cran: VennDiagram | Projects | Ecosyste.ms: Papers

10.1093/g3journal/jkaa055

Transcriptome analysis of Caenorhabditis elegans lacking heme peroxidase SKPO-1 reveals an altered response to Enterococcus faecalis
Cited by: 4
Author(s): Yi Liu, Daniel Martínez-Martínez, Clara L. Essmann, Melissa R. Cruz, Filipe Cabreiro, Danielle A. Garsin
Software Mentions: 5
Published: almost 4 years ago

10.7717/peerj.6806

Shared genomic outliers across two divergent population clusters of a highly threatened seagrass
Cited by: 25
Author(s): Nikki Leanne Phair, Robert J. Toonen, Ingrid S. Knapp, Sophie von der Heyden
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.6162

Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range
Cited by: 20
Author(s): Dandan Cheng, Zhongsai Tian, Liang Feng, Lin Xu, Hongmei Wang
Software Mentions: 5
Published: almost 6 years ago

10.3389/fonc.2021.663556

Identification of a Three-RNA Binding Proteins (RBPs) Signature Predicting Prognosis for Breast Cancer
Cited by: 14
Author(s): Yang Liu, Hefen Sun, Xuan Li, Qiqi Liu, Yuanyuan Zhao, Liangdong Li, Baojin Xu, Yifeng Hou, Wei Jin
Software Mentions: 5
Published: over 3 years ago

10.1093/bioinformatics/btx364

UpSetR: an R package for the visualization of intersecting sets and their properties
Cited by: 1,808
Author(s): Jake R. Conway, Alexander Lex, Nils Gehlenborg
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-020-07180-y

Transcriptome analysis reveals mechanism of early ripening in Kyoho grape with hydrogen peroxide treatment
Cited by: 22
Author(s): Da‐Long Guo, Zhenguang Wang, Mao-Song Pei, Lili Guo, Yi‐He Yu
Software Mentions: 5
Published: about 4 years ago

10.1186/s12889-020-09791-2

Burden of prediabetes, undiagnosed, and poorly or potentially sub-controlled diabetes: Lolland-Falster health study
Cited by: 7
Author(s): Neda Esmailzadeh Bruun-Rasmussen, George Napolitano, Allan Kofoed‐Enevoldsen, Stig E. Bojesen, Christina Ellervik, Knud Rasmussen, Randi Jepsen
Software Mentions: 5
Published: about 4 years ago

10.3389/fgene.2021.707713

Identification of Candidate Blood mRNA Biomarkers in Intracerebral Hemorrhage Using Integrated Microarray and Weighted Gene Co-expression Network Analysis
Cited by: 3
Author(s): Feng Jin, Lei Li, Yuehan Hao, Ling Tang, Yuye Wang, Zhiyi He
Software Mentions: 5
Published: over 3 years ago

10.7717/peerj.9644

Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters
Cited by: 26
Author(s): Giulia M. Marchioro, Bettina Glasl, Aschwin H. Engelen, Ester Á. Serrão, David G. Bourne, Nicole S. Webster, Pedro R. Frade
Software Mentions: 5
Published: over 4 years ago

10.3389/fnins.2021.622640

Integrated Multi-Omic Analyses of the Genomic Modifications by Gut Microbiome-Derived Metabolites of Epicatechin, 5-(4′-Hydroxyphenyl)-γ-Valerolactone, in TNFalpha-Stimulated Primary Human Brain Microvascular Endothelial Cells
Cited by: 13
Author(s): Karla Fabiola Corral-Jara, Saivageethi Nuthikattu, John C. Rutledge, Amparo C. Villablanca, Christine Morand, Hagen Schroeter, Dragan Milenković
Software Mentions: 5
Published: over 3 years ago

10.12688/wellcomeopenres.11253.2

A genomic atlas of human adrenal and gonad development
Cited by: 46
Author(s): Ignacio del Valle, Federica Buonocore, Andrew Duncan, Lin Lin, Martino Barenco, Rahul Parnaik, Sonia Shah, Michael Hubank, Dianne Gerrelli, John C. Achermann
Software Mentions: 5
Published: about 7 years ago

10.1186/s12985-017-0882-6

ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells
Cited by: 49
Author(s): Benxia Hu, Yongxia Huo, Liping Yang, Guijun Chen, Min‐Hua Luo, Jing Yang, Jumin Zhou
Software Mentions: 5
Published: about 7 years ago

10.1186/s10020-021-00345-9

Association of CASC18/miR-20a-3p/TGFB2 ceRNA axis with occult lymph node metastasis in tongue squamous cell carcinoma
Cited by: 5
Author(s): Bo Zhou, Yue Zhou, Ying Liu, Hailin Zhang, Huangxing Mao, Mingjing Peng, Anji Xu, Zan Li, Hui Wang, Haolei Tan, Huayi Ren, Xiao Yan Zhou, Ying Long
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2018.02212

A Class 1 Histone Deacetylase as Major Regulator of Secondary Metabolite Production in Aspergillus nidulans
Cited by: 29
Author(s): Angelo Pidroni, Birgit Faber, Gerald Brosch, Ingo Bauer, Stefan Graessle
Software Mentions: 5
Published: about 6 years ago

10.3389/fmicb.2019.01665

Spatial Environmental Heterogeneity Determines Young Biofilm Assemblages on Microplastics in Baltic Sea Mesocosms
Cited by: 97
Author(s): Katharina Kesy, Sonja Oberbeckmann, Bernd Kreikemeyer, Matthias Labrenz
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-021-07924-4

Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella)
Cited by: 10
Author(s): Yan He, Hongyan Yu, Hongling Zhao, Hua Zhu, Qingjing Zhang, Anqi Wang, Yubang Shen, Xiaoyan Xu, Jiale Li
Software Mentions: 5
Published: over 3 years ago

10.3390/microorganisms7010004

The Microbial Communities of Leaves and Roots Associated with Turtle Grass (Thalassia testudinum) and Manatee Grass (Syringodium filliforme) are Distinct from Seawater and Sediment Communities, but Are Similar between Species and Sampling Sites
Cited by: 41
Author(s): Kelly Ugarelli, Peeter Laas, Ulrich Stingl
Software Mentions: 5
Published: almost 6 years ago

10.3390/microorganisms8040559

Comparative Transcriptomics Reveals Distinct Gene Expressions of a Model Ciliated Protozoan Feeding on Bacteria-Free Medium, Digestible, and Digestion-Resistant Bacteria
Cited by: 9
Author(s): Songbao Zou, Qianqian Zhang, Jun Gong
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2018.00897

Lactobacillus frumenti Facilitates Intestinal Epithelial Barrier Function Maintenance in Early-Weaned Piglets
Cited by: 54
Author(s): Jun Hu, Lingli Chen, Wenyong Zheng, Min Shi, Liu Liu, Chunlin Xie, Xinkai Wang, Youguo Niu, Qiliang Hou, Xichen Xu, Baoyang Xu, Yimei Tang, Shengqian Zhou, Yiqin Yan, Tao Yang, Libao Ma, Xianghua Yan
Software Mentions: 5
Published: over 6 years ago

10.3390/microorganisms9020262

Bacterial Diversity and Community Composition Distribution in Cold-Desert Habitats of Qinghai–Tibet Plateau, China
Cited by: 7
Author(s): Wei Zhang, Ali Bahadur, Wasim Sajjad, Gaosen Zhang, Fahad Nasir, Binglin Zhang, Xiukun Wu, Guangxiu Lu, Tuo Chen
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-018-25015-5

Metabolic systems analysis of LPS induced endothelial dysfunction applied to sepsis patient stratification
Cited by: 22
Author(s): Sarah McGarrity, Ósk Anuforo, Haraldur Halldórsson, Andreas Bergmann, Skarphéđinn Halldórsson, Sirus Palsson, H Henriksen, Pär I. Johansson, Óttar Rolfsson
Software Mentions: 5
Published: over 6 years ago

10.3390/microorganisms9020347

Global Transcriptional Response of Methylorubrum extorquens to Formaldehyde Stress Expands the Role of EfgA and Is Distinct from Antibiotic Translational Inhibition
Cited by: 3
Author(s): Jannell V. Bazurto, Siavash Riazi, Simon D’Alton, Daniel E. Deatherage, Eric L. Bruger, Jeffrey E. Barrick, Christopher J. Marx
Software Mentions: 5
Published: almost 4 years ago

10.1002/ece3.6196

Competition with insectivorous ants as a contributor to low songbird diversity at low elevations in the eastern Himalaya
Cited by: 12
Author(s): K. Supriya, Trevor D. Price, Corrie S. Moreau
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2019.02587

Complementary DNA/RNA-Based Profiling: Characterization of Corrosive Microbial Communities and Their Functional Profiles in an Oil Production Facility
Cited by: 15
Author(s): Silvia J. Salgar-Chaparro, Laura L. Machuca
Software Mentions: 5
Published: about 5 years ago

10.18632/aging.102871

Prognostic value of immune-related genes in the tumor microenvironment of lung adenocarcinoma and lung squamous cell carcinoma
Cited by: 52
Author(s): Yan Qu, Bo Cheng, Ningsheng Shao, Yibin Jia, Qingxu Song, Bingxu Tan, Jianbo Wang
Software Mentions: 5
Published: over 4 years ago

10.1186/s40168-020-00823-y

Most dominant roles of insect gut bacteria: digestion, detoxification, or essential nutrient provision?
Cited by: 128
Author(s): Tianzhong Jing, Fenghui Qi, Zhiying Wang
Software Mentions: 5
Published: over 4 years ago

10.1073/pnas.2110758118

TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia
Cited by: 22
Author(s): Maike Bensberg, Olof Rundquist, Aida Selimović, Cathrine Lagerwall, Mikael Benson, Mika Gustafsson, Hartmut Vogt, Antonio Lentini, Colm E. Nestor
Software Mentions: 5
Published: over 3 years ago

10.1186/s40168-017-0304-4

Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome
Cited by: 145
Author(s): Yunzeng Zhang, Jin Xu, Nadia Riera, Tao Jin, Jinyun Li, Nian Wang
Software Mentions: 5
Published: over 7 years ago

10.3390/cells9061534

Transcriptomic microRNA Profiling of Dendritic Cells in Response to Gut Microbiota-Secreted Vesicles
Cited by: 13
Author(s): Natalia Díaz-Garrido, Sarah Bonnin, Marta Riera, Rosa Gíménez, Josefa Badı́a, Laura Baldomà
Software Mentions: 5
Published: over 4 years ago

10.3390/cells10081923

Overexpression and Activation of αvβ3 Integrin Differentially Affects TGFβ2 Signaling in Human Trabecular Meshwork Cells
Cited by: 11
Author(s): Mark S. Filla, Keith Meyer, Jennifer A. Faralli, Donna M. Peters
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2016.01363

The Willow Microbiome Is Influenced by Soil Petroleum-Hydrocarbon Concentration with Plant Compartment-Specific Effects
Cited by: 46
Author(s): Stacie Tardif, Étienne Yergeau, Julien Tremblay, Pierre Legendre, Lyle G. Whyte, Charles W. Greer
Software Mentions: 5
Published: about 8 years ago

10.3390/insects11090578

The Microbiome of Neotropical Water Striders and Its Potential Role in Codiversification
Cited by: 12
Author(s): Anakena M. Castillo, Kristin Saltonstall, Carlos F. Arias, Karina Chavarria, Luis A. Ramírez‐Camejo, Luis C. Mejía, Luis F. De León
Software Mentions: 5
Published: over 4 years ago

10.3390/cancers12061393

Anti-EGFR Therapy Induces EGF Secretion by Cancer-Associated Fibroblasts to Confer Colorectal Cancer Chemoresistance
Cited by: 37
Author(s): Colleen M. Garvey, Roy Lau, Alyssa Sanchez, Ren Sun, Emma Fong, Michael E. Doche, Oscar Chen, Anthony Jusuf, Heinz‐Josef Lenz, Brent K. Larson, Shannon M. Mumenthaler
Software Mentions: 5
Published: over 4 years ago

10.1186/s12974-017-0834-5

Myeloid C/EBPβ deficiency reshapes microglial gene expression and is protective in experimental autoimmune encephalomyelitis
Cited by: 17
Author(s): Marta Pulido-Salgado, José M. Vidal-Taboada, Gerardo Garcıa-Dıaz Barriga, Joan Serratosa, Tony Valente, Paola Castillo, Jonathan Matalonga, Marco Straccia, Josep M. Canals, Annabel F. Valledor, Carme Solà, Josep Saura
Software Mentions: 5
Published: over 7 years ago

10.3389/fmicb.2020.00571

Composition, Predicted Functions and Co-occurrence Networks of Rhizobacterial Communities Impacting Flowering Desert Events in the Atacama Desert, Chile
Cited by: 17
Author(s): Marcia Astorga-Eló, Qian Zhang, Giovanni Larama, Alexandra Stoll, Michael J. Sadowsky, Milko A. Jorquera
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2021.589160

Gene and Transposable Element Expression Evolution Following Recent and Past Polyploidy Events in Spartina (Poaceae)
Cited by: 9
Author(s): Delphine Giraud, Oscar Lima, Mathieu Rousseau‐Gueutin, Armel Salmon, Malika L. Aïnouche
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2016.01727

Gradual Changes of Gut Microbiota in Weaned Miniature Piglets
Cited by: 123
Author(s): Jun Hu, Yangfan Nie, Jian Wei Chen, Yong Zhang, Zhi‐Chang Wang, Qi-Wen Fan, Xianghua Yan
Software Mentions: 5
Published: about 8 years ago

10.3389/fonc.2019.01212

Stromal-Immune Score-Based Gene Signature: A Prognosis Stratification Tool in Gastric Cancer
Cited by: 114
Author(s): Hao Wang, Xiaosheng Wu, Yiming Chen
Software Mentions: 5
Published: about 5 years ago

10.3390/ijms21176033

Identification of Novel Targets of Knee Osteoarthritis Shared by Cartilage and Synovial Tissue
Cited by: 8
Author(s): Chenshuang Li, Zhong Zheng
Software Mentions: 5
Published: over 4 years ago

10.3390/ijms22020569

Cartilage Targets of Knee Osteoarthritis Shared by Both Genders
Cited by: 8
Author(s): Chenshuang Li, Zhong Zheng
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0208917

The hindgut microbiota of praying mantids is highly variable and includes both prey-associated and host-specific microbes
Cited by: 6
Author(s): Kara Tinker, Elizabeth A. Ottesen
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.10607

PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3
Cited by: 20
Author(s): Ho‐Ryun Chung, Chao Xu, Alisa Fuchs, Andreas Mund, Martin Lange, Hannah Staege, Tobias Schubert, Chuanbing Bian, Ilona Dunkel, Anton Eberharter, Catherine Regnard, Henrike Klinker, David Meierhofer, Luca Cozzuto, Andreas Winterpacht, Luciano Di Croce, Jinrong Min, Hans Will, Sarah Kinkley
Software Mentions: 4
Published: over 8 years ago

10.1186/s12936-021-03918-5

Transcriptome-based analysis of blood samples reveals elevation of DNA damage response, neutrophil degranulation, cancer and neurodegenerative pathways in Plasmodium falciparum patients
Cited by: 1
Author(s): Akua A. Karikari, Wasco Wruck, James Adjaye
Software Mentions: 4
Published: about 3 years ago

10.1186/s12864-021-07712-0

Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (1): specific signatures of stromal, glandular and luminal epithelial cells
Cited by: 8
Author(s): Wiruntita Chankeaw, Sandra Lignier, Christophe Richard, Theodoros Ntallaris, Mariam Raliou, Yongkang Guo, Damien Plassard, Claudia Bevilacqua, Olivier Sandra, Göran Andersson, P. Humblot, Gilles Charpigny
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-017-4183-7

Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana
Cited by: 49
Author(s): Xiaoning Zhang, Yi-Fei Shi, Jordan J. Powers, Niraj Gowda, Chong Zhang, Heba M. M. Ibrahim, Hannah B. Ball, Samuel Chen, Hua Lu, Stephen M. Mount
Software Mentions: 4
Published: about 7 years ago

10.3389/fpls.2012.00202

A High-Throughput Method for Illumina RNA-Seq Library Preparation
Cited by: 134
Author(s): Ravi Kumar, Yasunori Ichihashi, Seisuke Kimura, Daniel H. Chitwood, Lauren R. Headland, Jie Peng, Julin N. Maloof, Neelima Sinha
Software Mentions: 4
Published: almost 13 years ago

10.3389/fpls.2020.00765

Different Predictors Shape the Diversity Patterns of Epiphytic and Non-epiphytic Liverworts in Montane Forests of Uganda
Cited by: 3
Author(s): Karola Maul, Yu‐Mei Wei, Martin Nebel, Federico Luebert, Boon‐Chuan Ho, Dietmar Quandt, Michael Kessler
Software Mentions: 4
Published: over 4 years ago

10.3390/ijms20061370

Transcriptomic Impact of IMA-08401, a Novel AHR Agonist Resembling Laquinimod, on Rat Liver
Cited by: 3
Author(s): Stephenie D. Prokopec, Raimo Pohjanvirta, Selma Mahiout, Lars Pettersson, Paul C. Boutros
Software Mentions: 4
Published: over 5 years ago

10.1186/s12935-021-01939-3

Identification of an immune-related signature indicating the dedifferentiation of thyroid cells
Cited by: 10
Author(s): Xuemin Wang, Wen Peng, Chunyan Li, Rujia Qin, Zhaoming Zhong, Chuanzheng Sun
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0240037

Changes in root-associated fungal communities in Triticum aestivum ssp. spelta L. and Triticum aestivum ssp. vulgare L. under drought stress and in various soil processing
Cited by: 12
Author(s): Sylwia Salamon, Katarzyna Mikołajczak, Lidia Błaszczyk, Karolina Ratajczak, H. Sulewska
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0154315

VennPainter: A Tool for the Comparison and Identification of Candidate Genes Based on Venn Diagrams
Cited by: 61
Author(s): Guoliang Lin, Jing Chai, Shuo Yuan, Chao Mai, Li Cai, Robert W. Murphy, Wei Zhou, Jing Luo
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2019.01432

Innate Immune Genes Associated With Newcastle Disease Virus Load in Chick Embryos From Inbred and Outbred Lines
Cited by: 9
Author(s): Megan A. Schilling, Sahar Memari, Isabella M. Cattadori, Robab Katani, Amandus P. Muhairwa, Joram Buza, Peter J. Hudson
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0238420

Construction and analysis of a competing endogenous RNA network to reveal potential prognostic biomarkers for Oral Floor Squamous Cell Carcinoma
Cited by: 1
Author(s): Wenjing Zhang, Shuai Xu, Laner Shi, Zhangzhi Zhu, Xinying Xie
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0134168

Comparative Proteomics of Activated THP-1 Cells Infected with Mycobacterium tuberculosis Identifies Putative Clearance Biomarkers for Tuberculosis Treatment
Cited by: 19
Author(s): Benjawan Kaewseekhao, Vivek Naranbhai, Sittiruk Roytrakul, Wises Namwat, Atchara Paemanee, Viraphong Lulitanond, Angkana Chaiprasert, Kiatichai Faksri
Software Mentions: 4
Published: over 9 years ago

10.1534/g3.118.200585

Transcriptomic Plasticity in the Arthropod Generalist Tetranychus urticae Upon Long-Term Acclimation to Different Host Plants
Cited by: 36
Author(s): Simon Snoeck, Nicky Wybouw, Thomas Van Leeuwen, Wannes Dermauw
Software Mentions: 4
Published: about 6 years ago

10.1093/bib/bbw008

A benchmark of gene expression tissue-specificity metrics
Cited by: 231
Author(s): Nadezda Kryuchkova-Mostacci, Marc Robinson‐Rechavi
Software Mentions: 4
Published: almost 9 years ago

10.3389/fmicb.2018.02060

Local Functioning, Landscape Structuring: Drivers of Soil Microbial Community Structure and Function in Peatlands
Cited by: 6
Author(s): Sven Teurlincx, Amber Heijboer, Annelies J. Veraart, George A. Kowalchuk, Steven Declerck
Software Mentions: 4
Published: over 6 years ago

10.3390/jof7050335

Effect of Isolation Conditions on Diversity of Endolichenic Fungal Communities from a Foliose Lichen, Parmotrema tinctorum
Cited by: 10
Author(s): Ji Ho Yang, Seung‐Yoon Oh, Wonyong Kim, Jung-Jae Woo, Hyeonjae Kim, Jae‐Seoun Hur
Software Mentions: 4
Published: over 3 years ago

10.1038/s41388-019-1047-4

Targeting chemoresistant colorectal cancer via systemic administration of a BMP7 variant
Cited by: 23
Author(s): Veronica Veschi, Laura Rosa Mangiapane, Antonietta Nicotra, Simone Di Franco, Emanuela Scavo, Tiziana Apuzzo, Davide Stefano Sardina, Micol Eleonora Fiori, Antonina Benfante, Maria Luisa Colorito, Gianfranco Cocorullo, Felice Giuliante, Calogero Cipolla, Giuseppe Pistone, Maria Rita Bongiorno, Aroldo Rizzo, Courtney M. Tate, Xiaohua Wu, Scott W. Rowlinson, Louis F. Stancato, Matilde Todaro, Ruggero De Maria, Giorgio Stassi
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms21041518

The Molecular Mechanism of Perillaldehyde Inducing Cell Death in Aspergillus flavus by Inhibiting Energy Metabolism Revealed by Transcriptome Sequencing
Cited by: 18
Author(s): Chao Pan, Yongxin Li, Kunlong Yang, Famous Erhunmwunsee, Yan Ma, Xiaona He, Qingru Geng, Man Liu, Jun Tian
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2105-15-91

Differential meta-analysis of RNA-seq data from multiple studies
Cited by: 88
Author(s): Andrea Rau, Guillemette Marot, Florence Jaffrézic
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0208054

Agnostic detection of genomic alterations by holistic DNA structural interrogation
Cited by: 1
Author(s): Ryan K. Shultzaberger, Rachel E. Abrams, Challise J. Sullivan, Anthony Schmitt, T. W. Thompson, John Dresios
Software Mentions: 4
Published: about 6 years ago

10.1186/s13068-015-0248-5

Genome-wide analysis of the endoplasmic reticulum stress response during lignocellulase production in Neurospora crassa
Cited by: 52
Author(s): Fan Feng, Guoli Ma, Jingen Li, Qian Liu, J. Philipp Benz, Chaoguang Tian, Yanhe Ma
Software Mentions: 4
Published: over 9 years ago

10.1128/mBio.02613-19

The Cyclic AMP Receptor Protein Regulates Quorum Sensing and Global Gene Expression in Yersinia pestis during Planktonic Growth and Growth in Biofilms
Cited by: 23
Author(s): Jeremy T. Ritzert, G. Minasov, Ryan B. Embry, Matthew J. Schipma, K.J.F. Satchell
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13068-018-1164-2

Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies
Cited by: 40
Author(s): Anna Alessi, Susannah Bird, Nicola C. Oates, Yang Li, Adam Dowle, E. H. Novotny, Eduardo R. deAzevedo, Joseph P. Bennett, Igor Polikarpov, J. Peter W. Young, Simon J. McQueen‐Mason, Neil C. Bruce
Software Mentions: 4
Published: over 6 years ago

10.1042/BSR20193349

Integrated analysis of DNA methylation and mRNA expression profiles to identify key genes in head and neck squamous cell carcinoma
Cited by: 5
Author(s): Yu Jin, Xing Qin
Software Mentions: 4
Published: almost 5 years ago

10.3389/fimmu.2017.01372

Transcriptome Analysis of Circulating Immune Cell Subsets Highlight the Role of Monocytes in Zaire Ebola Virus Makona Pathogenesis
Cited by: 40
Author(s): Andrea Menicucci, Krista Versteeg, Courtney Woolsey, Chad E. Mire, Joan B. Geisbert, Robert W. Cross, Krystle N. Agans, Allen Jankeel, Thomas W. Geisbert, Ilhem Messaoudi
Software Mentions: 4
Published: about 7 years ago

10.18632/aging.202170

A three-gene signature based on tumour microenvironment predicts overall survival of osteosarcoma in adolescents and young adults
Cited by: 10
Author(s): Chun-Kai Wen, Hongxue Wang, Han Wang, Hao Yuan Mo, Weiying Zhong, Jing Tang, Yuefeng Lu, Wenxian Zhou, Aihua Tan, Yan Liu, Weimin Xie
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pgen.1007357

Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti
Cited by: 48
Author(s): George C. diCenzo, Alex B. Benedict, Marco Fondi, Graham C. Walker, Turlough M. Finan, Alessio Mengoni, Joel S. Griffitts
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pbio.3000849

In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age
Cited by: 203
Author(s): Nicole A P Lieberman, Vikas Peddu, Hong Xie, Lasata Shrestha, Meei Li Huang, Megan Mears, Maria N.B. Cajimat, Dennis A. Bente, Pei Yong Shi, Francesca T. Bovier, Pavitra Roychoudhury, Keith R. Jerome, Anne Moscona, Matteo Porotto, Alexander L. Greninger
Software Mentions: 4
Published: about 4 years ago

10.3389/fonc.2020.574977

Serum RNA Profiling in the 10-Years Period Prior to Diagnosis of Testicular Germ Cell Tumor
Cited by: 6
Author(s): Joshua Burton, Sinan Uğur Umu, Hilde Langseth, Tom Grotmol, Tom Kristian Grimsrud, Trine B. Haugen, Trine B. Rounge
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2021.701067

Nitrogen Supply and Host-Plant Genotype Modulate the Transcriptomic Profile of Plasmodiophora brassicae
Cited by: 3
Author(s): Kévin Gazengel, Yoann Aigu, Christine Lariagon, Mathilde Humeau, Antoine Gravot, Maria Manzanares-Dauleux, Stéphanie Daval
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-019-5530-7

Gene expression of Hanwoo satellite cell differentiation in longissimus dorsi and semimembranosus
Cited by: 17
Author(s): Sara de las Heras‐Saldana, Ki Yong Chung, Seung Hwan Lee, Cedric Gondro
Software Mentions: 4
Published: almost 6 years ago

10.3389/fonc.2020.615976

Identification of Core Genes and Screening of Potential Targets in Glioblastoma Multiforme by Integrated Bioinformatic Analysis
Cited by: 12
Author(s): Jian Yang, Qian Yang
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-021-07713-z

Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (2): impacts of post-partum negative energy balance on stromal, glandular and luminal epithelial cells
Cited by: 6
Author(s): Wiruntita Chankeaw, Sandra Lignier, Christophe Richard, Theodoros Ntallaris, Mariam Raliou, Yongkang Guo, Damien Plassard, Claudia Bevilacqua, Olivier Sandra, Gerhard Andersson, P. Humblot, Gilles Charpigny
Software Mentions: 4
Published: over 3 years ago

10.1186/s12870-018-1611-z

Phytohormone treatment induces generation of cryptic peptides with antimicrobial activity in the Moss Physcomitrella patens
Cited by: 25
Author(s): Igor Fesenko, Regina Azarkina, Ilya Kirov, Andrei Kniazev, Anna Filippova, Ekaterina N. Grafskaia, В. Н. Лазарев, Victor G. Zgoda, Ivan Butenko, Olga Bukato, Irina Lyapina, Dmitry Nazarenko, S. N. Elansky, Anna Mamaeva, В. Т. Иванов, Vadim M. Govorun
Software Mentions: 4
Published: almost 6 years ago

10.18632/aging.102190

Long non-coding RNA CASC19 is associated with the progression and prognosis of advanced gastric cancer
Cited by: 23
Author(s): Wenjie Wang, Changan Guo, Rui Li, Zipeng Xu, Jianping Yu, Ye Yan, Jun Zhao, Jing Wang, Wen-An Wang, An Zhang, Hongtao Li, Chen Wang, Hongbin Liu
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-84308-4

Elucidating the genetics of grain yield and stress-resilience in bread wheat using a large-scale genome-wide association mapping study with 55,568 lines
Cited by: 11
Author(s): Philomin Juliana, Ravi P. Singh, Jesse Poland, Sandesh Shrestha, Julio Huerta‐Espino, Velu Govindan, Suchismita Mondal, Leonardo Crespo‐Herrera, Uttam Kumar, Arun Kumar Joshi, Thomas Payne, Pradeep Kumar Bhati, Vipin Tomar, Franjel Consolacion, Jaime Amador Campos Serna
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-019-43483-1

Conserved, breed-dependent, and subline-dependent innate immune responses of Fayoumi and Leghorn chicken embryos to Newcastle disease virus infection
Cited by: 6
Author(s): Megan A. Schilling, Sahar Memari, Meredith Cavanaugh, Robab Katani, Melissa S. Deist, Jessica Radzio‐Basu, Susan J. Lamont, Joram Buza, Vivek Kapur
Software Mentions: 4
Published: over 5 years ago

10.3390/molecules21111431

Comparative Transcriptomic Analysis of Grape Berry in Response to Root Restriction during Developmental Stages
Cited by: 20
Author(s): Lu Feng, Qiong Lin, Di Wu, Shiping Wang, Dengliang Wang, Chongde Sun
Software Mentions: 4
Published: about 8 years ago

10.3389/fgene.2020.00478

Bioinformatics Analysis of Prognostic miRNA Signature and Potential Critical Genes in Colon Cancer
Cited by: 25
Author(s): Weigang Chen, Chang Gao, Yong Liu, Ying Wen, Xiaoling Hong, Zunnan Huang
Software Mentions: 4
Published: over 4 years ago

10.3389/fonc.2020.589168

NFATC2 Modulates Radiation Sensitivity in Dermal Fibroblasts From Patients With Severe Side Effects of Radiotherapy
Cited by: 0
Author(s): Joshua Dulong, Clara Kouakou, Yasmina Mesloub, Julie Rorteau, Sandra Moratille, Fabien Chevalier, Tatiana Vinasco-Sandoval, Michèle Martin, Jérôme Lamartine
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-019-42560-9

De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats
Cited by: 22
Author(s): Diana D. Moreno-Santillán, Carlos Machaín-Williams, Georgina Hernández-Montes, Jorge Ortega
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-64514-2

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype
Cited by: 12
Author(s): Sharon A. McGrath‐Morrow, Roland Ndeh, Kathryn A. Helmin, Basil Khuder, Cynthia Rothblum-Oviatt, Joseph M. Collaco, Jonathan H. Wright, Paul A. Reyfman, Howard M. Lederman, Benjamin D. Singer
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-89366-2

Comparative transcriptomics between Drosophila mojavensis and D. arizonae reveals transgressive gene expression and underexpression of spermatogenesis-related genes in hybrid testes
Cited by: 9
Author(s): Cecília Ártico Banho, Vincent Mérel, Thiago Y. Oliveira, Claudia M. A. Carareto, Cristina Vieira
Software Mentions: 4
Published: over 3 years ago

10.3390/microorganisms8121954

The Limits and Avoidance of Biases in Metagenomic Analyses of Human Fecal Microbiota
Cited by: 8
Author(s): Emma Bergsten, Denis Mestivier, Iradj Sobhani
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12866-019-1519-2

Assessment of the impact of different fecal storage protocols on the microbiota diversity and composition: a pilot study
Cited by: 16
Author(s): Shirin Moossavi, Phillip A. Engen, Reza Ghanbari, Stefan J. Green, Ankur Naqib, Faraz Bishehsari, Shahin Merat, Hossein Poustchi, Ali Keshavarzian, Reza Malekzadeh
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2021.658292

Cross-Talk Between Butyric Acid and Gut Microbiota in Ulcerative Colitis Following Fecal Microbiota Transplantation
Cited by: 21
Author(s): Haoming Xu, Honglan Huang, Jing Xu, Jie He, Chong Zhao, Yuling Peng, Hailan Zhao, Wenqi Huang, Chuangyu Cao, Yongjian Zhou, Yuqiang Nie
Software Mentions: 4
Published: over 3 years ago

10.1128/AEM.02470-17

Influence of Pig Farming on the Human Nasal Microbiota: Key Role of Airborne Microbial Communities
Cited by: 59
Author(s): Julia G. Kraemer, Alban Ramette, Suzanne Aebi, Anne Oppliger, Markus Hilty
Software Mentions: 4
Published: over 6 years ago

10.1186/s12865-014-0040-5

Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice
Cited by: 53
Author(s): Victor Greiff, Ulrike Menzel, Ulrike Haessler, Skylar C. Cook, Simon Friedensohn, Tarik A. Khan, Mark Pogson, Ina Hellmann, Sai T. Reddy
Software Mentions: 4
Published: about 10 years ago

10.1038/srep24048

RXR controlled regulatory networks identified in mouse brain counteract deleterious effects of Aβ oligomers
Cited by: 27
Author(s): Kyong Nyon Nam, Anaïs Mounier, Nicholas F. Fitz, Cody M. Wolfe, Jonathan Schug, Iliya Lefterov, Radosveta Koldamova
Software Mentions: 4
Published: over 8 years ago

10.3389/fcell.2021.735307

Transcriptomic Signatures of Airway Epithelium Infected With SARS-CoV-2: A Balance Between Anti-infection and Virus Load
Cited by: 3
Author(s): Lingzhang Meng, Houji Qin, Jingjie Zhao, Siyuan He, Qiuju Wei, Zechen Wang, Jiajia Shen, Suren R. Sooranna, Jian Song
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2021.610823

The Structure of Rhizosphere Fungal Communities of Wild and Domesticated Rice: Changes in Diversity and Co-occurrence Patterns
Cited by: 23
Author(s): Jingjing Chang, Yu Sun, Lei Tian, Ji Li, Shasha Luo, Fahad Nasir, Eiko E. Kuramae, Chunjie Tian
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-017-01032-8

Transcriptomic analysis reveals a previously unknown role for CD8+ T-cells in rVSV-EBOV mediated protection
Cited by: 28
Author(s): Andrea Menicucci, Suhas Sureshchandra, Andrea Marzi, Heinz Feldmann, Ilhem Messaoudi
Software Mentions: 4
Published: over 7 years ago

10.7150/jca.51321

AURKA and FAM83A are prognostic biomarkers and correlated with Tumor-infiltrating Lymphocytes in smoking related Lung Adenocarcinoma
Cited by: 7
Author(s): Mengyu Zhang, Huo Chen, Yingxiao Jiang, Jianyu Liu, Yi-Can Yang, Yunhong Yin, Yi-Qing Qu
Software Mentions: 4
Published: almost 4 years ago

10.1128/MRA.01195-19

GenePiper, a Graphical User Interface Tool for Microbiome Sequence Data Mining
Cited by: 7
Author(s): W. M. Tong, Yuen-Yan Chan
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-14-87

The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus
Cited by: 8
Author(s): Emanuel Heitlinger, Stephen Bridgett, Anna Montazam, Horst Taraschewski, Mark Blaxter
Software Mentions: 4
Published: almost 12 years ago

10.1093/gigascience/giz102

Metabolic responses of rice source and sink organs during recovery from combined drought and heat stress in the field
Cited by: 13
Author(s): Lovely Mae F Lawas, Alexander Erban, Joachim Kopka, S. V. Krishna Jagadish, Ellen Zuther, Dirk K. Hincha
Software Mentions: 4
Published: over 5 years ago

10.3390/ani10010144

Characterization of Anaerobic Rumen Fungal Community Composition in Yak, Tibetan Sheep and Small Tail Han Sheep Grazing on the Qinghai-Tibetan Plateau
Cited by: 16
Author(s): Wei Guo, Weiwei Wang, Sisi Bi, Ruijun Long, Farman Ullah, Muhammad Shafiq, Mi Zhou, Ying Zhang
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2021.643904

Predominant Microbial Colonizers in the Root Endosphere and Rhizosphere of Turfgrass Systems: Pseudomonas veronii, Janthinobacterium lividum, and Pseudogymnoascus spp.
Cited by: 10
Author(s): Qing Xia, Thomas W. Rufty, Wei Shi
Software Mentions: 4
Published: over 3 years ago

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