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: about 6 years ago

10.3389/fgene.2021.665888

A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells
Cited by: 2
Author(s): Simon Haile, Richard Corbett, Véronique G. LeBlanc, Lisa L. Wei, Stephen Pleasance, Steve Bilobram, Ka Ming Nip, Kirstin Brown, Eva Trinh, Jillian Smith, Diane L. Trinh, Miruna Bala, Eric Chuah, Robin Coope, Richard A. Moore, Andrew J. Mungall, Yongjun Zhao, Martin Hirst, Samuel Aparicio, İnanç Birol, Steven J.M. Jones, Marco A. Marra
Software Mentions: 13
Published: over 5 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: almost 7 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: over 5 years ago

10.1186/1471-2105-10-363

A novel R-package graphic user interface for the analysis of metabonomic profiles
Cited by: 51
Author(s): José Luis Izquierdo-García, Ignacio Rodríguez, Angelos Kyriazis, Palmira Villa, Pilar Barreiro Elorza, Manuel Desco, Jesús Ruíz-Cabello
Software Mentions: 13
Published: almost 17 years ago

10.3389/fneur.2020.579683

Development and Validation of a Five-Gene Signature to Predict Relapse-Free Survival in Multiple Sclerosis
Cited by: 6
Author(s): Fei Ye, Jie Liang, Jiaoxing Li, Haiyan Li, Wenli Sheng
Software Mentions: 13
Published: almost 6 years ago

10.1371/journal.pone.0135784

Comparison of Nine Statistical Model Based Warfarin Pharmacogenetic Dosing Algorithms Using the Racially Diverse International Warfarin Pharmacogenetic Consortium Cohort Database
Cited by: 38
Author(s): Rong Liu, Xi Li, Wei Zhang, Hong‐Hao Zhou
Software Mentions: 13
Published: about 11 years ago

10.7554/eLife.62915

ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data
Cited by: 9
Author(s): James W. Opzoomer, Jessica A Timms, Kevin Blighe, Thanos P. Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan G. Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca D. Ciccarelli, Peter J. Parker, Michaéla Fontenay, Paul R. Barber, James N. Arnold, Shahram Kordasti
Software Mentions: 13
Published: over 5 years ago

10.1002/ece3.5968

Contrasting responses to climate change at Himalayan treelines revealed by population demographics of two dominant species
Cited by: 23
Author(s): Kumar P. Mainali, Bharat Babu Shrestha, Ravi Kumar Sharma, Arjun Adhikari, Eliezer Gurarie, Michael C. Singer, Camille Parmesan
Software Mentions: 13
Published: over 6 years ago

10.1186/1748-7188-4-7

Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity
Cited by: 71
Author(s): Koji Kadota, Yuji Nakai, Kentaro Shimizu
Software Mentions: 13
Published: over 17 years ago

10.3389/fimmu.2019.02887

Meta-Analysis of in vitro-Differentiated Macrophages Identifies Transcriptomic Signatures That Classify Disease Macrophages in vivo
Cited by: 29
Author(s): Hung Jen Chen, Andrew Y. Li Yim, Guillermo R. Griffith, Wouter J. de Jonge, Marcel M.A.M. Mannens, Enrico Ferrero, Peter Henneman, Menno P.J. de Winther
Software Mentions: 13
Published: almost 7 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: over 5 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: almost 6 years ago

10.7717/peerj.5518

Random forest as a generic framework for predictive modeling of spatial and spatio-temporal variables
Cited by: 419
Author(s): Tomislav Hengl, Madlene Nussbaum, Marvin N. Wright, G.B.M. Heuvelink, Benedikt Gräler
Software Mentions: 13
Published: about 8 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

10.3390/v13061184

Age and Infectious Dose Significantly Affect Disease Progression after RHDV2 Infection in Naïve Domestic Rabbits
Cited by: 13
Author(s): Robyn N. Hall, Tegan King, Tiffany W. O’Connor, Andrew J. Read, Jane Arrow, Katherine Trought, Janine A. Duckworth, M. Treuting Piper, Tanja Strive
Software Mentions: 13
Published: over 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: over 5 years ago

10.1371/journal.pone.0206563

Nitrogen addition pulse has minimal effect in big sagebrush (Artemisia tridentata) communities on the Pinedale Anticline, Wyoming (USA)
Cited by: 1
Author(s): Christopher W. Beltz, Megan L. Mobley, Ingrid C. Burke
Software Mentions: 13
Published: over 7 years ago

10.1371/journal.pcbi.1008896

Multilevel selection favors fragmentation modes that maintain cooperative interactions in multispecies communities
Cited by: 8
Author(s): Gil J. B. Henriques, Simon van Vliet, Michael Doebeli
Software Mentions: 13
Published: about 5 years ago

10.3390/tropicalmed5020064

Disease Ecology of Rickettsial Species: A Data Science Approach
Cited by: 6
Author(s): Sergé Morand, Kittipong Chaisiri, Anamika Kritiyakan, Rawadee Kumlert
Software Mentions: 13
Published: over 6 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: about 6 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 9 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: about 7 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 5 years ago

10.1590/0074-02760170489

Single nucleotide polymorphisms of cytokine-related genes and association with clinical outcome in a Chagas disease case-control study from Brazil
Cited by: 10
Author(s): Lucia Elena Alvarado-Arnez, Angélica Martins Batista, Sílvia Marinho Martins Alves, Gloria Melo, Virgínia Maria Barros de Lorena, Cynthia Chester Cardoso, Isabela Resende Pereira, Cristina de Fátima Velloso Carrazzone, Antônio Guilherme Pacheco, Wilson Alves de Oliveira, Milton Ozório Moraes, Joseli Lannes-Vieira
Software Mentions: 13
Published: over 8 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: almost 7 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: over 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: about 5 years ago

10.1038/s41598-021-90901-4

Characteristics of preoperative steroid profiles and glucose metabolism in patients with primary aldosteronism developing adrenal insufficiency after adrenalectomy
Cited by: 3
Author(s): Xiao Wang, Daniel A. Heinrich, Sonja Kunz, Nina Heger, Lisa Sturm, Olaf Uhl, Felix Beuschlein, Martín Reincke, Martin Bidlingmaier
Software Mentions: 13
Published: over 5 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: about 5 years ago

10.1186/s12874-020-01121-9

COVID19-world: a shiny application to perform comprehensive country-specific data visualization for SARS-CoV-2 epidemic
Cited by: 19
Author(s): Cristian Tebé, Joan Valls, Pau Satorra, Aurelio Tobías
Software Mentions: 13
Published: about 6 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: almost 6 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: over 5 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: 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: over 7 years ago

10.1186/s13059-020-02001-7

Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing
Cited by: 7
Author(s): Jinyan Huang, Lijun Bai, Bowen Cui, Liang Wu, Liwen Wang, Zhiyin An, Shulin Ruan, Yue Yu, Xianyang Zhang, Jun Chen
Software Mentions: 13
Published: over 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: about 5 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

10.3389/fonc.2021.639013

Single-Cell Transcriptome Analysis Identifies Ligand–Receptor Pairs Associated With BCP-ALL Prognosis
Cited by: 3
Author(s): Liang Wu, Mingming Jiang, Ping Yu, Jianfeng Li, Wen Ouyang, Chong Feng, Wei Zhao, Yuting Dai, Jinyan Huang
Software Mentions: 13
Published: over 5 years ago

10.3390/nu12123626

Trajectories of Body Composition during Advanced Aging in Consideration of Diet and Physical Activity: A 20-Year Longitudinal Study
Cited by: 6
Author(s): Alexandra Jungert, Gerrit Eichner, Monika Neuhäuser‐Berthold
Software Mentions: 13
Published: almost 6 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: over 8 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

10.3389/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: over 5 years ago

10.12688/f1000research.10742.2

haploR: an R package for querying web-based annotation tools
Cited by: 20
Author(s): Ilya Y. Zhbannikov, Konstantin G. Arbeev, Svetlana V. Ukraintseva, Anatoliy I. Yashin
Software Mentions: 13
Published: over 9 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.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: almost 11 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

10.1111/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: 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

10.1186/1471-2164-14-46

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

10.7554/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: over 5 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

10.1002/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: over 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/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: about 6 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

10.1038/s41422-020-00453-x

Establishment of intestinal organoid cultures modeling injury-associated epithelial regeneration
Cited by: 39
Author(s): Molong Qu, Liang Xiong, Yulin Lyu, Xiannian Zhang, Jie Shen, Jingyang Guan, Peiyuan Chai, Lin Zheng, Boyao Nie, Cheng Li, Jun Xu, Hongkui Deng
Software Mentions: 13
Published: over 5 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 5 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: almost 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: about 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: about 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: almost 6 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: about 6 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: over 5 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: almost 6 years ago

10.1186/s13059-019-1739-7

CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data
Cited by: 33
Author(s): Rebekka Wegmann, Marilisa Neri, Sven Schuierer, Bilada Bilican, Huyen Hartkopf, Florian Nigsch, Felipa Mapa, Annick Waldt, Rachel Cuttat, Max R. Salick, Joe Raymond, Ajamete Kaykas, Guglielmo Roma, Caroline Gubser Keller
Software Mentions: 13
Published: about 7 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

10.1002/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: about 7 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: 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

10.1186/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: about 6 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: almost 10 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

10.3389/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: about 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

10.1093/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: about 8 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 8 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: over 6 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 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: almost 7 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: about 7 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

10.1186/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: almost 7 years ago

10.1186/s13059-019-1898-6

Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis
Cited by: 123
Author(s): Shuang Sun, Jiaqiang Zhu, Ying Ma, Xiang Zhou
Software Mentions: 13
Published: almost 7 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

10.1186/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: over 5 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: over 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: 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: over 7 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.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: almost 6 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

10.3389/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: almost 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: almost 7 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

10.1038/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: about 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: about 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

10.1038/srep42130

Dissecting the brown adipogenic regulatory network using integrative genomics
Cited by: 20
Author(s): Rachana Pradhan, Johannes Bues, Vincent Gardeux, Petra Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil K. Raghav, Bart Deplancke
Software Mentions: 13
Published: over 9 years ago

10.3389/fonc.2021.583547

Alternative Splicing Events in Tumor Immune Infiltration in Colorectal Cancer
Cited by: 5
Author(s): Shi Jian-yu, Yan-yan Bi, Bo Yu, Qingfeng Wang, Teng Dan, WU Dong-ning
Software Mentions: 13
Published: over 5 years ago