-019-57130-2

B4GALNT1 induces angiogenesis, anchorage independence growth and motility, and promotes tumorigenesis in melanoma by induction of ganglioside GM2/GD2
Cited by: 19
Author(s): Hideki Yoshida, Lisa Koodie, Kari Jacobsen, Ken Hanzawa, Yasuhide Miyamoto, Masato Yamamoto
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-58342-7

Whole-genome and time-course dual RNA-Seq analyses reveal chronic pathogenicity-related gene dynamics in the ginseng rusty root rot pathogen Ilyonectria robusta
Cited by: 17
Author(s): Yiming Guan, Meili Chen, Yingying Ma, Zhenglin Du, Yuan Ni, Li Yu, Jingfa Xiao, Yayu Zhang
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-58643-x

Integrated metabolomic and transcriptomic analyses identify critical genes in eicosapentaenoic acid biosynthesis and metabolism in the sea urchin Strongylocentrotus intermedius
Cited by: 12
Author(s): Heng Wang, Jun Ding, Siyu Ding, Yaqing Chang
Software Mentions: 1
Published: over 6 years ago

10.3389/fcimb.2018.00231

The Stringent Response-Regulated sRNA Transcriptome of Borrelia burgdorferi
Cited by: 20
Author(s): Dan Drecktrah, Laura S. Hall, Philipp Rescheneder, Meghan Lybecker, D. Scott Samuels
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-020-58629-9

Role of the imprinted allele of the Cdkn1c gene in mouse neocortical development
Cited by: 12
Author(s): Yui Imaizumi, Shohei Furutachi, Tomoyuki Watanabe, Hiroaki Miya, Daichi Kawaguchi, Yukiko Gotoh
Software Mentions: 1
Published: over 6 years ago

10.1007/s00239-019-09901-8

Eye Degeneration and Loss of otx5b Expression in the Cavefish Sinocyclocheilus tileihornes
Cited by: 9
Author(s): Zhuo Huang, Tom A. Titus, John H. Postlethwait, Fanwei Meng
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-020-58970-z

Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia
Cited by: 5
Author(s): Toni Grönroos, Artturi Mäkinen, Saara Laukkanen, Juha Mehtonen, Atte Nikkilä, Laura Oksa, Samuli Rounioja, Yanara Marincevic-Zuniga, Jessica Nordlund, Virva Pohjolainen, Timo Paavonen, Merja Heinäniemi, Olli Lohi
Software Mentions: 1
Published: over 6 years ago

10.3389/fcimb.2020.00066

Isoforms of Cathepsin B1 in Neurotropic Schistosomula of Trichobilharzia regenti Differ in Substrate Preferences and a Highly Expressed Catalytically Inactive Paralog Binds Cystatin
Cited by: 3
Author(s): Hana Dvořáková, Roman Leontovyč, Tomáš Macháček, Anthony J. O’Donoghue, Ondřej Šedo, Zbyněk Zdráhal, Charles S. Craik, Conor R. Caffrey, Petr Horák, Libor Mikeš
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1006422

Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis
Cited by: 68
Author(s): Ziwei Li, Shengpeng Wang, Cheng Junfeng, Chunxia Su, Zhong Songxiao, Qi Liu, Yuda Fang, Yao Yu, Hong Liu, Yun Zheng, Binglian Zheng
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1004043

Tomato Yield Heterosis Is Triggered by a Dosage Sensitivity of the Florigen Pathway That Fine-Tunes Shoot Architecture
Cited by: 82
Author(s): Ke Jiang, Katie L. Liberatore, Soon Ju Park, John Paul Alvarez, Zachary B. Lippman
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-020-59610-2

MiR-4435 is an UQCRB-related circulating miRNA in human colorectal cancer
Cited by: 10
Author(s): Ji Won Hong, Jung Min Kim, Jeong Eun Kim, Hee Cho, Dasol Kim, Wankyu Kim, Jisun Oh, Ho Jeong Kwon
Software Mentions: 1
Published: over 6 years ago

10.3389/fcimb.2017.00004

Repurposing Approach Identifies Auranofin with Broad Spectrum Antifungal Activity That Targets Mia40-Erv1 Pathway
Cited by: 64
Author(s): Shankar Thangamani, Matthew C. Maland, Haroon Mohammad, Pete E. Pascuzzi, Larisa Avramova, Carla M. Koehler, Tony R. Hazbun, Mohamed N. Seleem
Software Mentions: 1
Published: over 9 years ago

10.1007/s00109-020-01922-x

Opposite regulation of piRNAs, rRNAs and miRNAs in the blood after subarachnoid hemorrhage
Cited by: 2
Author(s): Rafał Morga, Małgorzata Borczyk, Michał Korostyński, Marcin Piechota, Dżesika Hoinkis, Sławomir Gołda, Tomasz Dziedzic, Agnieszka Słowik, Marek Moskała, Joanna Pera
Software Mentions: 1
Published: about 6 years ago

10.1007/s00109-020-01954-3

Investigating the importance of B cells and antibodies during Trichuris muris infection using the IgMi mouse
Cited by: 4
Author(s): Rinal Sahputra, Erin A. Murphy, Ruth Forman, Iris Mair, Muhammad Zaki Hidayatullah Fadlullah, Ari Waisman, Werner Müller, Kathryn J. Else
Software Mentions: 1
Published: about 6 years ago

10.3389/fcimb.2020.00097

RNA-Seq Revealed a Circular RNA-microRNA-mRNA Regulatory Network in Hantaan Virus Infection
Cited by: 64
Author(s): Shuang Lu, Ni Zhu, Weiwei Guo, Xin Wang, Kaiji Li, Jie Yan, Cuiping Jiang, Han Shi-yu, Hanmin Xiang, Xiaohan Wu, Yuanyuan Liu, Hairong Xiong, Liangjun Chen, Zuojiong Gong, Fan Luo, Wei Hou
Software Mentions: 1
Published: over 6 years ago

10.3389/fcimb.2020.575630

Comparative Transcriptomics of Shiga Toxin-Producing and Commensal Escherichia coli and Cytokine Responses in Colonic Epithelial Cell Culture Infections
Cited by: 2
Author(s): Lisa M. Harrison, David W. Lacher, Mark K. Mammel, Susan R. Leonard
Software Mentions: 1
Published: almost 6 years ago

10.3389/fcimb.2021.662563

Transcriptome Signatures Predict Phenotypic Variations of Candida auris
Cited by: 11
Author(s): Sabrina Jenull, Michael Tscherner, Nataliia D. Kashko, Raju Shivarathri, Anton Stoiber, Manju Chauhan, Andriy Petryshyn, Neeraj Chauhan, Karl Kuchler
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pntd.0005691

Effect of praziquantel on the differential expression of mouse hepatic genes and parasite ATP binding cassette transporter gene family members during Schistosoma mansoni infection
Cited by: 17
Author(s): Melissa C. Sanchez, Katina V. Krasnec, Amalia S. Parra, Christian von Cabanlong, Geoffrey N. Gobert, Boris Umylny, Pauline M. Cupit, Charles Cunningham
Software Mentions: 1
Published: about 9 years ago

10.3389/fcimb.2017.00045

Colistin Resistance in Acinetobacter baumannii MDR-ZJ06 Revealed by a Multiomics Approach
Cited by: 30
Author(s): Xiaoting Hua, Lilin Liu, Youhong Fang, Qiucheng Shi, Xi Li, Qiong Chen, Kezhang Shi, Yan Jiang, Hua Zhou, Yunsong Yu
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pntd.0005527

A third generation vaccine for human visceral leishmaniasis and post kala azar dermal leishmaniasis: First-in-human trial of ChAd63-KH
Cited by: 101
Author(s): Mohamed Osman, Anoop Mistry, Ada Keding, Rhian Gabe, Liz Cook, Sarah Forrester, Rebecca Wiggins, Stefania Di Marco, Stefano Colloca, Loredana Siani, Riccardo Cortese, Deborah F. Smith, Toni Aebischer, Paul M. Kaye, Charles Lacey
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-020-59691-z

Transcriptomic response to soybean meal-based diets as the first formulated feed in juvenile yellow perch (Perca flavescens)
Cited by: 14
Author(s): Megan M. Kemski, Chad A. Rappleye, Konrad Dąbrowski, Richard S. Bruno, Macdonald Wick
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1003834

The Serum Resistome of a Globally Disseminated Multidrug Resistant Uropathogenic Escherichia coli Clone
Cited by: 134
Author(s): Minh-Duy Phan, Kate M. Peters, Sohinee Sarkar, Samuel W. Lukowski, Luke P. Allsopp, Danilo Gomes Moriel, Maud E. S. Achard, Makrina Totsika, Vikki M. Marshall, Mathew Upton, Scott A. Beatson, Mark A. Schembri
Software Mentions: 1
Published: almost 13 years ago

10.3389/fcell.2020.579708

Transcriptome Analysis Reveals the Potential Role of Long Non-coding RNAs in Mammary Gland of Yak During Lactation and Dry Period
Cited by: 6
Author(s): Xiaoyun Wu, Xiaofang Zhou, Lin Xiong, Jie Pei, Xixi Yao, Chunnian Liang, Pengjia Bao, Min Chen, Xian Guo, Ping Yan
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-60351-5

Inner Mongolian Cashmere Goat Secondary Follicle Development Regulation Research Based on mRNA-miRNA Co-analysis
Cited by: 22
Author(s): Wenjing Han, Feng Yang, Zhihong Wu, Fei Guo, Junjie Zhang, Erhan Hai, Fangzheng Shang, Rui Su, Ruijun Wang, Zhiying Wang, Zhihong Liu, Yunlong Zhao, Zhixin Wang, Yanjun Zhang, Jinquan Li
Software Mentions: 1
Published: over 6 years ago

10.3389/fcell.2021.593677

The Cancer-Testis Long Non-coding RNA PCAT6 Facilitates the Malignant Phenotype of Ovarian Cancer by Sponging miR-143-3p
Cited by: 6
Author(s): Xiaofang Tan, Yang Shao, Yue Teng, Siyu Liu, Weijian Li, Lu Xue, Yuepeng Cao, Chongqi Sun, Jinhong Zhang, Jing Han, Xiaoli Wu, Hanzi Xu, Kaipeng Xie
Software Mentions: 1
Published: over 5 years ago

10.3390/nu13020468

Vitamin E Deficiency Disrupts Gene Expression Networks during Zebrafish Development
Cited by: 11
Author(s): Brian Head, Stephen A. Ramsey, Chrissa Kioussi, Robert L. Tanguay, Maret G. Traber
Software Mentions: 1
Published: over 5 years ago

10.3389/fcell.2021.727353

Multiomics Analysis of Neuroblastoma Cells Reveals a Diversity of Malignant Transformations
Cited by: 2
Author(s): Milda Narmontė, Povilas Gibas, Kristina Daniūnaitė, Juozas Gordevičius, Edita Kriukienė
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-020-62111-x

Combined transcriptomic and metabolomic analyses uncover rearranged gene expression and metabolite metabolism in tobacco during cold acclimation
Cited by: 26
Author(s): Jianing Xu, Zheng Chen, Fazhan Wang, Wei Jia, Zicheng Xu
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1008045

Discovery and characterization of variance QTLs in human induced pluripotent stem cells
Cited by: 55
Author(s): Abhishek Sarkar, Po-Yuan Tung, John Blischak, Jonathan E. Burnett, Yang Li, Matthew Stephens, Yoav Gilad
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-62255-w

microRNA and Metabolite Signatures Linked to Early Consequences of Lethal Radiation
Cited by: 11
Author(s): Nabarun Chakraborty, Aarti Gautam, Gregory P. Holmes-Hampton, Vidya P. Kumar, Swapan Kumar Biswas, Raina Kumar, Dana Hamad, George Dimitrov, Ayodele O. Olabisi, Rasha Hammamieh, Sanchita Ghosh
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-62507-9

Genetic and genomic analysis for cocoon yield traits in silkworm
Cited by: 11
Author(s): Shou-Min Fang, Qi Zhou, Qiuhan Yu, Ze Zhang
Software Mentions: 1
Published: over 6 years ago

10.3390/nu12113235

Animal and Cellular Studies Demonstrate Some of the Beneficial Impacts of Herring Milt Hydrolysates on Obesity-Induced Glucose Intolerance and Inflammation
Cited by: 10
Author(s): Rachel Durand, Adia Ouellette, Vanessa P. Houde, Frédéric Guénard, Thibaut Varin, Bruno Marcotte, Geneviève Pilon, Erwann Fraboulet, Marie‐Claude Vohl, André Marette, Laurent Bazinet
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1007511

Velvet domain protein VosA represses the zinc cluster transcription factor SclB regulatory network for Aspergillus nidulans asexual development, oxidative stress response and secondary metabolism
Cited by: 23
Author(s): Karl G. Thieme, Jennifer Gerke, Christoph Sasse, Oliver Valerius, Razieh Karimi, Antje K. Heinrich, Florian Finkernagel, Kristina M. Smith, Helge B. Bode, Michael Freitag, Arthur F. J. Ram, Gerhard H. Braus
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pgen.1007327

Role of duplicate genes in determining the tissue-selectivity of hereditary diseases
Cited by: 31
Author(s): Ruth Barshir, Idan Hekselman, Netta Shemesh, Moran Sharon, Lena Novack, Esti Yeger-Lotem
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1005666

A Cytosine Methytransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen
Cited by: 31
Author(s): Michael C. Chao, Shijia Zhu, Satoshi Kimura, Brigid M. Davis, Eric E. Schadt, Gang Fang, Matthew K. Waldor
Software Mentions: 1
Published: over 10 years ago

10.3389/fcell.2021.704341

NAT10-Mediated N4-Acetylcytidine of RNA Contributes to Post-transcriptional Regulation of Mouse Oocyte Maturation in vitro
Cited by: 11
Author(s): Yuting Xiang, Chuanchuan Zhou, Yanyan Zeng, Qi Guo, Jiana Huang, Taibao Wu, Jiawen Liu, Qiqi Liang, Haitao Zeng, Xiaoyan Liang
Software Mentions: 1
Published: about 5 years ago

10.3389/fcell.2019.00337

mTORC1-Rps15 Axis Contributes to the Mechanisms Underlying Global Translation Reduction During Senescence of Mouse Embryonic Fibroblasts
Cited by: 4
Author(s): Su Wu, Siyao Xu, Ruofei Li, Kecheng Li, Xiaoqin Zhong, Yingying Li, Zhifen Zhou, Yi Liu, Ran Feng, Jianfei Zheng, Zhou Songyang, Feng Liu
Software Mentions: 1
Published: over 6 years ago

10.3389/fcell.2021.713503

Establishment of Mouse Primed Stem Cells by Combination of Activin and LIF Signaling
Cited by: 2
Author(s): Mengyi Wei, Yanglin Chen, Chaoyue Zhao, Zheng Li, Baojiang Wu, Chen Chen, Xihe Li, Siqin Bao
Software Mentions: 1
Published: about 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568