Scientific Papers with Software Mentions

10.3390/cancers12051076

Tumor-Infiltrating CD8 T Cells Predict Clinical Breast Cancer Outcomes in Young Women
Cited by: 31
Author(s): Yong Won Jin, Pingzhao Hu
Software Mentions: 9
Published: about 6 years ago

A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer’s Disease
Cited by: 6
Author(s): Sze Chung Yuen, Hongmei Zhu, Siu-wai Leung
Software Mentions: 9
Published: over 6 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

10.1371/journal.pone.0056024

Novel Pancreatic Endocrine Maturation Pathways Identified by Genomic Profiling and Causal Reasoning
Cited by: 14
Author(s): Alex Gutteridge, J. Michael Rukstalis, Daniel Ziemek, Mark Tié, Lin Ji, Rebeca Ramos-Zayas, Nancy A. Nardone, Lisa D. Norquay, Martin Brenner, Kim San Tang, John D. McNeish, Rebecca K. Rowntree
Software Mentions: 9
Published: over 13 years ago

10.15252/msb.20209620

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models
Cited by: 166
Author(s): Chenling Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I. Jordan, Nir Yosef
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-021-93800-w

Year-round high abundances of the world’s smallest marine vertebrate (Schindleria) in the Red Sea and worldwide associations with lunar phases
Cited by: 4
Author(s): Vanessa Robitzch, Víctor Molina-Valdivia, Jaiber J. Solano‐Iguaran, Mauricio F. Landaeta, Michael L. Berumen
Software Mentions: 9
Published: almost 5 years ago

10.3390/mps4020028

The Transcriptome of SH-SY5Y at Single-Cell Resolution: A CITE-Seq Data Analysis Workflow
Cited by: 2
Author(s): Daniele Mercatelli, Nicola Balboni, Francesca De Giorgio, Emanuela Aleo, Caterina Garone, Federico M. Giorgi
Software Mentions: 9
Published: about 5 years ago

10.3390/metabo10030086

Local Phenomena Shape Backyard Soil Metabolite Composition
Cited by: 9
Author(s): Tra D Nguyen, Mahbobeh Lesani, Ines Forrest, Yunpeng Lan, Danya A. Dean, Quentin M. R. Gibaut, Yanting Guo, Ekram Hossain, Marcela Olvera, Hannah Panlilio, Adwaita R. Parab, Chao‐Yi Wu, Jean A. Bernatchez, Robert H. Cichewicz, Laura-Isobel McCall
Software Mentions: 9
Published: over 6 years ago

10.7150/jgen.41196

crispRdesignR: A Versatile Guide RNA Design Package in R for CRISPR/Cas9 Applications
Cited by: 2
Author(s): Dylan Beeber, Frédéric J. J. Chain
Software Mentions: 9
Published: over 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

10.1128/mBio.00399-21

Salmonella enterica Serovar Typhimurium SPI-1 and SPI-2 Shape the Global Transcriptional Landscape in a Human Intestinal Organoid Model System
Cited by: 12
Author(s): Anna-Lisa E. Lawrence, Basel H. Abuaita, Ryan P. Berger, David R. Hill, Sha Huang, Veda K. Yadagiri, Brooke Bons, Courtney Fields, Christiane E. Wobus, Jason R. Spence, Vincent B. Young, Mary X. O’Riordan
Software Mentions: 9
Published: almost 5 years ago

10.1016/j.csbj.2018.01.003

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
Cited by: 184
Author(s): Chang Xu
Software Mentions: 9
Published: over 8 years ago

10.1038/s41598-019-55434-x

QuantSeq. 3′ Sequencing combined with Salmon provides a fast, reliable approach for high throughput RNA expression analysis
Cited by: 28
Author(s): Susan M. Corley, Niamh M. Troy, Anthony Bosco, Marc R. Wilkins
Software Mentions: 9
Published: over 6 years ago

10.1186/s40168-021-01089-8

Remodeling of the maternal gut microbiome during pregnancy is shaped by parity
Cited by: 28
Author(s): Alexander S. F. Berry, Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, Kevin T. O’Brien, Ying Chen, Samuel Murray, Lydia A. Ramharack, Robert N. Baldassano, Thomas D. Parsons, Daniel P. Beiting
Software Mentions: 9
Published: almost 5 years ago

10.1038/s41598-020-76603-3

VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots
Cited by: 230
Author(s): Joachim Goedhart, Martijn S. Luijsterburg
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-019-55984-0

Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype
Cited by: 16
Author(s): Matej Mihelčić, Tomislav Šmuc, Fran Supek
Software Mentions: 9
Published: over 6 years ago

10.1097/MD.0000000000020115

The establishment and evaluation of a new model for the prediction of Children B-ALL based on TARGET
Cited by: 0
Author(s): Xiangyu Gao, Li Chen
Software Mentions: 9
Published: about 6 years ago

10.3390/genes12070995

Effects of the Developmental Regulator BOLITA on the Plant Metabolome
Cited by: 3
Author(s): Hugo Gerardo Lazcano-Ramírez, Roberto Gamboa-Becerra, Irving Jair Garcia-Lopez, Ricardo A. Chávez Montes, David Díaz-Ramírez, Octavio Martı́nez de la Vega, José Juan Ordaz-Ortíz, Stefan de Folter, Axel Tiessen-Favier, Robert Winkler, Nayelli Marsch-Martínez
Software Mentions: 9
Published: almost 5 years ago

10.1371/journal.pcbi.1009029

G2S3: A gene graph-based imputation method for single-cell RNA sequencing data
Cited by: 7
Author(s): Weimiao Wu, Yunqing Liu, Qile Dai, Xiting Yan, Zuoheng Wang
Software Mentions: 9
Published: about 5 years ago

10.7554/eLife.55862

Genomic architecture and evolutionary antagonism drive allelic expression bias in the social supergene of red fire ants
Cited by: 16
Author(s): Carlos Martínez-Ruiz, Rodrigo Pracana, Eckart Stolle, Carolina Ivon Paris, Richard A. Nichols, Yannick Wurm
Software Mentions: 9
Published: almost 6 years ago

10.3389/fninf.2017.00046

Software for Brain Network Simulations: A Comparative Study
Cited by: 42
Author(s): Ruben A. Tikidji-Hamburyan, Vikram K. Narayana, Zeki Bozkuş, Tarek El‐Ghazawi
Software Mentions: 9
Published: almost 9 years ago

10.3389/fneur.2021.713794

Seizure Forecasting Using a Novel Sub-Scalp Ultra-Long Term EEG Monitoring System
Cited by: 35
Author(s): Rachel E Stirling, Matias I. Maturana, Philippa J Karoly, Ewan S. Nurse, Kate McCutcheon, David B. Grayden, Steven G. Ringo, John M. Heasman, R. J. Hoare, Alan Lai, Wendyl D’Souza, Udaya Seneviratne, Linda Seiderer, Karen J. McLean, Kristian J Bulluss, Michael A. Murphy, Benjamin H. Brinkmann, Mark P. Richardson, Dean R. Freestone, Mark Cook
Software Mentions: 9
Published: almost 5 years ago

10.3390/ijms161226230

MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma
Cited by: 12
Author(s): Steffen Sass, Adriana Pitea, Kristian Unger, Julia Heß, Nikola S. Mueller, Fabian J. Theis
Software Mentions: 9
Published: over 10 years ago

10.1186/s13059-016-1000-6

Blood lipids influence DNA methylation in circulating cells
Cited by: 149
Author(s): Koen F. Dekkers, Maarten van Iterson, Roderick C. Slieker, Matthijs Moed, Marc Jan Bonder, M.A. van Galen, Hailiang Mei, Daria V. Zhernakova, Leonard H van den Berg, Joris Deelen, Jenny van Dongen, Diana van Heemst, Albert Hofman, Jouke Jan Hottenga, Carla Kallen, Casper G. Schalkwijk, Coen D. A. Stehouwer, Ettje F. Tigchelaar, André G. Uitterlinden, Gonneke Willemsen, Alexandra Zhernakova, Lude Franke, Peter A.C. ’t Hoen, Ritsert C. Jansen, Joyce B. J. van Meurs, Dorret I. Boomsma, Cornelia M. van Duijn, Marleen M.J. van Greevenbroek, Jan H. Veldink, Cisca Wijmenga, Erik W. van Zwet, P. Eline Slagboom, J. Wouter Jukema, Bastiaan T. Heijmans
Software Mentions: 9
Published: almost 10 years ago

10.1016/j.dib.2020.106651

Impact of malnutrition on survival in adult patients after elective cardiac surgery: Long-term follow up data
Cited by: 0
Author(s): Sergey Efremov, Tatiana Ionova, Tatiana Nikitina, Pavel E. Vedernikov, Timur Dzhumatov, Timofey S. Ovchinnikov, Abduvahhob A. Rashidov, Alexandr E Khomenko, Christian Stoppe, Daren K. Heyland, В. В. Ломиворотов
Software Mentions: 9
Published: over 5 years ago

10.1186/s13059-020-02141-w

Improved reference genome of the arboviral vector Aedes albopictus
Cited by: 61
Author(s): Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud‐Nissen, James K. Biedler, Flávia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna‐Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie, Atashi Sharma, Д. А. Карагодин, James Jenrette, Stephanie Gamez, Pascal Miesen, Patrick Masterson, Adalgisa Caccone, Maria V. Sharakhova, Zhijian Tu, Philippos Aris Papathanos, Ronald P. van Rij, Omar S. Akbari, Jeffrey R. Powell, Adam M. Phillippy, Mariangela Bonizzoni
Software Mentions: 9
Published: almost 6 years ago

10.26508/lsa.202000794

Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis
Cited by: 5
Author(s): Elisa Redl, Raheleh Sheibani-Tezerji, Crhistian de Jesus Cardona, Patricia Hamminger, Gerald Timelthaler, Melanie R. Hassler, Maša Zrimšek, Sabine Lagger, Thomas Dillinger, Lorena Hofbauer, Kristina Draganić, Andreas Tiefenbacher, Michael Kothmayer, C. Dietz, Bernard Ramsahoye, Lukas Kenner, Christoph Bock, Christian Seiser, Wilfried Ellmeier, Gabriele Schweikert, Gerda Egger
Software Mentions: 9
Published: over 5 years ago

10.7554/eLife.54756

ATR expands embryonic stem cell fate potential in response to replication stress
Cited by: 34
Author(s): Sina Atashpaz, Sara Samadi Shams, Javier Martín‐González, Endre Sebestyén, Negar Arghavanifard, Andrea Gnocchi, Eliene Albers, Simone Minardi, Giovanni Fagà, Paolo Soffientini, E. Allievi, Valeria Cancila, Ángela Bachi, Óscar Fernández-Capetillo, Claudio Tripodo, Francesco Ferrari, Andrés J. López-Contreras, Vincenzo Costanzo
Software Mentions: 9
Published: over 6 years ago

10.3389/fonc.2020.593760

Medication for Acromegaly Reduces Expression of MUC16, MACC1 and GRHL2 in Pituitary Neuroendocrine Tumour Tissue
Cited by: 4
Author(s): Rihards Saksis, Ivars Silamiķelis, Pola Laksa, Kaspars Megnis, Raitis Pečulis, Ilona Mandrika, Olesja Rogoza, Ramona Petrovska, Inga Balcere, Ilze Konrāde, Liva Steina, Jānis Stukēns, Austra Breikša, Jurijs Nazarovs, Jeļizaveta Sokolovska, Valdis Pīrāgs, Jānis Kloviņš, Vita Rovīte
Software Mentions: 9
Published: over 5 years ago

10.1186/s12862-021-01806-9

The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae)
Cited by: 8
Author(s): Polina Drozdova, Alena Kizenko, Alexandra Saranchina, Anton Gurkov, Maria Firulyova, E. B. Govorukhina, Maxim A. Timofeyev
Software Mentions: 9
Published: about 5 years ago

10.1155/2021/5633514

Roles of the Immune/Methylation/Autophagy Landscape on Single-Cell Genotypes and Stroke Risk in Breast Cancer Microenvironment
Cited by: 22
Author(s): Junyi Wu, Jun Qin, Lei Li, Kun-Dong Zhang, Yisheng Chen, Yang Li, Tao Jin, Jianrong Xu
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12859-019-2799-0

FastqPuri: high-performance preprocessing of RNA-seq data
Cited by: 22
Author(s): Paula Pérez-Rubio, Claudio Lottaz, Julia C. Engelmann
Software Mentions: 9
Published: about 7 years ago

10.1186/s13029-016-0059-5

A bedr way of genomic interval processing
Cited by: 19
Author(s): Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei‐Fei Liu, Paul C. Boutros
Software Mentions: 9
Published: over 9 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

10.1186/s12887-020-02431-z

Contemporary epidemiology of rising atrial septal defect trends across USA 1991–2016: a combined ecological geospatiotemporal and causal inferential study
Cited by: 28
Author(s): Albert Stuart Reece, Gary Kenneth Hulse
Software Mentions: 9
Published: over 5 years ago

10.1186/s12889-020-09748-5

Co-occurrence across time and space of drug- and cannabinoid- exposure and adverse mental health outcomes in the National Survey of Drug Use and Health: combined geotemporospatial and causal inference analysis
Cited by: 18
Author(s): Albert Stuart Reece, Gary Kenneth Hulse
Software Mentions: 9
Published: over 5 years ago

10.3389/fnana.2018.00010

Cerebral Artery Diameter in Inbred Mice Varies as a Function of Strain
Cited by: 23
Author(s): Baogang Qian, Robert F. Rudy, Tianxi Cai, Rose Du
Software Mentions: 9
Published: over 8 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

10.7554/eLife.28811

Sperm competition risk drives rapid ejaculate adjustments mediated by seminal fluid
Cited by: 32
Author(s): Michael Bartlett, Tammy E. Steeves, Neil J. Gemmell, Patrice Rosengrave
Software Mentions: 9
Published: over 8 years ago

10.3389/fphar.2020.607287

Netosis and Inflammasomes in Large Vessel Occlusion Thrombi
Cited by: 18
Author(s): Stephanie H. Chen, Xavier O. Scott, Yoandy Ferrer Marcelo, Vania W. Almeida, Patricia Blackwelder, Dileep R. Yavagal, Eric C. Peterson, Robert M. Starke, W. Dalton Dietrich, Robert W. Keane, Juan Pablo de Rivero Vaccari
Software Mentions: 9
Published: over 5 years ago

10.7717/peerj.9017

Population structure and microbial community diversity of two common tetillid sponges in a tropical reef lagoon
Cited by: 10
Author(s): Jake Ivan P. Baquiran, Michael Angelou L. Nada, Niño Posadas, Dana P. Manogan, Patrick C. Cabaitan, Cecilia Conaco
Software Mentions: 9
Published: about 6 years ago

10.1038/s41598-017-04141-6

The Microbiome of Endophytic, Wood Colonizing Bacteria from Pine Trees as Affected by Pine Wilt Disease
Cited by: 53
Author(s): Diogo Neves Proença, Romeu Francisco, Susanne Kublik, Anne Schöler, Gisle Vestergaard, Michael Schloter, Paula V. Morais
Software Mentions: 9
Published: about 9 years ago

10.1371/journal.pone.0241025

Genome-wide SNP analysis to assess the genetic population structure and diversity of Acrocomia species
Cited by: 13
Author(s): Brenda Gabriela Diaz, Maria Imaculada Zucchi, Alessandro Alves‐Pereira, Caléo Panhoca de Almeida, Aline Costa Lima Moraes, Suelen Alves Vianna, Joaquim Adelino de Azevedo-Filho, Carlos Augusto Colombo
Software Mentions: 9
Published: almost 5 years ago

10.3389/fgene.2019.01253

Benchmark and Parameter Sensitivity Analysis of Single-Cell RNA Sequencing Clustering Methods
Cited by: 56
Author(s): Monika Krzak, Yordan P. Raykov, Alexis Boukouvalas, Luisa Cutillo, Claudia Angelini
Software Mentions: 9
Published: over 6 years ago

10.3389/fninf.2015.00019

ANNarchy: a code generation approach to neural simulations on parallel hardware
Cited by: 65
Author(s): Julien Vitay, Helge Ülo Dinkelbach, Fred H. Hamker
Software Mentions: 9
Published: almost 11 years ago

10.1038/s42003-021-01948-y

High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers
Cited by: 9
Author(s): Chrats Melkonian, Lucas Fillinger, Siavash Atashgahi, Ulisses Nunes da Rocha, Eric Kuiper, Brett G. Olivier, Martin Braster, Willi Gottstein, Rick Helmus, John R. Parsons, Hauke Smidt, Marcelle van der Waals, Jan Gerritse, Bernd W. Brandt, Wilfred F. M. Röling, Douwe Molenaar, Rob J.M. van Spanning
Software Mentions: 9
Published: about 5 years ago

10.1177/1179546820951793

Carotid Plaque Morphology is Similar in Patients with Reduced and Normal Renal Function
Cited by: 1
Author(s): Caroline Heijl, Fredrik Kahn, Andreas Edsfeldt, Christoffer Tengryd, Jan Nilsson, Isabel Gonçalves
Software Mentions: 9
Published: over 6 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

10.1111/tpj.15190

Subgenome evolution in allotetraploid plants
Cited by: 19
Author(s): Matteo Schiavinato, Alexandrina Bodrug‐Schepers, Juliane C. Dohm, Heinz Himmelbauer
Software Mentions: 9
Published: over 5 years ago

10.3389/fmicb.2021.649517

Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST
Cited by: 15
Author(s): Carlus Deneke, Laura Uelze, Holger Brendebach, Simon H. Tausch, Burkhard Malorny
Software Mentions: 9
Published: about 5 years ago

10.3390/vaccines8010138

From Bivariate to Multivariate Analysis of Cytometric Data: Overview of Computational Methods and Their Application in Vaccination Studies
Cited by: 12
Author(s): Simone Lucchesi, Simone Furini, Donata Medaglini, Annalisa Ciabattini
Software Mentions: 9
Published: over 6 years ago

10.3389/fpls.2019.01380

The Development of Hyperspectral Distribution Maps to Predict the Content and Distribution of Nitrogen and Water in Wheat (Triticum aestivum)
Cited by: 52
Author(s): Brooke Bruning, Huajian Liu, Chris Brien, Bettina Berger, Mervyn K. Lewis, Trevor Garnett
Software Mentions: 9
Published: over 6 years ago

10.3389/fmicb.2020.575707

Evaluating the Potential Antibiotic Resistance Status in Environment Based on the Trait of Microbial Community
Cited by: 9
Author(s): Zhiguo Su, Bei Huang, Quanquan Mu, Donghui Wen
Software Mentions: 9
Published: over 5 years ago

10.1155/2020/4252580

A Novel RNA-Seq-Based Model for Preoperative Prediction of Lymph Node Metastasis in Oral Squamous Cell Carcinoma
Cited by: 7
Author(s): Bo Qiao, Min Zhao, Jing Wu, Huan Wu, Yiming Zhao, Fanhao Meng, Yu Tian, Situo Wang, Jianxin Shi, Haizhong Zhang
Software Mentions: 9
Published: almost 6 years ago

10.1371/journal.pone.0193164

Mosquito pornoscopy: Observation and interruption of Aedes aegypti copulation to determine female polyandric event and mixed progeny
Cited by: 10
Author(s): Danilo O. Carvalho, Samira Chuffi, Rafaella Sayuri Ioshino, I. C. S. Marques, Regina Fini, Maria Karina Costa, Helena Rocha Corrêa de Araújo, André Luis Costa-da-Silva, Bianca Burini Kojin, Margareth Lara Capurro
Software Mentions: 9
Published: over 8 years ago

10.1186/s12859-020-03669-1

TRIP - T cell receptor/immunoglobulin profiler
Cited by: 11
Author(s): Maria Th. Kotouza, Katerina Gemenetzi, Chrysi Galigalidou, Elisavet Vlachonikola, Nikolaos Pechlivanis, Andreas Agathangelidis, Raphael Sandaltzopoulos, Pericles A. Mitkas, Kostas Stamatopoulos, Anastasia Chatzidimitriou, Fotis Psomopoulos
Software Mentions: 9
Published: over 5 years ago

10.1126/sciadv.abg1921

Environmental vulnerability of the global ocean epipelagic plankton community interactome
Cited by: 47
Author(s): Samuel Chaffron, Erwan Delage, Marko Budinich, Damien Vintache, Nicolas Henry, Charlotte Nef, Mathieu Ardyna, Ahmed A. Zayed, Pedro C. Junger, Pierre E. Galand, Connie Lovejoy, Alison E. Murray, Hugo Sarmento, Tara Oceans Coordinators, Silvia G. Acinas, Marcel Babin, Daniele Iudicone, Olivier Jaillon, Eric Karsenti, Patrick Wincker, Lee Karp‐Boss, Matthew B. Sullivan, Chris Bowler, Colomban de Vargas, Damien Eveillard
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12864-018-4870-z

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data
Cited by: 11
Author(s): Joseph C. Devlin, Thomas Battaglia, Martin J. Blaser, Kelly V. Ruggles
Software Mentions: 9
Published: almost 8 years ago

10.3389/fonc.2021.616976

A Nomogram for Preoperative Estimation of Microvascular Invasion Risk in Hepatocellular Carcinoma: Single-Center Analyses With Internal Validation
Cited by: 5
Author(s): Jiarui Yang, Shuguang Zhu, Juanjuan Yong, Xia Long, Xiangjun Qian, Jiawei Yang, Xueqiao Hu, Yuxuan Li, Chusi Wang, Wenguang Peng, Lei Zhang, Meihai Deng, Weidong Pan
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-017-13506-w

Associations of interactions between NLRP3 SNPs and HLA mismatch with acute and extensive chronic graft-versus-host diseases
Cited by: 15
Author(s): Hidekazu Takahashi, Naoko Okayama, Natsu Yamaguchi, Yuta Miyahara, Yasuo Morishima, Yutaka Suehiro, Takahiro Yamasaki, Koji Tamada, Satoshi Takahashi, Arinobu Tojo, Shigetaka Asano, Tsuyoshi Tanabe
Software Mentions: 9
Published: over 8 years ago

10.3389/fphys.2013.00278

Methods and approaches in the topology-based analysis of biological pathways
Cited by: 162
Author(s): Cristina Mitrea, Zeinab Taghavi, Behzad Bokanizad, Samer Najeeb Hanoudi, Rebecca Tagett, Michèle Donato, Călin Voichiţa, Sorin Drăghici
Software Mentions: 9
Published: over 13 years ago

10.18632/aging.103508

Radiomics-based prediction of survival in patients with head and neck squamous cell carcinoma based on pre- and post-treatment 18F-PET/CT
Cited by: 26
Author(s): Zheran Liu, Yuan Cao, Wei Diao, Yue Cheng, Zhiyun Jia, Xingchen Peng
Software Mentions: 9
Published: almost 6 years ago

10.12688/f1000research.20916.2

Fast effect size shrinkage software for beta-binomial models of allelic imbalance
Cited by: 11
Author(s): Joshua P. Zitovsky, Michael I. Love
Software Mentions: 9
Published: over 5 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

10.1038/s41598-018-31780-0

DNA hypermethylation and differential gene expression associated with Klinefelter syndrome
Cited by: 67
Author(s): Anne Skakkebæk, Morten Muhlig Nielsen, Christian Trolle, Søren Vang, Henrik Hornshøj, Jakob Hedegaard, Mikkel Wallentin, Anders Bojesen, Jens Michael Hertz, Jens Fedder, John R. Østergaard, Jakob Skou Pedersen, Claus Højbjerg Gravholt
Software Mentions: 9
Published: almost 8 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/fpsyg.2019.02174

Expanding the Map of Intrinsic and Extrinsic Aspirations Using Network Analysis and Multidimensional Scaling: Examining Four New Aspirations
Cited by: 24
Author(s): Frank Martela, Emma L. Bradshaw, Richard M. Ryan
Software Mentions: 9
Published: over 6 years ago

10.12688/f1000research.22731.2

Fast analysis of scATAC-seq data using a predefined set of genomic regions
Cited by: 10
Author(s): Valentina Giansanti, Ming Tang, Davide Cittaro
Software Mentions: 9
Published: about 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

10.3389/fpubh.2021.679406

The Mediating Role of Placental Weight Change in the Association Between Prenatal Exposure to Thallium and Birth Weight: A Prospective Birth Cohort Study
Cited by: 4
Author(s): He Zhou, Xiangrong Sun, Yiding Wang, Yufeng Ye, Hanwei Chen, Qingsong Chen, Guanhao He, Jiaqi Wang, Xin Liu, Moran Dong, Dengzhou Chen, Guimin Chen, Lifang Yuan, Jianpeng Xiao, Jianxiong Hu, Weilin Zeng, Zuhua Rong, Qianqian Zhang, Mengya Zhou, Lingchuan Guo, Yanyun Lv, Jingjie Fan, Yudong Pu, Wenjun Ma, Bo Zhang, Tao Liu
Software Mentions: 9
Published: almost 5 years ago

10.1042/BSR20201604

Novel prognostic prediction model constructed through machine learning on the basis of methylation-driven genes in kidney renal clear cell carcinoma
Cited by: 11
Author(s): Weihao Tang, Ying Cao, Xiaoke Ma
Software Mentions: 9
Published: almost 6 years ago

10.3389/fimmu.2021.592303

Machine Learning Identifies Complicated Sepsis Course and Subsequent Mortality Based on 20 Genes in Peripheral Blood Immune Cells at 24 H Post-ICU Admission
Cited by: 35
Author(s): Shayantan Banerjee, Akram Mohammed, Hector R. Wong, Nades Palaniyar, Rishikesan Kamaleswaran
Software Mentions: 9
Published: over 5 years ago

10.3389/fpls.2014.00078

Plasma membrane lipidâ€“protein interactions affect signaling processes in sterol-biosynthesis mutants in Arabidopsis thaliana
Cited by: 24
Author(s): Henrik Zauber, Asdrúbal Burgos, Prashanth Garapati, Waltraud X. Schulze
Software Mentions: 9
Published: over 12 years ago

10.3389/fninf.2016.00008

PyRhO: A Multiscale Optogenetics Simulation Platform
Cited by: 20
Author(s): Benjamin D. Evans, Sarah Jarvis, Simon R. Schultz, Konstantin Nikolić
Software Mentions: 9
Published: over 10 years ago

10.18632/aging.104064

Clinical and prognostic pan-cancer analysis of m6A RNA methylation regulators in four types of endocrine system tumors
Cited by: 29
Author(s): Kai Li, Hui Luo, Hui Luo, Xiao Zhu
Software Mentions: 9
Published: over 5 years ago

10.3390/s19224824

Validation of Wireless Sensors for Psychophysiological Studies
Cited by: 9
Author(s): Pedro Silva Moreira, Pedro Chaves, Rúben Dias, Nuno Dias, Pedro R. Almeida
Software Mentions: 9
Published: over 6 years ago

10.3389/fphys.2018.01945

A Quantitative Comparison of Clinically Employed Parameters in the Assessment of Acute Cerebral Ischemia Using Dynamic Susceptibility Contrast Magnetic Resonance Imaging
Cited by: 1
Author(s): Christian Našel, Uros Klickovic, Heike-Marie Kührer, Kersten Villringer, Jochen B. Fiebach, Arno Villringer, Ewald Moser
Software Mentions: 9
Published: over 7 years ago

10.1038/s41398-020-0738-5

A polygenic predictor of treatment-resistant depression using whole exome sequencing and genome-wide genotyping
Cited by: 32
Author(s): Chiara Fabbri, Siegfried Kasper, Alexander Kautzky, Joseph Zohar, Daniel Souery, Stuart Montgomery, Diego Albani, Gianluigi Forloni, Panagiotis Ferentinos, Dan Rujescu, Julien Mendlewicz, Rudolf Uher, Cathryn M. Lewis, Alessandro Serretti
Software Mentions: 9
Published: over 6 years ago

10.1186/s12859-018-2287-y

miRge 2.0 for comprehensive analysis of microRNA sequencing data
Cited by: 54
Author(s): Yin Lu, Alexander S. Baras, Marc K. Halushka
Software Mentions: 9
Published: almost 8 years ago

10.3390/ijerph18084052

The Impact of Temperature on the Risk of COVID-19: A Multinational Study
Cited by: 5
Author(s): Ya‐Chen Yang, Jason Lee
Software Mentions: 9
Published: about 5 years ago

10.3389/fncel.2020.00065

Single-Cell Analysis of Neuroinflammatory Responses Following Intracranial Injection of G-Deleted Rabies Viruses
Cited by: 29
Author(s): Kee Wui Huang, Bernardo L. Sabatini
Software Mentions: 9
Published: over 6 years ago

10.3389/fcell.2021.643603

Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain
Cited by: 8
Author(s): Samuel E. Ross, Daniel Hesselson, Ozren Bogdanović
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0209402

Assessing the potential for competition between Pacific Halibut (Hippoglossus stenolepis) and Arrowtooth Flounder (Atheresthes stomias) in the Gulf of Alaska
Cited by: 6
Author(s): Cheryl L. Barnes, Anne H. Beaudreau, Mary E. Hunsicker, Lorenzo Ciannelli
Software Mentions: 9
Published: over 7 years ago

10.3389/fpls.2019.01355

In-Field Detection and Quantification of Septoria Tritici Blotch in Diverse Wheat Germplasm Using Spectral–Temporal Features
Cited by: 22
Author(s): Jonas Anderegg, Andreas Hund, Petteri Karisto, Alexey Mikaberidze
Software Mentions: 9
Published: over 6 years ago

10.3389/fnbeh.2019.00036

Prolonged Bat Call Exposure Induces a Broad Transcriptional Response in the Male Fall Armyworm (Spodoptera frugiperda; Lepidoptera: Noctuidae) Brain
Cited by: 13
Author(s): Scott D Cinel, Steven J. Taylor
Software Mentions: 9
Published: over 7 years ago

10.3389/fcimb.2020.00137

Microbiotyping the Sinonasal Microbiome
Cited by: 15
Author(s): Ahmed Bassiouni, S. Paramasivan, Arron Shiffer, Matthew R. Dillon, Emily K. Cope, Clare Cooksley, Mahnaz Ramezanpour, Sophia Moraitis, Mohammad Javed Ali, Benjamin S. Bleier, Claudio Callejas, Marjolein Cornet, Richard Douglas, Daniel Lorena Dutra, Christos Georgalas, Richard J. Harvey, Peter H. Hwang, Amber U. Luong, Rodney J. Schlosser, Pongsakorn Tantilipikorn, Marc A. Tewfik, Sarah Vreugde, Peter John Wormald, J. Gregory Caporaso, Alkis James Psaltis
Software Mentions: 9
Published: about 6 years ago

10.1111/1755-0998.13362

Chromosome‐scale assembly of the genome of <i>Salix</i><i>dunnii</i> reveals a male‐heterogametic sex determination system on chromosome 7
Cited by: 24
Author(s): Li He, Kai‐Hua Jia, Rengang Zhang, Yuan Wang, Tian-Le Shi, Zhichao Li, Si-Wen Zeng, Xin-Jie Cai, Natascha D. Wagner, Elvira Hörandl, Aline Muyle, Ke Yang, Deborah Charlesworth, Jian‐Feng Mao
Software Mentions: 9
Published: over 5 years ago

10.1534/g3.120.401193

MoBPS - Modular Breeding Program Simulator
Cited by: 33
Author(s): Torsten Pook, Martin Schlather, Henner Simianer
Software Mentions: 9
Published: about 6 years ago

10.3389/fimmu.2018.02074

Epigenetic Enhancer Marks and Transcription Factor Binding Influence Vκ Gene Rearrangement in Pre-B Cells and Pro-B Cells
Cited by: 13
Author(s): Eden Kleiman, Salvatore Loguercio, Ann J. Feeney
Software Mentions: 9
Published: almost 8 years ago

10.1371/journal.pone.0254491

Learning epistatic gene interactions from perturbation screens
Cited by: 2
Author(s): Kieran Elmes, Fabian Schmich, Ewa Szczurek, Jeremy L. Jenkins, Niko Beerenwinkel, Alex Gavryushkin
Software Mentions: 9
Published: almost 5 years ago

10.3389/fpsyg.2019.01507

A Primer to (Cross-Cultural) Multi-Group Invariance Testing Possibilities in R
Cited by: 147
Author(s): Ronald Fischer, Johannes Alfons Karl
Software Mentions: 9
Published: almost 7 years ago

10.3389/fnmol.2021.664912

Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for Cognition
Cited by: 9
Author(s): Sergio Espeso‐Gil, Aliaksei Z. Holik, Sarah Bonnin, Shalu Jhanwar, Sandhya Chandrasekaran, Roger Piqué-Regi, Júlia Albaigès-Ràfols, Michael P. Maher, Jon Permanyer, Manuel Irimia, Marc R. Friedländer, Meritxell Pons-Espinal, Schahram Akbarian, Mara Dierssen, Philipp G. Maass, Charlotte N. Hor, Stephan Ossowski
Software Mentions: 9
Published: about 5 years ago

10.1038/s41409-020-01186-6

Early bilirubinemia after allogeneic stem cell transplantation—an endothelial complication
Cited by: 7
Author(s): Hao Dai, Olaf Penack, Aleksandar Radujkovic, David Schult, Joshua Majer-Lauterbach, Igor Wolfgang Blau, Lars Bullinger, Sihe Jiang, Carsten Müller‐Tidow, Peter Dreger, Thomas Luft
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-020-77201-z

An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae
Cited by: 3
Author(s): José Córdoba-Caballero, Pedro Seoane, Fernando M. Jabato, James R. Perkins, Manuel Manchado, M. Gonzalo Claros
Software Mentions: 9
Published: over 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

10.3389/fpsyg.2020.599788

Faster Visual Information Processing in Video Gamers Is Associated With EEG Alpha Amplitude Modulation
Cited by: 5
Author(s): Yannik Hilla, Jörg von Mankowski, Julia Föcker, Paul Sauseng
Software Mentions: 9
Published: over 5 years ago

10.1186/s12870-019-1679-0

Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon
Cited by: 34
Author(s): Alejandro Sanz-Carbonell, Maria Carmen Marqués, Alexander Bustamante, Mario A. Fares, Guillermo Rodrigo, Gustavo Gómez
Software Mentions: 9
Published: over 7 years ago