bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2021.615893

Transcriptome Profiling Reveals a Novel Mechanism of Antiviral Immunity Upon Sacbrood Virus Infection in Honey Bee Larvae (Apis cerana)
Cited by: 10
Author(s): Yanjun Guo, Zhengyi Zhang, Mingsheng Zhuang, Liuhao Wang, Kai Li, Jun Yao, Huipeng Yang, Jiaxing Huang, Ya Hao, Ying Fan, Hira Mannan, Jie Wu, Yanping Chen, Jilian Li
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2018.00356

Comparative Genomics of the Baltic Sea Toxic Cyanobacteria Nodularia spumigena UHCC 0039 and Its Response to Varying Salinity
Cited by: 12
Author(s): Jonna Teikari, Songjun Hou, Matti Wahlsten, Wolfgang R. Hess, Kaarina Sivonen
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2017.00180

Critical Issues in Mycobiota Analysis
Cited by: 63
Author(s): Bettina Halwachs, Nandhitha Madhusudhan, Robert Krause, R. Henrik Nilsson, Christine Moissl-Eichinger, Christoph Högenauer, Gerhard G. Thallinger, Gregor Gorkiewicz
Software Mentions: 1
Published: over 9 years ago

10.1002/cam4.2097

Circulating PD‐1 (+) cells may participate in immune evasion in peripheral T‐cell lymphoma and chidamide enhance antitumor activity of PD‐1 (+) cells
Cited by: 10
Author(s): Wei Zhang, Haorui Shen, Yan Zhang, Wei Wang, Shaoxuan Hu, Dongmei Zou, Daobin Zhou
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2016.01545

New Genes Involved in Osmotic Stress Tolerance in Saccharomyces cerevisiae
Cited by: 18
Author(s): Ramón González, Pilar Morales, Jordi Tronchoni, Gustavo Cordero-Bueso, Enrico Vaudano, Manuel Quirós, Maïté Novo, Rafael Torres‐Pérez, Eva Valero
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12935-020-01295-8

Construction of a metastasis-associated ceRNA network reveals a prognostic signature in lung cancer
Cited by: 22
Author(s): Qing Cao, Zewen Dong, Shuzhen Liu, Guoyan An, Bianbian Yan, Lei Lei
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2016.00078

Integrated Translatomics with Proteomics to Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae
Cited by: 31
Author(s): Xiao-Yan Yang, Kui He, Gaofei Du, Xiaohui Wu, Guangchuang Yu, Yunlong Pan, Gong Zhang, Xia Sun, Qing‐Yu He
Software Mentions: 1
Published: over 10 years ago

10.3389/fmicb.2021.651744

Growth on Formic Acid Is Dependent on Intracellular pH Homeostasis for the Thermoacidophilic Methanotroph Methylacidiphilum sp. RTK17.1
Cited by: 11
Author(s): Carlo R. Carere, Kiel Hards, Kathryn Wigley, Luke Carman, Karen M. Houghton, Gregory M. Cook, Matthew B. Stott
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2019.02452

Single-Cell RNA Sequencing of Plant-Associated Bacterial Communities
Cited by: 10
Author(s): Qin Ma, Heike Bücking, Jose L. Gonzalez-Hernandez, Senthil Subramanian
Software Mentions: 1
Published: almost 7 years ago

10.7554/eLife.47262

Sex-specific transcriptomic responses to changes in the nutritional environment
Cited by: 39
Author(s): M. Florencia Camus, Matthew D. W. Piper, Max Reuter
Software Mentions: 1
Published: about 7 years ago

10.3389/fmicb.2017.01266

Long-Term Rock Phosphate Fertilization Impacts the Microbial Communities of Maize Rhizosphere
Cited by: 54
Author(s): Ubiana C. Silva, Julliane Dutra Medeiros, Laura Hora Rios Leite, Daniel Morais, Sara Cuadros-Orellana, Carlos A. S. Oliveira, U. G. de P. Lana, E. A. Gomes, Vera Lúcia dos Santos
Software Mentions: 1
Published: about 9 years ago

10.3389/fmicb.2016.00880

Genetic Manipulation of Competition for Nitrate between Heterotrophic Bacteria and Diatoms
Cited by: 41
Author(s): Rachel E. Diner, Sarah M. Schwenck, John P. McCrow, Hong Zheng, Andrew E. Allen
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2018.00299

Temporal Expression Dynamics of Plant Biomass-Degrading Enzymes by a Synthetic Bacterial Consortium Growing on Sugarcane Bagasse
Cited by: 22
Author(s): Diego Javier Jiménez, Maryam Chaib De Mares, Joana Falcão Salles
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2019.00848

Adaptation of the Human Gut Microbiota Metabolic Network During the First Year After Birth
Cited by: 11
Author(s): Alvaro Fuertes, Sergio Pérez-Burillo, Iñigo Apaolaza, Yvonne Vallès, M. Pilar Francino, José Ángel Rufián-Henares, Francisco J. Planes
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2016.01279

Demethylase Inhibitor Fungicide Resistance in Pyrenophora teres f. sp. teres Associated with Target Site Modification and Inducible Overexpression of Cyp51
Cited by: 55
Author(s): Wesley J. Mair, Wei‐Wei Deng, Jonathan Mullins, Samuel West, Penghao Wang, Naghmeh Besharat, Simon R. Ellwood, Richard P. Oliver, Francisco J. López-Ruiz
Software Mentions: 1
Published: about 10 years ago

10.3389/fmicb.2018.02569

Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems
Cited by: 39
Author(s): Mina Bižić-Ionescu, Danny Ionescu, Hans‐Peter Grossart
Software Mentions: 1
Published: almost 8 years ago

10.3389/fmicb.2015.00631

Changes in gene expression of Prymnesium parvum induced by nitrogen and phosphorus limitation
Cited by: 36
Author(s): Zhenfeng Liu, Amy E. Koid, Ramón Terrado, Victoria Campbell, David A. Caron, Karla B. Heidelberg
Software Mentions: 1
Published: about 11 years ago

10.3389/fmicb.2018.00189

Functional Genomics and Phylogenetic Evidence Suggest Genus-Wide Cobalamin Production by the Globally Distributed Marine Nitrogen Fixer Trichodesmium
Cited by: 10
Author(s): Nathan G. Walworth, Michael D. Lee, Christopher Suffridge, Pingping Qu, Fei-Xue Fu, Mak A. Saito, Eric A. Webb, Sergio A. Sañudo‐Wilhelmy, David A. Hutchins
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2020.539702

Calcineurin Regulates Conidiation, Chlamydospore Formation and Virulence in Fusarium oxysporum f. sp. lycopersici
Cited by: 10
Author(s): Yi-Hsuan Hou, Li-Hang Hsu, Hsuan-Fu Wang, Yu-Hsin Lai, Ying-Lien Chen
Software Mentions: 1
Published: almost 6 years ago

10.3389/fmicb.2019.01622

Molecular Signatures of Non-typeable Haemophilus influenzae Lung Adaptation in Pediatric Chronic Lung Disease
Cited by: 13
Author(s): Ammar Aziz, Derek S. Sarovich, Elizabeth Nosworthy, Jemima Beissbarth, Anne B. Chang, Heidi Smith‐Vaughan, Erin P. Price, Tegan M. Harris
Software Mentions: 1
Published: about 7 years ago

10.3389/fmicb.2018.00752

Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 – A Harmful Bloom Algae
Cited by: 30
Author(s): Mohammad Moniruzzaman, Eric R. Gann, Steven W. Wilhelm
Software Mentions: 1
Published: over 8 years ago

10.1002/cam4.3963

Pivotal factors associated with the immunosuppressive tumor microenvironment and melanoma metastasis
Cited by: 21
Author(s): Chuan Zhang, Dan Dang, Lele Cong, Hongyan Sun, Xianling Cong
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2016.01465

Exploratory Investigation of Bacteroides fragilis Transcriptional Response during In vitro Exposure to Subinhibitory Concentration of Metronidazole
Cited by: 7
Author(s): Michele Cristine Ribeiro de Freitas, Juliana Alves Resende, Alessandra Barbosa Ferreira-Machado, Guadalupe del Rosario Quispe Saji, Ana Tereza Ribeiro de Vasconcelos, Vânia Lúcia da Silva, Marisa Fabiana Nicolás, Cláudio Galuppo Diniz
Software Mentions: 1
Published: almost 10 years ago

10.3389/fmicb.2018.02308

Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells
Cited by: 7
Author(s): Gaofeng Ni, Sebastian Canizales, Elias Broman, Domenico Simone, Viraja R. Palwai, Daniel Lundin, Margarita López-Fernández, Tom Sleutels, Mark Dopson
Software Mentions: 1
Published: almost 8 years ago

10.3389/fmicb.2020.01096

ClpV3 of the H3-Type VI Secretion System (H3-T6SS) Affects Multiple Virulence Factors in Pseudomonas aeruginosa
Cited by: 14
Author(s): Yanqi Li, Lin Chen, Pansong Zhang, Anjali Y. Bhagirath, Kangmin Duan
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2019.02640

Diversity Distribution and Assembly Mechanisms of Planktonic and Benthic Microeukaryote Communities in Intertidal Zones of Southeast Fujian, China
Cited by: 20
Author(s): Jie Kong, Ying Wang, Alan Warren, Bangqin Huang, Ping Sun
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2018.03266

Multi-Method Characterization of the Human Circulating Microbiome
Cited by: 103
Author(s): Emma Whittle, Martin O. Leonard, Rebecca D Harrison, Timothy W. Gant, Daniel Tonge
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2015.01262

Identification of Genetic Modules Mediating the Jekyll and Hyde Interaction of Dinoroseobacter shibae with the Dinoflagellate Prorocentrum minimum
Cited by: 42
Author(s): Hui Wang, Jürgen Tomasch, Victoria Michael, Sabin Bhuju, Michael Jarek, Jörn Petersen, Irene Wagner‐Döbler
Software Mentions: 1
Published: almost 11 years ago

10.7554/eLife.07125

The acinar differentiation determinant PTF1A inhibits initiation of pancreatic ductal adenocarcinoma
Cited by: 117
Author(s): Nathan M. Krah, Jean–Paul De La O, Galvin H. Swift, Chinh Q. Hoang, Spencer G. Willet, Fong Chen Pan, Gabriela M Cash, Mary P. Bronner, Christopher V.E. Wright, Raymond J. MacDonald, L. Charles Murtaugh
Software Mentions: 1
Published: about 11 years ago

10.3389/fimmu.2020.594243

Effects of In Vivo Gluten Challenge on PBMC Gene Expression Profiles in Diet Treated Celiac Disease
Cited by: 4
Author(s): Dawit A. Yohannes, Andrea de Kauwe, Katri Kaukinen, Kalle Kurppa, Markku Mäki, Robert P. Anderson, Sten Linnarsson, Dario Greco, Päivi Saavalainen
Software Mentions: 1
Published: over 5 years ago

10.3389/fimmu.2019.02394

IFN-Lambda 3 Mediates Antiviral Protection Against Porcine Epidemic Diarrhea Virus by Inducing a Distinct Antiviral Transcript Profile in Porcine Intestinal Epithelia
Cited by: 35
Author(s): Liang Li, Mei Xue, Fang Fu, Liang Yin, Li Feng, Pinghuang Liu
Software Mentions: 1
Published: almost 7 years ago

10.3389/fimmu.2018.01372

CD19+CD24hiCD38hi B Cells Are Expanded in Juvenile Dermatomyositis and Exhibit a Pro-Inflammatory Phenotype After Activation Through Toll-Like Receptor 7 and Interferon-α
Cited by: 60
Author(s): Christopher Piper, Meredyth G Ll Wilkinson, Claire T. Deakin, G. Otto, S Dowle, Chantal L. Duurland, Stuart Adams, Emiliano Marasco, Elizabeth C. Rosser, Anna Radziszewska, Rita Carsetti, Yiannis Ioannou, Philip L. Beales, Daniel Kelberman, David Isenberg, Claudia Mauri, Kiran Nistala, Lucy R. Wedderburn
Software Mentions: 1
Published: about 8 years ago

10.7554/eLife.64330

SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung
Cited by: 40
Author(s): Alan E. Mast, Alisa S. Wolberg, David Gailani, Michael R. Garvin, Christiane Alvarez, J Izaak Miller, Bruce J. Aronow, Daniel Jacobson
Software Mentions: 1
Published: over 5 years ago

10.1002/2211-5463.13059

Quantitative comparison of the mRNA content of human iPSC‐derived motor neurons and their extracellular vesicles
Cited by: 4
Author(s): Kentaro Otake, Keiko Adachi-Tominari, Hiroaki Nagai, Masayo Saito, Osamu Sano, Yoshihiko Hirozane, Hidehisa Iwata
Software Mentions: 1
Published: over 5 years ago

10.1096/fj.201701558R

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

10.7554/eLife.51002

Hidden long-range memories of growth and cycle speed correlate cell cycles in lineage trees
Cited by: 18
Author(s): Erika E Kuchen, Nils B. Becker, Nina Claudino, Thomas Höfer
Software Mentions: 1
Published: over 6 years ago

10.12688/f1000research.9094.2

Selective inhibition of ASIC1a confers functional and morphological neuroprotection following traumatic spinal cord injury
Cited by: 6
Author(s): Liam M. Koehn, Natassya M. Noor, Qing Dong, Sing-Yan Er, Lachlan D. Rash, Glenn F. King, Katarzyna M. Dzięgielewska, NR Saunders, Mark D. Habgood
Software Mentions: 1
Published: almost 10 years ago

10.12688/f1000research.3928.2

edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens
Cited by: 68
Author(s): Zhiyin Dai, Julie Sheridan, Linden J. Gearing, Darcy Moore, Shian Su, Sam Wormald, Stephen Wilcox, Liam O’Connor, Ross A. Dickins, Marnie E. Blewitt, Matthew E. Ritchie
Software Mentions: 1
Published: almost 12 years ago

10.1186/s40164-021-00230-5

Blocking siglec-10hi tumor-associated macrophages improves anti-tumor immunity and enhances immunotherapy for hepatocellular carcinoma
Cited by: 26
Author(s): Nan Xiao, Xiao‐Dong Zhu, Kangshuai Li, Yifan Chen, Xuefeng Li, Bin Xu, Ming Lei, Jiejie Xu, Hui–Chuan Sun
Software Mentions: 1
Published: about 5 years ago

10.1093/emph/eow010

Human fibroblasts display a differential focal adhesion phenotype relative to chimpanzee
Cited by: 5
Author(s): Alexander S. Advani, Annie Y. Chen, Courtney C. Babbitt
Software Mentions: 1
Published: over 10 years ago

10.1111/eva.13024

Age‐dependent expression of cancer‐related genes in a long‐lived seabird
Cited by: 4
Author(s): Richard Meitern, Jérôme Fort, Mathieu Giraudeau, Kalev Rattiste, Elin Sild, Tuul Sepp
Software Mentions: 1
Published: about 6 years ago

10.1186/s13227-016-0050-x

Conserved expression of vertebrate microvillar gene homologs in choanocytes of freshwater sponges
Cited by: 42
Author(s): Jesús F. Peña, Alexandre Alié, Daniel J. Richter, Lingyu Wang, Noriko Funayama, Scott Nichols
Software Mentions: 1
Published: about 10 years ago

10.1186/s13227-016-0044-8

HOX gene complement and expression in the planarian Schmidtea mediterranea
Cited by: 73
Author(s): Ko W. Currie, David D. R. Brown, Shujun Zhu, Changjiang Xu, Véronique Voisin, Gary D. Bader, Bret J. Pearson
Software Mentions: 1
Published: over 10 years ago

10.1098/rsob.140024

Sex-biased expression of microRNAs inDrosophila melanogaster
Cited by: 38
Author(s): A. De Marco
Software Mentions: 1
Published: over 12 years ago

10.1002/cam4.719

Transcriptome profiling reveals novel gene expression signatures and regulating transcription factors of <scp>TGF</scp> β ‐induced epithelial‐to‐mesenchymal transition
Cited by: 32
Author(s): Liutao Du, Shota Yamamoto, Brian L. Burnette, Danshang Huang, Kun Gao, Neema Jamshidi, Michael Kuo
Software Mentions: 1
Published: about 10 years ago

10.1155/2020/8591892

Fuzheng Huayu Recipe Prevented and Treated CCl4-Induced Mice Liver Fibrosis through Regulating Polarization and Chemotaxis of Intrahepatic Macrophages via CCL2 and CX3CL1
Cited by: 14
Author(s): Man Zhang, Hongliang Liu, Kai Huang, Yuan Peng, Tao Yue, Changqing Zhao, Xudong Hu, Chenghai Liu
Software Mentions: 1
Published: almost 6 years ago

10.1155/2021/5584099

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

10.1186/s13072-018-0241-x

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

10.1002/cam4.2071

Candidate genes involved in metastasis of colon cancer identified by integrated analysis
Cited by: 24
Author(s): Yiming Zhou, Yiwen Zang, Yi Yang, Jianbin Xiang, Zongyou Chen
Software Mentions: 1
Published: over 7 years ago

10.1186/s13072-015-0013-9

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

10.1289/ehp.1408188

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

10.1186/s12940-017-0288-3

Genome-wide gene by lead exposure interaction analysis identifies UNC5D as a candidate gene for neurodevelopment
Cited by: 18
Author(s): Zhao‐Xi Wang, Birgit Claus Henn, Chaolong Wang, Yongyue Wei, Su Li, Ryan Sun, Han Chen, Peter J. Wagner, Quan Lu, Xihong Lin, Robert O. Wright, David C. Bellinger, Molly L. Kile, Maitreyi Mazumdar, Martha María Téllez‐Rojo, Lourdes Schnaas, David C. Christiani
Software Mentions: 1
Published: about 9 years ago

10.1186/s12940-020-00666-y

Epigenome-wide association study for pesticide (Permethrin and DEET) induced DNA methylation epimutation biomarkers for specific transgenerational disease
Cited by: 12
Author(s): Jennifer L. M. Thorson, Daniel Beck, Millissia Ben Maamar, Eric Nilsson, Michael K. Skinner
Software Mentions: 1
Published: almost 6 years ago

10.1002/cam4.3406

Seven immune‐related genes prognostic power and correlation with tumor‐infiltrating immune cells in hepatocellular carcinoma
Cited by: 22
Author(s): Tiantian Liu, Hao Wu, Jianni Qi, Chengyong Qin, Qing Zhu
Software Mentions: 1
Published: about 6 years ago

10.1093/eep/dvaa022

Effect of concentration and duration of particulate matter exposure on the transcriptome and DNA methylome of bronchial epithelial cells
Cited by: 12
Author(s): Steven K. Huang, Priya Tripathi, Lada A. Koneva, Raymond G. Cavalcante, N. Craig, Anne M. Scruggs, Maureen A. Sartor, Furong Deng, Yahong Chen
Software Mentions: 1
Published: over 5 years ago

10.1093/eep/dvy026

Fatherhood alters gene expression within the MPOA
Cited by: 7
Author(s): Adele M. H. Seelke, Jessica Bond, Trent C Simmons, Nikhil Joshi, Matthew L. Settles, Danielle S. Stolzenberg, Mijke Rhemtulla, Karen L. Bales
Software Mentions: 1
Published: almost 8 years ago

10.1002/ece3.7581

Comparative transcriptomics of albino and warningly‐coloured caterpillars
Cited by: 4
Author(s): Juan A. Galarza
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.64250

Stretch-activated ion channels identified in the touch-sensitive structures of carnivorous Droseraceae plants
Cited by: 40
Author(s): Carl Procko, Swetha E. Murthy, William T Keenan, Seyed Ali Reza Mousavi, Tsegaye Dabi, Adam Coombs, Erik Procko, Lisa Baird, Ardem Patapoutian, Joanne Chory
Software Mentions: 1
Published: over 5 years ago

10.1002/ece3.7889

Transcriptomic response of Daphnia magna to nitrogen‐ or phosphorus‐limited diet
Cited by: 3
Author(s): Zhimeng Xu, Yingdong Li, Meng Li, Hongbin Liu
Software Mentions: 1
Published: about 5 years ago

10.15252/embr.202051660

Plasmodium transcription repressor AP2‐O3 regulates sex‐specific identity of gene expression in female gametocytes
Cited by: 21
Author(s): Zhenkui Li, Huiting Cui, Jiepeng Guan, Cong Liu, Zhengang Yang, Jing Yuan
Software Mentions: 1
Published: over 5 years ago

10.15252/embr.201744853

The dynamic recruitment of <scp>TRBP</scp> to neuronal membranes mediates dendritogenesis during development
Cited by: 22
Author(s): Anna Antoniou, Sharof Khudayberdiev, Agata Idziak, Silvia Bicker, Ralf Jacob, Gerhard Schratt
Software Mentions: 1
Published: over 8 years ago

10.15252/embr.201949942

SMaRT lncRNA controls translation of a G‐quadruplex‐containing mRNA antagonizing the DHX36 helicase
Cited by: 18
Author(s): Julie Martone, Davide Mariani, Tiziana Santini, Adriano Setti, Sama Shamloo, Alessio Colantoni, Francesca Capparelli, Alessandro Paiardini, Dacia Dimartino, Mariangela Morlando, Irene Bozzoni
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.65735

circPTPN12/miR-21–5 p/∆Np63α pathway contributes to human endometrial fibrosis
Cited by: 17
Author(s): Minmin Song, Guangfeng Zhao, Haixiang Sun, Simin Yao, Zhenhua Zhou, Pengju Jiang, Qianwen Wu, Hui Zhu, Huiyan Wang, Chenyan Dai, Jingmei Wang, Ruotian Li, Yun Cao, Haining Lv, Dan Liŭ, Jianwu Dai, Yan Zhou, Yali Hu
Software Mentions: 1
Published: about 5 years ago

10.3390/cancers12092524

Influence of Intratumor Microbiome on Clinical Outcome and Immune Processes in Prostate Cancer
Cited by: 33
Author(s): Jiayan Ma, Aditi Gnanasekar, Abby Lee, Wei Tse Li, Martin Haas, Jessica Wang‐Rodriguez, Eric Y. Chang, Mahadevan Rajasekaran, Weg M. Ongkeko
Software Mentions: 1
Published: about 6 years ago

10.3390/cancers13174412

DHX30 Coordinates Cytoplasmic Translation and Mitochondrial Function Contributing to Cancer Cell Survival
Cited by: 6
Author(s): Bartolomeo Bosco, Annalisa Rossi, Dario Rizzotto, Meriem Hadjer Hamadou, Alessandra Bisio, Sebastiano Giorgetta, Alicia Perzolli, Francesco Bonollo, Angéline Gaucherot, Frédéric Catez, Jean‐Jacques Diaz, Erik Dassi, Alberto Inga
Software Mentions: 1
Published: about 5 years ago

10.3390/cancers12092417

TIM-3 Expression Is Downregulated on Human NK Cells in Response to Cancer Targets in Synergy with Activation
Cited by: 16
Author(s): Tram N. Dao, Sagar M. Utturkar, Nadia A. Lanman, Sandro Matosevic
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0053562

Transcriptomic Analyses of Sexual Dimorphism of the Zebrafish Liver and the Effect of Sex Hormones
Cited by: 57
Author(s): Wei Zheng, Hongyan Xu, Siew Hong Lam, Huaien Luo, R. Krishna Murthy Karuturi, Zhiyuan Gong
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0189051

Reprogramming pancreatic stellate cells via p53 activation: A putative target for pancreatic cancer therapy
Cited by: 30
Author(s): Maya Saison-Ridinger, Kathleen E. DelGiorno, Tejia Zhang, Annabelle Kraus, Randall French, Dawn Jaquish, Crystal Tsui, Galina Erikson, Benjamin T. Spike, Maxim N. Shokhirev, Christopher Liddle, Ruth T. Yu, Michael Downes, Ronald M. Evans, Alan Saghatelian, Andrew M. Lowy, Geoffrey M. Wahl
Software Mentions: 1
Published: almost 9 years ago

10.7554/eLife.46012

CCN1 interlinks integrin and hippo pathway to autoregulate tip cell activity
Cited by: 34
Author(s): Myo-Hyeon Park, Ae kyung Kim, Sarala Manandhar, Su-Young Oh, Gil-Jin Jang, Kang Li, Dongwon Lee, Do Young Hyeon, Sunhee Lee, Hye-Eun Lee, Tae‐Lin Huh, Sang Heon Suh, Daehee Hwang, Kyunghee Byun, Hae-Chul Park, You Mie Lee
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0060668

Identification of Transcriptome SNPs for Assessing Allele-Specific Gene Expression in a Super-Hybrid Rice Xieyou9308
Cited by: 13
Author(s): Rongrong Zhai, Feng Yue, Xiaodeng Zhan, Xihong Shen, Weiming Wu, Ping Yü, Yingxin Zhang, Daibo Chen, Huimin Wang, Zhou Lin, Shifeng Cheng
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0058363

Transcriptomic Events Involved in Melon Mature-Fruit Abscission Comprise the Sequential Induction of Cell-Wall Degrading Genes Coupled to a Stimulation of Endo and Exocytosis
Cited by: 69
Author(s): Jorge Corbacho, F. Romojaro, Jean‐Claude Pech, Alain Latché, M.C. Gómez-Jiménez
Software Mentions: 1
Published: over 13 years ago

10.1002/cam4.4167

A robust signature of immune‐related long non‐coding RNA to predict the prognosis of bladder cancer
Cited by: 10
Author(s): Cong Lai, Zhenyu Wu, Zhuohang Li, Hao Yu, Kuiqing Li, Zhuang Tang, Cheng Liu, Kecheng Xu
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0131153

Global Transcriptome Profiles of 'Meyer' Zoysiagrass in Response to Cold Stress
Cited by: 28
Author(s): Shanjun Wei, Zhenlin Du, Fei Gao, Xiang Ke, Jing Li, Jianxiu Liu, Yijun Zhou
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0177938

Transcriptomic analysis of the response of Pseudomonas fluorescens to epigallocatechin gallate by RNA-seq
Cited by: 20
Author(s): Xiaoxiang Liu, Shen Bimiao, Peng Du, Nan Wang, Jiaxue Wang, Jiànróng Lǐ, Aijun Sun
Software Mentions: 1
Published: over 9 years ago

10.7554/eLife.59469

Adrenergic activation modulates the signal from the Reissner fiber to cerebrospinal fluid-contacting neurons during development
Cited by: 20
Author(s): Yasmine Cantaut-Belarif, Adeline Orts-Del’Immagine, Margot Penru, Guillaume Pézeron, Claire Wyart, Pierre-Luc Bardet
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0132624

Genome-Wide Identification of Differentially Expressed Genes Associated with the High Yielding of Oleoresin in Secondary Xylem of Masson Pine (Pinus massoniana Lamb) by Transcriptomic Analysis
Cited by: 22
Author(s): Qinghua Liu, Zhichun Zhou, Yongcheng Wei, Danyu Shen, Zhong‐Ping Feng, Shanping Hong
Software Mentions: 1
Published: about 11 years ago

10.1098/rsob.200413

Parallel evolution of trehalose production machinery in anhydrobiotic animals via recurrent gene loss and horizontal transfer
Cited by: 14
Author(s): Yuichiro Hara, Reira Shibahara, Koyuki Kondo, Wataru Abe, Takekazu Kunieda
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0234448

Transcriptomic analyses revealed the effect of Funneliformis mosseae on genes expression in Fusarium oxysporum
Cited by: 1
Author(s): Xueqi Zhang, Li Bai, Na Guo, Baiyan Cai
Software Mentions: 1
Published: about 6 years ago

10.1515/med-2020-0190

Identification of four genes associated with cutaneous metastatic melanoma
Cited by: 7
Author(s): Ji Chen, Yuming Li, Kai Yang, Yumei Gao, Yan Sha, Dong Xiao, Xiaohong Liang, Zhongqin Cheng
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0192625

Transcriptome variations among human embryonic stem cell lines are associated with their differentiation propensity
Cited by: 23
Author(s): Chengbo Sun, Jiawen Zhang, Dongmin Zheng, Wang Jian, Huanming Yang, Xi Zhang
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0242159

Variation in intrinsic resistance of pea aphids to parasitoid wasps: A transcriptomic basis
Cited by: 4
Author(s): Ailsa H. C. McLean, Benjamin J. Parker
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0207050

Hypothalamic transcriptome analysis reveals the neuroendocrine mechanisms in controlling broodiness of Muscovy duck (Cairina moschata)
Cited by: 11
Author(s): Pengfei Ye, Min Li, Wang Liao, Kai Ge, Sihua Jin, Cheng Zhang, Xingyong Chen
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0124083

Analyses of the Complete Genome and Gene Expression of Chloroplast of Sweet Potato [Ipomoea batata]
Cited by: 40
Author(s): Yan Ling, Xianjun Lai, Xuedan Li, Changhe Wei, Xuemei Tan, Yizheng Zhang
Software Mentions: 1
Published: over 11 years ago

10.1515/med-2020-0237

Key pathways in prostate cancer with SPOP mutation identified by bioinformatic analysis
Cited by: 2
Author(s): Guanxiong Ding, Jian Sun, Lianhua Jiang, Peng Gao, Qing Zhou, Jianqing Wang, Shijun Tong
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0124421

Global Gene Expression of Kosteletzkya virginica Seedlings Responding to Salt Stress
Cited by: 17
Author(s): Xiaoli Tang, Hongyan Wang, Chunlin Shao, Hongbo Shao
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0172161

Liver X receptor agonist treatment significantly affects phenotype and transcriptome of APOE3 and APOE4 Abca1 haplo-deficient mice
Cited by: 13
Author(s): Alexis Y. Carter, Florent Letronne, Nicholas F. Fitz, Anaïs Mounier, Cody M. Wolfe, Kyong Nyon Nam, Valerie L. Reeves, Hafsa Kamboh, Iliya Lefterov, Radosveta Koldamova
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0248700

Interpretation of the absorbed constituents and pharmacological effect of Spica Schizonepetae extract on non-small cell lung cancer
Cited by: 6
Author(s): Shuai Wang, Xinxin Yang, Wei Wang, Yunkun Zhang, Tianjiao Li, Lin Zhao, Yong-Rui Bao, Xin-He Meng
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.28415

Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions
Cited by: 54
Author(s): Jason A. Morrison, Rebecca McLennan, Lauren A. Wolfe, Madelaine Gogol, Samuel R. Meier, Mary Cathleen McKinney, Jessica M. Teddy, Laura Holmes, Craig L. Semerad, Andrew Box, Hua Li, Kathryn Hall, Anoja Perera, Paul M. Kulesa
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0187973

Profiling analysis of circulating microRNA in peripheral blood of patients with class IV lupus nephritis
Cited by: 46
Author(s): Elkin Navarro Quiroz, Lisandro Pacheco-Lugo, Roberto Navarro-Quiroz, Hernán Lorenzi, Pierine España-Puccini, Yirys Díaz-Olmos, Lisneth Almendrales, Valeria Olave, Henry J. González-Tórres, Anderson Díaz-Pérez, Aída Ortiz Domínguez, Antonio Iglesias, Raúl García, Gustavo Aroca
Software Mentions: 1
Published: almost 9 years ago

10.7554/eLife.50346

Disruption of entire Cables2 locus leads to embryonic lethality by diminished Rps21 gene expression and enhanced p53 pathway
Cited by: 2
Author(s): Tra Thi Huong Dinh, Hiroyoshi Iseki, Seiya Mizuno, Saori Iijima-Mizuno, Yoko Tanimoto, Yoko Daitoku, Kayoko Kato, Yuko Hamada, Ammar Shaker Hamed Hasan, Hayate Suzuki, Katsuyuki Murata, Masafumi Muratani, Masatsugu Ema, Jun-Dal Kim, Junji Ishida, Akiyoshi Fukamizu, Mitsuyasu Kato, Satoru Takahashi, Ken‐ichi Yagami, Valerie Wilson, Ruth M. Arkell, Fumihiro Sugiyama
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0123025

Transcriptome Analysis and Its Application in Identifying Genes Associated with Fruiting Body Development in Basidiomycete Hypsizygus marmoreus
Cited by: 48
Author(s): Jinjing Zhang, Ang Ren, Hui Chen, Mingwen Zhao, Liang Shi, Mingjie Chen, Hong Wang, Zhen Feng
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0139324

Comprehensive Identification of Sexual Dimorphism-Associated Differentially Expressed Genes in Two-Way Factorial Designed RNA-Seq Data on Japanese Quail (Coturnix coturnix japonica)
Cited by: 11
Author(s): Kelsey Caetano-Anollés, Minseok Seo, Sandra L. Rodriguez-Zas, Jae-Don Oh, Jae Yong Han, Kichoon Lee, Tae Sub Park, Sangsu Shin, Jiao Jiao Zhang, Mrinmoy Ghosh, Dong Kee Jeong, Seoae Cho, Heebal Kim, Ki Duk Song, Hak Kyo Lee
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0226599

Genome-wide identification and expression profile of the MADS-box gene family in Erigeron breviscapus
Cited by: 11
Author(s): Wen Tang, Yayi Tu, Xiaoyu Cheng, Lili Zhang, Hengling Meng, Xin Zhao, Wei Zhang, Bin He
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0180600

Genome-wide identification of Hami melon miRNAs with putative roles during fruit development
Cited by: 9
Author(s): Hong Zhang, Lan Yin, Huaisong Wang, Guangzhi Wang, Xiaofeng Ma, Meihua Li, Haibo Wu, Qihua Fu, Yi Zhang, Yi Huiuk
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0112630

High-Throughput Sequencing Approach Uncovers the miRNome of Peritoneal Endometriotic Lesions and Adjacent Healthy Tissues
Cited by: 38
Author(s): Merli Saare, Kadri Rekker, Triin Laisk, Deniss Sõritsa, Anne Mari Roost, Jaak Simm, Agne Velthut-Meikas, Kuelli Samuel, Tauno Metsalu, Helle Karro, Andrei Sõritsa, Andres Salumets, Maire Peters
Software Mentions: 1
Published: almost 12 years ago

10.1515/med-2021-0276

Four long noncoding RNAs act as biomarkers in lung adenocarcinoma
Cited by: 3
Author(s): Zhihui Zhang, Liu Yang, Yujiang Li, Yingxi Wu, Xiang Li, Xu Wu
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0141390

Mantle Branch-Specific RNA Sequences of Moon Scallop Amusium pleuronectes to Identify Shell Color-Associated Genes
Cited by: 9
Author(s): Ronglian Huang, Zhe Zheng, Qingheng Wang, Xiyang Zhao, Yuewen Deng, Yu Jiao, Xiaodong Du
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12935-020-01221-y

A long non-coding RNA LINC00461-dependent mechanism underlying breast cancer invasion and migration via the miR-144-3p/KPNA2 axis
Cited by: 12
Author(s): Qiang Zhang, Xiaoyan Jin, Wei Shi, Xin Chen, Wenyang Pang, Xiang Yu, Linjun Yang
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0211182

Screening of the candidate genes related to low-temperature tolerance of Fenneropenaeus chinensis based on high-throughput transcriptome sequencing
Cited by: 13
Author(s): Xianhong Meng, Lijun Dong, Xiaoli Shi, Xupeng Li, Juan Sui, Kun Luo, Sheng Luan, Baolong Chen, Baoxiang Cao, Jiawang Cao, Jie Kong
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0110712

Genome-Scale Transcriptome Analysis of the Alpine “Glasshouse” Plant Rheum nobile (Polygonaceae) with Special Translucent Bracts
Cited by: 8
Author(s): Lizhong Wang, Haihong Zhou, Han jinsoo, Richard I. Milne, Mingyu Wang, Bingbing Liu
Software Mentions: 1
Published: almost 12 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

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Papers Mentioning edgeR 6,568