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: almost 8 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: over 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: almost 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: about 7 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: about 6 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: almost 10 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

10.1371/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: about 8 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: about 6 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: over 6 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: almost 5 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

10.3389/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: 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: almost 9 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

10.1371/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/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

10.18632/aging.202831

Seven interferon gamma response genes serve as a prognostic risk signature that correlates with immune infiltration in lung adenocarcinoma
Cited by: 11
Author(s): Boyang Yao, Lixin Wang, Heyong Wang, Jinxia Bao, Qiwen Li, Fengzhi Yu, Wenjing Zhu, Li Zhang, Wang Li, Gu Zhan, Ke Fei, Peng Zhang, Fan Zhang, Xiaoying Huang
Software Mentions: 13
Published: about 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: 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: about 6 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: 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: 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: almost 5 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

10.3390/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: 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

10.3389/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/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: over 5 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

10.1371/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: almost 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

10.1038/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

10.3389/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

10.18632/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: about 5 years ago

10.1186/s12859-015-0794-7

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Cited by: 47
Author(s): Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 13
Published: over 10 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: almost 9 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/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

10.12688/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: about 7 years ago

10.1186/s13059-020-02071-7

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data
Cited by: 56
Author(s): Ralph Patrick, David T. Humphreys, Vaibhao Janbandhu, Alicia Oshlack, Joshua W. K. Ho, Richard P. Harvey, Kitty Lo
Software Mentions: 13
Published: almost 6 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

10.1186/1471-2164-14-46

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

10.1038/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: over 4 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

10.3389/fgene.2019.00317

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis
Cited by: 549
Author(s): Geng Chen, Baitang Ning, Tieliu Shi
Software Mentions: 13
Published: about 7 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: almost 6 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

10.12688/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/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

10.3389/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: almost 6 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: about 6 years ago

10.1016/j.mbplus.2019.04.001

Pan-Cancer analysis of the expression and regulation of matrisome genes across 32 tumor types
Cited by: 37
Author(s): Valerio Izzi, Juho Lakkala, Raman Devarajan, Anni Kääriäinen, Jarkko Koivunen, Ritva Heljasvaara, Taina Pihlajaniemi
Software Mentions: 13
Published: over 7 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

10.1186/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

10.3389/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/s12859-021-04142-3

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
Cited by: 11
Author(s): Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise A Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordóñez, Andrew E. Jaffe, Leonardo Collado‐Torres
Software Mentions: 13
Published: about 5 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: almost 6 years ago

10.1186/s12868-019-0538-0

28th Annual Computational Neuroscience Meeting: CNS*2019
Cited by: 3
Author(s):
Software Mentions: 13
Published: over 6 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

10.1371/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: almost 7 years ago

10.3389/fgene.2021.652189

Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance
Cited by: 11
Author(s): Chirag Gupta, Venkategowda Ramegowda, Supratim Basu, Andy Pereira
Software Mentions: 13
Published: almost 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: 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: 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: almost 5 years ago

10.1111/mec.15422

Ecological and evolutionary drivers of haemoplasma infection and bacterial genotype sharing in a Neotropical bat community
Cited by: 21
Author(s): Daniel J. Becker, Kelly A. Speer, Alexis M. Brown, M. Brock Fenton, Alex D. Washburne, Sonia Altizer, Daniel G. Streicker, Raina K. Plowright, Vladimir E. Chizhikov, Nancy B. Simmons, Dmitriy V. Volokhov
Software Mentions: 13
Published: about 6 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

10.7554/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: about 5 years ago

10.1186/s12859-021-04057-z

Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
Cited by: 21
Author(s): Hao Chen, Yan Lu, Dongsheng Lu, Shuhua Xu
Software Mentions: 13
Published: about 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: almost 6 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: 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: about 7 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: 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: almost 7 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

10.1186/s12864-017-4423-x

Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis
Cited by: 31
Author(s): Claudia Cava, Gloria Bertoli, Antonio Colaprico, Catharina Olsen, Gianluca Bontempi, Isabella Castiglioni
Software Mentions: 12
Published: over 8 years ago

10.1371/journal.pone.0229330

StructuRly: A novel shiny app to produce comprehensive, detailed and interactive plots for population genetic analysis
Cited by: 22
Author(s): Nicola G. Criscuolo, Claudia Angelini
Software Mentions: 12
Published: over 6 years ago

10.1093/molbev/msaa128

Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression
Cited by: 25
Author(s): Xavier Grau‐Bové, Sean Tomlinson, Andrias O. O’Reilly, Nicholas J. Harding, Alistair Miles, Dominic Kwiatkowski, Martin Donnelly, David Weetman
Software Mentions: 12
Published: about 6 years ago

10.1371/journal.pgen.1009141

A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank
Cited by: 68
Author(s): Junyang Qian, Yosuke Tanigawa, Wenfei Du, Matthew Aguirre, Chris Chang, Robert Tibshirani, Manuel A. Rivas, Trevor Hastie
Software Mentions: 12
Published: over 5 years ago

10.26508/lsa.202000770

In vivo CRISPR/Cas9 knockout screen: TCEAL1 silencing enhances docetaxel efficacy in prostate cancer
Cited by: 12
Author(s): Linda Rushworth, Victoria Harle, Peter Repiščák, William Clark, Robin Shaw, Holly Hall, Martin Bushell, Hing Y. Leung, Rachana Patel
Software Mentions: 12
Published: over 5 years ago

10.1111/test.12258

Some teaching resources using R with illustrative examples exploring COVID ‐19 data
Cited by: 0
Author(s): Arthur Berg, Nour Hawila
Software Mentions: 12
Published: almost 5 years ago

10.1371/journal.pone.0202824

Allometry predicts trabecular bone structural properties in the carnivoran jaw joint
Cited by: 6
Author(s): Matthew Wysocki, Z. Jack Tseng
Software Mentions: 12
Published: almost 8 years ago

10.12688/f1000research.14013.2

Taxa: An R package implementing data standards and methods for taxonomic data
Cited by: 23
Author(s): Zachary Foster, Scott Chamberlain, Niklaus J. Grünwald
Software Mentions: 12
Published: over 7 years ago

10.1111/gcb.14581

Structural and functional responses of invertebrate communities to climate change and flow regulation in alpine catchments
Cited by: 61
Author(s): Daniel Bruno, Óscar Belmar, Anthony Maire, Adrien Morel, Bernard Dumont, Thibault Datry
Software Mentions: 12
Published: over 7 years ago

10.1186/s12862-016-0661-9

Breeding system, shell size and age at sexual maturity affect sperm length in stylommatophoran gastropods
Cited by: 4
Author(s): Dénes Schmera, Julia Pizá, Ellen Reinartz, Sylvain Ursenbacher, Bruno Baur
Software Mentions: 12
Published: about 10 years ago

10.1371/journal.pone.0239197

Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signatures
Cited by: 13
Author(s): Weston R. Bodily, Brian H. Shirts, Tom Walsh, Süleyman Gülsüner, Mary‐Claire King, Alyssa Parker, Moom R. Roosan, Stephen R. Piccolo
Software Mentions: 12
Published: over 5 years ago

10.1186/s13073-016-0384-y

XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits
Cited by: 131
Author(s): Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C. Knight
Software Mentions: 12
Published: over 9 years ago

10.3390/nu13082639

Infants’ First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental Cohorts
Cited by: 18
Author(s): Chiara-Maria Homann, Connor A J Rossel, Sara Dizzell, Liene Bervoets, Julia Simioni, Jenifer Li, Elizabeth Gunn, Michael G. Surette, Russell J. de Souza, Monique Mommers, Eileen K. Hutton, Katherine M. Morrison, John Penders, Niels van Best, Jennifer C. Stearns
Software Mentions: 12
Published: almost 5 years ago

10.3389/fgene.2019.01079

HiCeekR: A Novel Shiny App for Hi-C Data Analysis
Cited by: 13
Author(s): Lucio Di Filippo, Dario Righelli, Miriam Gagliardi, Maria R. Matarazzo, Claudia Angelini
Software Mentions: 12
Published: over 6 years ago

10.1128/mBio.02782-18

Fitness Cost of Aflatoxin Production in Aspergillus flavus When Competing with Soil Microbes Could Maintain Balancing Selection
Cited by: 21
Author(s): Milton T. Drott, Tracy Debenport, Steven A. Higgins, Daniel H. Buckley, Michael G. Milgroom
Software Mentions: 12
Published: over 7 years ago

10.7554/eLife.52465

Navigating the garden of forking paths for data exclusions in fear conditioning research
Cited by: 87
Author(s): Tina B. Lonsdorf, Maren Klingelhöfer-Jens, Marta Andreatta, Tom Beckers, Anastasia Chalkia, Anna Gerlicher, Valerie L. Jentsch, Shira Meir Drexler, Gaëtan Mertens, Jan Richter, Rachel Sjouwerman, Julia Wendt, Christian J. Merz
Software Mentions: 12
Published: over 6 years ago

10.1186/s40168-020-0793-4

Separating the signal from the noise in metagenomic cell-free DNA sequencing
Cited by: 26
Author(s): Philip Burnham, Nardhy Gómez-López, Michael Heyang, Alexandre Pellan Cheng, Joan Sesing Lenz, Darshana Dadhania, John Richard Lee, Manikkam Suthanthiran, Roberto Romero, Iwijn De Vlaminck
Software Mentions: 12
Published: over 6 years ago

10.1186/s12935-021-01900-4

Role of tumor mutation burden-related signatures in the prognosis and immune microenvironment of pancreatic ductal adenocarcinoma
Cited by: 16
Author(s): Rong Tang, Xiaomeng Liu, Wei Wang, Jie Hua, Jin Xu, Chen Liang, Qingcai Meng, Jiang Liu, Bo Zhang, Yu Lei, Si Shi
Software Mentions: 12
Published: about 5 years ago

10.1186/s12859-021-04028-4

scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data
Cited by: 12
Author(s): Bobby Ranjan, Florian Schmidt, Wenjie Sun, Jinyu Park, Mohammad Amin Honardoost, Joanna H.J. Tan, Nirmala Arul Rayan, Shyam Prabhakar
Software Mentions: 12
Published: about 5 years ago

10.1186/s12919-016-0015-z

Analysis of gene expression to predict dynamics of future hypertension incidence in type 2 diabetic patients
Cited by: 8
Author(s): Piotr Radkowski, Gracjan Wątor, Jan Skupień, Anna Bogdali, Paweł Wołkow
Software Mentions: 12
Published: over 9 years ago

10.12688/f1000research.12874.2

Measuring evolutionary rates of proteins in a structural context
Cited by: 5
Author(s): Dariya K. Sydykova, Benjamin R. Jack, Scott R. Spielman, Claus O. Wilke
Software Mentions: 12
Published: over 8 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: about 7 years ago

10.3390/insects11080535

Impacts of Dietary Nutritional Composition on Larval Development and Adult Body Composition in the Yellow Fever Mosquito (Aedes aegypti)
Cited by: 15
Author(s): Tess van Schoor, Erin Taylor Kelly, Nicole Tam, Geoffrey M. Attardo
Software Mentions: 12
Published: almost 6 years ago

10.1186/s13071-017-2054-3

GIS-supported epidemiological analysis on canine Angiostrongylus vasorum and Crenosoma vulpis infections in Germany
Cited by: 41
Author(s): Pavlo Maksimov, Carlos Hermosilla, Anja Taubert, Christoph Staubach, Carola Sauter‐Louis, Franz Josef Conraths, Majda Globokar Vrhovec, Nikola Pantchev
Software Mentions: 12
Published: over 9 years ago

10.1002/ece3.7130

QuoVidi: An open‐source web application for the organization of large‐scale biological treasure hunts
Cited by: 8
Author(s): Guillaume Lobet, Charlotte Descamps, Lola Leveau, Alain Guillet, Jean-François Rees
Software Mentions: 12
Published: over 5 years ago