cran: ggplot2 | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0199277

Predictive performance of six mortality risk scores and the development of a novel model in a prospective cohort of patients undergoing valve surgery secondary to rheumatic fever
Cited by: 13
Author(s): Omar Asdrúbal Vilca Mejía, Manuel J. Antunes, Maxim Goncharov, Luís Alberto Oliveira Dallan, Elinthon Tavares Veronese, Gisele Aparecida Lapenna, Luiz Augusto Ferreira Lisboa, Carlos Manuel de Almeida Brandão, Jorge P. Zubelli, Flávio Tarasoutchi, Pablo Maria Alberto Pomerantzeff, Fábio Biscegli Jatene
Software Mentions: 13
Published: over 7 years ago

10.1099/mgen.0.000492

Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes
Cited by: 13
Author(s): Chun Shen Lim, Vitina Sozzi, Margaret Littlejohn, Lilly Yuen, Nadia Warner, Brigid Betz‐Stablein, Fabio Luciani, Peter Revill, Chris M. Brown
Software Mentions: 13
Published: about 5 years ago

10.1038/s41598-020-78747-8

Non-invasive assessment of skeletal muscle fibrosis in mice using nuclear magnetic resonance imaging and ultrasound shear wave elastography
Cited by: 6
Author(s): Aurea B. Martins-Bach, Damien Bachasson, E. Araujo, Lucas Soustelle, Paulo Loureiro de Sousa, Y. Fromes, Pierre Carlier
Software Mentions: 13
Published: about 5 years ago

10.1186/s13068-019-1584-7

A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock
Cited by: 14
Author(s): Karel Sedlář, Jan Kolek, Markus Gruber, Katerina Jureckova, Barbora Branská, Gergely Csaba, Maryna Vasylkivska, Ralf Zimmer, Petra Patáková, Ivo Provazník
Software Mentions: 13
Published: over 6 years ago

10.3389/fonc.2020.01767

Ovarian Blood Sampling Identifies Junction Plakoglobin as a Novel Biomarker of Early Ovarian Cancer
Cited by: 6
Author(s): Florian Weiland, Noor A. Lokman, Manuela Klingler‐Hoffmann, Thomas W. Jobling, Andrew N. Stephens, Karin Sundfeldt, Peter Hoffmann, Martin K. Oehler
Software Mentions: 13
Published: over 5 years ago

10.1038/s41598-019-49160-7

Early life determinants induce sustainable changes in the gut microbiome of six-year-old children
Cited by: 27
Author(s): Silvia Gschwendtner, Hani Kang, Elisabeth Thiering, Susanne Kublik, Bärbel U. Foesel, Holger Schulz, Susanne Krauss‐Etschmann, Joachim Heinrich, Anne Schöler, Michael Schloter, Marie Standl
Software Mentions: 13
Published: over 6 years ago

10.3389/fmicb.2021.713523

Dispersal Limitation Plays Stronger Role in the Community Assembly of Fungi Relative to Bacteria in Rhizosphere Across the Arable Area of Medicinal Plant
Cited by: 15
Author(s): Guozhuang Zhang, Guangfei Wei, Fang Wei, Zhongjian Chen, Min He, Shuo Jiao, Yong Wang, Lixin Dong, Shilin Chen
Software Mentions: 13
Published: over 4 years ago

10.1186/s13059-017-1305-0

Splatter: simulation of single-cell RNA sequencing data
Cited by: 575
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 13
Published: over 8 years ago

10.1099/mgen.0.000583

rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data
Cited by: 5
Author(s): Ivan Sserwadda, Gerald Mboowa
Software Mentions: 13
Published: over 4 years ago

10.1002/ece3.6520

Growth and survival of the superorganism: Ant colony macronutrient intake and investment
Cited by: 3
Author(s): Yeisson Gutiérrez, Tung Phung, Harald Mumma, Arden Ambrose‐Winters, Christoph Scherber, Chris R. Smith
Software Mentions: 13
Published: over 5 years ago

10.7554/eLife.57116

shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data
Cited by: 35
Author(s): Kenichi Shimada, John A. Bachman, Jeremy Muhlich, Timothy J. Mitchison
Software Mentions: 13
Published: about 5 years ago

10.1186/s40168-018-0569-2

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes
Cited by: 107
Author(s): Joshua P. Earl, Nithin D. Adappa, Jarosław Król, Archana Bhat, Sergey Balashov, Rachel Ehrlich, James N. Palmer, Alan D. Workman, Mariel Blasetti, Bhaswati Sen, Jocelyn Hammond, Noam A. Cohen, Garth D. Ehrlich, Joshua Chang Mell
Software Mentions: 13
Published: over 7 years ago

10.7554/eLife.50087

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle
Cited by: 58
Author(s): Elias T Friman, Cédric Deluz, Antonio C. A. Meireles-Filho, Subashika Govindan, Vincent Gardeux, Bart Deplancke, David M. Suter
Software Mentions: 13
Published: about 6 years ago

10.18632/oncotarget.6716

Integrative bioinformatic analyses of an oncogenomic profile reveal the biology of endometrial cancer and guide drug discovery
Cited by: 5
Author(s): Henry Sung Ching Wong, Yung‐Shun Juan, Mei-Shin Wu, Yan Feng Zhang, Yi‐Hsiang Hsu, Huang-Hui Chen, Weimin Liu, Wei Chiao Chang
Software Mentions: 13
Published: about 10 years ago

10.3389/fmicb.2020.02033

Plasmid Interactions Can Improve Plasmid Persistence in Bacterial Populations
Cited by: 24
Author(s): João Alves Gama, Rita Zilhão, Francisco Dionísio
Software Mentions: 13
Published: over 5 years ago

10.3389/fonc.2021.678694

A Novel Ferroptosis-Related Pathway for Regulating Immune Checkpoints in Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Su Gao, Hailong Ruan, Jingchong Liu, Yuenan Liu, Di Liu, Junwei Tong, Jian Shi, Hongmei Yang, Tianbo Xu, Xiaoping Zhang
Software Mentions: 13
Published: over 4 years ago

10.1371/journal.pone.0253148

Enhancing monitoring of rewilding progress through wildlife tracking and remote sensing
Cited by: 1
Author(s): Julia Carolina Mata, Robert Buitenwerf, Jens‐Christian Svenning
Software Mentions: 13
Published: over 4 years ago

10.3389/fpls.2021.628439

The History of Lentil (Lens culinaris subsp. culinaris) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace Accessions
Cited by: 19
Author(s): Marta Liber, Isabel Margarida Duarte, Ana-Teresa Maia, Hugo R. Oliveira
Software Mentions: 13
Published: almost 5 years ago

10.1186/s12917-019-1962-1

Network analysis of dairy cattle movement and associations with bovine tuberculosis spread and control in emerging dairy belts of Ethiopia
Cited by: 21
Author(s): Getnet Abie Mekonnen, Gobena Ameni, James Wood, Stefan Berg, Andrew J. K. Conlan
Software Mentions: 13
Published: over 6 years ago

10.3389/fpls.2021.633651

Improving Wheat Yield Prediction Using Secondary Traits and High-Density Phenotyping Under Heat-Stressed Environments
Cited by: 6
Author(s): Mohammad Zillur Rahman, Jared Crain, Atena Haghighattalab, Ravi P. Singh, Jesse Poland
Software Mentions: 13
Published: over 4 years ago

10.1186/s13023-020-01520-7

Identification of risk features for complication in Gaucher’s disease patients: a machine learning analysis of the Spanish registry of Gaucher disease
Cited by: 11
Author(s): Marcio Andrade‐Campos, Laura López de Frutos, Jorge J. Cebolla, Irene Serrano-Gonzalo, Blanca Medrano-Engay, Mercedes Roca-Espiau, Beatriz Gomez-Barrera, Jorge Pérez-Heredia, D. Íñiguez, Pilar Giraldo
Software Mentions: 13
Published: over 5 years ago

10.12688/f1000research.8986.2

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
Cited by: 483
Author(s): Ben J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie, Susan Holmes
Software Mentions: 13
Published: over 9 years ago

10.7554/eLife.54186

Epigenetic inheritance of circadian period in clonal cells
Cited by: 12
Author(s): Yan Li, Yongli Shan, Gokhul Kilaru, Stefano Berto, Guang-Zhong Wang, Kimberly Cox, Seung-Hee Yoo, Shao Nian Yang, Genevieve Konopka, Joseph S. Takahashi
Software Mentions: 13
Published: over 5 years ago

10.3389/fonc.2021.643104

TRIM68, PIKFYVE, and DYNLL2: The Possible Novel Autophagy- and Immunity-Associated Gene Biomarkers for Osteosarcoma Prognosis
Cited by: 10
Author(s): Jie Jiang, Dachang Liu, Guoyong Xu, Tuo Liang, Chaojie Yu, Shijie Liao, Liyi Chen, Shengsheng Huang, Xuhua Sun, Ming Yi, Zide Zhang, Zhaojun Lu, Zequn Wang, Jiarui Chen, Tianyou Chen, Hao Li, Yuanlin Yao, Wu‐Hua Chen, Hao Guo, Chong Liu, Xinli Zhan
Software Mentions: 13
Published: almost 5 years ago

10.1186/s12967-021-02889-0

Pan-cancer characterization of metabolism-related biomarkers identifies potential therapeutic targets
Cited by: 6
Author(s): Guoshu Bi, Yunyi Bian, Jiaqi Liang, Jiacheng Yin, Runmei Li, Mengnan Zhao, Yiwei Huang, Tao Lu, Cheng Zhan, Hong Fan, Qun Wang
Software Mentions: 13
Published: over 4 years ago

10.1038/s42003-021-01842-7

Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer
Cited by: 35
Author(s): Ling Cai, Hongyu Liu, Fang Huang, Junya Fujimoto, Luc Girard, Jun Chen, Yongwen Li, Yu An Zhang, Dhruba Deb, Victor Stastny, Karine Pozo, Christin S. Kuo, Gaoxiang Jia, Chendong Yang, Wei Zou, Adeeb Alomar, Kenneth E. Huffman, Mahboubeh Papari-Zareei, Lin Yang, Benjamin J. Drapkin, Esra A. Akbay, David S. Shames, Ignacio I. Wistuba, Tao Wang, Jane E. Johnson, Guanghua Xiao, Ralph J. DeBerardinis, John D. Minna, Yang Xie, Adi F. Gazdar
Software Mentions: 13
Published: almost 5 years ago

10.1186/s42523-020-0023-1

Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species
Cited by: 31
Author(s): Joan E. Edwards, Sudarshan A. Shetty, Pim van den Berg, Faith Burden, D.A. van Doorn, W.F. Pellikaan, J. Dijkstra, Hauke Smidt
Software Mentions: 13
Published: almost 6 years ago

10.3389/fneur.2020.00539

Longitudinal Effects of Immediate and Delayed Estradiol on Cognitive Performance in a Spatial Maze and Hippocampal Volume in Menopausal Macaques Under an Obesogenic Diet
Cited by: 6
Author(s): Benjamin Zimmerman, Payel Kundu, Zheng Liu, Henryk F. Urbanski, Christopher D. Kroenke, Steven G. Kohama, Cynthia L. Bethea, Jacob Raber
Software Mentions: 13
Published: over 5 years ago

10.1186/s12864-021-07542-0

Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn
Cited by: 8
Author(s): Songlin Guo, Shouxiong Huang, Xi Jiang, Haiyang Hu, Dingding Han, Carlos S. Moreno, Genevieve Fairbrother, David A. Hughes, Mark Stoneking, Philipp Khaitovich
Software Mentions: 13
Published: almost 5 years ago

10.7554/eLife.62587

Selfing is the safest sex for Caenorhabditis tropicalis
Cited by: 30
Author(s): Luke M. Noble, John G Yuen, Lewis Stevens, Nicolas Moya, Riaad Persaud, Marc Moscatelli, Jacqueline L. Jackson, Gaotian Zhang, Rojin Chitrakar, L. Ryan Baugh, Christian Braendle, Erik C. Andersen, Hannah S. Seidel, Matthew V. Rockman
Software Mentions: 13
Published: about 5 years ago

10.1186/s12885-020-07695-3

Comprehensive analysis of prognostic gene signatures based on immune infiltration of ovarian cancer
Cited by: 18
Author(s): Shi-Bai Yan, Jinling Fang, Yongcai Chen, Yong Xie, Siyou Zhang, Xiaohui Zhu, Fang Fěng
Software Mentions: 13
Published: about 5 years ago

10.1002/bjs5.50138

Global variation in anastomosis and end colostomy formation following left‐sided colorectal resection
Cited by: 16
Author(s): GlobalSurg Collaborative
Software Mentions: 13
Published: almost 7 years ago

10.7554/eLife.61980

Metabolomic profiling of rare cell populations isolated by flow cytometry from tissues
Cited by: 43
Author(s): Andrew W. DeVilbiss, Zhiyu Zhao, Misty S. Martin-Sandoval, Jessalyn M. Ubellacker, Alpaslan Tasdogan, Michalis Agathocleous, Thomas P. Mathews, Sean J. Morrison
Software Mentions: 13
Published: about 5 years ago

10.2196/mental.9946

Predicting Caller Type From a Mental Health and Well-Being Helpline: Analysis of Call Log Data
Cited by: 9
Author(s): Alexander Grigorash, Siobhan O’Neill, Raymond Bond, Colette Ramsey, Chérie Armour, Maurice Mulvenna
Software Mentions: 13
Published: over 7 years ago

10.3389/fgene.2020.00620

An Analysis Regarding the Association Between the ISLR Gene and Gastric Carcinogenesis
Cited by: 13
Author(s): Shu Li, Wei Zhao, Manyi Sun
Software Mentions: 13
Published: over 5 years ago

10.1186/s12864-020-07204-7

Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow trout
Cited by: 5
Author(s): Pratima Chapagain, Donald M. Walker, Timothy D. Leeds, Beth M. Cleveland, Mohamed Salem
Software Mentions: 13
Published: about 5 years ago

10.1186/s12864-019-5700-7

RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
Cited by: 14
Author(s): Patrick Perkins, Serina Mazzoni-Putman, Anna N. Stepanova, José M. Alonso, Steffen Heber
Software Mentions: 13
Published: over 6 years ago

10.1002/jgh3.12451

Presence and type of decompensation affects outcomes in autoimmune hepatitis upon treatment with corticosteroids
Cited by: 1
Author(s): Sanchit Sharma, Samagra Agarwal, Kanica Kaushal, Abhinav Anand, Deepak Gunjan, Rajni Yadav, Sanchit Sharma
Software Mentions: 13
Published: about 5 years ago

10.1186/s12859-020-03922-7

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions
Cited by: 3
Author(s): Krutika S. Gaonkar, Fédérico Marini, Komal S. Rathi, Payal Jain, Yuankun Zhu, Nicholas A. Chimicles, Miguel Brown, Ammar S. Naqvi, Bo Zhang, Phillip B. Storm, John M. Maris, Pichai Raman, Adam Resnick, Konstantin Strauch, Jaclyn N. Taroni, Jo Lynne Rokita
Software Mentions: 13
Published: about 5 years ago

10.3389/fmolb.2021.689224

Immune-Related lncRNA Signature for Predicting the Immune Landscape of Head and Neck Squamous Cell Carcinoma
Cited by: 13
Author(s): Yin Ji, Xiaohui Li, Caifeng Lv, Xian He, Xiaoqin Luo, Sen Li, Wenjian Hu
Software Mentions: 13
Published: over 4 years ago

10.3389/fcell.2021.709022

Identification of the Role and Clinical Prognostic Value of Target Genes of m6A RNA Methylation Regulators in Glioma
Cited by: 24
Author(s): Peilin Cong, Tingmei Wu, Xinwei Huang, Huazheng Liang, Xiaofei Gao, Li Tian, Wanrong Li, Aiwen Chen, Hanxi Wan, Mengfan He, Danqing Dai, Zhen Li, Lize Xiong
Software Mentions: 13
Published: over 4 years ago

10.1186/s12939-016-0350-8

Are health care inequalities unfair? A study on public attitudes in 23 countries
Cited by: 25
Author(s): Olaf von dem Knesebeck, Nico Vonneilich, Tae Jun Kim
Software Mentions: 13
Published: almost 10 years ago

10.12688/f1000research.6379.2

regionReport: Interactive reports for region-level and feature-level genomic analyses
Cited by: 2
Author(s): Leonardo Collado‐Torres, Andrew E. Jaffe, Jeffrey T. Leek
Software Mentions: 13
Published: over 9 years ago

10.3389/fimmu.2021.709493

Development of a Novel Immune Infiltration-Based Gene Signature to Predict Prognosis and Immunotherapy Response of Patients With Cervical Cancer
Cited by: 12
Author(s): Sihui Yu, Xi Li, Jiawen Zhang, Sufang Wu
Software Mentions: 13
Published: over 4 years ago

10.3934/mbe.2020007

Development of a tissue augmented Bayesian model for expression quantitative trait loci analysis
Cited by: 1
Author(s): Yonghua Zhuang, Kristen J. Wade, Laura Saba, Katerina Kechris
Software Mentions: 13
Published: about 6 years ago

10.12688/f1000research.8967.2

An end to end workflow for differential gene expression using Affymetrix microarrays
Cited by: 16
Author(s): Bernd Klaus, Stefanie Reisenauer
Software Mentions: 13
Published: over 7 years ago

10.1128/AEM.01225-21

Dynamics of the Human Nasal Microbiota and Staphylococcus aureus CC398 Carriage in Pig Truck Drivers across One Workweek
Cited by: 7
Author(s): Anna Cäcilia Ingham, Tinna Ravnholt Urth, Raphael N. Sieber, Marc Stegger, Sofie Marie Edslev, Øystein Angen, Anders Rhod Larsen
Software Mentions: 13
Published: over 4 years ago

10.3389/fimmu.2021.652677

The Contribution of Serum Complement Component 3 Levels to 90-Day Mortality in Living Donor Liver Transplantation
Cited by: 2
Author(s): Saeko Fukui, Masaaki Hidaka, Shoichi Fukui, Shimpei Morimoto, Takanobu Hara, Akihiko Soyama, Tomohiko Adachi, Hajime Matsushima, Takayuki Tanaka, Mai Fuchigami, Hiroo Hasegawa, Katsunori Yanagihara, Susumu Eguchi
Software Mentions: 13
Published: over 4 years ago

10.1186/s13227-020-0147-0

Elongation during segmentation shows axial variability, low mitotic rates, and synchronized cell cycle domains in the crustacean, Thamnocephalus platyurus
Cited by: 9
Author(s): Savvas J. Constantinou, Nicole Duan, Lisa M. Nagy, Ariel D. Chipman, Terri A. Williams
Software Mentions: 13
Published: about 6 years ago

10.12688/f1000research.19236.3

Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures
Cited by: 11
Author(s): Dharmesh D. Bhuva, Momeneh Foroutan, Yi Xie, Ruqian Lyu, Joseph Cursons, Melissa J. Davis
Software Mentions: 13
Published: over 6 years ago

10.1371/journal.pcbi.1007859

Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease
Cited by: 10
Author(s): Christine Tataru, Maude M. David
Software Mentions: 13
Published: almost 6 years ago

10.7554/eLife.67784

Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe
Cited by: 26
Author(s): Ella Katz, Jiajie Li, Benjamin Jaegle, Haim Ashkenazy, R. Shawn Abrahams, Clement Bagaza, Samuel Holden, Chris J Pires, Ruthie Angelovici, Daniel J. Kliebenstein
Software Mentions: 13
Published: almost 5 years ago

10.1371/journal.pone.0212956

Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation
Cited by: 24
Author(s): Colin Lischik, Leonie Adelmann, Joachim Wittbrodt
Software Mentions: 13
Published: almost 7 years ago

10.1186/s12859-021-04268-4

A comprehensive database for integrated analysis of omics data in autoimmune diseases
Cited by: 10
Author(s): Jordi Martorell-Marugán, Raúl López-Domínguez, Adrián García-Moreno, Daniel Toro-Domínguez, Juan Antonio Villatoro-García, Guillermo Barturen, Adoración Martín-Gómez, Kevin Troulé, Gonzalo Gómez‐López, Fátima Al‐Shahrour, Víctor González‐Rumayor, María Peña‐Chilet, Joaquín Dopazo, Julio Sáez-Rodríguez, Marta E. Alarcón‐Riquelme, Pedro Carmona-Sáez
Software Mentions: 13
Published: over 4 years ago

10.1371/journal.pcbi.1003000

Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq
Cited by: 55
Author(s): Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G. Svärd
Software Mentions: 13
Published: almost 13 years ago

10.1038/s42003-021-02335-3

A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues
Cited by: 9
Author(s): José M. Ranz, Pablo M. González, Bryan D. Clifton, Nestor O. Nazario-Yepiz, Pablo Luis Hernández-Cervantes, María J. Palma-Martínez, Dulce I. Valdivia, Andrés Jiménez-Kaufman, Megan Lu, Therese A. Markow, Cei Abreu‐Goodger
Software Mentions: 13
Published: over 4 years ago

10.18632/aging.202976

Development and validation of epithelial mesenchymal transition-related prognostic model for hepatocellular carcinoma
Cited by: 7
Author(s): Xuequan Wang, Ziming Xing, Huihui Xu, Haihua Yang, Tongjing Xing
Software Mentions: 13
Published: almost 5 years ago

10.1038/s42003-021-01887-8

The impact of locomotion on the brain evolution of squirrels and close relatives
Cited by: 23
Author(s): Ornella Bertrand, Hans P. Püschel, Julia A. Schwab, Mary Silcox, Stephen L. Brusatte
Software Mentions: 13
Published: almost 5 years ago

10.1128/AEM.01096-17

Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data
Cited by: 58
Author(s): Laura M. Carroll, Jasna Kovač, Robert W. Miller, Martin Wiedmann
Software Mentions: 13
Published: over 8 years ago

10.1186/s12859-019-2787-4

flowDiv: a new pipeline for analyzing flow cytometric diversity
Cited by: 9
Author(s): Bruno Wanderley, Daniel Araújo, María Victoria Quiroga, André Megali Amado, Adrião Duarte Dória Neto, Hugo Sarmento, Sebastián Metz, Fernando Unrein
Software Mentions: 13
Published: over 6 years ago

10.1177/0271678X17713901

Modified structural network backbone in the contralesional hemisphere chronically after stroke in rat brain
Cited by: 21
Author(s): Michel R.T. Sinke, Willem M. Otte, Maurits Pa van Meer, Annette van der Toorn, Rick M. Dijkhuizen
Software Mentions: 13
Published: over 8 years ago

10.1371/journal.pone.0178783

Pharmacokinetics of caspofungin acetate to guide optimal dosing in cats
Cited by: 8
Author(s): Jana Leshinsky, Andrew J. McLachlan, David J. R. Foster, Ross Norris, Vanessa R. Barrs
Software Mentions: 13
Published: over 8 years ago

10.3389/fmicb.2021.616013

Distribution of Bacterial Endophytes in the Non-lesion Tissues of Potato and Their Response to Potato Common Scab
Cited by: 7
Author(s): Wencong Shi, Gaoya Su, Mingcong Li, Bing Wang, Runmao Lin, Yang Yu-tian, Tao Wei, Bo Zhou, Zheng Gao
Software Mentions: 13
Published: about 5 years ago

10.3389/fgene.2021.690530

Predicting the Survival and Immune Landscape of Colorectal Cancer Patients Using an Immune-Related lncRNA Pair Model
Cited by: 3
Author(s): Chi Ma, Xin Zhang, Xudong Zhao, Nan Zhang, Sixin Zhou, Yonghui Zhang, Peiyu Li
Software Mentions: 13
Published: over 4 years ago

10.3390/ijms22031075

A Novel Epigenetic Machine Learning Model to Define Risk of Progression for Hepatocellular Carcinoma Patients
Cited by: 7
Author(s): Luca Bedon, Michele Dal Bo, Monica Mossenta, Davide Busato, Giuseppe Toffoli, Maurizio Polano
Software Mentions: 13
Published: about 5 years ago

10.3389/fmicb.2019.00665

Microbial Diversity and Connectivity in Deep-Sea Sediments of the South Atlantic Polar Front
Cited by: 31
Author(s): Gilda Varliero, Christina Bienhold, Florian Schmid, Antje Boetius, Massimiliano Molari
Software Mentions: 13
Published: almost 7 years ago

10.1186/s13073-021-00893-z

Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers
Cited by: 18
Author(s): Alaric W. D’Souza, Manish Boolchandani, Sanket Patel, Gianluca Galazzo, Jarne M. van Hattem, Maris S Arcilla, Damian C. Melles∗, Menno D. de Jong, Constance Schultsz, Gautam Dantas, John Penders
Software Mentions: 13
Published: over 4 years ago

10.3389/fvets.2019.00406

An Epidemiological and Economic Simulation Model to Evaluate Strategies for the Control of Bovine Virus Diarrhea in Germany
Cited by: 17
Author(s): Jörn Gethmann, Carolina Probst, Jason Bassett, Pascal Blunk, Philipp Hövel, Franz Josef Conraths
Software Mentions: 13
Published: about 6 years ago

10.3390/ijms21010019

Use of QSAR Global Models and Molecular Docking for Developing New Inhibitors of c-src Tyrosine Kinase
Cited by: 8
Author(s): Robert Ancuceanu, Bogdan Ionel Tamba, C. Stoicescu, Mihaela Dinu
Software Mentions: 13
Published: about 6 years ago

10.3389/fonc.2021.697948

Development and Validation of a Nomogram and a Comprehensive Prognostic Analysis of an LncRNA-Associated Competitive Endogenous RNA Network Based on Immune-Related Genes for Locally Advanced Rectal Cancer With Neoadjuvant Therapy
Cited by: 2
Author(s): Fang-Ze Wei, Shiwen Mei, Zhijie Wang, Jianan Chen, Huan Shen, Fen Zhao, Juan Li, Tixian Xiao, Qian Liu
Software Mentions: 13
Published: over 4 years ago

10.3390/cancers11010091

The Potential Mechanism of Bufadienolide-Like Chemicals on Breast Cancer via Bioinformatics Analysis
Cited by: 5
Author(s): Yingbo Zhang, Xiaomin Tang, Yuxin Pang, Luqi Huang, Dan Wang, Chao Yuan, Xuan Hu, Liping Qu
Software Mentions: 13
Published: about 7 years ago

10.3389/fvets.2019.00045

Exploring Uncertainty in Canine Cancer Data Sources Through Dasymetric Refinement
Cited by: 5
Author(s): Gianluca Boo, Stefan Leyk, Sara Irina Fabrikant, Ricarda Graf, Andreas Pospischil
Software Mentions: 13
Published: almost 7 years ago

10.1186/s13073-020-00823-5

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients
Cited by: 169
Author(s): Anna C. Aschenbrenner, Maria Mouktaroudi, Benjamin Krämer, Marie Oestreich, Nikolaos Antonakos, Melanie Nuesch-Germano, Konstantina Gkizeli, Lorenzo Bonaguro, Nico Reusch, Kevin Baßler, Maria Saridaki, Rainer Knoll, Tal Pecht, Theodore S. Kapellos, Sarandia Doulou, Charlotte Kröger, Miriam Herbert, Lisa Holsten, Arik Horne, Ioanna Gemünd, Nikoletta Rovina, Shobhit Agrawal, K. Dahm, Martina van Uelft, Anna Drews, Lena Lenkeit, Niklas Bruse, Jelle Gerretsen, Jannik Gierlich, Matthias Becker, Kristian Händler, Michael Kraut, Heidi Theis, Simachew Abebe Mengiste, Elena De Domenico, Jonas Schulte-Schrepping, Lea Seep, Jan Raabe, Christoph Hoffmeister, Michael ToVinh, Verena Keitel, Gereon J Rieke, Valentina Talevi, Dirk Skowasch, N. Ahmad Aziz, Peter Pickkers, Frank L. van de Veerdonk, Mihai G. Netea, Joachim L. Schultze, Matthijs Kox, Monique M.B. Breteler, Jacob Nattermann, Antonia Koutsoukou, Evangelos J. Giamarellos‐Bourboulis, Thomas Ulas
Software Mentions: 13
Published: about 5 years ago

10.3390/ijms21134674

The Inflammasome Adaptor Protein ASC in Mild Cognitive Impairment and Alzheimer’s Disease
Cited by: 37
Author(s): Xavier O. Scott, Marisa E. Stephens, Marie C. Desir, W. Dalton Dietrich, Robert W. Keane, Juan Pablo de Rivero Vaccari
Software Mentions: 13
Published: over 5 years ago

10.1371/journal.pgen.1009291

Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci
Cited by: 30
Author(s): Marisa E. Miller, Eric S. Nazareno, Susan M. Rottschaefer, Jakob Riddle, Daniel A. Pereira, Feng Li, Hoa Nguyen-Phuc, Eva C Henningsen, Antoine Persoons, Diane G. O. Saunders, Eva H. Stukenbrock, Peter N. Dodds, Shahryar F. Kianian, Melania Figueroa
Software Mentions: 13
Published: about 5 years ago

10.1371/journal.pone.0140989

The Increase in Animal Mortality Risk following Exposure to Sparsely Ionizing Radiation Is Not Linear Quadratic with Dose
Cited by: 35
Author(s): Benjamin Haley, Tatjana Paunesku, David J. Grdina, Gayle E. Woloschak
Software Mentions: 13
Published: about 10 years ago

10.1186/s13072-020-00343-x

BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks
Cited by: 29
Author(s): Lőrinc Sándor Pongor, Jacob M. Gross, Roberto Vera Alvarez, Junko Murai, Sang‐Min Jang, Hongliang Zhang, Christophe E. Redon, Haiqing Fu, Shar-yin N. Huang, Bhushan Thakur, Adrian Baris, Leonardo Mariño‐Ramírez, David Landsman, Mirit I. Aladjem, Yves Pommier
Software Mentions: 13
Published: almost 6 years ago

10.3389/fmicb.2021.689262

Monitoring of Antimicrobial Resistance to Aminoglycosides and Macrolides in Campylobacter coli and Campylobacter jejuni From Healthy Livestock in Spain (2002–2018)
Cited by: 9
Author(s): Vicente Lopez-Chavarrias, María Ugarte‐Ruiz, Carmen Bárcena, Adolfo Olarra, María Teresa Antonio García, José Luís Saez, Cristina de Frutos, Tania Serrano, I. Abad Perez, M. Moreno, Lucas Domı́nguez, Julio Álvarez
Software Mentions: 13
Published: over 4 years ago

10.3389/fmicb.2020.02028

Assessment of Inter-Laboratory Variation in the Characterization and Analysis of the Mucosal Microbiota in Crohn’s Disease and Ulcerative Colitis
Cited by: 8
Author(s): Jake C. Szamosi, Jessica D. Forbes, John W. Copeland, Natalie Knox, Shahrokh Shekarriz, Laura Rossi, Morag Graham, Christine Bonner, David S. Guttman, Gary Van Domselaar, Michael G. Surette, Çharles N. Bernstein
Software Mentions: 13
Published: over 5 years ago

10.1186/s13072-020-00380-6

Distinctive epigenomic alterations in NF1-deficient cutaneous and plexiform neurofibromas drive differential MKK/p38 signaling
Cited by: 7
Author(s): Jamie Grit, Benjamin K. Johnson, Patrick S. Dischinger, Curt J. Essenburg, Marie Adams, Stacy Campbell, Kai Pollard, Christine A. Pratilas, Tim Triche, Carrie R. Graveel, Matthew R. Steensma
Software Mentions: 13
Published: about 5 years ago

10.3390/microorganisms9010092

Grapevine Microbiota Reflect Diversity among Compartments and Complex Interactions within and among Root and Shoot Systems
Cited by: 23
Author(s): Joel F. Swift, Megan E. Hall, Zachary N. Harris, Misha T. Kwasniewski, Allison J. Miller
Software Mentions: 13
Published: about 5 years ago

10.1371/journal.pone.0193437

Delineating modern variation from extinct morphology in the fossil record using shells of the Eastern Box Turtle (Terrapene carolina)
Cited by: 8
Author(s): Natasha Vitek
Software Mentions: 13
Published: almost 8 years ago

10.1186/s13073-021-00904-z

An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility
Cited by: 33
Author(s): Liuyang Wang, Thomas J Balmat, Alejandro L. Antonia, Florica J. Constantine, Ricardo Henao, Thomas W. Burke, Andy Ingham, Micah T. McClain, Ephraim L. Tsalik, Emily R Ko, Geoffrey S. Ginsburg, Mark DeLong, Xiling Shen, Christopher W. Woods, Elizabeth R. Hauser, Dennis C. Ko
Software Mentions: 13
Published: over 4 years ago

10.3390/curroncol28040269

Evaluating the Impact of the COVID-19 Pandemic on New Cancer Diagnoses and Oncology Care in Manitoba
Cited by: 14
Author(s): Kathleen Decker, Pascal Lambert, Allison Feely, Oliver Bucher, Julian O. Kim, Pamela Hebbard, Maclean Thiessen, Tunji Fatoye, Marshall Pitz, Rashmi Koul, Piotr Czaykowski
Software Mentions: 13
Published: over 4 years ago

10.1093/gigascience/giz088

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping
Cited by: 5
Author(s): Luis Francisco Hernández Sánchez, Bram Burger, Carlos Horro, Antonio Fabregat, Stefan Johansson, Pål Rasmus Njølstad, Harald Barsnes, Henning Hermjakob, Marc Vaudel
Software Mentions: 12
Published: over 6 years ago

10.3390/microorganisms9071526

Exploring the Individual Bacterial Microbiota of Questing Ixodes ricinus Nymphs
Cited by: 2
Author(s): Aurélien Alafaci, Alexandre Crépin, Sabine Beaubert, Jean‐Marc Berjeaud, Vincent Delafont, Julien Verdon
Software Mentions: 12
Published: over 4 years ago

10.1186/s13073-021-00869-z

Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home
Cited by: 13
Author(s): Quinten R Ducarmon, Elisabeth M. Terveer, Sam Nooij, Michelle N Bloem, Karuna E W Vendrik, Monique A. A. Caljouw, Ingrid M J G Sanders, S.M. van Dorp, M.C. Wong, Romy D. Zwittink, Ed J. Kuijper
Software Mentions: 12
Published: almost 5 years ago

10.3389/fmicb.2019.00697

Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must
Cited by: 28
Author(s): Kimmo Sirén, Sarah S.T. Mak, Chrats Melkonian, Christian Carøe, Jan H. Swiegers, Douwe Molenaar, Ulrich Fischer, M. Thomas P. Gilbert
Software Mentions: 12
Published: almost 7 years ago

10.3389/fgene.2020.00906

Construction and Validation of Novel Diagnostic and Prognostic DNA Methylation Signatures for Hepatocellular Carcinoma
Cited by: 7
Author(s): Ran Li, Liyan Shui, Junling Jia, Chao Wu
Software Mentions: 12
Published: over 5 years ago

10.3389/fgene.2019.01200

Dysregulation of MicroRNA Regulatory Network in Lower Extremities Arterial Disease
Cited by: 22
Author(s): Anna Bogucka‐Kocka, Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Łukasz Komsta, Przemysław Kołodziej, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki
Software Mentions: 12
Published: about 6 years ago

10.3389/fphar.2021.726529

CD3D, GZMK, and KLRB1 Are Potential Markers for Early Diagnosis of Rheumatoid Arthritis, Especially in Anti-Citrullinated Protein Antibody-Negative Patients
Cited by: 8
Author(s): Junqin Lu, Yihui Bi, Yapeng Zhu, Hanyu Shi, Wenxiu Duan, Jian Zhou
Software Mentions: 12
Published: over 4 years ago

10.3390/plants10050879

Multivariate Analysis of Morpho-Physiological Traits Reveals Differential Drought Tolerance Potential of Bread Wheat Genotypes at the Seedling Stage
Cited by: 26
Author(s): Mohammed Mohi-Ud-Din, Md. Alamgir Hossain, Md. Motiar Rohman, Md. Nesar Uddin, Md. Sabibul Haque, Jalal Uddin Ahmed, Akbar Hossain, Mohamed M. Hassan, Mohammad Golam Mostofa
Software Mentions: 12
Published: almost 5 years ago

10.1371/journal.pgen.1006111

Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes
Cited by: 109
Author(s): Sébastian Lequime, Albin Fontaine, Meriadeg Ar Gouilh, Isabelle Moltini-Conclois, Louis Lambrechts
Software Mentions: 12
Published: over 9 years ago

10.1038/s41598-021-89066-x

Lagged recovery of fish spatial distributions following a cold-water perturbation
Cited by: 3
Author(s): Masumi Robertson, Gao Jin, Paul M. Regular, M. J. Morgan, Fan Zhang
Software Mentions: 12
Published: almost 5 years ago

10.3389/fgene.2018.00278

RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus)
Cited by: 11
Author(s): Carolina N. Correia, Kirsten E. McLoughlin, Nicolas C. Nalpas, David A. Magee, John A. Browne, Kévin Rue-Albrecht, Stephen V. Gordon, David E. MacHugh
Software Mentions: 12
Published: over 7 years ago

10.1038/s41598-021-86989-3

Stability and individual variability of social attachment in imprinting
Cited by: 15
Author(s): Bastien S. Lemaire, Daniele Rucco, Mathilde Josserand, Giorgio Vallortígara, Elisabetta Versace
Software Mentions: 12
Published: almost 5 years ago

10.3389/fgene.2021.667610

The Construction and Analysis of ceRNA Network and Immune Infiltration in Kidney Renal Clear Cell Carcinoma
Cited by: 10
Author(s): Lugang Deng, Peixi Wang, Zhi Qu, Nan Liu
Software Mentions: 12
Published: over 4 years ago

10.3389/fgene.2021.689159

Analyzing Roles of NUSAP1 From Clinical, Molecular Mechanism and Immune Perspectives in Hepatocellular Carcinoma
Cited by: 3
Author(s): Wenjie Zhu, Jian Xu, Zehao Chen, Jianxin Jiang
Software Mentions: 12
Published: over 4 years ago

10.3389/fgene.2020.00363

Novel Immune-Related Gene Signature for Risk Stratification and Prognosis of Survival in Lower-Grade Glioma
Cited by: 114
Author(s): Mingwei Zhang, Xuezhen Wang, Xiaoping Chen, Qiuyu Zhang, Jinsheng Hong
Software Mentions: 12
Published: almost 6 years ago

10.1038/s41598-021-86286-z

Construction and validation of a metabolic risk model predicting prognosis of colon cancer
Cited by: 5
Author(s): Didi Zuo, Chao Li, Tao Liu, Meng Yue, Jiantao Zhang, Guang Ning
Software Mentions: 12
Published: almost 5 years ago

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Papers Mentioning ggplot2 11,441