Ecosyste.ms: Papers

10.3389/fonc.2021.644416

An Inflammatory Response-Related Gene Signature Can Impact the Immune Status and Predict the Prognosis of Hepatocellular Carcinoma
Cited by: 62
Author(s): Zhuo Lin, Xu Qian, Dan Miao, Fang Yu
Software Mentions: 16
Published: over 3 years ago

10.3390/jcm10051089

Prediction of Neurologically Intact Survival in Cardiac Arrest Patients without Pre-Hospital Return of Spontaneous Circulation: Machine Learning Approach
Cited by: 4
Author(s): Dong-Woo Seo, Hahn Yi, Hyun‐Jin Bae, Youn-Jung Kim, Cheol Ho Sohn, Won Young Kim, Kyung-Taek Lim, Namkug Kim, Youn-Jung Kim
Software Mentions: 13
Published: over 3 years ago

10.3390/nu12123626

Trajectories of Body Composition during Advanced Aging in Consideration of Diet and Physical Activity: A 20-Year Longitudinal Study
Cited by: 6
Author(s): Alexandra Jungert, Gerrit Eichner, Monika Neuhäuser‐Berthold
Software Mentions: 13
Published: almost 4 years ago

10.3389/fgene.2021.706907

ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram
Cited by: 97
Author(s): Chunhui Gao, Guangchuang Yu, Peng Cai
Software Mentions: 12
Published: about 3 years ago

10.3389/fmicb.2017.01553

Effect of Pre-weaning Diet on the Ruminal Archaeal, Bacterial, and Fungal Communities of Dairy Calves
Cited by: 58
Author(s): Juliana Dias, Marcos Inácio Marcondes, Melline Fontes Noronha, Rafael Tassinari Resende, F. S. Machado, Hilário Cuquetto Mantovani, Kimberly A. Dill‐McFarland, Garret Suen
Software Mentions: 12
Published: over 7 years ago

10.18632/aging.202871

A novel focal adhesion related gene signature for prognostic prediction in hepatocellular carcinoma
Cited by: 4
Author(s): Zhuo Lin, Dan Miao, Xu Qian, Xiaodong Wang, Fang Yu
Software Mentions: 12
Published: over 3 years ago

10.1038/s41598-021-86396-8

Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
Cited by: 15
Author(s): Miriam I. Brandt, Florence Pradillon, Blandine Trouche, Nicolas Henry, Cathy Liautard‐Haag, Marie-Anne Cambon-Bonavita, Valérie Cueff-Gauchard, Patrick Wincker, Caroline Belser, Julie Poulain, Sophie Arnaud‐Haond, Daniela Zeppilli
Software Mentions: 11
Published: over 3 years ago

10.1007/s00394-020-02351-9

Gluten intake and metabolic health: conflicting findings from the UK Biobank
Cited by: 13
Author(s): Inken Behrendt, Mathias Faßhauer, Gerrit Eichner
Software Mentions: 11
Published: over 4 years ago

10.1016/j.dnarep.2021.103158

Damage-Net: A program for DNA repair meta-analysis identifies a network of novel repair genes that facilitate cancer evolution
Cited by: 1
Author(s): Aldo S. Bader, Martin Bushell
Software Mentions: 10
Published: about 3 years ago

10.3389/fgene.2020.576566

Systematic Profiling of Immune Risk Model to Predict Survival and Immunotherapy Response in Head and Neck Squamous Cell Carcinoma
Cited by: 9
Author(s): Xingyu Liu, Jiarui Chen, Wei Lu, Zhao-Yi Zeng, Jiali Li, Xueping Jiang, Yanping Gao, Yan Gong, Qiuji Wu, Conghua Xie
Software Mentions: 9
Published: about 4 years ago

10.3389/fmicb.2020.610269

Zebra Mussel Holobionts Fix and Recycle Nitrogen in Lagoon Sediments
Cited by: 15
Author(s): Ugo Marzocchi, Stefano Bonaglia, Anastasija Zaiko, Grazia Marina Quero, Irma Vybernaite‐Lubiene, Tobia Politi, Aurelija Samuilovienė, Mindaugas Žilius, Marco Bartoli, Ulisse Cardini
Software Mentions: 8
Published: almost 4 years ago

10.3390/ijms22073618

Transcriptome Analyses of Myometrium from Fibroid Patients Reveals Phenotypic Differences Compared to Non-Diseased Myometrium
Cited by: 9
Author(s): Emmanuel N. Paul, Gregory W. Burns, Tyler J. Carpenter, Joshua Grey, Asgerally T. Fazleabas, Jose M. Teixeira
Software Mentions: 8
Published: over 3 years ago

10.1042/BSR20204456

A new m6A methylation-related gene signature for prognostic value in patient with urothelial carcinoma of the bladder
Cited by: 9
Author(s): Bin Zheng, Jianwei Wang, Guiting Zhao, Xiaoxu Chen, Zhongshun Yao, Wei He, Wei He
Software Mentions: 8
Published: over 3 years ago

10.3389/fmicb.2019.02736

Habitat Heterogeneity and Connectivity: Effects on the Planktonic Protist Community Structure at Two Adjacent Coastal Sites (the Lagoon and the Gulf of Venice, Northern Adriatic Sea, Italy) Revealed by Metabarcoding
Cited by: 14
Author(s): Simona Armeli Minicante, Roberta Piredda, Grazia Marina Quero, Stefania Finotto, Fabrizio Bernardi Aubry, Mauro Bastianini, Alessandra Pugnetti, Adriana Zingone
Software Mentions: 8
Published: almost 5 years ago

10.3389/fpls.2021.675760

Genotype-Specific Expression and NLR Repertoire Contribute to Phenotypic Resistance Diversity in Plantago lanceolata
Cited by: 4
Author(s): Pezhman Safdari, Layla Höckerstedt, Mikael Brosché, Jarkko Salojärvi, Anna‐Liisa Laine
Software Mentions: 8
Published: over 3 years ago

10.3389/fmicb.2020.00789

Unraveling the Diversity of Eukaryotic Microplankton in a Large and Deep Perialpine Lake Using a High Throughput Sequencing Approach
Cited by: 18
Author(s): Nico Salmaso, Bruno Adriano, Massimo Pindo
Software Mentions: 7
Published: over 4 years ago

10.1038/srep39527

Synergetic effects of DNA methylation and histone modification during mouse induced pluripotent stem cell generation
Cited by: 13
Author(s): Guiying Wang, Rong Weng, Yuanyuan Lan, Xudong Guo, Qidong Liu, Xiaoqin Liu, Chenqi Lu, Jiuhong Kang
Software Mentions: 7
Published: almost 8 years ago

10.1038/srep19899

Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds
Cited by: 34
Author(s): Pui Yi Yung, Letizia Lo Grasso, Abeed Fatima Mohidin, Enzo Acerbi, Jamie Hinks, Thomas Seviour, Enrico Marsili, Federico M. Lauro
Software Mentions: 7
Published: almost 9 years ago

10.1126/sciadv.aaz5373

Freezing and water availability structure the evolutionary diversity of trees across the Americas
Cited by: 47
Author(s): Rocío Cortés, R. Toby Pennington, Tim R. Baker, Fernanda Coelho de Souza, Danilo M. Neves, Charles C. Davis, Juan J. Armestó, Ary Olivera-Filho, Kyle G. Dexter
Software Mentions: 7
Published: over 4 years ago

10.18632/aging.202417

Overexpression of TICRR and PPIF confer poor prognosis in endometrial cancer identified by gene co-expression network analysis
Cited by: 13
Author(s): Linlin Yang, Yunxia Cui, Xiao Sun, Yudong Wang
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0118867

A Deep Catalog of Autosomal Single Nucleotide Variation in the Pig
Cited by: 22
Author(s): Erica Bianco, Bruno Nevado, Sebastián E. Ramos-Onsins, Miguel Pérez‐Enciso
Software Mentions: 6
Published: over 9 years ago

10.3390/microorganisms8101554

HybridMine: A Pipeline for Allele Inheritance and Gene Copy Number Prediction in Hybrid Genomes and Its Application to Industrial Yeasts
Cited by: 6
Author(s): Soukaina Timouma, Jean-Marc Schwartz, Daniela Delneri
Software Mentions: 6
Published: about 4 years ago

10.3389/fonc.2021.631803

Prognostic and Predictive Value of m6A “Eraser” Related Gene Signature in Gastric Cancer
Cited by: 14
Author(s): Xin Xu, Enbo Zhou, Jun Zheng, Chihao Zhang, Yinghua Zou, Jiayun Lin, Jiwei Yu
Software Mentions: 6
Published: over 3 years ago

10.18632/aging.202446

A novel five-lncRNA signature panel improves high-risk survival prediction in patients with cholangiocarcinoma
Cited by: 11
Author(s): Xiaozai Xie, Yi Wang, Sina Zhang, Jialiang Li, Zhengping Yu, Xiwei Ding, Long‐Yun Ye, Peirong Gong, Qing Zhu, Junjian Li, Zi-Yan Chen, Xinfei Yao, Zhifeng Du, Qian Zeng, Hanbin Chen, Zhen Yang, Gang Chen
Software Mentions: 5
Published: almost 4 years ago

10.3390/cells10030693

Voluntary Wheel Running Did Not Alter Gene Expression in 5xfad Mice, but in Wild-Type Animals Exclusively after One-Day of Physical Activity
Cited by: 2
Author(s): Anna Wierczeiko, Lena Gammel, Konstantin Radyushkin, Vu Thu Thuy Nguyen, Hristo Todorov, Susanne Gerber, Kristina Endres
Software Mentions: 5
Published: over 3 years ago

10.3390/diagnostics10090617

microRNA Expression Profile in Single Hormone Receptor-Positive Breast Cancers Is Mainly Dependent on HER2 Status—A Pilot Study
Cited by: 6
Author(s): Michał Kunc, Marta Popęda, Magdalena Niemira, Anna Szałkowska, Michał Bieńkowski, Rafał Pęksa, Aleksandra Łacko, Barbara Radecka, Marcin Braun, Joanna Pikiel, Maria Litwiniuk, Katarzyna Pogoda, Ewa Iżycka‐Świeszewska, Adam Krętowski, Anna Żaczek, Wojciech Biernat, Elżbieta Senkus
Software Mentions: 5
Published: over 4 years ago

10.3389/fpls.2021.621561

Transcriptome Analysis Reveals Photoperiod-Associated Genes Expressed in Rice Anthers
Cited by: 14
Author(s): Shiyu Sun, Duoxiang Wang, Jingbin Li, Yaqi Lei, Gang Li, Wenguo Cai, Xiangxiang Zhao, Wanqi Liang, Dabing Zhang
Software Mentions: 5
Published: over 3 years ago

10.18632/oncotarget.13252

Prognostic and predictive values of CDK1 and MAD2L1 in lung adenocarcinoma
Cited by: 81
Author(s): Yuan-Xiang Shi, Tao Zhu, Ting Zou, Wei Zhuo, Yixin Chen, Ma-Sha Huang, Wei Zheng, Chenjing Wang, Xi Li, Xiao‐Yuan Mao, Wei Zhang, Hong‐Hao Zhou, Ji‐Ye Yin, Zhao‐Qian Liu
Software Mentions: 5
Published: about 8 years ago

10.3390/ani10101764

The Effect of Coconut Oil Addition to Feed of Pigs on Rectal Microbial Diversity and Bacterial Abundance
Cited by: 12
Author(s): Michal Rolinec, Juraj Medo, Michal Gábor, Martina Miluchová, D. Bíro, Milan Šimko, Miroslav Juráček, Ondrej Hanušovský, Zuzana Schubertová, Branislav Gálik
Software Mentions: 4
Published: about 4 years ago

10.3389/fpls.2017.01939

De novo Transcriptome Assembly and Comparison of C3, C3-C4, and C4 Species of Tribe Salsoleae (Chenopodiaceae)
Cited by: 19
Author(s): Maximilian Lauterbach, Hanno Schmidt, Kumari Billakurthi, Thomas Hankeln, Peter Westhoff, Udo Gowik, Gudrun Kadereit
Software Mentions: 4
Published: about 7 years ago

10.3389/fnsyn.2021.660718

Dichotomic Hippocampal Transcriptome After Glutamatergic vs. GABAergic Deletion of the Cannabinoid CB1 Receptor
Cited by: 0
Author(s): Diego Pascual Cuadrado, Anna Wierczeiko, Charlotte Hewel, Susanne Gerber, Beat Lutz
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0248213

De novo identification and targeted sequencing of SSRs efficiently fingerprints Sorghum bicolor sub-population identity
Cited by: 2
Author(s): John P. Baggett, Richard L. Tillett, Elizabeth A. Cooper, Melinda K. Yerka
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pbio.3000891

Interphase-arrested Drosophila embryos activate zygotic gene expression and initiate mid-blastula transition events at a low nuclear-cytoplasmic ratio
Cited by: 19
Author(s): I. Strong, Xianfu Lei, Fang Chen, Kai Yuan, Patrick H. O’Farrell
Software Mentions: 4
Published: about 4 years ago

10.3390/ijms21176060

Sperm Proteome after Interaction with Reproductive Fluids in Porcine: From the Ejaculation to the Fertilization Site
Cited by: 12
Author(s): Chiara Luongo, Leopoldo González-Brusi, Paula Cots-Rodríguez, M. J. Izquierdo-Rico, Manuel A. Bueno Sánchez, Francisco Alberto García–Vázquez
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2019.01713

Comparative Genomics of Marine Sponge-Derived Streptomyces spp. Isolates SM17 and SM18 With Their Closest Terrestrial Relatives Provides Novel Insights Into Environmental Niche Adaptations and Secondary Metabolite Biosynthesis Potential
Cited by: 20
Author(s): Eduardo L. Almeida, Andrés Felipe Carrillo Rincón, Stephen A. Jackson, Alan D. W. Dobson
Software Mentions: 4
Published: over 5 years ago

10.3389/fphys.2021.655059

Transcriptomic and Metabolomic Data Reveal the Key Metabolic Pathways Affecting Streltzoviella insularis (Staudinger) (Lepidoptera: Cossidae) Larvae During Overwintering
Cited by: 5
Author(s): Jiahe Pei, Yecheng Xu, Shixiang Zong, Lili Ren
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pbio.0050057

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs
Cited by: 501
Author(s): Kristin D. Kasschau, Noah Fahlgren, Elisabeth J. Chapman, Christopher Sullivan, Jason S. Cumbie, Scott A. Givan, James C. Carrington
Software Mentions: 3
Published: almost 18 years ago

10.3390/cells9122642

Common Factors in Neurodegeneration: A Meta-Study Revealing Shared Patterns on a Multi-Omics Scale
Cited by: 30
Author(s): Nicolas Ruffini, Susanne Klingenberg, Susann Schweiger, Susanne Gerber
Software Mentions: 3
Published: almost 4 years ago

10.7717/peerj.12059

Distribution and diversity of myxomycetes in Tiantangzhai National Forest Park, China
Cited by: 2
Author(s): Min Li, Gaowei Wang, Yang Gao, Ming-Zhu Dou, Ziqi Wang, Shi Yan, Shuanglin Chen
Software Mentions: 3
Published: about 3 years ago

10.3390/microorganisms8091370

Homogenization of Endosymbiont Communities Hosted by Equatorial Corals during the 2016 Mass Bleaching Event
Cited by: 7
Author(s): Sudhanshi S. Jain, Lutfi Afiq‐Rosli, Bar Feldman, Oren Levy, Jun Wei Phua, Benjamin J. Wainwright, Danwei Huang
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-018-4778-7

Dynamic transcriptome profiling towards understanding the morphogenesis and development of diverse feather in domestic duck
Cited by: 10
Author(s): Jing Yang, Yanhua Qu, Yuan Huang, Fumin Lei
Software Mentions: 3
Published: over 6 years ago

10.1186/s41065-019-0101-0

Integrated identification of key genes and pathways in Alzheimer’s disease via comprehensive bioinformatical analyses
Cited by: 25
Author(s): Tingting Yan, Feng Ding, Yan Zhao
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-83875-w

Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome
Cited by: 15
Author(s): Zhigang Han, Peter S. Thuy‐Boun, Wayne Pfeiffer, Vincent F. Vartabedian, Ali Torkamani, John R. Teijaro, Dennis W. Wolan
Software Mentions: 2
Published: over 3 years ago

10.3389/fvets.2021.633858

Antibiotic Resistance in Agricultural Soil and Crops Associated to the Application of Cow Manure-Derived Amendments From Conventional and Organic Livestock Farms
Cited by: 16
Author(s): Leire Jauregi, Lur Epelde, Itziar Alkorta, Carlos Garbisu
Software Mentions: 2
Published: over 3 years ago