cran: Julia | Projects | Ecosyste.ms: Papers

10.7554/eLife.53350

The natverse, a versatile toolbox for combining and analysing neuroanatomical data
Cited by: 128
Author(s): Alexander Shakeel Bates, James D. Manton, Sridhar R. Jagannathan, Marta Costa, Philipp Schlegel, Torsten Rohlfing, Gregory Jefferis
Software Mentions: 17
Published: over 4 years ago

10.1534/g3.119.400018

BGData - A Suite of R Packages for Genomic Analysis with Big Data
Cited by: 23
Author(s): Alexander Grueneberg, Gustavo de los Campos
Software Mentions: 16
Published: over 5 years ago

10.1093/jas/skaa402

ASAS-NANP SYMPOSIUM: prospects for interactive and dynamic graphics in the era of data-rich animal science1
Cited by: 4
Author(s): Gota Morota, Hao Cheng, Dianne Cook, Emi Tanaka
Software Mentions: 15
Published: almost 4 years ago

10.1016/j.xpro.2021.100837

Protocol for hybrid flux balance, statistical, and machine learning analysis of multi-omic data from the cyanobacterium Synechococcus sp. PCC 7002
Cited by: 3
Author(s): Supreeta Vijayakumar, Claudio Angione
Software Mentions: 13
Published: about 3 years ago

10.1186/s40679-018-0060-y

An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data
Cited by: 11
Author(s): Laurent P. René de Cotret, Martin Otto, Mark J. Stern, Bradley J. Siwick
Software Mentions: 12
Published: about 6 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: about 8 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: almost 5 years ago

10.1186/s41044-019-0043-6

A substrate for modular, extensible data-visualization
Cited by: 6
Author(s): Jordan Matelsky, Joseph Downs, Hannah Cowley, Brock Wester, William Gray-Roncal
Software Mentions: 11
Published: almost 5 years ago

10.1371/journal.pone.0209358

QuantumInformation.jl—A Julia package for numerical computation in quantum information theory
Cited by: 11
Author(s): Piotr Gawron, Dariusz Kurzyk, Łukasz Pawela
Software Mentions: 10
Published: almost 6 years ago

10.12688/f1000research.7118.2

DREAMTools: a Python package for scoring collaborative challenges
Cited by: 9
Author(s): Thomas Cokelaer, Mukesh Bansal, Christopher Bare, Erhan Bilal, Brian M. Bot, Elias Chaibub Neto, Federica Eduati, Alberto de la Fuente, Mehmet Gönen, Steven M. Hill, Bruce Hoff, Jonathan R. Karr, Robert Küffner, Michael P. Menden, Pablo Meyer, Raquel Norel, Abhishek Pratap, Robert J. Prill, Matthew T. Weirauch, James C. Costello, Gustavo Stolovitzky, Julio Sáez-Rodríguez
Software Mentions: 10
Published: over 8 years ago

10.1016/j.devcel.2018.01.022

Innate Immune Response and Off-Target Mis-splicing Are Common Morpholino-Induced Side Effects in Xenopus
Cited by: 40
Author(s): George E. Gentsch, Thomas Spruce, Rita S. Monteiro, Nick Owens, Stephen R. Martin, James C. Smith
Software Mentions: 10
Published: almost 7 years ago

10.1128/mSystems.00917-20

FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses
Cited by: 7
Author(s): Matthew Chung, Ricky S. Adkins, John Mattick, Katie R. Bradwell, Amol Shetty, Lisa Sadzewicz, Luke J. Tallon, Claire M. Fraser, David A. Rasko, Anup Mahurkar, Julie C. Dunning Hotopp
Software Mentions: 8
Published: almost 4 years ago

10.1016/j.epidem.2020.100425

Responsible modelling: Unit testing for infectious disease epidemiology
Cited by: 6
Author(s): Tim Lucas, Timothy M. Pollington, Emma L Davis, T. Déirdre Hollingsworth
Software Mentions: 8
Published: about 4 years ago

10.7554/eLife.65654

Quantitative control of noise in mammalian gene expression by dynamic histone regulation
Cited by: 2
Author(s): Tan D, Rui Chen, Yuejian Mo, Shu Gu, Jiao Ma, Wei Xu, Xibin Lu, Hongtao He, Fan Jiang, Weimin Fan, Yili Wang, Xi Chen, Wei Huang
Software Mentions: 8
Published: over 3 years ago

10.1186/s13059-019-1639-x

CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing
Cited by: 23
Author(s): K. Sato, Koki Tsuyuzaki, Kentaro Shimizu, Itoshi Nikaido
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0256990

Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins
Cited by: 11
Author(s): Joe G Greener, David T. Jones
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0208561

Open source software in quantum computing
Cited by: 87
Author(s): Mark Fingerhuth, Tomáš Babej, Peter Wittek
Software Mentions: 7
Published: about 6 years ago

10.1007/s12559-020-09773-x

Deep Learning in Mining Biological Data
Cited by: 197
Author(s): Mufti Mahmud, M. Shamim Kaiser, TM McGinnity, Amir Hussain
Software Mentions: 7
Published: almost 4 years ago

10.3389/fimmu.2021.665312

An IRF1-IRF4 Toggle-Switch Controls Tolerogenic and Immunogenic Transcriptional Programming in Human Langerhans Cells
Cited by: 8
Author(s): James Davies, Andrés F. Vallejo, Sofía Sirvent, Gemma Porter, Kalum Clayton, Yamkela Qumbelo, Patrick S. Stumpf, Jonathan West, Clive M. Gray, Nyaradzo T. L. Chigorimbo‐Murefu, Ben D. MacArthur, Marta E. Polak
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pgen.1009303

Creating artificial human genomes using generative neural networks
Cited by: 51
Author(s): Burak Yelmen, Aurélien Decelle, Linda Ongaro, Davide Marnetto, Corentin Tallec, Francesco Montinaro, Cyril Furtlehner, Luca Pagani, Flora Jay
Software Mentions: 7
Published: almost 4 years ago

10.1128/mBio.00905-21

Functional and Comparative Analysis of Centromeres Reveals Clade-Specific Genome Rearrangements in Candida auris and a Chromosome Number Change in Related Species
Cited by: 10
Author(s): Aswathy Narayanan, Rakesh Netha Vadnala, Promit Ganguly, Pavitra Selvakumar, Shivaprakash M Rudramurthy, Rajendra Prasad, Arunaloke Chakrabarti, Rahul Siddharthan, Kaustuv Sanyal
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0254749

Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node
Cited by: 2
Author(s): Christopher Schölzel, Valeria Blesius, Gernot Ernst, Alexander Goesmann, Andreas Dominik
Software Mentions: 7
Published: over 3 years ago

10.3389/fninf.2019.00014

Visbrain: A Multi-Purpose GPU-Accelerated Open-Source Suite for Multimodal Brain Data Visualization
Cited by: 44
Author(s): Etienne Combrisson, Raphaël Vallat, Christian O’Reilly, Mainak Jas, Annalisa Pascarella, Anne-Lise Saive, Thomas Thiery, David Meunier, Dmitrii Altukhov, Tarek Lajnef, Perrine Ruby, Aymeric Guillot, Karim Jerbi
Software Mentions: 7
Published: almost 6 years ago

10.3389/fninf.2018.00030

Information-Theoretical Analysis of EEG Microstate Sequences in Python
Cited by: 13
Author(s): Frederic von Wegner, Helmut Laufs
Software Mentions: 7
Published: over 6 years ago

10.1038/s42003-021-02553-9

QSPcc reduces bottlenecks in computational model simulations
Cited by: 2
Author(s): Danilo Tomasoni, Alessio Paris, Stefano Giampiccolo, Federico Reali, Giulia Simoni, Luca Marchetti, Chanchala Kaddi, Susana Neves-Zaph, Corrado Priami, Karim Azer, Rosario Lombardo
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pcbi.1008495

Confidence intervals by constrained optimization—An algorithm and software package for practical identifiability analysis in systems biology
Cited by: 5
Author(s): Ivan I. Borisov, Eugeniy Metelkin
Software Mentions: 6
Published: about 4 years ago

10.1107/S1600576715022396

COD::CIF::Parser: an error-correcting CIF parser for the Perl language
Cited by: 131
Author(s): Andrius Merkys, Antanas Vaitkus, Justas Butkus, Mykolas Okulič-Kazarinas, Visvaldas Kairys, S. Gražulis
Software Mentions: 6
Published: almost 9 years ago

10.1186/s12859-020-03707-y

A sparse Bayesian factor model for the construction of gene co-expression networks from single-cell RNA sequencing count data
Cited by: 11
Author(s): Michael Sekula, Jeremy Gaskins, Susmita Datta
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pcbi.1008326

Using interactive digital notebooks for bioscience and informatics education
Cited by: 10
Author(s): Alan Davies, Frances Hooley, Peter Causey-Freeman, Iliada Eleftheriou, Georgina Moulton
Software Mentions: 6
Published: about 4 years ago

10.1186/s13321-020-0415-y

The C++ programming language in cheminformatics and computational chemistry
Cited by: 13
Author(s): Dmitrii N. Rassokhin
Software Mentions: 6
Published: almost 5 years ago

10.12688/f1000research.29032.2

Sustainable data analysis with Snakemake
Cited by: 502
Author(s): Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Förster, Soohyun Lee, Sven Twardziok, Alexander Kanitz, Andreas Wilm, Manuel Holtgrewe, Sven Rahmann, Sven Nahnsen, Johannes Köster
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.47898

CTCF confers local nucleosome resiliency after DNA replication and during mitosis
Cited by: 52
Author(s): Nick Owens, Thaleia Papadopoulou, Nicola Festuccia, Alexandra Tachtsidi, Inma González, Agnès Dubois, Sandrine Vandormael-Pournin, Elphège P. Nora, Benoit G. Bruneau, Michel Cohen-Tannoudji, Pablo Navarro
Software Mentions: 6
Published: about 5 years ago

10.3389/fninf.2015.00005

Neuroinformatics and the The Insight ToolKit
Cited by: 6
Author(s): Brian B. Avants, Hans J. Johnson, Nicholas J. Tustison
Software Mentions: 5
Published: over 9 years ago

10.3389/frobt.2018.00060

Inform: Efficient Information-Theoretic Analysis of Collective Behaviors
Cited by: 24
Author(s): Douglas Moore, Gabriele Valentini, Sara Imari Walker, Michael Levin
Software Mentions: 5
Published: over 6 years ago

10.1038/s42003-021-01753-7

Universal probabilistic programming offers a powerful approach to statistical phylogenetics
Cited by: 14
Author(s): Fredrik Ronquist, Jan Kudlicka, Viktor Senderov, Johannes Borgström, Nicolas Lartillot, Daniel Lundén, Lawrence M. Murray, Thomas B. Schön, David Broman
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.csbj.2020.06.033

Integration of single-cell multi-omics for gene regulatory network inference
Cited by: 37
Author(s): Xinlin Hu, Yaohua Hu, Fanjie Wu, Ricky Wai Tak Leung, Jing Qin
Software Mentions: 5
Published: almost 5 years ago

10.7717/peerj.8717

Genomic analysis of variability in Delta-toxin levels between Staphylococcus aureus strains
Cited by: 10
Author(s): Michelle Su, James T. Lyles, Robert A. Petit, Jessica Peterson, Michelle Hargita, Huaqiao Tang, Claudia Solís-Lemus, Cassandra L. Quave, Timothy D. Read
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-021-82196-2

Benchmarking of numerical integration methods for ODE models of biological systems
Cited by: 22
Author(s): Philipp Städter, Yannik Schälte, Leonard Schmiester, Jan Hasenauer, Paul Stapor
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-018-2583-6

hoDCA: higher order direct-coupling analysis
Cited by: 4
Author(s): Michael Schmidt, Kay Hamacher
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pcbi.1006828

Scalable nonlinear programming framework for parameter estimation in dynamic biological system models
Cited by: 15
Author(s): Sungho Shin, Ophelia S. Venturelli, Víctor M. Zavala
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-54492-5

Prediction of leukocyte counts during paediatric acute lymphoblastic leukaemia maintenance therapy
Cited by: 3
Author(s): Santeri Karppinen, Olli Lohi, Matti Vihola
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1007982

It’s about time: Analysing simplifying assumptions for modelling multi-step pathways in systems biology
Cited by: 17
Author(s): Niklas Korsbo, Henrik Jönsson
Software Mentions: 4
Published: over 4 years ago

10.3390/e23010117

Probabilistic Models with Deep Neural Networks
Cited by: 3
Author(s): Andrés R. Masegosa, Rafael Cabañas, Helge Langseth, Thomas D. Nielsen, Antonio Salmerón
Software Mentions: 4
Published: almost 4 years ago

10.7717/peerj-cs.161

An integrated platform for intuitive mathematical programming modeling using LaTeX
Cited by: 4
Author(s): Charalampos Triantafyllidis, Lazaros G. Papageorgiou
Software Mentions: 4
Published: over 6 years ago

10.1073/pnas.1921536117

Spontaneous formation of autocatalytic sets with self-replicating inorganic metal oxide clusters
Cited by: 35
Author(s): Haralampos N. Miras, Cole Mathis, Weimin Xuan, De‐Liang Long, Robert Pow, Leroy Cronin
Software Mentions: 4
Published: over 4 years ago

10.1002/ece3.6049

Climate connectivity of the bobcat in the Great Lakes region
Cited by: 6
Author(s): Robby R. Marrotte, Jeff Bowman, Paul J. Wilson
Software Mentions: 4
Published: almost 5 years ago

10.1107/S2052252520008830

Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering
Cited by: 11
Author(s): Yen-Lin Chen, Lois Pollack
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-020-03711-2

VFFVA: dynamic load balancing enables large-scale flux variability analysis
Cited by: 6
Author(s): Marouen Ben Guebila
Software Mentions: 4
Published: about 4 years ago

10.1186/s13104-020-05371-0

FINET: Fast Inferring NETwork
Cited by: 9
Author(s): Anyou Wang, Rong Hai
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pcbi.1008278

Optimising age coverage of seasonal influenza vaccination in England: A mathematical and health economic evaluation
Cited by: 6
Author(s): Edward M. Hill, Stavros Petrou, Henry Forster, Simon de Lusignan, Ivelina Yonova, Matthew James Keeling
Software Mentions: 4
Published: about 4 years ago

10.1186/s13148-018-0504-1

Identifying mislabeled and contaminated DNA methylation microarray data: an extended quality control toolset with examples from GEO
Cited by: 82
Author(s): Jonathan Heiss, Allan C. Just
Software Mentions: 4
Published: over 6 years ago

10.1021/acs.jctc.1c00159

Beyond Tripeptides Two-Step Active Machine Learning for Very Large Data sets
Cited by: 18
Author(s): Alexander van Teijlingen, Tell Tuttle
Software Mentions: 4
Published: over 3 years ago

10.1093/gigascience/giaa044

Iterative hard thresholding in genome-wide association studies: Generalized linear models, prior weights, and double sparsity
Cited by: 9
Author(s): Benjamin B. Chu, Kevin L. Keys, Christopher A. German, Hua Zhou, Jin Zhou, Eric M. Sobel, Janet S. Sinsheimer, Kenneth Lange
Software Mentions: 4
Published: over 4 years ago

10.1093/gigascience/giaa127

GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets
Cited by: 6
Author(s): Miroslav Kratochvíl, Oliver Hunewald, Laurent Heirendt, Vasco Verissimo, Jiřı́ Vondrášek, Venkata Satagopam, Reinhard Schneider, Christophe Trefois, Markus Ollert
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0213535

Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8
Cited by: 22
Author(s): Mio Takeuchi, Haruka Ozaki, Satoshi Hiraoka, Yoichi Kamagata, Susumu Sakata, Hideyoshi Yoshioka, Wataru Iwasaki
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0092721

Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners
Cited by: 134
Author(s): Carlo Baldassi, Marco Zamparo, Christoph Feinauer, Andrea Procaccini, Riccardo Zecchina, Martin Weigt, Andrea Pagnani
Software Mentions: 4
Published: over 10 years ago

10.3389/fninf.2018.00087

Xolotl: An Intuitive and Approachable Neuron and Network Simulator for Research and Teaching
Cited by: 10
Author(s): Srinivas Gorur-Shandilya, Alec Hoyland, Eve Marder
Software Mentions: 4
Published: about 6 years ago

10.3389/fgene.2021.655638

Alternative Ways of Computing the Numerator Relationship Matrix
Cited by: 4
Author(s): Mohammad Ali Nilforooshan, Dorian J. Garrick, B. L. Harris
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.11305

Characterizing a psychiatric symptom dimension related to deficits in goal-directed control
Cited by: 353
Author(s): Claire M. Gillan, Michal Kosinski, Robert Whelan, Elizabeth A. Phelps, Nathaniel D. Daw
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0225392

Evidence in support of chromosomal sex influencing plasma based metabolome vs APOE genotype influencing brain metabolome profile in humanized APOE male and female mice
Cited by: 22
Author(s): Yuan Shang, Aarti Mishra, Tian Wang, Yiwei Wang, Maunil K. Desai, Shuhua Chen, Zisu Mao, Loi Do, Adam Bernstein, Theodore P. Trouard, Roberta Dı́az Brinton
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0228520

Compressive Big Data Analytics: An ensemble meta-algorithm for high-dimensional multisource datasets
Cited by: 5
Author(s): Simeone Marino, Yangyu Zhao, Nina Zhou, Yiwang Zhou, Arthur W. Toga, Lu Zhao, Yingsi Jian, Yichen Yang, Yehu Chen, Qiucheng Wu, Jessica Wild, Brandon C Cummings, Ivo D. Dinov
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pcbi.1009058

A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2
Cited by: 9
Author(s): Edward M. Hill, Benjamin D. Atkins, Matthew James Keeling, Louise Dyson, Michael J. Tildesley
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-88875-4

Synthetic single cell RNA sequencing data from small pilot studies using deep generative models
Cited by: 5
Author(s): Martin Treppner, Adrián Salas-Bastos, Moritz Hess, Stefan Lenz, Tanja Vogel, Harald Binder
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-86087-4

Microdroplet-based one-step RT-PCR for ultrahigh throughput single-cell multiplex gene expression analysis and rare cell detection
Cited by: 13
Author(s): Jennifer Ma, Gary Tran, Alwin M. D. Wan, Elton T. Young, Eugenia Kumacheva, Norman N. Iscove, Peter W. Zandstra
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-40873-3

PTMselect: optimization of protein modifications discovery by mass spectrometry
Cited by: 13
Author(s): Renaud T Perchey, Laure Tonini, Marie Tosolini, Jean‐Jacques Fournié, Frédéric Lopez, Arnaud Besson, Frédéric Pont
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12859-019-2664-1

Predicting clinically promising therapeutic hypotheses using tensor factorization
Cited by: 5
Author(s): Jin Yao, Mark R. Hurle, Matthew R. Nelson, Pankaj Agarwal
Software Mentions: 3
Published: almost 6 years ago

10.1038/s12276-021-00612-z

Epigenetic dysregulation of immune-related pathways in cancer: bioinformatics tools and visualization
Cited by: 5
Author(s): Anders Berglund, Ryan M. Putney, Imène Hamaidi, Sungjune Kim
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-61257-y

Signals of anticipation of reward and of mean reward rates in the human brain
Cited by: 6
Author(s): Roberto Viviani, Lisa Dommes, Julia Bosch, Michael Steffens, Anna Paul, Katharina Schneider, Julia Stingl, Petra Beschoner
Software Mentions: 3
Published: almost 5 years ago

10.1093/bioinformatics/btaa861

Inferring signaling pathways with probabilistic programming
Cited by: 1
Author(s): David Merrell, Anthony Gitter
Software Mentions: 3
Published: about 4 years ago

10.3390/ph11020057

Changing Trends in Computational Drug Repositioning
Cited by: 121
Author(s): Jaswanth Yella, Suryanarayana Yaddanapudi, Yunguan Wang, Anil G. Jegga
Software Mentions: 3
Published: over 6 years ago

10.1186/s13195-018-0410-y

Genome-wide association study for variants that modulate relationships between cerebrospinal fluid amyloid-beta 42, tau, and p-tau levels
Cited by: 14
Author(s): Taylor J. Maxwell, Chris Corcoran, Jorge L. Del‐Aguila, John Budde, Yuetiva Deming, Carlos Cruchaga, Alison Goate, John S. K. Kauwe
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-017-10842-9

Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration
Cited by: 7
Author(s): Ofir Shukron, M. Hauer, David Holcman
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.824

CauseMap: fast inference of causality from complex time series
Cited by: 14
Author(s): M. Cyrus Maher, Ryan D. Hernández
Software Mentions: 3
Published: almost 10 years ago

10.7717/peerj.909

<tt>DCEMRI.jl</tt>: a fast, validated, open source toolkit for dynamic contrast enhanced MRI analysis
Cited by: 23
Author(s): David Stanley Smith, Xia Li, Lori R. Arlinghaus, Thomas E. Yankeelov, E. Brian Welch
Software Mentions: 3
Published: over 9 years ago

10.3390/e23060666

Count Data Time Series Modelling in Julia—The CountTimeSeries.jl Package and Applications
Cited by: 4
Author(s): Manuel Stapper
Software Mentions: 3
Published: over 3 years ago

10.1098/rsos.202169

Projecting a second wave of COVID-19 in Japan with variable interventions in high-risk settings
Cited by: 13
Author(s): Sung-mok Jung, Akira Endo, Ryô Kinoshita, Hiroshi Nishiura
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-018-28701-6

Reconciling differences in natural tags to infer demographic and genetic connectivity in marine fish populations
Cited by: 30
Author(s): Ruth Patrick, Susanne E. Tanner, Maria Ana Aboim, Rita P. Vasconcelos, Jean Laroche, Grégory Charrier, Montse Pérez, Pablo Presa, Bronwyn M. Gillanders, Henrique N. Cabral
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0244107

A new formulation of compartmental epidemic modelling for arbitrary distributions of incubation and removal times
Cited by: 2
Author(s): P. Hernández, Carlos Peña, Alberto Ramos, J.J. Gómez-Cadenas
Software Mentions: 3
Published: almost 4 years ago

10.3325/cmj.2019.60.369

Tensors all around us
Cited by: 1
Author(s): Branimir K. Hackenberger
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-018-2510-x

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow
Cited by: 54
Author(s): Jonathan Ozik, Nicholson Collier, Justin M. Wozniak, Charles M. Macal, Chase Cockrell, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Randy Heiland, Gary An, Paul Macklin
Software Mentions: 3
Published: about 6 years ago

10.3390/v13071240

PhaLP: A Database for the Study of Phage Lytic Proteins and Their Evolution
Cited by: 15
Author(s): Bjorn Criel, Steff Taelman, Wim Van Criekinge, Michiel Stock, Yves Briers
Software Mentions: 3
Published: over 3 years ago

10.1016/j.dib.2020.106627

Image-based data on strain fields of microstructures with porosity defects
Cited by: 0
Author(s): Pranav Milind Khanolkar, Saurabh Basu, Christopher McComb
Software Mentions: 3
Published: almost 4 years ago

10.15252/msb.20198982

Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome
Cited by: 98
Author(s): Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Maike Kathrin Aurich, Ronan M. T. Fleming
Software Mentions: 3
Published: over 4 years ago

10.3389/frobt.2019.00020

Simulating Active Inference Processes by Message Passing
Cited by: 24
Author(s): T.W. van de Laar, Bert de Vries
Software Mentions: 3
Published: over 5 years ago

10.3758/s13415-020-00799-0

Sympathetic involvement in time-constrained sequential foraging
Cited by: 6
Author(s): Neil M. Dundon, Neil Garrett, Viktoriya Babenko, Matt Cieslak, Nathaniel D. Daw, Scott T. Grafton
Software Mentions: 3
Published: over 4 years ago

10.1016/j.cels.2017.08.014

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures
Cited by: 386
Author(s): Thalia E. Chan, Michael Stumpf, Ann C. Babtie
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1007074

Perturbing low dimensional activity manifolds in spiking neuronal networks
Cited by: 20
Author(s): Emil Wärnberg, Arvind Kumar
Software Mentions: 3
Published: over 5 years ago

10.3389/fphys.2020.00954

Fine-Tuning of Energy Levels Regulates SUC2 via a SNF1-Dependent Feedback Loop
Cited by: 8
Author(s): Sebastian Persson, Niek Welkenhuysen, Sviatlana Shashkova, Marija Cvijović
Software Mentions: 3
Published: over 4 years ago

10.1093/genetics/iyaa043

Translating insights from the seed metabolome into improved prediction for lipid-composition traits in oat (Avena sativaL.)
Cited by: 15
Author(s): Malachy T. Campbell, Haixiao Hu, Trevor H. Yeats, Melanie Caffe‐Treml, Lucı́a Gutiérrez, Kevin P. Smith, Mark E. Sorrells, Michael A. Gore, Jean Luc Jannink
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1005362

Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes
Cited by: 18
Author(s): Mohammadkarim Saeedghalati, Farnoush Farahpour, Bettina Budeus, Anja Lange, Astrid M. Westendorf, Marc Seifert, Ralf Küppers, Daniel Hoffmann
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pcbi.1007983

Task-evoked activity quenches neural correlations and variability across cortical areas
Cited by: 52
Author(s): Takuya Ito, Scott L. Brincat, Markus Siegel, Ravi D. Mill, Biyu J. He, Earl K. Miller, Horacio G. Rotstein, Michael W. Cole
Software Mentions: 3
Published: over 4 years ago

10.1099/mgen.0.000146

MentaLiST – A fast MLST caller for large MLST schemes
Cited by: 36
Author(s): Pedro Feijão, Hua-Ting Yao, Daniel Fornika, Jennifer L. Gardy, William Hsiao, Cédric Chauve, Leonid Chindelevitch
Software Mentions: 3
Published: almost 7 years ago

10.1007/s11306-019-1588-0

Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing
Cited by: 55
Author(s): Kevin Mendez, Leighton Pritchard, Stacey N. Reinke, David Broadhurst
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0243485

Local hypergraph clustering using capacity releasing diffusion
Cited by: 4
Author(s): Rania Ibrahim, David F. Gleich
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-019-2743-3

AUTALASSO: an automatic adaptive LASSO for genome-wide prediction
Cited by: 17
Author(s): Patrik Waldmann, Maja Ferenčaković, Gábor Mészáros, Negar Khayatzadeh, Ino Čurik, Johann Sölkner
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1007996

A mathematical model for persistent post-CSD vasoconstriction
Cited by: 3
Author(s): Shixin Xu, Junbiao Chang, C. C. Chow, K. C. Brennan, Huaxiong Huang
Software Mentions: 3
Published: over 4 years ago

10.3389/fninf.2019.00003

From the Wet Lab to the Web Lab: A Paradigm Shift in Brain Imaging Research
Cited by: 5
Author(s): Anisha Keshavan, Jean‐Baptiste Poline
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pcbi.1005425

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers
Cited by: 52
Author(s): Björn Grüning, Helena Rasche, Boris Rebolledo‐Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1008266

A mesoscopic simulator to uncover heterogeneity and evolutionary dynamics in tumors
Cited by: 8
Author(s): Juan Jiménez-Sánchez, Álvaro Martínez-Rubio, Антон Попов, Julián Pérez-Beteta, Youness Azimzade, David Molina-García, Juan Belmonte-Beitia, Gabriel F. Calvo, Víctor M. Pérez‐García
Software Mentions: 3
Published: almost 4 years ago

10.17269/s41997-020-00470-8

cchsflow: an open science approach to transform and combine population health surveys
Cited by: 0
Author(s): Warsame Yusuf, Rostyslav Vyuha, Carol Bennett, Yulric Sequeira, Courtney Maskerine, Manuel Dujovny
Software Mentions: 3
Published: over 3 years ago

Projects: cran: Julia

Papers Mentioning Julia 304