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: over 5 years ago

10.1371/journal.pone.0159046

Accuracy and Calibration of Computational Approaches for Inpatient Mortality Predictive Modeling
Cited by: 13
Author(s): Christos T. Nakas, Narayan Schütz, Marcus Werners, Alexander Benedikt Leichtle
Software Mentions: 13
Published: about 10 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: about 5 years ago

10.1371/journal.pone.0243241

CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis
Cited by: 15
Author(s): Sebastian Hupfauf, Mohammad Etemadi, Marina Fernández-Delgado Juárez, María Gómez-Brandòn, Heribert Insam, Sabine Marie Podmirseg
Software Mentions: 13
Published: over 5 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: over 7 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: over 5 years ago

10.1186/s12859-016-1457-z

Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq
Cited by: 55
Author(s): Claire Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim
Software Mentions: 13
Published: over 9 years ago

10.1007/s12035-018-1112-y

Differentiation-Induced Remodelling of Store-Operated Calcium Entry Is Independent of Neuronal or Glial Phenotype but Modulated by Cellular Context
Cited by: 5
Author(s): Claire Whitworth, Christopher P.F. Redfern, Timothy R. Cheek
Software Mentions: 13
Published: about 8 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: about 6 years ago

10.1007/s10875-020-00908-1

Targeted Proteomics Reveals Inflammatory Pathways that Classify Immune Dysregulation in Common Variable Immunodeficiency
Cited by: 13
Author(s): Roos-Marijn Berbers, Julia Drylewicz, Pauline M. Ellerbroek, Joris M. van Montfrans, Virgil A. S. H. Dalm, P. Martin van Hagen, Baerbel Keller, Klaus Warnatz, Annick van de Ven, J.M. van Laar, Stefan Nierkens, Helen L. Leavis
Software Mentions: 13
Published: over 5 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: almost 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: over 5 years ago

10.12688/f1000research.12512.1

lakemorpho: Calculating lake morphometry metrics in R
Cited by: 15
Author(s): Jeffrey W. Hollister, Joseph Stachelek
Software Mentions: 13
Published: almost 9 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: over 5 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: about 8 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: almost 6 years ago

10.1038/srep36460

Overlooked habitat of a vulnerable gorgonian revealed in the Mediterranean and Eastern Atlantic by ecological niche modelling
Cited by: 28
Author(s): Joana Boavida, Jorge Assis, Inga Silva, Ester A. Serrão
Software Mentions: 13
Published: over 9 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: about 9 years ago

10.1038/s41598-018-21217-z

Spatially-explicit valuation of coastal wetlands for cyclone mitigation in Australia and China
Cited by: 32
Author(s): Xiaoguang Ouyang, Joe Lee, Rod M. Connolly, Martin J. Kainz
Software Mentions: 13
Published: over 8 years ago

10.3389/fpls.2020.01206

Similar Arbuscular Mycorrhizal Fungal Communities in 31 Durum Wheat Cultivars (Triticum turgidum L. var. durum) Under Field Conditions in Eastern Canada
Cited by: 16
Author(s): Franck Stefani, Sarah Dupont, Mario Laterrière, Ron Knox, Yuefeng Ruan, Chantal Hamel, Mohamed Hijri
Software Mentions: 13
Published: almost 6 years ago

10.1186/s12859-020-03774-1

Hypercluster: a flexible tool for parallelized unsupervised clustering optimization
Cited by: 7
Author(s): Lili M. Blumenberg, Kelly V. Ruggles
Software Mentions: 13
Published: almost 6 years ago

10.1186/1471-2164-14-46

Systems infection biology: a compartmentalized immune network of pig spleen challenged with Haemophilus parasuis
Cited by: 9
Author(s): Ming Zhao, Xiangdong Liu, Xinyun Li, Hongbo Chen, Hui Jin, Rui Zhou, Mengjin Zhu, Shuhong Zhao
Software Mentions: 13
Published: over 13 years ago

10.3390/microorganisms9050945

Diversity and Geographical Structure of Xanthomonas citri pv. citri on Citrus in the South West Indian Ocean Region
Cited by: 4
Author(s): Olivier Pruvost, Damien Richard, Karine Boyer, Stéphanie Javegny, Claudine Boyer, Frédéric Chiroleu, Pierre Grygiel, Evelyne Parvedy, Isabelle Robène, Véronique Maillot-Lebon, Abdou Azali Hamza, Kanta Kumar Lobin, Marc Naiken, Christian Vernière
Software Mentions: 13
Published: over 5 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: almost 6 years ago

10.3389/fbioe.2021.614324

One-Time Optimization of Advanced T Cell Culture Media Using a Machine Learning Pipeline
Cited by: 9
Author(s): Paul Grzesik, Sebastian C. Warth
Software Mentions: 13
Published: about 5 years ago

10.3389/fimmu.2020.620716

Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help
Cited by: 14
Author(s): Elena Merino Tejero, Danial Lashgari, Rodrigo García-Valiente, Xuefeng Gao, Fabien Crauste, Philippe A. Robert, Michael Meyer‐Hermann, María Rodríguez Martínez, S. Marieke van Ham, Jeroen E. J. Guikema, Huub Hoefsloot, Antoine H. C. van Kampen
Software Mentions: 13
Published: over 5 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: almost 9 years ago

10.3390/cancers13174311

Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging
Cited by: 15
Author(s): Daria Lazic, Florian Kromp, Fikret Rifatbegovic, Peter Repiščák, Michael Kirr, Filip Mívalt, Florian Halbritter, Marie Bernkopf, Andrea Bileck, Marek Ussowicz, Inge M. Ambros, Peter F. Ambros, Christopher Gerner, Ruth Ladenstein, Christian Ostalecki, Sabine Taschner‐Mandl
Software Mentions: 13
Published: almost 5 years ago

10.1186/s13059-020-02151-8

Alignment and mapping methodology influence transcript abundance estimation
Cited by: 80
Author(s): Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro
Software Mentions: 13
Published: almost 6 years ago

10.1186/s12859-015-0453-z

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis
Cited by: 41
Author(s): Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido
Software Mentions: 13
Published: over 11 years ago

10.1098/rspb.2021.0219

Collaboration enhances career progression in academic science, especially for female researchers
Cited by: 9
Author(s): Jessica E. M. van der Wal, Rose Thorogood, Nicholas P. C. Horrocks
Software Mentions: 13
Published: almost 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: over 7 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

10.3389/fonc.2020.629909

Identification of an Immune Gene-Associated Prognostic Signature and Its Association With a Poor Prognosis in Gastric Cancer Patients
Cited by: 15
Author(s): Xiaoqing Guan, Zhiyuan Xu, Runzhe Chen, Jiang‐Jiang Qin, Xiangdong Cheng
Software Mentions: 13
Published: over 5 years ago

10.1007/s00248-020-01635-1

Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral Composition
Cited by: 12
Author(s): Irina Tanuwidjaja, Cordula Vogel, Geertje Johanna Pronk, Anne Schöler, Susanne Kublik, Gisle Vestergaard, Ingrid Kögel‐Knabner, Mirna Mrkonjić Fuka, Michael Schloter, Stefanie Schulz
Software Mentions: 13
Published: over 5 years ago

10.1186/s12935-020-01362-0

Immune-related long non-coding RNA signature identified prognosis and immunotherapeutic efficiency in bladder cancer (BLCA)
Cited by: 40
Author(s): Rui Cao, Lushun Yuan, Bo Ma, Gang Wang, Ye Tian
Software Mentions: 13
Published: about 6 years ago

10.1128/mBio.02275-17

A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus <i>Puccinia striiformis</i> f. sp. <i>tritici</i> Reveals High Interhaplotype Diversity
Cited by: 99
Author(s): Benjamin Schwessinger, Jana Sperschneider, William S. Cuddy, Diana Garnica, Marisa E. Miller, Jennifer Taylor, Peter N. Dodds, Melania Figueroa, Robert Park, John P. Rathjen
Software Mentions: 13
Published: over 8 years ago

10.1371/journal.pone.0212669

Batch adjustment by reference alignment (BARA): Improved prediction performance in biological test sets with batch effects
Cited by: 3
Author(s): Robin Gradin, Malin Lindstedt, Henrik J. Johansson
Software Mentions: 13
Published: over 7 years ago

10.1186/s12859-019-3251-1

BISR-RNAseq: an efficient and scalable RNAseq analysis workflow with interactive report generation
Cited by: 17
Author(s): Venkat Sundar Gadepalli, Hatice Gülçin Özer, Ayse Selen Yilmaz, Maciej Pietrzak, Amy Webb
Software Mentions: 13
Published: over 6 years ago

10.1038/s41398-021-01596-0

Autoantibody profiles associated with clinical features in psychotic disorders
Cited by: 6
Author(s): August Jernbom Falk, Cherrie Galletly, David R. Just, Catherine Toben, Bernhard T. Baune, Scott Clark, Dennis Liu, Peter Nilsson, Anna Månberg, Klaus Oliver Schubert
Software Mentions: 13
Published: almost 5 years ago

10.1186/s13321-020-00455-2

spyrmsd: symmetry-corrected RMSD calculations in Python
Cited by: 23
Author(s): Rocco Meli, Philip C. Biggin
Software Mentions: 13
Published: almost 6 years ago

10.1016/j.xpro.2021.100837

Protocol for hybrid flux balance, statistical, and machine learning analysis of multi-omic data from the cyanobacterium Synechococcus sp. PCC 7002
Cited by: 3
Author(s): Supreeta Vijayakumar, Claudio Angione
Software Mentions: 13
Published: over 4 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: over 5 years ago

10.1371/journal.pone.0250817

#MaskOn! #MaskOff! Digital polarization of mask-wearing in the United States during COVID-19
Cited by: 48
Author(s): Jun Lang, Wesley W. Erickson, Zhuo Jing–Schmidt
Software Mentions: 13
Published: about 5 years ago

10.1093/bib/bbz158

Toward a gold standard for benchmarking gene set enrichment analysis
Cited by: 74
Author(s): Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Software Mentions: 13
Published: over 6 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: over 5 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: almost 7 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: about 5 years ago

10.3390/ijms22062790

Differential Methylation in the GSTT1 Regulatory Region in Sudden Unexplained Death and Sudden Unexpected Death in Epilepsy
Cited by: 4
Author(s): Steffan Noe Christiansen, Stine Jacobsen, Jeppe Dyrberg Andersen, Marie-Louise Kampmann, Linea C Trudsø, Karsten Olsen, Jacob Tfelt-Hansen, Jytte Banner, Niels Morling
Software Mentions: 13
Published: over 5 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: almost 5 years ago

10.1371/journal.pcbi.1007113

Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes
Cited by: 28
Author(s): Claire Bomkamp, Shreejoy J. Tripathy, Carolina Bengtsson Gonzales, Jens Hjerling-Leffler, Ann Marie Craig, Paul Pavlidis
Software Mentions: 13
Published: about 7 years ago

10.3390/cancers13163922

Transcriptomic Profiling Reveals Novel Candidate Genes and Signalling Programs in Breast Cancer Quiescence and Dormancy
Cited by: 4
Author(s): Lewis A. Quayle, Amy Spicer, Penelope D. Ottewell, Ingunn Holen
Software Mentions: 13
Published: almost 5 years ago

10.1002/ece3.5645

Testing adaptive hypotheses on the evolution of larval life history in acorn and stalked barnacles
Cited by: 11
Author(s): Christine Ewers‐Saucedo, Paula Pappalardo
Software Mentions: 13
Published: almost 7 years ago

10.1186/s12859-019-3029-5

CAGEfightR: analysis of 5′-end data using R/Bioconductor
Cited by: 35
Author(s): Malte Thodberg, Axel Thieffry, Kristoffer Vitting-Seerup, Robin Andersson, Albin Sandelin
Software Mentions: 13
Published: almost 7 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: over 5 years ago

10.1002/ece3.5586

Life history alterations upon oral and hemocoelic bacterial exposure in the butterfly Melitaea cinxia
Cited by: 1
Author(s): Luisa Woestmann, Dimitri Stucki, Marjo Saastamoinen
Software Mentions: 13
Published: almost 7 years ago

10.12688/f1000research.7082.3

EvolQG - An R package for evolutionary quantitative genetics
Cited by: 31
Author(s): Diogo Melo, Guilherme Garcia, Alex Hubbe, Ana Paula A. Assis, Gabriel Marroig
Software Mentions: 13
Published: over 9 years ago

10.3390/e22020203

An Analysis of Smart Contracts Security Threats Alongside Existing Solutions
Cited by: 18
Author(s): Antonio López Vivar, Alberto Turégano Castedo, Ana Lucila Sandoval Orozco, Luis Javier García Villalba
Software Mentions: 13
Published: over 6 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: about 6 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: almost 8 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: over 7 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: over 5 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: about 6 years ago

10.12688/f1000research.17548.2

Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
Cited by: 8
Author(s): Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
Software Mentions: 13
Published: over 7 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: almost 5 years ago

10.3389/fninf.2020.572068

Rxnat: An Open-Source R Package for XNAT-Based Repositories
Cited by: 0
Author(s): Adrian Gherman, John Muschelli, Brian Caffo, Ciprian M. Crainiceanu
Software Mentions: 13
Published: over 5 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: almost 6 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: almost 6 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: about 7 years ago

10.3389/fimmu.2021.730346

Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens
Cited by: 6
Author(s): Brandi T. Johnson‐Weaver, Hae Woong Choi, Hui Yang, Joshua A. Granek, Cliburn Chan, Soman N. Abraham, Herman F. Staats
Software Mentions: 13
Published: almost 5 years ago

10.3389/fonc.2020.01317

The Potential of Five Immune-Related Prognostic Genes to Predict Survival and Response to Immune Checkpoint Inhibitors for Soft Tissue Sarcomas Based on Multi-Omic Study
Cited by: 17
Author(s): Hao Gu, Lu-Lu Lin, Zhang Chao, Min Yang, Hongshan Zhong, Renxiong Wei
Software Mentions: 13
Published: about 6 years ago

10.1186/s40168-020-00861-6

Reservoirs of antimicrobial resistance genes in retail raw milk
Cited by: 41
Author(s): Jinxin Liu, Yongxu Zhu, Michele Jay-Russell, Danielle G. Lemay, David A. Mills
Software Mentions: 13
Published: about 6 years ago

10.4049/immunohorizons.1900097

Mass Cytometry Defines Virus-Specific CD4+ T Cells in Influenza Vaccination
Cited by: 3
Author(s): Priyanka B. Subrahmanyam, Tyson H. Holmes, Derek Lin, Laura F. Su, Gerlinde Obermoser, Jacques Banchereau, Virginia Pascual, Adolfo Garcı́a-Sastre, Randy A. Albrecht, Karolina Palucka, Mark M. Davis, Holden T. Maecker
Software Mentions: 13
Published: over 5 years ago

10.1371/journal.pone.0242502

Timeliness of immunisation with the pentavalent vaccine at different levels of the health care system in the Lao People’s Democratic Republic: A cross-sectional study
Cited by: 3
Author(s): Lisa Hefele, Sengdavanh Syphan, Dalouny Xayavong, Anousin Homsana, Daria Kleine, Phetsavanh Chanthavilay, Phonethipsavanh Nouanthong, Kinnaly Xaydalasouk, Outavong Phathammavong, Somxay Billamay, Anonh Xeuatvongsa, Daniel Reinharz, Antony P. Black, Claude P. Muller
Software Mentions: 13
Published: over 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: over 5 years ago

10.3389/fbioe.2020.00515

Construction of a Competitive Endogenous RNA Network for Pancreatic Adenocarcinoma Based on Weighted Gene Co-expression Network Analysis and a Prognosis Model
Cited by: 4
Author(s): Jing Wang, Jinzhu Xiang, Xueling Li
Software Mentions: 13
Published: about 6 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: about 8 years ago

10.1007/s41114-018-0015-6

Computer algebra in gravity research
Cited by: 20
Author(s): Malcolm MacCallum
Software Mentions: 13
Published: almost 8 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: over 5 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 5 years ago

10.1186/s12859-021-04210-8

Contrastive self-supervised clustering of scRNA-seq data
Cited by: 28
Author(s): Madalina Ciortan, Matthieu Defrance
Software Mentions: 13
Published: about 5 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: about 5 years ago

10.1093/bioinformatics/bty713

Bigmelon: tools for analysing large DNA methylation datasets
Cited by: 47
Author(s): T.J. Gorrie-Stone, Melissa Smart, Ayden Saffari, Karim Malki, Eilís Hannon, Joe Burrage, Jonathan Mill, Meena Kumari, Leonard C Schalkwyk
Software Mentions: 13
Published: almost 8 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: about 6 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: about 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: over 5 years ago

10.3389/fcimb.2021.688256

Machine Learning Uses Chemo-Transcriptomic Profiles to Stratify Antimalarial Compounds With Similar Mode of Action
Cited by: 1
Author(s): Ashleigh van Heerden, Roelof van Wyk, Lyn-Marié Birkholtz
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: over 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: over 6 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: over 6 years ago

10.1186/s13046-020-01684-x

KIAA1522 potentiates TNFα-NFκB signaling to antagonize platinum-based chemotherapy in lung adenocarcinoma
Cited by: 11
Author(s): Boshi Wang, Tiantian Jing, Wei‐Lin Jin, Biaohua Chen, Chengsi Wu, Ming-Rong Wang, Yizhen Liu
Software Mentions: 13
Published: almost 6 years ago

10.1186/s12861-018-0163-7

Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells
Cited by: 4
Author(s): Anna Mantsoki, Guillaume Devailly, Anagha Joshi
Software Mentions: 13
Published: over 8 years ago

10.2196/16810

Blockchain-Authenticated Sharing of Genomic and Clinical Outcomes Data of Patients With Cancer: A Prospective Cohort Study
Cited by: 29
Author(s): Benjamin S. Glicksberg, Shohei Burns, R. Currie, A. Clark Griffin, Zhen Jane Wang, David Haussler, Theodore C. Goldstein, Eric A. Collisson
Software Mentions: 13
Published: over 6 years ago

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: about 8 years ago

10.1371/journal.pone.0018657

Who Shares? Who Doesn't? Factors Associated with Openly Archiving Raw Research Data
Cited by: 172
Author(s): Heather Piwowar
Software Mentions: 13
Published: about 15 years ago

10.1002/ece3.7657

Disentangling demographic effects of red deer on chamois population dynamics
Cited by: 9
Author(s): Valerio Donini, Luca Pedrotti, Francesco Ferretti, Luca Corlatti
Software Mentions: 13
Published: about 5 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: about 6 years ago

10.1371/journal.pone.0253546

Tone and genes: New cross-linguistic data and methods support the weak negative effect of the “derived” allele of ASPM on tone, but not of Microcephalin
Cited by: 1
Author(s): Dan Dediu
Software Mentions: 13
Published: about 5 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: over 6 years ago

10.1371/journal.pcbi.1008880

Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD
Cited by: 20
Author(s): Yannick Marcon, Tom Bishop, Demetris Avraam, Xavier Escribà-Montagut, Patricia Ryser-Welch, SM Wheater, Paul R. Burton, Juan R. González
Software Mentions: 13
Published: over 5 years ago