10.1007/s00429-018-1628-y

Diffusion MRI-based cortical connectome reconstruction: dependency on tractography procedures and neuroanatomical characteristics
Cited by: 61
Author(s): Michel R.T. Sinke, Willem M. Otte, Daan Christiaens, Oliver Schmitt, Alexander Leemans, Annette van der Toorn, R. Angela Sarabdjitsingh, Marian Joëls, Rick M. Dijkhuizen
Software Mentions: 12
Published: over 8 years ago

10.3390/microorganisms9071526

Exploring the Individual Bacterial Microbiota of Questing Ixodes ricinus Nymphs
Cited by: 2
Author(s): Aurélien Alafaci, Alexandre Crépin, Sabine Beaubert, Jean‐Marc Berjeaud, Vincent Delafont, Julien Verdon
Software Mentions: 12
Published: almost 5 years ago

10.1371/journal.pone.0251323

The role of multiple metabolic genes in predicting the overall survival of colorectal cancer: A study based on TCGA and GEO databases
Cited by: 2
Author(s): Weijun Shi, Xincan Li, Shuai Xu, Hexin Wen, Tianwen Chen, Huazhang Wu, Mulin Liu
Software Mentions: 12
Published: almost 5 years ago

10.1371/journal.pone.0244005

DDRP: Real-time phenology and climatic suitability modeling of invasive insects
Cited by: 13
Author(s): Brittany S. Barker, Leonard B. Coop, Tyson Wepprich, Fritzi S. Grevstad, Gericke Cook
Software Mentions: 12
Published: over 5 years ago

10.3390/insects10090271

Comparison of Twelve Ant Species and Their Susceptibility to Fungal Infection
Cited by: 13
Author(s): Nick Bos, Viljami Kankaanpää-Kukkonen, Dalial Freitak, Dimitri Stucki, Liselotte Sundström
Software Mentions: 12
Published: almost 7 years ago

10.1111/jcmm.16605

Leptin receptor is a key gene involved in the immunopathogenesis of thyroid‐associated ophthalmopathy
Cited by: 3
Author(s): Ziyi Chen, Zhe Chen, Jingya Wang, Meng Zhang, Xiaofei Wang, Deji Cuomu, Bingyin Shi, Yue Wang
Software Mentions: 12
Published: about 5 years ago

10.1099/mgen.0.000499

A comprehensive and high-quality collection of Escherichia coli genomes and their genes
Cited by: 32
Author(s): Gal Horesh, Grace A. Blackwell, Gerry Tonkin‐Hill, Jukka Corander, Eva Heinz, Nicholas R. Thomson
Software Mentions: 12
Published: over 5 years ago

10.1186/s12942-017-0097-5

Estimating the prevalence of 26 health-related indicators at neighbourhood level in the Netherlands using structured additive regression
Cited by: 18
Author(s): Jan van de Kassteele, Laurens Zwakhals, Oscar Breugelmans, Caroline Ameling, Carolien van den Brink
Software Mentions: 12
Published: almost 9 years ago

10.1186/s12937-021-00692-7

A review of statistical methods for dietary pattern analysis
Cited by: 103
Author(s): Junkang Zhao, Zhiyao Li, Qian Gao, Haifeng Zhao, Shuting Chen, Ling-Qiao Huang, Yiyun Wang, Tong Wang
Software Mentions: 12
Published: about 5 years ago

10.12688/f1000research.8839.3

A cross-package Bioconductor workflow for analysing methylation array data
Cited by: 80
Author(s): Jovana Maksimovic, Belinda Phipson, Alicia Oshlack
Software Mentions: 12
Published: about 9 years ago

10.1038/srep26451

Glycosyltransferase Gene Expression Profiles Classify Cancer Types and Propose Prognostic Subtypes
Cited by: 52
Author(s): Jahanshah Ashkani, Kevin J. Naidoo
Software Mentions: 12
Published: about 10 years ago

10.1186/s13148-019-0729-7

Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease
Cited by: 26
Author(s): Mikko Konki, Maia Malonzo, Ida Karlsson, Noora Lindgrén, Bishwa Ghimire, Johannes Smolander, Noora M. Scheinin, Miina Ollikainen, Asta Laiho, Laura L. Elo, Tapio Lönnberg, Matias Röyttä, Nancy L. Pedersen, Jaakko Kaprio, Harri Lähdesmäki, Juha O. Rinne, Riikka Lund
Software Mentions: 12
Published: almost 7 years ago

10.1371/journal.pone.0205742

The calm during the storm: Snowfall events decrease the movement rates of grey wolves (Canis lupus)
Cited by: 10
Author(s): Amanda Droghini, Stan Boutin
Software Mentions: 12
Published: over 7 years ago

10.1111/gcb.15637

Impacts of climate change on aquatic insects in temperate alpine regions: Complementary modeling approaches applied to Swiss rivers
Cited by: 6
Author(s): Pablo Timoner, Marc Fasel, Seyed Saeid Ashraf Vaghefi, Pierre Marle, Emmanuel Castella, Frédéric Moser, Anthony Lehmann
Software Mentions: 12
Published: about 5 years ago

10.1155/2021/6656926

The Preference, Effect, and Prognosis of Intra-Aortic Balloon Counterpulsation in Acute Myocardial Infarction Complicated by Cardiogenic Shock Patients: A Retrospective Cohort Study
Cited by: 0
Author(s): Wenjun Wang, Fang Yang, Xixiang Lin, Qin Zhong, Zongren Li, Xu Chen, Junfeng Wang, Kunlun He
Software Mentions: 12
Published: over 5 years ago

10.1186/s12859-021-04178-5

WEScover: selection between clinical whole exome sequencing and gene panel testing
Cited by: 3
Author(s): In-Hee Lee, Yufei Lin, William Jefferson Alvarez, Carles Hernández-Ferrer, Kenneth D. Mandl, Sek Won Kong
Software Mentions: 12
Published: about 5 years ago

10.1371/journal.ppat.1005548

Determinants of Arbovirus Vertical Transmission in Mosquitoes
Cited by: 90
Author(s): Sébastian Lequime, Paul Rácz, Louis Lambrechts
Software Mentions: 12
Published: about 10 years ago

10.1534/g3.120.401527

rdmc: An Open Source R Package Implementing Convergent Adaptation Models of Lee and Coop (2017)
Cited by: 2
Author(s): Silas Tittes
Software Mentions: 12
Published: almost 6 years ago

10.1371/journal.pone.0152098

Combining Soil Databases for Topsoil Organic Carbon Mapping in Europe
Cited by: 37
Author(s): Ece Aksoy, Yusuf Yiğini, Luca Montanarella
Software Mentions: 12
Published: about 10 years ago

10.1186/s12859-019-3096-7

Moiety modeling framework for deriving moiety abundances from mass spectrometry measured isotopologues
Cited by: 9
Author(s): Jianya Huan, Hunter N. B. Moseley
Software Mentions: 12
Published: over 6 years ago

10.1371/journal.pone.0195065

Dengue forecasting in São Paulo city with generalized additive models, artificial neural networks and seasonal autoregressive integrated moving average models
Cited by: 48
Author(s): Oswaldo Santos Baquero, Lidia Maria Reis Santana, Francisco Chiaravalloti Neto
Software Mentions: 12
Published: about 8 years ago

10.7554/eLife.65751

Visualizing anatomically registered data with brainrender
Cited by: 64
Author(s): Federico Claudi, Adam L. Tyson, Luigi Petrucco, Troy W. Margrie, Rubén Portugues, Tiago Branco
Software Mentions: 12
Published: over 5 years ago

10.1186/s12911-017-0500-y

Predicting two-year survival versus non-survival after first myocardial infarction using machine learning and Swedish national register data
Cited by: 53
Author(s): John Wallert, Mattia Tomasoni, Guy Madison, Claes Held
Software Mentions: 12
Published: almost 9 years ago

10.3390/insects12020180

Unexpected Effects of Local Management and Landscape Composition on Predatory Mites and Their Food Resources in Vineyards
Cited by: 16
Author(s): Stefan Möth, Andreas Walzer, Markus Redl, Božana Petrović, Christoph Hoffmann, Silvia Winter
Software Mentions: 12
Published: over 5 years ago

10.3389/fimmu.2021.698236

Comprehensive Analysis of Clinical Significance, Immune Infiltration and Biological Role of m6A Regulators in Early-Stage Lung Adenocarcinoma
Cited by: 3
Author(s): Bolun Zhou, Shugeng Gao
Software Mentions: 12
Published: over 4 years ago

10.1002/ece3.8020

Functional groups in piscivorous fishes
Cited by: 8
Author(s): Michalis Mihalitsis, David R. Bellwood
Software Mentions: 12
Published: almost 5 years ago

10.1186/s12889-021-11065-4

Who or what is to blame? Examining sociodemographic relationships to beliefs about causes, control, and responsibility for cancer and chronic disease prevention in Alberta, Canada
Cited by: 5
Author(s): Kimberley D. Curtin, Mathew Thomson, Candace I. J. Nykiforuk
Software Mentions: 12
Published: about 5 years ago

10.1093/molbev/msaa128

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

10.1186/s13059-019-1790-4

Identifying significantly impacted pathways: a comprehensive review and assessment
Cited by: 113
Author(s): Tuan-Minh Nguyen, Adib Shafi, Tin Nguyen, Sorin Drăghici
Software Mentions: 12
Published: over 6 years ago

10.3389/fgene.2019.01079

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

10.1186/s12859-018-2367-z

Biotite: a unifying open source computational biology framework in Python
Cited by: 54
Author(s): Patrick Kunzmann, Kay Hamacher
Software Mentions: 12
Published: over 7 years ago

10.3390/toxins12070433

Low Doses of Mycotoxin Mixtures below EU Regulatory Limits Can Negatively Affect the Performance of Broiler Chickens: A Longitudinal Study
Cited by: 26
Author(s): Oluwatobi Kolawole, A. Graham, Caroline Julie Donaldson, B. Owens, Wilfred A. Abia, Julie Meneely, M. Alcorn, Lisa Connolly, Chris Elliott
Software Mentions: 12
Published: almost 6 years ago

10.1371/journal.pone.0236305

Defining the sediment prokaryotic communities of the Indian River Lagoon, FL, USA, an Estuary of National Significance
Cited by: 7
Author(s): David J. Bradshaw, Nicholas J. Dickens, John H. Trefry, Peter J. McCarthy
Software Mentions: 12
Published: over 5 years ago

10.3390/biom11020338

Fungal X-Intrinsic Protein Aquaporin from Trichoderma atroviride: Structural and Functional Considerations
Cited by: 1
Author(s): Maroua Ben Amira, Mohamed Faize, Magnus Karlsson, Mukesh Dubey, Magdalena Frąc, Jacek Panek, Boris Fumanal, Aurélie Gousset-Dupont, Jean-Louis Julien, Hatem Chaar, Daniel Auguin, Robin Mom, Philippe Label, Jean-Stéphane Venisse
Software Mentions: 12
Published: over 5 years ago

10.3389/fimmu.2020.01659

Conventional and Computational Flow Cytometry Analyses Reveal Sustained Human Intrathymic T Cell Development From Birth Until Puberty
Cited by: 2
Author(s): Marieke Lavaert, Brecht Valcke, Bart Vandekerckhove, Georges Leclercq, Kai Ling Liang, Tom Taghon
Software Mentions: 12
Published: almost 6 years ago

10.1155/2021/6653247

A Risk Signature with Nine Stemness Index-Associated Genes for Predicting Survival of Patients with Uterine Corpus Endometrial Carcinoma
Cited by: 9
Author(s): Haoya Xu, Ruoyao Zou, Jiyu Liu, Li Zhu
Software Mentions: 12
Published: over 5 years ago

10.4269/ajtmh.20-0757

A Computational Modeling Study of COVID-19 in Bangladesh
Cited by: 7
Author(s): Irtesam Mahmud Khan, Ubydul Haque, Samiha Kaisar, Md. Saidur Rahman
Software Mentions: 12
Published: over 5 years ago

10.1186/s12862-016-0661-9

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

10.3389/fmolb.2021.681526

Identification of Key Biomarkers and Immune Infiltration in Systemic Juvenile Idiopathic Arthritis by Integrated Bioinformatic Analysis
Cited by: 2
Author(s): Min Zhang, Rongxin Dai, Qianqian Zhao, Lina Zhou, Yunfei An, Xuemei Tang, Xiaodong Zhao
Software Mentions: 12
Published: almost 5 years ago

10.1371/journal.pone.0225900

PyRates—A Python framework for rate-based neural simulations
Cited by: 10
Author(s): Richard Gast, Daniel Rose, Christoph Salomon, Harald E. Möller, Nikolaus Weiskopf, Thomas R. Knösche
Software Mentions: 12
Published: over 6 years ago

10.1038/srep18871

LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights
Cited by: 37
Author(s): Xinran Dong, Yun Huang, Xiao Wang, Weidong Tian
Software Mentions: 12
Published: over 10 years ago

10.7554/eLife.52465

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

10.3389/fmicb.2020.01116

Crop Management Impacts the Soybean (Glycine max) Microbiome
Cited by: 41
Author(s): Reid Longley, Zachary A Noel, Gian Maria Niccolò Benucci, Martin I. Chilvers, Frances Trail, Gregory Bonito
Software Mentions: 12
Published: about 6 years ago

10.7717/peerj.9847

Prognostic implications of metabolism-associated gene signatures in colorectal cancer
Cited by: 21
Author(s): Yifei Miao, Qiutian Li, Jiangtao Wang, Wuxia Quan, Chen Li, Yuan Yang, Denghai Mi
Software Mentions: 12
Published: almost 6 years ago

10.1093/gigascience/gix037

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics
Cited by: 48
Author(s): Leonardo Perez de Souza, Thomas Naake, Takayuki Tohge, Alisdair R. Fernie
Software Mentions: 12
Published: about 9 years ago

10.12688/f1000research.9501.2

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Cited by: 693
Author(s): Aaron T. L. Lun, Davis J. McCarthy, John C. Marioni
Software Mentions: 12
Published: over 9 years ago

10.1186/s12920-017-0303-0

Classifying cancer genome aberrations by their mutually exclusive effects on transcription
Cited by: 8
Author(s): Jonathan Dayton, Stephen R. Piccolo
Software Mentions: 12
Published: over 8 years ago

10.26508/lsa.202000770

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

10.1002/ece3.7294

Determinants of habitat suitability models transferability across geographically disjunct populations: Insights from <i>Vipera ursinii urs</i> <i>inii</i>
Cited by: 8
Author(s): Francesco Cerasoli, Aurélien Besnard, Marc-Antoine Marchand, Paola D’Alessandro, Mattia Iannella, Maurizio Biondi
Software Mentions: 12
Published: over 5 years ago

10.7554/eLife.58993

Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns
Cited by: 23
Author(s): Kathleen Greenham, Ryan C. Sartor, Stevan Zorich, Ping Lou, Todd C. Mockler, C. Robertson McClung
Software Mentions: 12
Published: over 5 years ago

10.1371/journal.pone.0075146

NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations
Cited by: 29
Author(s): Ivan Merelli, Píetro Lió, Luciano Milanesi
Software Mentions: 12
Published: almost 13 years ago

10.1093/gigascience/giab011

The case for using mapped exonic non-duplicate reads when reporting RNA-sequencing depth: examples from pediatric cancer datasets
Cited by: 2
Author(s): Holly C. Beale, Jacquelyn Roger, Matthew Cattle, Liam T. McKay, Drew Thompson, Katrina Learned, A. Geoffrey Lyle, Ellen Kephart, R. Currie, Du Linh Lam, Lauren Sanders, Jacob Pfeil, John Vivian, Isabel Bjork, Sofie R. Salama, David Haussler, Olena M. Vaske
Software Mentions: 12
Published: over 5 years ago

10.1002/ece3.6606

Evolution of breeding plumages in birds: A multiple‐step pathway to seasonal dichromatism in New World warblers (Aves: Parulidae)
Cited by: 16
Author(s): Ryan S. Terrill, Glenn F. Seeholzer, Jared D. Wolfe
Software Mentions: 12
Published: almost 6 years ago

10.3390/ani11020485

Action Recognition Using a Spatial-Temporal Network for Wild Felines
Cited by: 9
Author(s): Liqi Feng, Yaqin Zhao, Yang Sun, Wenxuan Zhao, Jiaxi Tang
Software Mentions: 12
Published: over 5 years ago

10.1007/s00216-020-03093-7

Repeated double cross-validation applied to the PCA-LDA classification of SERS spectra: a case study with serum samples from hepatocellular carcinoma patients
Cited by: 23
Author(s): Elisa Gurian, Alessia Di Silvestre, Elisa Mitri, Devis Pascut, Claudio Tiribelli, Mauro Giuffrè, Lory Saveria Crocè, Valter Sergo, Alois Bonifacio
Software Mentions: 12
Published: over 5 years ago

10.1371/journal.pgen.1009141

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

10.1186/s12859-020-03803-z

NBZIMM: negative binomial and zero-inflated mixed models, with application to microbiome/metagenomics data analysis
Cited by: 38
Author(s): Xinyan Zhang, Nengjun Yi
Software Mentions: 12
Published: over 5 years ago

10.1002/ece3.5295

<i>Acacia dealbata</i> invasion in Chile: Surprises from climatic niche and species distribution models
Cited by: 12
Author(s): Bárbara Langdon, Aníbal Pauchard, Ramiro O. Bustamante
Software Mentions: 12
Published: almost 7 years ago

10.3389/fmicb.2019.02597

New Insights Into Cinnamoyl Esterase Activity of Oenococcus oeni
Cited by: 9
Author(s): Ingrid Collombel, Chrats Melkonian, Douwe Molenaar, Francisco M. Campos, Tim Hogg
Software Mentions: 12
Published: over 6 years ago

10.12688/f1000research.14013.2

Taxa: An R package implementing data standards and methods for taxonomic data
Cited by: 23
Author(s): Zachary Foster, Scott Chamberlain, Niklaus J. Grünwald
Software Mentions: 12
Published: almost 8 years ago

10.1186/s13073-016-0384-y

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

10.1186/s13059-019-1900-3

Benchmarking principal component analysis for large-scale single-cell RNA-sequencing
Cited by: 60
Author(s): Koki Tsuyuzaki, Hiroyuki Sato, K. Sato, Itoshi Nikaido
Software Mentions: 12
Published: over 6 years ago

10.3389/fgene.2021.655536

Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges
Cited by: 30
Author(s): Jiajia Li, Zusen Fan, Weiling Zhao, Xiaobo Zhou
Software Mentions: 12
Published: about 5 years ago

10.3389/fsufs.2020.561517

Predictive Models May Complement or Provide an Alternative to Existing Strategies for Assessing the Enteric Pathogen Contamination Status of Northeastern Streams Used to Provide Water for Produce Production
Cited by: 19
Author(s): Daniel Weller, Tanzy Love, Alexandra Belias, Martin Wiedmann
Software Mentions: 12
Published: over 5 years ago

10.3389/fmicb.2017.01553

Effect of Pre-weaning Diet on the Ruminal Archaeal, Bacterial, and Fungal Communities of Dairy Calves
Cited by: 58
Author(s): Juliana Dias, Marcos Inácio Marcondes, Melline Fontes Noronha, Rafael Tassinari Resende, F. S. Machado, Hilário Cuquetto Mantovani, Kimberly A. Dill‐McFarland, Garret Suen
Software Mentions: 12
Published: almost 9 years ago

10.1002/ece3.7992

Using Delaunay triangulation to sample whole‐specimen color from digital images
Cited by: 5
Author(s): Jennifer J Valvo, J. David Aponte, Mitch J Daniel, Kenna Dwinell, Helen Rodd, David Houle, Kimberly A. Hughes
Software Mentions: 12
Published: almost 5 years ago

10.1371/journal.pone.0191956

Carotenoid coloration and health status of urban Eurasian kestrels (Falco tinnunculus)
Cited by: 24
Author(s): Petra Sumasgutner, Marius Adrion, Anita Gamauf
Software Mentions: 12
Published: over 8 years ago

10.1007/s12032-017-0963-9

The identification of key genes and pathways in hepatocellular carcinoma by bioinformatics analysis of high-throughput data
Cited by: 107
Author(s): Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Software Mentions: 12
Published: about 9 years ago

10.7554/eLife.60474

The effect of hybridization on transposable element accumulation in an undomesticated fungal species
Cited by: 26
Author(s): Mathieu Hénault, Souhir Marsit, Guillaume Charron, Christian R. Landry
Software Mentions: 12
Published: almost 6 years ago

10.3390/plants10050879

Multivariate Analysis of Morpho-Physiological Traits Reveals Differential Drought Tolerance Potential of Bread Wheat Genotypes at the Seedling Stage
Cited by: 26
Author(s): Mohammed Mohi-Ud-Din, Md. Alamgir Hossain, Md. Motiar Rohman, Md. Nesar Uddin, Md. Sabibul Haque, Jalal Uddin Ahmed, Akbar Hossain, Mohamed M. Hassan, Mohammad Golam Mostofa
Software Mentions: 12
Published: about 5 years ago

10.26508/lsa.202001004

CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data
Cited by: 21
Author(s): Almut Luetge, Joanna Zyprych-Walczak, Urszula Brykczynska Kunzmann, Helena L. Crowell, Daniela Calini, Dheeraj Malhotra, Charlotte Soneson, Mark D. Robinson
Software Mentions: 12
Published: about 5 years ago

10.1002/cam4.2786

FOLFOX treatment response prediction in metastatic or recurrent colorectal cancer patients via machine learning algorithms
Cited by: 24
Author(s): Wei Lu, Dongliang Fu, Xianglong Kong, Zhiheng Huang, Maxwell Hwang, Yaowu Zhu, Liubo Chen, Kai Jiang, Xinlin Li, Yihua Wu, Jun Li, Ying Yuan, Kefeng Ding
Software Mentions: 12
Published: over 6 years ago

10.7554/eLife.63003

Short-term exposure to intermittent hypoxia leads to changes in gene expression seen in chronic pulmonary disease
Cited by: 17
Author(s): Gang Wu, Yin Yeng Lee, Evelyn M. Gulla, Andrew Potter, Joseph A. Kitzmiller, Marc D. Ruben, Nathan Salomonis, JA Whitsett, Lauren J. Francey, John B. Hogenesch, Smith Dl
Software Mentions: 12
Published: over 5 years ago

10.3389/fonc.2020.596822

Predictive Model and Precaution for Oral Mucositis During Chemo-Radiotherapy in Nasopharyngeal Carcinoma Patients
Cited by: 10
Author(s): Peijing Li, Kaixin Li, Tengchuan Jin, Hua Lin, Jun Fang, Shengchun Yang, Wei‐Chih Shen, Jia Chen, Jiang Zhang, Xiaozhong Chen, Ming Chen, Yuanyuan Chen
Software Mentions: 12
Published: over 5 years ago

10.1371/journal.pone.0197176

Investigation of protein quaternary structure via stoichiometry and symmetry ınformation
Cited by: 12
Author(s): Selçuk Korkmaz, José M. Duarte, Andreas Prlić, Dinçer Göksülük, Gökmen Zararsız, Osman Saraçbaşı, S.K. Burley, Peter W. Rose
Software Mentions: 12
Published: about 8 years ago

10.1186/s12885-021-07788-7

Comprehensive analysis of genomic mutation signature and tumor mutation burden for prognosis of intrahepatic cholangiocarcinoma
Cited by: 14
Author(s): Rui Zhang, Qi Li, Jiao Fu, Z C Jin, Jingbo Su, Jian Zhang, Chen Chen, Zhimin Geng, Dong Zhang
Software Mentions: 12
Published: over 5 years ago

10.3389/fimmu.2021.647832

Large-Scale Gene Expression Signatures Reveal a Microbicidal Pattern of Activation in Mycobacterium leprae-Infected Monocyte-Derived Macrophages With Low Multiplicity of Infection
Cited by: 9
Author(s): Thyago Leal-Calvo, Bruna Letícia Martins, Daniele Ferreira de Faria Bertoluci, Patrícia Sammarco Rosa, Rodrigo Mendes de Camargo, G. Germano, Vânia Niéto Brito de Souza, Ana Carla Pereira Latini, Milton Ozório Moraes
Software Mentions: 12
Published: about 5 years ago

10.1038/s41598-020-69239-w

Neural innervation as a potential trigger of morphological color change and sexual dimorphism in cichlid fish
Cited by: 14
Author(s): Yipeng Liang, Axel Meyer, Claudius F. Kratochwil
Software Mentions: 12
Published: almost 6 years ago

10.1186/s13567-021-00981-3

Immunogenicity and protective efficacy of a Streptococcus suis vaccine composed of six conserved immunogens
Cited by: 8
Author(s): Christine Weiße, Denise Dittmar, Beata Jakóbczak, Volker Florian, Nicole Schütze, Gottfried Alber, Kristin Klose, Stephan Michalik, Peter Valentin‐Weigand, Uwe Völker, Christoph Georg Baums
Software Mentions: 12
Published: almost 5 years ago

10.1038/s41598-020-73812-8

Synbiotic feed supplementation significantly improves lipid utilization and shows discrete effects on disease resistance in rainbow trout (Oncorhynchus mykiss)
Cited by: 10
Author(s): Kasper Rømer Villumsen, Maki Ohtani, Torunn Forberg, Elisabeth Aasum, John Tinsley, Anders Miki Bojesen
Software Mentions: 12
Published: over 5 years ago

10.1038/s41598-021-89066-x

Lagged recovery of fish spatial distributions following a cold-water perturbation
Cited by: 3
Author(s): Masumi Robertson, Gao Jin, Paul M. Regular, M. J. Morgan, Fan Zhang
Software Mentions: 12
Published: about 5 years ago

10.3389/fonc.2019.01361

Development and Validation of an RNA-Seq-Based Prognostic Signature in Neuroblastoma
Cited by: 28
Author(s): Jianguo Zhou, Bo Liang, Sanli Jin, Hui-Ling Liao, Guocheng Du, Long Cheng, Hu Ma, Udo S. Gaipl
Software Mentions: 12
Published: over 6 years ago

10.3389/fgene.2020.00968

Systematic Transcriptome Analysis of Noise-Induced Hearing Loss Pathogenesis Suggests Inflammatory Activities and Multiple Susceptible Molecules and Pathways
Cited by: 6
Author(s): Quan Wang, Yilin Shen, Hongbo Hu, Fan Cui, Andi Zhang, Rui Ding, Bin Ye, Ming Xiang
Software Mentions: 12
Published: almost 6 years ago

10.7717/peerj.11923

Signature identification of relapse-related overall survival of early lung adenocarcinoma after radical surgery
Cited by: 2
Author(s): Peng Han, Jiaqi Yue, Kangle Kong, Shan Huang, Pei Cao, Yu Deng, Ли Фан, Bo Zhao
Software Mentions: 12
Published: almost 5 years ago

10.1002/aps3.1227

Open‐source data reveal how collections‐based fungal diversity is sensitive to global change
Cited by: 24
Author(s): Carrie Andrew, Ulf Büntgen, Simon Egli, Béatrice Senn-Irlet, John‐Arvid Grytnes, Jacob Heilmann‐Clausen, Lynne Boddy, Claus Bässler, Alan C. Gange, Einar Heegaard, Klaus Høiland, Paul M. Kirk, Irmgard Krisai‐Greilhuber, Thomas W. Kuyper, Håvard Kauserud
Software Mentions: 12
Published: over 7 years ago

10.7717/peerj.5661

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia
Cited by: 17
Author(s): Camila Duarte Ritter, Alexander Zizka, Fabian Roger, Hanna Tuomisto, Christopher J. Barnes, R. Henrik Nilsson, Alexandre Antonelli
Software Mentions: 12
Published: over 7 years ago

10.3389/fmicb.2018.02312

Experimental Evidence of Functional Group-Dependent Effects of Tree Diversity on Soil Fungi in Subtropical Forests
Cited by: 26
Author(s): Christina Weißbecker, Tesfaye Wubet, Guillaume Lentendu, Peter Kühn, Thomas Scholten, Helge Bruelheide, François Buscot
Software Mentions: 12
Published: over 7 years ago

10.1002/cam4.4126

Hypoxia‐related lncRNAs to build prognostic classifier and reveal the immune characteristics of EGFR wild type and low expression of PD‐L1 squamous and adenocarcinoma NSCLC
Cited by: 4
Author(s): Fang Zhao, Min Wang, Jie Zhu
Software Mentions: 12
Published: almost 5 years ago

10.1186/s12868-017-0372-1

26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3
Cited by: 5
Author(s): Adam J. H. Newton, Alexandra H Seidenstein, Robert A. McDougal, Alberto Pérez-Cervera, Gemma Huguet, Tere M. Seara, Caroline Haimerl, David Angulo-García, Alessandro Torcini, Rosa Cossart, Arnaud Malvache, K. Skiker, Mounir Maouene, Gianmarco Ragognetti, Letizia Lorusso, Andrea Viggiano, Angelo Marcelli, Rosa Senatore, Antonio Parziale, Sebastiano Stramaglia, M. Pellicoro, Lucia Angelini, Enrico Amico, Hannelore Aerts, Jesús M. Cortés, Steven Laureys, Daniele Marinazzo, Iege Bassez, Luca Faes, Hannes Almgren, Adeel Razi, Frederik Van de Steen, Ruth M. Krebs, Hannelore Aerts, Lida Kanari, Paweł Dłotko, Martina Scolamiero, Ran Levi, Julian C. Shillcock, Christiaan Pj de Kock, Katharina Heß, Henry Markram, Cheng Ly, Gary Marsat, Tom Gillespie, Malin Sandström, Mathew Abrams, Jeffrey S. Grethe, Maryann E. Martone, Robin De Gernier, Sergio Solinas, Christian Rössert, Marc Haelterman, Serge Massar, Valentina Pasquale, Vito Paolo Pastore, Sergio Martinoia, Paolo Massobrio, Cristiano Capone, Núria Tort-Colet, María V. Sánchez-Vives, Maurizio Mattia, Ali Almasi, Shaun L. Cloherty, David B. Grayden, Yan T. Wong, M. Ibbotson, Hamish Meffin, Luke Y. Prince, Krasimira Tsaneva-Atanasova, Jack R. Mellor, Annalisa Mazzoni, Manuela Rosa, J. Carpaneto, Luigi Romito, Alberto Priori, Silvestro Micera, Rosanna Migliore, Carmen Alina Lupaşcu, Francesco Franchina, Luca Bologna, Armando Romani, Sára Sáray, Werner Van Geit, Szabolcs Káli, Alex Thomson, Audrey Mercer, Sigrun Lange, Joanne Falck, Eilif Müller, Felix Schürmann, Dmitry Todorov, Robert Capps, William Barnett, Yaroslav I. Molkov, Federico Devalle, Diego Pazó, Ernest Montbrió, Gabriela Mochol, Habiba Azab, Benjamin Y. Hayden, Rubén Moreno‐Bote, Pragathi Priyadharsini Balasubramani, Srinivasa Chakravarthy, Vignayanandam Ravindernath Muddapu, Medorian D. Gheorghiu, Bartul Mimica, Jonathan Withlock, Raul C. Mureșan, Jennifer L. Zick, Kelsey Schultz, Rachael K. Blackman, Matthew V. Chafee, Theoden I. Netoff, Nicholas Roberts, Vivek Nagaraj, Andrew Lamperski, Logan L. Grado, Matthew D. Johnson, David Darrow, Davide Lonardoni, Hayder Amin, Stefano Di Marco, Alessandro Maccione, Luca Berdondini, Thierry Nieus, Marcel Stimberg, Dan F. M. Goodman, Thomas Nowotny, Veronika Koren, Valentin Dragoi, Klaus Obermayer, Samy Castro, Mariano Fernández, Wael El-Deredy, Ke Xu, Jean P. Maidana, Patricio Orio, Wei‐Liang Chen, Iain Hepburn, Francesco Casalegno, Adrien Devresse, A. G. Ovcharenko, Fernando Pereira, Fabien Delalondre, Erik De Schutter, Peter Bratby, Andrew R. Gallimore, Guido Klingbeil, Criseida Zamora, Yunliang Zang, Patrick Crotty, Eric Palmerduca, Alberto Antonietti, Claudia Casellato, Csaba Erö, Egidio D’Angelo, Marc‐Oliver Gewaltig, Alessandra Pedrocchi, Ilja Bytschok, Dominik Dold, Johannes Schemmel, K. Meier, Mihai A. Petrovici, Hui-An Shen, Simone Carlo Surace, Jean-Pascal Pfister, Baptiste Lefebvre, Olivier Marre, Pierre Yger, Athanasia Papoutsi, Jiyoung Park, Ryan T. Ash, Stelios M. Smirnakis, Panayiota Poirazi, Richard A. Felix, Alexander G. Dimitrov, Christine V. Portfors, Silvia Daun, Tibor Tóth, Joanna Jędrzejewska‐Szmek, Nadine Kabbani, Kim T. Blackwel, Bahar Moezzi, Natalie Schaworonkow, Lukas Plogmacher, Mitchell R. Goldsworthy, Brenton Hordacre, Mark D. McDonnell, Nicolangelo Iannella, Michael C. Ridding, Jochen Triesch, Reinoud Maex, Karen Safaryan, Volker Steuber, Rongxiang Tang, Yi‐Yuan Tang, Darya V. Verveyko, Alexey Brazhe, Andrey Yu. Verisokin, Dmitry E. Postnov, Cengiz Günay, Gabriella Panuccio, Michèle Giugliano, Astrid A. Prinz, Pablo Varona, M. I. Rabinovich, Jack E. Denham, Thomas Ranner, Netta Cohen, Maria Reva, Nelson Rebola, Tekla Kirizs, Zoltán Nusser, David A. DiGregorio, Eirini Mavritsaki, Panos Rentzelas, Nikul H. Ukani, Adam Tomkins, Chung-Heng Yeh, Wesley Bruning, Allison L. Fenichel, Yiyin Zhou, Yu-Chi Huang, Dorian Florescu, Carlos L. Ortiz, Paul Richmond, Chung-Chuan Lo, Daniel Coca, Ann‐Shyn Chiang, Aurel A. Lazar, Jennifer Creaser, Congping Lin, Peter Ashwin, Jon T. Brown, Thomas Ridler, Daniel Levenstein, Brendon O. Watson, György Buzsáki, John Rinzel, Rodica Curtu, Anh Trung Nguyen, Sahand Assadzadeh, P. A. Robinson, Paula Sanz‐Leon, Caroline Garcia Forlim, Lírio Onofre Baptista de Almeida, Reynaldo D. Pinto, Francisco B. Rodríguez, Ángel Lareo, Aarón Montero, Thiago Mosqueiro, Ramón Huerta, Vinicio Changoluisa, Vinícius Lima Cordeiro, Cesar Ceballos, Nilton L. Kamiji, Antonio Roque, William W. Lytton, Andrew T. Knox, Joshua J. C. Rosenthal, Svitlana Popovych, Liqing Liu, Bin A. Wang, Christian Grefkes, Gereon R. Fink, Nils Rosjat, Abraham Perez-Trujillo, Andrés Espinal, Marco Aurelio Sotelo-Figueroa, Iván Cruz-Aceves, Horacio Rostro-González, Martin Zapotocky, Martina Hoskovcová, J Kopecká, Olga Ulmanová, Evžen Růžička, Matthias Gärtner, Sevil Duvarci, Jochen Roeper, Gerd‐Helge Schneider, Štefan Albert, Katharina Schmack, Michiel W. H. Remme, Susanne Schreiber, Michele Migliore, Stefano Maximiliano Antonel, Jean-Denis Courcol, Sami Utku Çelikok, Eva M. Navarro-López, Neslihan Serap Şengör, Rahmi Elibol, Mustafa Y. Özdemir, Tianyi Li, Angelo Arleo, Denis Sheynikhovich, Akihiro Nakamura, Masanori Shimono, Youngjo Song, Sol Park, Ilhwan Choi, Jaeseung Jeong, Hee‐Sup Shin, Sadra Sadeh, Padraig Gleeson, R. Angus Silver, Alexandra P. Chatzikalymniou, Frances K. Skinner, Francisco B. Rodríguez, Roberto C. Sotero, Loreen Hertäg, Owen Mackwood, Henning Sprekeler, Steffen Puhlmann, Simon Weber, David Higgins, Laura Naumann, Ramakrisnan Iyer, Ştefan Mihalaş, Valentina Ticcinelli, Tomislav Stankovski, Peter V. E. McClintock, Aneta Stefanovska, Predrag Janjić, Dimitar Solev, Gerald Seifert, Ljupčo Kocarev, Christian Steinhäuser, Mehrdad Salmasi, Stefan Glasauer, Martin B. Stemmler, Danke Zhang, Chi Zhang, Armen Stepanyants, Julia Goncharenko, Lieke Kros, Neil Davey, Chris I. De Zeeuw, Freek E. Hoebeek, Ankur Sinha, Roderick Adams, Michael Schmuker, Maria Psarrou, Maria J. Schilstra, Benjamin Torben‐Nielsen, Christoph Metzner, Achim Schweikard, Tuomo Mäki‐Marttunen, Bartosz Zurowski, Daniele Marinazzo, Luca Faes, Sebastiano Stramaglia, H Jordan, Simon M. Stringer, Elżbieta Gajewska-Dendek, Piotr Suffczyński, Nicoladie D. Tam, George Zouridakis, Luca Pollonini, Mojtaba Madadi Asl, Alireza Valizadeh, Peter A. Tass, Andreas Nold, Wei Fan, Sara Konrad, Heiko Endle, Johannes Vogt, Tatjana Tchumatchenko, Juliane Herpich, Christian Tetzlaff, Jannik Luboeinski, Timo Nachstedt, Manuel Ciba, Andreas Bahmer, Christiane Thielemann, Eric S. Kuebler, Joseph S. Tauskela, Jean-Philippe Thivierge, Rembrandt Bakker, María García‐Amado, Marian Evangelio, Francisco Clascá, Paul Tiesinga, Christopher L. Buckley, Taro Toyoizumi, Alexis Dubreuil, Rémi Monasson, Alessandro Treves, Davide Spalla, Sophie Rosay, Florence I. Kleberg, Willy Wong, Bruno de Oliveira Floriano, Toshihiko Matsuo, Tetsuya Uchida, D. Dibenedetto, Kâmil Uludağ, Abdorreza Goodarzinick, Maximilian Schmidt, Claus C. Hilgetag, Markus Diesmann, Sacha J. van Albada, Michael Fauth, Mark C. W. van Rossum, Manuel Reyes-Sánchez, Rodrigo Amaducci, Carlos Múñiz, Irene Elices, David Arroyo, Rafael Levi, Ben Cohen, Carson C. Chow, Shashaank Vattikuti, Elena Bertolotti, Raffaella Burioni, Matteo di Volo, A. Vezzani, Bayar Menzat, Tim P. Vogels, Nobuhiko Wagatsuma, Susmita Saha, Reena Kapoor, Robert R. Kerr, John Wagner, Luis C. G. del Molino, Guangyu Robert Yang, Jorge F. Mejías, Xiaojing Wang, Hanbing Song, Joseph W. Goodliffe, Jennifer I. Luebke, Christina M. Weaver, John Thomas, Nishant Sinha, Nikhita Shaju, Tomasz Maszczyk, Jing Jin, Sydney S. Cash, Justin Dauwels, M. Brandon Westover, Maryam Karimian, Michelle Moerel, Peter De Weerd, Thomas Burwick, Ronald L. Westra, Romesh Abeysuriya, Jonathan Hadida, Stamatios N. Sotiropoulos, Saâd Jbabdi, Mark W. Woolrich, Chama Bensmail, Borys Wróbel, Xiaolong Zhou, Zilong Ji, Xiao Liu, Xin Yan, Si Wu, Wang Xiao, Mingsha Zhang, Netanel Ofer, Orit Shefi, Gur Yaari, Ted Carnevale, Amit Majumdar, Subhashini Sivagnanam, Kenneth Yoshimoto, Elena Y. Smirnova, Dmitry V. Amakhin, Sergey L. Malkin, Aleksey V. Zaitsev, Anton V. Chizhov, Margarita Zaleshina, Alexander Zaleshin, Victor J. Barranca, George Zhu, Quinton M. Skilling, Daniel Maruyama, Nicolette Ognjanovski, Sara J. Aton, Michal Zochowski, Jiaxing Wu, Sara J. Aton, Scott Rich, Victoria Booth, Maral Budak, Salvador Dura‐Bernal, Samuel A. Neymotin, Benjamin A. Suter, Gordon M. Shepherd, Melvin Felton, Alfred B. Yu, David L. Boothe, Kelvin S. Oie, Piotr J. Franaszczuk, Sergey A. Shuvaev, Batuhan Başerdem, Anthony M. Zador, Alexei A. Koulakov, Víctor J. López‐Madrona, Ernesto Pereda, Claudio R. Mirasso, Santiago Canals, Stefano Masoli, Udaya Bhaskar Rongala, Anton Spanne, Henrik Jörntell, Calogero Maria Oddo, A. Vartanov, Anastasia Neklyudova, S. Kozlovskiy, A. Kiselnikov, J. Marakshina, Maria Teleńczuk, Bartosz Teleńczuk, Alain Destexhe, Paula T. Kuokkanen, Anna Kraemer, Thomas McColgan, Catherine Carr, Richard Kempter
Software Mentions: 12
Published: almost 9 years ago

10.1099/mgen.0.000131

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
Cited by: 370
Author(s): Martin Hunt, Alison E. Mather, Leonor Sánchez-Busó, Andrew J. Page, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris
Software Mentions: 12
Published: over 8 years ago

10.1371/journal.pone.0243295

Polish is quantitatively different on quartzite flakes used on different worked materials
Cited by: 12
Author(s): Antonella Pedergnana, Ivan Calandra, Adrian Evans, Konstantin Bob, Andreas Hildebrandt, Andreu Ollé
Software Mentions: 12
Published: over 5 years ago

10.3390/metabo7020030

Evaluation of Classifier Performance for Multiclass Phenotype Discrimination in Untargeted Metabolomics
Cited by: 33
Author(s): Patrick J. Trainor, Andrew P. DeFilippis, N. Shesh
Software Mentions: 12
Published: about 9 years ago

10.3389/fgene.2021.689159

Analyzing Roles of NUSAP1 From Clinical, Molecular Mechanism and Immune Perspectives in Hepatocellular Carcinoma
Cited by: 3
Author(s): Wenjie Zhu, Jian Xu, Zehao Chen, Jianxin Jiang
Software Mentions: 12
Published: almost 5 years ago

10.7717/peerj.10849

modelBuildR: an R package for model building and feature selection with erroneous classifications
Cited by: 3
Author(s): Maximilian Knoll, Jennifer Furkel, Jürgen Debus, Amir Abdollahi
Software Mentions: 12
Published: over 5 years ago

10.3390/ani11010026

Do Canine Behavioural Assessments and Characteristics Predict the Human-Dog Interaction When Walking on a Leash in a Shelter Setting?
Cited by: 4
Author(s): Hao-Yu Shih, Mandy Paterson, Fillipe Georgiou, Clive J. C. Phillips
Software Mentions: 12
Published: over 5 years ago

10.1186/s13059-021-02493-x

Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish
Cited by: 7
Author(s): Hyo Sik Jang, Yujie Chen, Jiaxin Ge, Alicia N Wilkening, Yiran Hou, Hyung Joo Lee, You Rim Choi, Rebecca F. Lowdon, Xiaoyun Xing, Daofeng Li, Charles Kaufman, Stephen L. Johnson, Ting Wang
Software Mentions: 12
Published: over 4 years ago

10.3389/fgene.2019.01200

Dysregulation of MicroRNA Regulatory Network in Lower Extremities Arterial Disease
Cited by: 22
Author(s): Anna Bogucka‐Kocka, Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Łukasz Komsta, Przemysław Kołodziej, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki
Software Mentions: 12
Published: over 6 years ago

10.3390/cancers11091248

Gastric Normal Adjacent Mucosa Versus Healthy and Cancer Tissues: Distinctive Transcriptomic Profiles and Biological Features
Cited by: 28
Author(s): Sabino Russi, Giovanni Calice, Vitalba Ruggieri, Simona Laurino, Francesco La Rocca, Elena Amendola, Cinzia Lapadula, Debora Compare, Gerardo Nardone, Pellegrino Musto, Mario De Felice, Geppino Falco, Pietro Zoppoli
Software Mentions: 12
Published: almost 7 years ago

10.7554/eLife.38579

FoxA1 and FoxA2 drive gastric differentiation and suppress squamous identity in NKX2-1-negative lung cancer
Cited by: 52
Author(s): Soledad A. Camolotto, S. R. Pattabiraman, Timothy Mosbruger, Alex Jones, Veronika K Belova, Grace Orstad, Mitchell Streiff, Lydia Salmond, Chris Stubben, Klaus H. Kaestner, Eric L. Snyder
Software Mentions: 12
Published: over 7 years ago

10.1186/s13059-019-1795-z

A comparison of automatic cell identification methods for single-cell RNA sequencing data
Cited by: 361
Author(s): Tamim Abdelaal, Lieke Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel J. T. Reinders, Ahmed Mahfouz
Software Mentions: 12
Published: almost 7 years ago