10.1186/s13040-019-0201-4

Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies
Cited by: 3
Author(s): Elisabetta Manduchi, Patryk Orzechowski, Marylyn D. Ritchie, Jason H. Moore
Software Mentions: 9
Published: almost 7 years ago

10.3390/ijms151221788

Interactome Mapping Reveals Important Pathways in Skeletal Muscle Development of Pigs
Cited by: 3
Author(s): Jianhua Cao, Tinghua Huang, Xinyun Li, Zhao Song
Software Mentions: 9
Published: over 11 years ago

10.1038/s42003-018-0171-y

Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species
Cited by: 33
Author(s): Stefan Reuscher, Tomohisa Furuta, Kanako Bessho‐Uehara, Michele Cosi, Kshirod K. Jena, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Motoyuki Ashikari
Software Mentions: 9
Published: over 7 years ago

10.1038/s41598-019-56288-z

Interactions with humans are jointly influenced by life history stage and social network factors and reduce group cohesion in moor macaques (Macaca maura)
Cited by: 26
Author(s): Kristen S. Morrow, Hunter Glanz, Putu Oka Ngakan, Erin P. Riley
Software Mentions: 9
Published: over 6 years ago

10.1186/s13073-020-00731-8

Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy
Cited by: 28
Author(s): Anna Reustle, Moreno Di Marco, Carolin Meyerhoff, Annika Nelde, Juliane S. Walz, Stefan Winter, Siahei Kandabarau, Florian Büttner, Mathias Haag, Linus Backert, Daniel J. Kowalewski, Steffen Rausch, Jörg Hennenlotter, Viktoria Stühler, Marcus Scharpf, Falko Fend, Arnulf Stenzl, Hans‐Georg Rammensee, Jens Bedke, Stefan Stevanović, Matthias Schwab, Elke Schaeffeler
Software Mentions: 9
Published: about 6 years ago

10.1002/cam4.2774

Identification of prognostic genes in adrenocortical carcinoma microenvironment based on bioinformatic methods
Cited by: 39
Author(s): Xiao Li, Yang Gao, Zicheng Xu, Zheng Zhang, Yuxiao Zheng, Feng Qi
Software Mentions: 9
Published: over 6 years ago

10.1093/bioinformatics/btw763

ontologyX: a suite of R packages for working with ontological data
Cited by: 66
Author(s): Daniel Greene, Sylvia Richardson, Ernest Turro
Software Mentions: 9
Published: over 9 years ago

10.1186/s12859-015-0537-9

A strategy to build and validate a prognostic biomarker model based on RT-qPCR gene expression and clinical covariates
Cited by: 6
Author(s): Maud Tournoud, Audrey Larue, Marie-Angélique Cazalis, Fabienne Venet, Alexandre Pachot, Guillaume Monneret, Alain Lepape, Jean‐Baptiste Veyrieras
Software Mentions: 9
Published: about 11 years ago

10.1371/journal.pbio.3001365

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
Cited by: 34
Author(s): Alexander K. Tice, David Žihala, Tomáš Pánek, Robert E. Jones, Eric D. Salomaki, Serafim Nenarokov, Fabien Burki, Marek Eliáš, Laura Eme, Andrew J. Roger, Antonis Rokas, Xing‐Xing Shen, Jürgen F. H. Strassert, Martin Kolísko, Matthew W. Brown
Software Mentions: 9
Published: almost 5 years ago

10.1186/s40621-021-00327-9

Non-fatal senior pickleball and tennis-related injuries treated in United States emergency departments, 2010–2019
Cited by: 6
Author(s): Harold B. Weiss, Jacob Dougherty, Charles DiMaggio
Software Mentions: 9
Published: about 5 years ago

10.1186/s13045-020-00941-y

A single-cell survey of cellular hierarchy in acute myeloid leukemia
Cited by: 39
Author(s): Jinliang Wu, Yanyu Xiao, Jie Sun, Huiyu Sun, Haide Chen, Yuanyuan Zhu, Haidong Fu, Chengxuan Yu, E Weigao, Shih‐Wei Lai, Lifeng Ma, Jiaqi Li, Lijiang Fei, Mengmeng Jiang, Jingjing Wang, Fang Ye, Renying Wang, Ziyu Zhou, Guodong Zhang, Tingyue Zhang, Qiong Ding, Zou Wang, Sheng Hao, Lizhen Liu, Weiyan Zheng, Jingsong He, Weijia Huang, Yungui Wang, Jin Xie, Tiefeng Li, Tao Cheng, Xiaoping Han, He Huang, Guoji Guo
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-017-18927-1

Species Distribution Modelling: Contrasting presence-only models with plot abundance data
Cited by: 107
Author(s): Vitor Hugo Freitas Gomes, Stéphanie D. IJff, Niels Raes, Iêda Leão do Amaral, Rafael de Paiva Salomão, Luiz de Souza Coêlho, Francisca Dionízia de Almeida Matos, Carolina V. Castilho, Diógenes de Andrade Lima Filho, Dairon Cárdenas López, Juan Ernesto Guevara, William E. Magnusson, Oliver L. Phillips, Florian Wittmann, Marcelo de Jesus Veiga Carim, Maria Pires Martins, Mariana Victória Irume, Daniel Sabatier, Jean‐François Molino, Olaf Bánki, José Renan da Silva Guimarães, Nigel C. A. Pitman, Maria Teresa Fernandez Piedade, Abel Monteagudo Mendoza, Bruno Garcia Luize, Eduardo Martins Venticinque, Evlyn Márcia Moraes de Leão Novo, Percy Núñez Vargas, Thiago Sanna Freire Silva, Ângelo Gilberto Manzatto, John Terborgh, Neidiane Farias Costa Reis, Juan Carlos Montero, Katia Regina Casula, Beatriz Schwantes Marimon, Ben‐Hur Marimon, Eurídice N. Honorio Coronado, Ted R. Feldpausch, Álvaro Duque, Charles E. Zartman, Nicolás Castaño Arboleda, Timothy J. Killeen, Bonifacio Mostacedo, Rodolfo Vásquez, Jochen Schöngart, Rafael Leandro de Assis, Marcelo Brilhante de Medeiros, Marcelo F. Simon, Ana Andrade, William F. Laurance, José Luís Camargo, Layon Oreste Demarchi, Susan G. Laurance, Emanuelle de Sousa Farias, Henrique E. M. Nascimento, Juan David Cardenas Revilla, Adriano Costa Quaresma, Flávia R. C. Costa, Ima Célia Guimarães Vieira, Bruno Barçante Ladvocat Cintra, Hernán Castellanos, Roel Brienen, Pablo R. Stevenson, Yuri Oliveira Feitosa, Joost F. Duivenvoorden, Gerardo A. Aymard C., Hugo F. Mogollón, Natália Targhetta, J. A. Comiskey, Alberto Vicentini, Aline Lopes, Gabriel Damasco, Nállarett Dávila, Roosevelt García‐Villacorta, Carolina Levis, Juliana Schietti, Priscila Souza, Thaíse Emilio, Alfonso Alonso, David Neill, Francisco Dallmeier, Leandro Valle Ferreira, Alejandro Araujo‐Murakami, Daniel Praia, Dário Dantas do Amaral, Fernanda Antunes Carvalho, Fernanda Coelho de Souza, Kenneth J. Feeley, Luzmila Arroyo, Marcelo Petratti Pansonato, Rogério Gribel, Boris Villa, Juan Carlos Licona, Paul V. A. Fine, Carlos Cerón, Christopher Baraloto, Eliana M. Jimenez, Juliana Stropp, Julien Engel, Marcos Silveira, M. C. Peñuela, Pascal Pétronelli, P.J.M. Maas, Raquel Thomas-Caesar, Terry W. Henkel, Doug Daly, Marcos Ríos Paredes, Tim R. Baker, Alfredo Fuentes, Carlos A. Peres, Jérôme Chave, Jose Luis Marcelo‐Peña, Kyle G. Dexter, Miles R. Silman, Peter M. Jørgensen, R. Toby Pennington, Anthony Di Fiore, Fernando Cornejo Valverde, Juan Fernando Phillips, Gonzalo Rivas‐Torres, Patricio von Hildebrand, Tinde van Andel, Ademir Roberto Ruschel, Adriana Prieto, Agustín Rudas, Bruce Hoffman, César I. A. Vela, Edelcílio Marques Barbosa, Egleé L. Zent, George Pepe Gallardo Gonzales, Hilda Paulette Dávila Doza, Íres Paula de Andrade Miranda, Jean-Louis Guillaumet, Linder Felipe Mozombite Pinto, Luiz Carlos de Matos Bonates, Natalino Silva, Ricardo Zárate Gómez, Stanford Zent, Therany Gonzales, Vincent Vos, Yadvinder Malhi, Alexandre Adalardo de Oliveira, Ángela Cano, Bianca Weiss Albuquerque, Corine Vriesendorp, Diego F. Correa, Emilio Vilanova Torre, Gregory van der Heijden, Hirma Ramírez‐Angulo, José Ferreira Ramos, Kenneth R. Young, Maíra da Rocha, Marcelo Trindade Nascimento, María Natalia Umaña Medina, Milton Tirado, Ophelia Wang, Rodrigo Sierra, Armando Torres‐Lezama, Casimiro Mendoza, Cid Ferreira, Cláudia Baider, Daniel Villarroel, Henrik Balslev, Italo Mesones, Ligia Estela Urrego Giraldo, Luisa Fernanda Casas, Manuel Augusto Ahuite Reategui, Reynaldo Linares-Palomino, Roderick Zagt, Sasha Cárdenas, William Farfán-Ríos, Adeilza Felipe Sampaio, Daniela Pauletto, Elvis H. Valderrama Sandoval, Freddy Ramírez Arévalo, Isau Huamantupa‐Chuquimaco, Karina García-Cabrera, Lionel Hernández, Luis Valenzuela Gamarra, Miguel Alexiades, Susamar Pansini, Walter Palacios Cuenca, William Milliken, Joana Ricardo, Gabriela Lopez‐Gonzalez, Edwin Pos, Hans ter Steege
Software Mentions: 9
Published: over 8 years ago

10.3389/fpls.2018.01673

Genetic and Pathogenicity Diversity of Aphanomyces euteiches Populations From Pea-Growing Regions in France
Cited by: 19
Author(s): Anne Quillévéré‐Hamard, Gwenola Le Roy, Anne Moussart, Alain Baranger, Didier Andrivon, Marie‐Laure Pilet‐Nayel, Christophe Le May
Software Mentions: 9
Published: over 7 years ago

10.3390/cancers13040917

Novel Gene Signatures Predictive of Patient Recurrence-Free Survival and Castration Resistance in Prostate Cancer
Cited by: 18
Author(s): Jun Ai, Baotong Zhang, Zhiqian Zhang, Hailiang Hu, Jiangtao Dong
Software Mentions: 9
Published: over 5 years ago

10.7717/peerj.10008

A model of twenty-three metabolic-related genes predicting overall survival for lung adenocarcinoma
Cited by: 3
Author(s): Zhenyu Zhao, Boxue He, Qidong Cai, Pengfei Zhang, Ping Xiong, Yuqian Zhang, Hui Xie, Xiang Wang
Software Mentions: 9
Published: over 5 years ago

10.1038/s41421-021-00274-1

Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19
Cited by: 21
Author(s): Yun Tan, Wei Zhang, Zhaoqin Zhu, Na Qiao, Yun Ling, Mingquan Guo, Tong Yin, Hai Fang, Xiaoguang Xu, Gang Lu, Peipei Zhang, Shuangshuang Yang, Ziyu Fu, Dongguo Liang, Yinyin Xie, Ruihong Zhang, Lu Jiang, Shuting Yu, Jing Lu, Fang-Ying Jiang, Jian Chen, Chenlu Xiao, Shengyue Wang, Shuo Chen, Xiu‐Wu Bian, Hongzhou Lu, Feng Liu, Sai‐Juan Chen
Software Mentions: 9
Published: about 5 years ago

10.1111/evo.13072

Niche divergence facilitated by fine‐scale ecological partitioning in a recent cichlid fish adaptive radiation
Cited by: 37
Author(s): Antonia G. P. Ford, Lukas Rüber, Jason Newton, Kanchon K. Dasmahapatra, J.D. Balarin, Kristoffer Bruun, Julia J. Day
Software Mentions: 9
Published: over 9 years ago

10.1186/s12889-018-5041-5

Dairy product consumption and risk of hip fracture: a systematic review and meta-analysis
Cited by: 67
Author(s): Shanshan Bian, Junfeng Hu, Kai Zhang, Yunguo Wang, Miaohui Yu, Jie Ma
Software Mentions: 9
Published: over 8 years ago

10.7717/peerj.7155

Nature representation in South American protected areas: country contrasts and conservation priorities
Cited by: 16
Author(s): Germán Baldi, Santiago A. Schauman, Marcos Texeira, Sofía Marinaro, Osvaldo A. Martin, Patricia Gandini, Estéban G. Jobbágy
Software Mentions: 9
Published: almost 7 years ago

10.1186/s12859-016-1321-1

GEN3VA: aggregation and analysis of gene expression signatures from related studies
Cited by: 17
Author(s): Gregory W. Gundersen, Kathleen M. Jagodnik, Holly Woodland, Nicholas F. Fernandez, Kevin Sani, Anders B. Dohlman, Peter M.U. Ung, Caroline D. Monteiro, Avner Schlessinger, Avi Ma’ayan
Software Mentions: 9
Published: over 9 years ago

10.1155/2020/8816070

Progressive and Prognostic Performance of an Extracellular Matrix-Receptor Interaction Signature in Gastric Cancer
Cited by: 20
Author(s): Xiangchou Yang, Liping Chen, Yuting Mao, Zijing Hu, Min He
Software Mentions: 9
Published: over 5 years ago

10.3389/fimmu.2019.00413

Transcriptional Profiles of California Sea Lion Peripheral NK and CD+8 T Cells Reflect Ecological Regionalization and Infection by Oncogenic Viruses
Cited by: 4
Author(s): Ignacio Peñín, Mónica Eugenia Figueroa-Cabañas, Fabiola Guerrero-de la Rosa, Luis A. Soto-García, Roberto Álvarez-Martínez, Adriana Flores-Morán, Karina Acevedo‐Whitehouse
Software Mentions: 9
Published: over 7 years ago

10.1111/mec.15648

Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species
Cited by: 11
Author(s): Christian Rellstab, Stefan Zoller, Christian Sailer, Andrew Tedder, Félix Gugerli, Kentaro Shimizu, Rolf Holderegger, Alex Widmer, Martin C. Fischer
Software Mentions: 9
Published: over 5 years ago

10.1038/s41419-019-1775-y

A new bioavailable fenretinide formulation with antiproliferative, antimetabolic, and cytotoxic effects on solid tumors
Cited by: 34
Author(s): Isabella Orienti, Federica Francescangeli, Maria Laura De Angelis, Katia Fecchi, Lucilla Bongiorno-Borbone, Michele Signore, Angelo Peschiaroli, Alessandra Boe, Alessandro Bruselles, Angelita Costantino, Adriana Eramo, Valentina Salvati, Giovanni Sette, Paola Contavalli, Lello Zolla, Toshihiko Oki, Toshio Kitamura, Massimo Spada, Alessandro Giuliani, Marta Baiocchi, Filippo La Torre, Gerry Melino, Marco Tartaglia, Ruggero De Maria, Ann Zeuner
Software Mentions: 9
Published: almost 7 years ago

10.1002/jgf2.349

Relationship between medical students’ career priority and specialty choice: A nationwide multicenter survey
Cited by: 6
Author(s): Kenya Ie, Akiko Murata, Masao Tahara, Manabu Komiyama, Shuhei Ichikawa, Yousuke Takemura, Hirotaka Onishi
Software Mentions: 9
Published: about 6 years ago

10.1186/s12864-015-1676-0

deGPS is a powerful tool for detecting differential expression in RNA-sequencing studies
Cited by: 14
Author(s): Chengcai Chu, Zhiming Fang, Xing Hua, Yaning Yang, Enguo Chen, Allen W. Cowley, Mingyu Liang, Pengyuan Liu, Yan Lu
Software Mentions: 9
Published: about 11 years ago

10.1186/s13059-015-0702-5

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
Cited by: 128
Author(s): Alexander Kanitz, Foivos Gypas, Andreas Gruber, Andreas Gruber, Georges Martín, Mihaela Zavolan
Software Mentions: 9
Published: almost 11 years ago

10.1186/1471-2164-16-S6-S3

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application
Cited by: 54
Author(s): Mattia D’Antonio, Paolo D’Onorio De Meo, Matteo Pallocca, Ernesto Picardi, Anna Maria D’Erchia, Raffaele Calogero, Tiziana Castrignanò, Graziano Pesole
Software Mentions: 9
Published: about 11 years ago

10.1186/s13059-020-02096-y

Demystifying “drop-outs” in single-cell UMI data
Cited by: 66
Author(s): Tae Hyun Kim, Xiang Zhou, Mengjie Chen
Software Mentions: 9
Published: almost 6 years ago

10.3390/ijms22042214

How Are the Flower Structure and Nectar Composition of the Generalistic Orchid Neottia ovata Adapted to a Wide Range of Pollinators?
Cited by: 8
Author(s): Emilia Brzosko, Andrzej Bajguz, Magdalena Chmur, Justyna Burzyńska, Edyta Jermakowicz, Paweł Mirski, Piotr Zieliński
Software Mentions: 9
Published: over 5 years ago

10.1186/s40168-020-00977-9

Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas
Cited by: 84
Author(s): Alice Baniel, Katherine R. Amato, Jacinta C. Beehner, Thore J. Bergman, Arianne Mercer, Rachel F. Perlman, Lauren Petrullo, Laurie J Reitsema, Sierra Sams, Amy Lu, Noah Snyder‐Mackler
Software Mentions: 9
Published: over 5 years ago

10.1186/s13040-020-00213-y

Ideas for how informaticians can get involved with COVID-19 research
Cited by: 17
Author(s): Jason H. Moore, Ian Barnett, Mary Regina Boland, Yong Chen, George Demiris, Graciela Gonzalez-Hernandez, Daniel S. Herman, Blanca E. Himes, Rebecca A. Hubbard, Dokyoon Kim, Jeffrey S. Morris, Danielle L. Mowery, Marylyn D. Ritchie, Li Shen, Ryan J. Urbanowicz, John H. Holmes
Software Mentions: 9
Published: about 6 years ago

10.3389/fmed.2021.604694

A Simple-to-Use Web-Based Calculator for Survival Prediction in Acute Respiratory Distress Syndrome
Cited by: 0
Author(s): Yong Liu, Jian Liu, Liang Huang
Software Mentions: 9
Published: over 5 years ago

10.1016/j.celrep.2020.108308

Developmental Gene Expression Differences between Humans and Mammalian Models
Cited by: 34
Author(s): Margarida Cardoso-Moreira, Ioannis Sarropoulos, Britta Velten, Matthew Mort, David Neil Cooper, Wolfgang Huber, Henrik Kaessmann
Software Mentions: 9
Published: over 5 years ago

10.1128/mSphere.00097-18

Influential Parameters for the Analysis of Intracellular Parasite Metabolomics
Cited by: 11
Author(s): Maureen A. Carey, Vincent Covelli, Audrey C. Brown, Gregory L. Medlock, Mareike Haaren, Jessica G. Cooper, Jason A. Papin, Jennifer L. Guler
Software Mentions: 9
Published: about 8 years ago

10.1128/mSystems.00474-21

Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics
Cited by: 12
Author(s): Elizabeth A. McDaniel, Francisco Moya-Flores, Natalie K. Beach, Pamela Y. Camejo, Ben O. Oyserman, Matthew Kizaric, Eng Hoe Khor, Daniel R. Noguera, Katherine D. McMahon
Software Mentions: 9
Published: almost 5 years ago

10.1098/rspb.2020.1728

Cost-free lifespan extension via optimization of gene expression in adulthood aligns with the developmental theory of ageing
Cited by: 7
Author(s): Martin I. Lind, Hanne Carlsson, Elizabeth M. L. Duxbury, Edward Ivimey‐Cook, Alexei A. Maklakov
Software Mentions: 9
Published: over 5 years ago

10.1186/s12935-019-0846-6

Integrated analysis reveals potential long non-coding RNA biomarkers and their potential biological functions for disease free survival in gastric cancer patients
Cited by: 34
Author(s): Ching‐Li Cheng, Qicai Wang, Mengting Zhu, Kelong Liu, Zhiqiao Zhang
Software Mentions: 9
Published: about 7 years ago

10.1371/journal.pcbi.1008918

Genome-wide analysis of lncRNA stability in human
Cited by: 17
Author(s): Kaiwen Shi, Tao Liu, Hanjiang Fu, Wuju Li, Xiaofei Zheng
Software Mentions: 9
Published: about 5 years ago

10.1038/s41598-021-86871-2

Family-based gene-environment interaction using sequence kernel association test (FGE-SKAT) for complex quantitative traits
Cited by: 0
Author(s): Chao-Yu Guo, Reng-Hong Wang, Hsin-Chou Yang
Software Mentions: 9
Published: about 5 years ago

10.1172/jci.insight.138729

CD28 costimulation drives tumor-infiltrating T cell glycolysis to promote inflammation
Cited by: 45
Author(s): Kathryn E. Beckermann, Rachel Hongo, Xiang Ye, Kirsten Young, Katie Carbonell, Diana C Contreras Healey, Peter J. Siska, Sierra Barone, Caroline E. Roe, Christof C. Smith, Benjamin G. Vincent, Frank M. Mason, Jonathan M. Irish, W. Kimryn Rathmell, Jeffrey C. Rathmell
Software Mentions: 9
Published: almost 6 years ago

10.1186/s12859-018-2254-7

Netpredictor: R and Shiny package to perform drug-target network analysis and prediction of missing links
Cited by: 12
Author(s): Abhik Seal, David Wild
Software Mentions: 9
Published: almost 8 years ago

10.3389/fimmu.2021.719628

Comprehensive Characterization of RNA Processing Factors in Gastric Cancer Identifies a Prognostic Signature for Predicting Clinical Outcomes and Therapeutic Responses
Cited by: 17
Author(s): Shenghan Lou, Fanzheng Meng, Xin Yin, Yao Zhang, Bangling Han, Yingwei Xue
Software Mentions: 9
Published: almost 5 years ago

10.1038/s41598-020-61932-0

Low FVC/TLC in Preserved Ratio Impaired Spirometry (PRISm) is associated with features of and progression to obstructive lung disease
Cited by: 20
Author(s): Spyridon Fortis, Alejandro P. Comellas, Victor Kim, Richard Casaburi, John E. Hokanson, James D. Crapo, Edwin K. Silverman, Emily S. Wan
Software Mentions: 9
Published: over 6 years ago

10.1038/s41598-019-50540-2

Deciphering bacterial and fungal endophyte communities in leaves of two maple trees with green islands
Cited by: 23
Author(s): Franziska Wemheuer, Bernd Wemheuer, Rolf Daniel, Stefan Vidal
Software Mentions: 9
Published: over 6 years ago

10.1186/s12889-021-10715-x

Assessing critical gaps in COVID-19 testing capacity: the case of delayed results in Ecuador
Cited by: 28
Author(s): Irene Torres, Rachel Sippy, Fernando Sacoto
Software Mentions: 9
Published: about 5 years ago

10.1002/ece3.5309

Evidence of strong stabilizing effects on the evolution of boreoeutherian (Mammalia) dental proportions
Cited by: 16
Author(s): Tesla A. Monson, Jean‐Renaud Boisserie, Marianne F. Brasil, Selene M. Clay, Rena R. Dvoretzky, Shruti Ravindramurthy, Christopher A. Schmitt, Antoine Souron, Risa Takenaka, Peter S. Ungar, Sunwoo Yoo, Michael Zhou, Madeleine E. Zuercher, Leslea J. Hlusko
Software Mentions: 9
Published: about 7 years ago

10.3389/fgene.2020.00785

Systematic Evaluation of the Diagnostic and Prognostic Significance of Competitive Endogenous RNA Networks in Prostate Cancer
Cited by: 3
Author(s): Zihu Guo, Han Liang, Yingxue Fu, Ziyin Wu, Yaohua Ma, Yueping Liu, Haiqing Wang, Li Jiang, Shengnan Liang, Zhenzhong Wang, Furong Li, Wei Xiao, Jingbo Wang, Yonghua Wang
Software Mentions: 9
Published: almost 6 years ago

10.3389/fcimb.2020.582187

Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface
Cited by: 11
Author(s): Austin Yan, James Butcher, David Mack, Alain Stintzi
Software Mentions: 9
Published: over 5 years ago

10.3389/fgene.2021.623424

Correlations Between Tumor Mutation Burden and Immunocyte Infiltration and Their Prognostic Value in Colon Cancer
Cited by: 17
Author(s): Zhangjian Zhou, Xin Xie, Xuan Wang, Xin Zhang, Wenxin Li, Tuanhe Sun, Yifan Cai, Jianhua Wu, Chengxue Dang, Hao Zhang
Software Mentions: 9
Published: over 5 years ago

10.1002/ece3.7437

Mixing tree species associated with arbuscular or ectotrophic mycorrhizae reveals dual mycorrhization and interactive effects on the fungal partners
Cited by: 14
Author(s): Heike Heklau, Nicole Schindler, François Buscot, Nico Eisenhauer, Olga Ferlian, Luis Daniel Prada-Salcedo, Helge Bruelheide
Software Mentions: 9
Published: about 5 years ago

10.12688/f1000research.27868.3

WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data
Cited by: 5
Author(s): Konstantinos Geles, Domenico Palumbo, Assunta Sellitto, Giorgio Giurato, Eleonora Cianflone, Fabiola Marino, Daniele Torella, Valeria Mirici Cappa, Giovanni Nassa, Roberta Tarallo, Alessandro Weisz, Francesca Rizzo
Software Mentions: 9
Published: almost 5 years ago

10.3389/fgene.2019.00460

Learning Causal Biological Networks With the Principle of Mendelian Randomization
Cited by: 37
Author(s): Md. Bahadur Badsha, Audrey Qiuyan Fu
Software Mentions: 9
Published: about 7 years ago

10.2196/26823

Predicting Biologic Therapy Outcome of Patients With Spondyloarthritis: Joint Models for Longitudinal and Survival Analysis
Cited by: 3
Author(s): Carolina Barata, Ana Maria Rodrigues, Helena Canhão, Susana Vinga, Alexandra M. Carvalho
Software Mentions: 9
Published: almost 5 years ago

10.1371/journal.pgen.1009259

Loss of endocytosis-associated RabGEF1 causes aberrant morphogenesis and altered autophagy in photoreceptors leading to retinal degeneration
Cited by: 9
Author(s): Passley Hargrove-Grimes, Anupam Mondal, Jessica Gumerson, Jacob Nellissery, Angel Aponte, Linn Gieser, Haohua Qian, Robert N Fariss, Juan S. Bonifacino, Tiansen Li, Anand Swaroop
Software Mentions: 9
Published: over 5 years ago

10.2196/16442

Quality Awareness and Its Influence on the Evaluation of App Meta-Information by Physicians: Validation Study
Cited by: 8
Author(s): Urs‐Vito Albrecht, Theodor Framke, Ute von Jan
Software Mentions: 9
Published: over 6 years ago

10.3390/pathogens10091221

Prevalence of Vector-Borne Pathogens in Reproductive and Non-Reproductive Tissue Samples from Free-Roaming Domestic Cats in the South Atlantic USA
Cited by: 5
Author(s): Charlotte Manvell, Kelli Ferris, Ricardo G. Maggi, Edward B. Breitschwerdt, Erin Lashnits
Software Mentions: 9
Published: almost 5 years ago

10.1186/1471-2148-14-9

Caves as microrefugia: Pleistocene phylogeography of the troglophilic North American scorpion Pseudouroctonus reddelli
Cited by: 36
Author(s): Robert W. Bryson, Lorenzo Prendini, Warren E. Savary, Peter B. Pearman
Software Mentions: 9
Published: over 12 years ago

10.3389/fcell.2020.00268

Comparative Transcriptome Landscape of Mouse and Human Hearts
Cited by: 14
Author(s): Tatsuya Anzai, Takanori Yamagata, Hideki Uosaki
Software Mentions: 9
Published: about 6 years ago

10.3758/s13414-018-1538-3

Bottom-up attention capture with distractor and target singletons defined in the same (color) dimension is not a matter of feature uncertainty
Cited by: 11
Author(s): Hanna Weichselbaum, Ulrich Ansorge
Software Mentions: 9
Published: about 8 years ago

10.7554/eLife.60188

Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cells
Cited by: 42
Author(s): Kristen L. Wells, Corey N. Miller, Andreas R. Gschwind, Wei Wu, Jonah D Phipps, Mark S. Anderson, Lars M. Steinmetz
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pcbi.1008778

Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells
Cited by: 4
Author(s): Jared Brown, Christopher Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Michael P. Schwartz, Amy Van Aartsen, John Steill, Scott Swanson, Ron Stewart, James A. Thomson, Christina Kendziorski
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0078009

Frequency Response and Gap Tuning for Nonlinear Electrical Oscillator Networks
Cited by: 0
Author(s): Harish S. Bhat, Garnet J. Vaz
Software Mentions: 9
Published: over 12 years ago

10.7150/thno.53092

Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy
Cited by: 7
Author(s): Xin Lai, Florian S. Dreyer, Martina Cantone, Martin Eberhardt, Kerstin F. Gerer, Tanushree Jaitly, Steffen Uebe, Christopher Lischer, Arif B. Ekici, Jürgen Wittmann, Hans‐Martin Jäck, Niels Schaft, Jan Dörrie, Julio Vera
Software Mentions: 9
Published: over 5 years ago

10.1007/s13755-020-00105-9

Predicting risk of stillbirth and preterm pregnancies with machine learning
Cited by: 43
Author(s): Aki Koivu, Mikko Sairanen
Software Mentions: 9
Published: over 6 years ago

10.26508/lsa.202000658

Predicting gene regulatory networks from cell atlases
Cited by: 7
Author(s): Andreas Fønss Møller, Kedar Nath Natarajan
Software Mentions: 9
Published: almost 6 years ago

10.7717/peerj.4473

pcr: an R package for quality assessment, analysis and testing of qPCR data
Cited by: 72
Author(s): Mahmoud Ahmed, Deok Ryong Kim
Software Mentions: 9
Published: over 8 years ago

10.1016/j.ebiom.2015.09.027

Distinct Transcriptional and Anti-Mycobacterial Profiles of Peripheral Blood Monocytes Dependent on the Ratio of Monocytes: Lymphocytes
Cited by: 58
Author(s): Vivek Naranbhai, Helen A. Fletcher, Rachel Tanner, Matthew K. O’Shea, Helen McShane, Benjamin P. Fairfax, Julian C. Knight, Adrian V. S. Hill
Software Mentions: 9
Published: over 10 years ago

10.1371/journal.pone.0129213

Association between Influenza A Virus Infection and Pigs Subpopulations in Endemically Infected Breeding Herds
Cited by: 35
Author(s): Andrés Díaz, Andrés Pérez, Srinand Sreevatsan, Peter Davies, Marie Culhane, Montserrat Torremorell
Software Mentions: 9
Published: about 11 years ago

10.1038/s41437-018-0059-0

Unexpected mixed-mode transmission and moderate genetic regulation of Symbiodinium communities in a brooding coral
Cited by: 46
Author(s): Kate M. Quigley, Patricia A. Warner, Line K. Bay, Bette L. Willis
Software Mentions: 9
Published: over 8 years ago

10.1007/s11831-017-9244-1

FEMPAR: An Object-Oriented Parallel Finite Element Framework
Cited by: 38
Author(s): Santiago Badia, Alberto F. Martı́n, Javier Príncipe
Software Mentions: 9
Published: over 8 years ago

10.1186/s13073-020-00786-7

A cell-of-origin epigenetic tracer reveals clinically distinct subtypes of high-grade serous ovarian cancer
Cited by: 11
Author(s): Pietro Lo Riso, Carlo Emanuele Villa, Gilles Gasparoni, Andrea Vingiani, Raffaele Luongo, Anna Manfredi, Annemarie Jungmann, Alessia Bertolotti, Francesca Borgo, Annalisa Garbi, Michela Lupia, Pasquale Laise, Vivek Das, Giancarlo Pruneri, Giuseppe Viale, Nicoletta Colombo, Teresa Manzo, Luigi Nezi, Ugo Cavallaro, Davide Cacchiarelli, Jörn Walter, Giuseppe Testa
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0192157

Tissue analyses reveal a potential immune-adjuvant function of FAP-1 positive fibroblasts in non-small cell lung cancer
Cited by: 30
Author(s): Thomas K. Kilvaer, Mehrdad Rakaee, Turid Hellevik, Arne Östman, Carina Strell, Roy M. Bremnes, Lill-Tove Busund, Tom Dønnem, Iñigo Martínez-Zubiaurre
Software Mentions: 9
Published: over 8 years ago

10.1186/s41065-021-00196-8

Dynamic co-expression modular network analysis in nonalcoholic fatty liver disease
Cited by: 4
Author(s): Jing Zheng, WU Hui-zhong, Zhiying Zhang, Songqiang Yao
Software Mentions: 9
Published: almost 5 years ago

10.26508/lsa.202000757

multicrispr: gRNA design for prime editing and parallel targeting of thousands of targets
Cited by: 16
Author(s): Aditya Bhagwat, Johannes Graumann, René Wiegandt, Mette Bentsen, Jordan M. Welker, Carsten Kuenne, Jens Preussner, Thomas Braun, Mario Looso
Software Mentions: 9
Published: almost 6 years ago

10.1093/jmcb/mjaa052

Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropouts
Cited by: 18
Author(s): Lihua Zhang, Shihua Zhang
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pcbi.1007276

Benchmarking network propagation methods for disease gene identification
Cited by: 29
Author(s): Sergio Picart‐Armada, Steven J. Barrett, David Willé, Alexandre Perera-Lluna, Alex Gutteridge, Benoît H. Dessailly
Software Mentions: 9
Published: almost 7 years ago

10.3390/s110908855

A Semantic Sensor Web for Environmental Decision Support Applications
Cited by: 45
Author(s): Alasdair J. G. Gray, Jason Sadler, Oleksandr Kit, Kostis Kyzirakos, Manos Karpathiotakis, Jean-Paul Calbimonte, Kevin Page, Raúl García‐Castro, Alex Frazer, Ixent Galpin, Alvaro A. A. Fernandes, Norman W. Paton, Óscar Corcho, Manolis Koubarakis, David De Roure, Kirk Martinez, Asuncíon Gómez-Pérez
Software Mentions: 9
Published: almost 15 years ago

10.1016/j.celrep.2019.01.041

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types
Cited by: 510
Author(s): Gianni Monaco, Bernett Lee, Weili Xu, Seri Mustafah, You Yi Hwang, Christophe Carré, Nicolas Burdin, Lucian Visan, Michele Ceccarelli, Michael Poidinger, Alfred Zippelius, João Pedro de Magalhães, Anis Larbi
Software Mentions: 9
Published: over 7 years ago

10.1186/s12859-020-03910-x

multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data
Cited by: 48
Author(s): Sebastian Canzler, Jörg Hackermüller
Software Mentions: 9
Published: over 5 years ago

10.3390/ijms22031399

DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
Cited by: 5
Author(s): Salim Ghannoum, Waldir Leoncio Netto, Damiano Fantini, Benjamin Ragan-Kelley, Amirabbas Parizadeh, Emma Jonasson, Anders Ståhlberg, Hesso Farhan, Alvaro Köhn‐Luque
Software Mentions: 9
Published: over 5 years ago

10.1530/EC-21-0027

Tumor growth rate in pancreatic neuroendocrine tumor patients undergoing PRRT with 177Lu-DOTATATE
Cited by: 4
Author(s): Olof Pettersson, Katarzyna Fröss-Baron, Joakim Crona, Anders Sundín
Software Mentions: 9
Published: about 5 years ago

10.1016/j.celrep.2020.108546

RTEL1 Regulates G4/R-Loops to Avert Replication-Transcription Collisions
Cited by: 33
Author(s): Panagiotis Kotsantis, Sandra Segura-Bayona, Pol Margalef, Paulina Marzec, Phil Ruis, Graeme Hewitt, Roberto Bellelli, Harshil Patel, Robert Goldstone, Anna R. Poetsch, Simon J. Boulton
Software Mentions: 9
Published: over 5 years ago

10.1186/s12859-016-0994-9

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments
Cited by: 79
Author(s): Ran Bi, Peng Liu
Software Mentions: 9
Published: about 10 years ago

10.3389/fonc.2021.695006

Tumor-Infiltrating PD-1hiCD8+-T-Cell Signature as an Effective Biomarker for Immune Checkpoint Inhibitor Therapy Response Across Multiple Cancers
Cited by: 7
Author(s): Zhenyu Yang, Yulan Deng, Jinghui Cheng, Shiyou Wei, Hao Luo, Lunxu Liu
Software Mentions: 9
Published: almost 5 years ago

10.3389/fmicb.2020.01536

Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations
Cited by: 13
Author(s): Elias Broman, Xiaole Sun, Christian Stranne, Marco Salgado, Stefano Bonaglia, M. C. Geibel, Martin Jakobsson, Alf Norkko, Christoph Humborg, Francisco J. A. Nascimento
Software Mentions: 9
Published: almost 6 years ago

10.1038/s41598-017-17704-4

High STAP1 expression in DUX4-rearranged cases is not suitable as therapeutic target in pediatric B-cell precursor acute lymphoblastic leukemia
Cited by: 10
Author(s): Elisabeth M. P. Steeghs, Marjolein Bakker, Alex Q. Hoogkamer, Judith M. Boer, Quirine J. Hartman, Femke Stalpers, Gabriele Escherich, Valérie de Haas, Hester A. de Groot-Kruseman, Rob Pieters, Monique L. den Boer
Software Mentions: 9
Published: over 8 years ago

10.1038/s41598-020-59292-w

Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering
Cited by: 5
Author(s): Johanne Ahrenfeldt, Madina Waisi, Isabella Charlotte Loft, Philip Thomas Lanken Conradsen Clausen, Rosa Lundbye Allesøe, Judit Szarvas, René S. Hendriksen, Frank Møller Aarestrup, Ole Lund
Software Mentions: 9
Published: over 6 years ago

10.1186/s12915-018-0518-3

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3
Cited by: 21
Author(s): Angelika Schmidt, Francesco Marabita, Narsis A. Kiani, Catharina C. Groß, Henrik J. Johansson, Szabolcs Éliás, Sini Rautio, Matilda Eriksson, Sunjay Jude Fernandes, Gilad Silberberg, Ubaid Ullah, Urvashi Bhatia, Harri Lähdesmäki, Janne Lehtiö, David Gomez-Cabrero, Heinz Wiendl, Riitta Lahesmaa, Jesper Tegnér
Software Mentions: 9
Published: about 8 years ago

10.12688/f1000research.15824.3

sPop: Age-structured discrete-time population dynamics model in C, Python, and R
Cited by: 3
Author(s): Kamil Erguler
Software Mentions: 9
Published: over 5 years ago

10.1111/1755-0998.13030

DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition
Cited by: 26
Author(s): Lukas Weilguny, Robert Kofler
Software Mentions: 9
Published: almost 7 years ago

10.1186/s12866-020-1704-3

The canine oral microbiome: variation in bacterial populations across different niches
Cited by: 36
Author(s): Avika Ruparell, Taichi Inui, Ruth Staunton, Corrin Wallis, Oliver Deusch, Lucy J. Holcombe
Software Mentions: 9
Published: over 6 years ago

10.3389/fninf.2021.561689

QDECR: A Flexible, Extensible Vertex-Wise Analysis Framework in R
Cited by: 13
Author(s): Sander Lamballais, Ryan L. Muetzel
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pone.0212024

Spatial and temporal development of deltamethrin resistance in malaria vectors of the Anopheles gambiae complex from North Cameroon
Cited by: 23
Author(s): Stanislas Mandeng, Herman Parfait Awono-Ambene, Jude D. Bigoga, Wolfgang Eyisap Ekoko, Achille Binyang, Michael Piameu, Lili Ranaise Mbakop, Betrand Nono Fesuh, Narcisse Mvondo, Raymond Tabue, Philippe Nwane, R. Mimpfoundi, Jean-Claude Toto, Immo Kleinschmidt, Tessa B. Knox, Abraham Mnzava, Martin J. Donnelly, Étienne Fondjo, Josiane Etang
Software Mentions: 9
Published: over 7 years ago

10.1371/journal.pone.0224186

Studying global processing in autism and attention-deficit/hyperactivity disorder with gaze movements: The example of a copying task
Cited by: 2
Author(s): Divya Seernani, Chara Ioannou, K. Damania, Kurt P. Spindler, Holger Hill, Tom Foulsham, Nikolaos Smyrnis, Stephan Bender, Christian Fleischhaker, Monica Biscaldi, Ulrich W. Ebner‐Priemer, Christoph Klein
Software Mentions: 9
Published: about 6 years ago

10.1186/s13062-021-00293-8

Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers
Cited by: 7
Author(s): Sergio Romera-Giner, Zoraida Andreu Martínez, Francisco García‐García, Marta R. Hidalgo
Software Mentions: 9
Published: about 5 years ago

10.7717/peerj.6746

Deterministic processes dominate soil microbial community assembly in subalpine coniferous forests on the Loess Plateau
Cited by: 19
Author(s): Pengyu Zhao, Jiabing Bao, Xue Wang, Yi Liu, Cui Li, Bo Chai
Software Mentions: 9
Published: about 7 years ago

10.1186/s12885-020-6638-5

Multiple m6A RNA methylation modulators promote the malignant progression of hepatocellular carcinoma and affect its clinical prognosis
Cited by: 33
Author(s): Nanfang Qu, Sanyu Qin, Xuemei Zhang, Xiaotong Bo, Zhengchun Liu, Chao Tan, Guiqiong Wen, Haixing Jiang
Software Mentions: 9
Published: over 6 years ago

10.3389/fcell.2021.654504

Role of CXCR4 as a Prognostic Biomarker Associated With the Tumor Immune Microenvironment in Gastric Cancer
Cited by: 5
Author(s): Yuyang Gu, Wenyue Gu, Rongrong Xie, Zhi Chen, Tongpeng Xu, Zhenghua Fei
Software Mentions: 9
Published: almost 5 years ago

10.3389/fphys.2018.00680

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
Cited by: 59
Author(s): Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loı̈c Paulevé
Software Mentions: 9
Published: about 8 years ago