pypi: matplotlib | Projects | Ecosyste.ms: Papers

10.3389/fninf.2013.00052

A framework for streamlining research workflow in neuroscience and psychology
Cited by: 12
Author(s): Jonas Kubilius
Software Mentions: 25
Published: almost 11 years ago

Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere
Cited by: 96
Author(s): Robyn J. Wright, Morgan G. I. Langille, Tony R. Walker
Software Mentions: 23
Published: about 4 years ago

10.3389/fninf.2019.00057

Comparing Open-Source Toolboxes for Processing and Analysis of Spike and Local Field Potentials Data
Cited by: 14
Author(s): Valentina A. Unakafova, Alexander Gail
Software Mentions: 23
Published: over 5 years ago

10.3389/fmicb.2020.550420

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline
Cited by: 91
Author(s): Daniel Straub, Nia Blackwell, Adrian Langarica‐Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst
Software Mentions: 22
Published: about 4 years ago

10.1371/journal.pgen.1009065

Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study
Cited by: 49
Author(s): Marco Galardini, Olivier Clermont, Agnès Baron, Bede P. Busby, Sara Dion, Sören Schubert, Pedro Beltrão, Erick Denamur
Software Mentions: 20
Published: about 4 years ago

10.1093/bioinformatics/bty149

NanoPack: visualizing and processing long-read sequencing data
Cited by: 1,423
Author(s): Wouter De Coster, Svenn D’Hert, Darrin T. Schultz, Marc Cruts, Christine Van Broeckhoven
Software Mentions: 18
Published: over 6 years ago

10.1186/s12880-021-00551-1

Sensitivity analysis for interpretation of machine learning based segmentation models in cardiac MRI
Cited by: 14
Author(s): Markus J. Ankenbrand, Liliia Shainberg, Michael Hock, David Lohr, Laura M. Schreiber
Software Mentions: 18
Published: over 3 years ago

10.1186/s40168-019-0702-x

Understanding microbial community dynamics to improve optimal microbiome selection
Cited by: 193
Author(s): Robyn J. Wright, Matthew I. Gibson, Joseph Alexander Christie-Oleza
Software Mentions: 18
Published: over 5 years ago

10.1084/jem.20200920

Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment
Cited by: 57
Author(s): Kristen E. Pauken, Osmaan Shahid, Kaitlyn A. Lagattuta, Kelly Mahuron, Jacob M. Luber, Margaret M. Lowe, Lüping Huang, Conor P. Delaney, Jaclyn M. Long, Megan E. Fung, Kathleen Newcomer, Katy K. Tsai, Melissa Chow, Samantha Guinn, Juhi R. Kuchroo, Kelly P. Burke, Jason M. Schenkel, Michael D. Rosenblum, Adil Daud, Arlene H. Sharpe, Meromit Singer
Software Mentions: 17
Published: over 3 years ago

10.1371/journal.pone.0230416

The citation advantage of linking publications to research data
Cited by: 131
Author(s): Giovanni Colavizza, Iain Hrynaszkiewicz, Isla Staden, Kirstie Whitaker, Barbara McGillivray
Software Mentions: 16
Published: over 4 years ago

10.3389/fnins.2014.00067

Flexible multivariate hemodynamics fMRI data analyses and simulations with PyHRF
Cited by: 11
Author(s): Vincent Thomas, Solveig Badillo, Laurent Risser, Lotfi Chaâri, Christine Bakhous, Florence Forbes, Philippe Ciuciu
Software Mentions: 14
Published: over 10 years ago

10.1186/s40679-016-0031-0

Analyzing microtomography data with Python and the scikit-image library
Cited by: 22
Author(s): Emmanuelle Gouillart, Juan Nunez-Iglesias, Stéfan van der Walt
Software Mentions: 14
Published: almost 8 years ago

10.1039/d0sc05337f

A data-driven perspective on the colours of metal–organic frameworks
Cited by: 14
Author(s): Kevin Maik Jablonka, Seyed Mohamad Moosavi, Mehrdad Asgari, Christopher P. Ireland, Luc Patiny, Berend Smit
Software Mentions: 14
Published: almost 4 years ago

10.12688/f1000research.15140.2

Recommendations for the packaging and containerizing of bioinformatics software
Cited by: 32
Author(s): Bjoern Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian D. O’Connor, Fábio Madeira, Victoria Domínguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jiménez, BioContainers Community, Yasset Perez‐Riverol
Software Mentions: 14
Published: over 5 years ago

10.1186/s13742-016-0147-0

2015 Brainhack Proceedings
Cited by: 6
Author(s): R. Cameron Craddock, Pierre Bellec, Daniel S. Margules, B. Nolan Nichols, Jörg P. Pfannmöller, AmanPreet Badhwar, David Kennedy, Jean‐Baptiste Poline, Roberto Toro, Ben Cipollini, Ariel Rokem, Daniel J. Clark, Krzysztof J. Gorgolewski, Daniel J. Clark, Samir Das, Cécile Madjar, Ayan Sengupta, Zia Mohades, Sébastien Déry, Weiran Deng, Eric Earl, Damion V. Demeter, Kate Mills, Glad Mihai, Luka Ružić, Nick Ketz, Andrew E. Reineberg, Marianne C. Reddan, Anne-Lise Goddings, Javier Gonzalez‐Castillo, Caroline Froehlich, Gil Dekel, Daniel S. Margulies, Ben D. Fulcher, Tristan Glatard, Reza Adalat, Natacha Beck, R. Bernard, Najmeh Khalili-Mahani, Pierre Rioux, Marc-Étienne Rousseau, Alan C. Evans, Yaroslav Halchenko, Matteo Visconti di Oleggio Castello, Raúl Hernández-Pérez, Edgar Abarca Morales, Laura V. Cuaya, Kaori Ito, Sook‐Lei Liew, Hans J. Johnson, Erik Kan, Julia Anglin, Michael R. Borich, Neda Jahanshad, Paul Thompson, Marcel Falkiewicz, Julia M. Huntenburg, David O’Connor, Michael P. Milham, Ramon Fraga Pereira, Anibal Sólon Heinsfeld, Alexandre R. Franco, Augusto Buchweitz, Felipe Meneguzzi, Rickson C. Mesquita, Luis C. T. Herrera, Daniela Dentico, Vanessa Sochat, Julio E. Villalon‐Reina, Eleftherios Garyfallidis
Software Mentions: 14
Published: about 8 years ago

10.1186/s12864-016-3278-x

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data
Cited by: 131
Author(s): Joshua G. Dunn, Jonathan S. Weissman
Software Mentions: 14
Published: almost 8 years ago

10.7554/eLife.55913

An image-based data-driven analysis of cellular architecture in a developing tissue
Cited by: 22
Author(s): Jonas Hartmann, Mie Wong, Elisa Cristina de Proença Rodrigues Gallo, Darren Gilmour
Software Mentions: 14
Published: over 4 years ago

10.1186/s13059-019-1783-3

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
Cited by: 20
Author(s): Kathleen C. Keough, Svetlana Lyalina, Michael P. Olvera, Sean Whalen, Bruce R. Conklin, Katherine S. Pollard
Software Mentions: 14
Published: about 5 years ago

10.3390/jcm10051089

Prediction of Neurologically Intact Survival in Cardiac Arrest Patients without Pre-Hospital Return of Spontaneous Circulation: Machine Learning Approach
Cited by: 4
Author(s): Dong-Woo Seo, Hahn Yi, Hyun‐Jin Bae, Youn-Jung Kim, Cheol Ho Sohn, Won Young Kim, Kyung-Taek Lim, Namkug Kim, Youn-Jung Kim
Software Mentions: 13
Published: over 3 years ago

10.1371/journal.pcbi.1007113

Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes
Cited by: 28
Author(s): Claire Bomkamp, Shreejoy J. Tripathy, Carolina Bengtsson Gonzales, Jens Hjerling-Leffler, Ann Marie Craig, Paul Pavlidis
Software Mentions: 13
Published: over 5 years ago

10.1128/mBio.02275-17

A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity
Cited by: 99
Author(s): Benjamin Schwessinger, Jana Sperschneider, William S. Cuddy, Diana Garnica, Marisa E. Miller, Jennifer Taylor, Peter N. Dodds, Melania Figueroa, Robert Park, John P. Rathjen
Software Mentions: 13
Published: over 6 years ago

10.1186/s12859-021-04057-z

Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
Cited by: 21
Author(s): Hao Chen, Yan Lu, Dongsheng Lu, Shuhua Xu
Software Mentions: 13
Published: over 3 years ago

10.1186/s12859-020-03774-1

Hypercluster: a flexible tool for parallelized unsupervised clustering optimization
Cited by: 7
Author(s): Lili M. Blumenberg, Kelly V. Ruggles
Software Mentions: 13
Published: about 4 years ago

10.7717/peerj.11376

ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses
Cited by: 4
Author(s): Natasha Pavlovikj, João Carlos Gomes-Neto, Jitender S. Deogun, Andrew K. Benson
Software Mentions: 12
Published: over 3 years ago

10.1186/s13059-018-1563-5

CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis
Cited by: 27
Author(s): Vivien A.C. Schoonenberg, Mitchel A Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello, Daniel E. Bauer
Software Mentions: 12
Published: about 6 years ago

10.1016/j.heliyon.2021.e06236

: A neuroscientist's sound toolkit
Cited by: 2
Author(s): N. Jeremy Hill, Scott W.J. Mooney, Glen T. Prusky
Software Mentions: 12
Published: almost 4 years ago

10.3389/fimmu.2020.00444

JunB Controls Intestinal Effector Programs in Regulatory T Cells
Cited by: 8
Author(s): Joshua D. Wheaton, Maria Ciofani
Software Mentions: 12
Published: over 4 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: about 6 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: about 5 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: almost 4 years ago

10.1038/s42003-021-01941-5

CENP-A overexpression promotes distinct fates in human cells, depending on p53 status
Cited by: 23
Author(s): Daniel Jeffery, Alberto Gatto, Katrina Podsypanina, Charlène Renaud-Pageot, Rebeca Ponce Landete, Lorraine Bonneville, Marie Dumont, Daniele Fachinetti, Geneviève Almouzni
Software Mentions: 12
Published: over 3 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 3 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 3 years ago

10.1371/journal.pone.0238835

Analyzing the fine structure of distributions
Cited by: 35
Author(s): Michael C. Thrun, Tino Gehlert, Alfred Ultsch
Software Mentions: 12
Published: about 4 years ago

10.3389/fninf.2018.00092

Multimodal Modeling of Neural Network Activity: Computing LFP, ECoG, EEG, and MEG Signals With LFPy 2.0
Cited by: 96
Author(s): Espen Hagen, Solveig Næss, Torbjørn V. Ness, Gaute T. Einevoll
Software Mentions: 12
Published: almost 6 years ago

10.1038/s41598-020-65015-y

Toffee – a highly efficient, lossless file format for DIA-MS
Cited by: 9
Author(s): Brett Tully
Software Mentions: 11
Published: over 4 years ago

10.1186/s13321-017-0215-1

ChemSAR: an online pipelining platform for molecular SAR modeling
Cited by: 39
Author(s): Jie Dong, Zhi Jiang Yao, Min Zhu, Ning Ning Wang, Ben Lü, Alex F. Chen, Ai Ping Lu, Hongyu Miao, Wen Zeng, Dong Sheng Cao
Software Mentions: 11
Published: over 7 years ago

10.3389/fnins.2020.00919

HYGRIP: Full-Stack Characterization of Neurobehavioral Signals (fNIRS, EEG, EMG, Force, and Breathing) During a Bimanual Grip Force Control Task
Cited by: 10
Author(s): Pablo Ortega, Tong Zhao, A. Aldo Faisal
Software Mentions: 11
Published: about 4 years ago

10.1371/journal.pone.0256339

Sex-specific spatial use of the winter foraging areas by Magellanic penguins and assessment of potential conflicts with fisheries during winter dispersal
Cited by: 6
Author(s): Samanta Dodino, Nicolás A. Lois, Luciana Riccialdelli, Michael J. Polito, Klemens Pütz, Andrea Raya Rey
Software Mentions: 11
Published: about 3 years ago

10.7717/peerj.4395

COREMIC: a web-tool to search for a niche associated CORE MICrobiome
Cited by: 17
Author(s): Richard R. Rodrigues, Nyle C. Rodgers, Xiaowei Wu, Mark A. Williams
Software Mentions: 11
Published: over 6 years ago

10.1098/rsif.2010.0230

Multi-camera real-time three-dimensional tracking of multiple flying animals
Cited by: 164
Author(s): Andrew Straw, Kristin Branson, Titus R. Neumann, Michael H. Dickinson
Software Mentions: 11
Published: over 14 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: over 4 years ago

10.1038/s41598-018-31154-6

Instant Clue: A Software Suite for Interactive Data Visualization and Analysis
Cited by: 156
Author(s): Hendrik Nolte, Thomas MacVicar, Frederik Tellkamp, Marcus Krüger
Software Mentions: 11
Published: about 6 years ago

10.3390/ijerph17031093

Teleconsultations between Patients and Healthcare Professionals in Primary Care in Catalonia: The Evaluation of Text Classification Algorithms Using Supervised Machine Learning
Cited by: 14
Author(s): Francesc López Seguí, Ricardo Ander Egg Aguilar, Gabriel de Maeztu, Anna García‐Altés, Francesc García Cuyàs, Sandra M. Walsh, Marta Sagarra Castro, Josep Vidal-Alaball
Software Mentions: 11
Published: over 4 years ago

10.1371/journal.pone.0225734

PyLandStats: An open-source Pythonic library to compute landscape metrics
Cited by: 19
Author(s): Martí Bosch
Software Mentions: 11
Published: almost 5 years ago

10.3389/fonc.2021.709077

Pyroptosis-Related Gene Signatures Can Robustly Diagnose Skin Cutaneous Melanoma and Predict the Prognosis
Cited by: 57
Author(s): Anji Ju, Jintian Tang, Shuohua Chen, Yan Fu, Yongzhang Luo
Software Mentions: 11
Published: over 3 years ago

10.1107/S1600577518016570

Automated data collection and real-time data analysis suite for serial synchrotron crystallography
Cited by: 34
Author(s): Shibom Basu, Jakub Wojciech Kaminski, Ezequiel Panepucci, Chia‐Ying Huang, Rangana Warshamanage, Meitian Wang, Justyna Aleksandra Wojdyla
Software Mentions: 11
Published: almost 6 years ago

10.1186/s40168-019-0714-6

A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments
Cited by: 78
Author(s): Jiarui Chen, Shelby E. McIlroy, Anand Asundi, David M. Baker, Gianni Panagiotou
Software Mentions: 11
Published: over 5 years ago

10.3389/fchem.2021.722087

PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems
Cited by: 0
Author(s): Matej Medvecký, Manolis Mandalakis
Software Mentions: 10
Published: about 3 years ago

10.1038/s41597-020-00725-6

An annotated dataset of bioacoustic sensing and features of mosquitoes
Cited by: 5
Author(s): Dinarte Vasconcelos, Nuno Nunes, João Gomes
Software Mentions: 10
Published: almost 4 years ago

10.1093/bioinformatics/btaa073

Coolpup.py: versatile pile-up analysis of Hi-C data
Cited by: 86
Author(s): Ilya M. Flyamer, Robert S. Illingworth, Wendy A. Bickmore
Software Mentions: 10
Published: almost 5 years ago

10.1029/2019EA001004

Open‐Source Software Analysis Tool to Investigate Space Plasma Turbulence and Nonlinear DYNamics (ODYN)
Cited by: 6
Author(s): E. Teodorescu, Marius Echim
Software Mentions: 10
Published: over 4 years ago

10.1186/s12859-021-04037-3

InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification
Cited by: 8
Author(s): Dominik J. E. Waibel, Sayedali Shetab Boushehri, Carsten Marr
Software Mentions: 10
Published: over 3 years ago

10.7717/peerj.453

scikit-image: image processing in Python
Cited by: 3,381
Author(s): Stéfan van der Walt, Johannes L. Schönberger, Juan Nunez-Iglesias, François Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, Tony Yu
Software Mentions: 10
Published: over 10 years ago

10.1016/j.dib.2020.105195

Dataset of depressive posts in Russian language collected from social media
Cited by: 12
Author(s): Sergazy Narynov, Daniyar Mukhtarkhanuly, Batyrkhan Omarov
Software Mentions: 10
Published: over 4 years ago

10.7554/eLife.62210

Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells
Cited by: 18
Author(s): Balyn W. Zaro, Joseph J. Noh, Victoria L. Mascetti, János Demeter, Benson M. George, Monika Żukowska, Gunsagar S. Gulati, Rahul Sinha, Ryan A. Flynn, Allison Banuelos, Allison Zhang, Adam C. Wilkinson, Peter K. Jackson, Irving L. Weissman
Software Mentions: 10
Published: almost 4 years ago

10.3390/md18100515

Applying a Chemogeographic Strategy for Natural Product Discovery from the Marine Cyanobacterium Moorena bouillonii
Cited by: 6
Author(s): Christopher A. Leber, C. Benjamin Naman, Lena Keller, Jehad Almaliti, Eduardo J. E. Caro‐Diaz, Evgenia Glukhov, V. Joseph, Sajeevan Thavarool Puthiyedathu, Andres Joshua Reyes, Jason S. Biggs, Te Li, Ye Yuan, Shan He, Xiaojun Yan, William H. Gerwick
Software Mentions: 10
Published: about 4 years ago

10.3390/ijms22157974

Transcriptomic and Metabolic Network Analysis of Metabolic Reprogramming and IGF-1 Modulation in SCA3 Transgenic Mice
Cited by: 4
Author(s): Yu Te Lin, Yong Shiou Lin, Wen Cheng, Jui-Chih Chang, Yi Chun Chao, Chin San Liu, An-Chi Wei
Software Mentions: 10
Published: over 3 years ago

10.15252/msb.202010108

Joint cell segmentation and cell type annotation for spatial transcriptomics
Cited by: 40
Author(s): Russell Littman, Zachary Hemminger, Robert T. Foreman, Douglas Arneson, Guanglin Zhang, Fernando Gómez‐Pinilla, Xia Yang, Roy Wollman
Software Mentions: 10
Published: over 3 years ago

10.3389/fgene.2018.00461

TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma
Cited by: 4
Author(s): Kathryn O’Neill, Wen‐Wei Liao, Asmita Patel, Molly Gale Hammell
Software Mentions: 10
Published: about 6 years ago

10.1186/s12864-021-07388-6

Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential
Cited by: 3
Author(s): Niels A. Zondervan, Vítor A. P. Martins dos Santos, María Suárez-Diez, Edoardo Saccenti
Software Mentions: 10
Published: almost 4 years ago

10.3389/fninf.2013.00041

LFPy: a tool for biophysical simulation of extracellular potentials generated by detailed model neurons
Cited by: 121
Author(s): Henrik Lindén, Espen Hagen, Szymon Łȩski, Espen Skjønsberg Norheim, Klas H. Pettersen, Gaute T. Einevoll
Software Mentions: 10
Published: almost 11 years ago

10.1038/s41598-021-89904-y

Feasibility of predicting allele specific expression from DNA sequencing using machine learning
Cited by: 5
Author(s): Zhenhua Zhang, Freerk van Dijk, Nigel Klein, Mariëlle van Gijn, Lude Franke, Richard J. Sinke, Morris A. Swertz, K. Joeri van der Velde
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-020-80308-y

A novel retinal ganglion cell quantification tool based on deep learning
Cited by: 22
Author(s): Luca Masin, Marie Claes, Steven Bergmans, Lien Cools, Lien Andries, Benjamin Davis, Lieve Moons, Lies De Groef
Software Mentions: 10
Published: almost 4 years ago

10.1371/journal.pone.0253010

Community evolution on Stack Overflow
Cited by: 11
Author(s): Iraklis Moutidis, Hywel T. P. Williams
Software Mentions: 10
Published: over 3 years ago

10.1016/j.dnarep.2021.103158

Damage-Net: A program for DNA repair meta-analysis identifies a network of novel repair genes that facilitate cancer evolution
Cited by: 1
Author(s): Aldo S. Bader, Martin Bushell
Software Mentions: 10
Published: about 3 years ago

10.1128/mSystems.00065-20

Subspecies Niche Specialization in the Oral Microbiome Is Associated with Nasopharyngeal Carcinoma Risk
Cited by: 19
Author(s): Justine W. Debelius, Tingting Huang, Yonglin Cai, Alexander Ploner, Donal Barrett, Xiaoying Zhou, Xue Xiao, Yancheng Li, Jian Liao, Yuming Zheng, Guangwu Huang, Hans‐Olov Adami, Yi Xin Zeng, Zhe Zhang, Ye W
Software Mentions: 10
Published: about 4 years ago

10.1534/genetics.119.302662

Polygenic Adaptation to an Environmental Shift: Temporal Dynamics of Variation Under Gaussian Stabilizing Selection and Additive Effects on a Single Trait
Cited by: 47
Author(s): Kevin R. Thornton
Software Mentions: 9
Published: almost 5 years ago

10.1186/s13062-021-00293-8

Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers
Cited by: 7
Author(s): Sergio Romera-Giner, Zoraida Andreu Martínez, Francisco García‐García, Marta R. Hidalgo
Software Mentions: 9
Published: over 3 years ago

10.3390/metabo11030133

Correlation of Metabolic Profiles of Plasma and Cerebrospinal Fluid of High-Grade Glioma Patients
Cited by: 9
Author(s): Artem D. Rogachev, Н. А. Алемасов, В. А. Иванисенко, Nikita V. Ivanisenko, E. V. Gaisler, Olga Oleshko, С. В. Чересиз, С. В. Мишинов, В. В. Ступак, Andrey G. Pokrovsky
Software Mentions: 9
Published: over 3 years ago

10.1099/mgen.0.000511

Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain
Cited by: 12
Author(s): Matthew P. Moore, Iain L. Lamont, David Williams, Steve Paterson, Iréna Kukavica-Ibrulj, Nicholas P. Tucker, D. Kenna, Jane F. Turton, Julie Jeukens, Luca Freschi, Bryan A. Wee, Nicholas J. Loman, Stephen Holden, Susan Manzoor, Peter M. Hawkey, Kevin W Southern, Martin Walshaw, Roger C. Levesque, Joanne L. Fothergill, Craig Winstanley
Software Mentions: 9
Published: over 3 years ago

10.7717/peerj-cs.227

Component-oriented acausal modeling of the dynamical systems in Python language on the example of the model of the sucker rod string
Cited by: 5
Author(s): Volodymyr Kopei, Oleh Onysko, Vitalii Panchuk
Software Mentions: 9
Published: about 5 years ago

10.1172/jci.insight.141683

CD84 is a regulator of the immunosuppressive microenvironment in Multiple Myeloma
Cited by: 15
Author(s): Hadas Lewinsky, Emine Gulsen Gunes, Keren David, Lihi Radomir, Matthias P. Kramer, Bianca Pellegrino, Michal Perpinial, Jing Chen, Ting He, Anthony G. Mansour, Kun yu Teng, Supriyo Bhattacharya, Enrico Caserta, Estelle Troadec, Peter Lee, Mingye Feng, Jonathan J. Keats, Amrita Krishnan, Michael Rosenzweig, Jianhua Yu, Michael A. Caligiuri, Yosef Cohen, Olga Shevetz, Shirly Becker-Herman, Flavia Pichiorri, Steven T. Rosen, Idit Shachar
Software Mentions: 9
Published: almost 4 years ago

10.1186/s13040-019-0201-4

Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies
Cited by: 3
Author(s): Elisabetta Manduchi, Patryk Orzechowski, Marylyn D. Ritchie, Jason H. Moore
Software Mentions: 9
Published: over 5 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: about 3 years ago

10.1186/s12864-020-06892-5

Machine learning based imputation techniques for estimating phylogenetic trees from incomplete distance matrices
Cited by: 15
Author(s): Ananya Bhattacharjee, Md. Shamsuzzoha Bayzid
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0235930

Neither per, nor tim1, nor cry2 alone are essential components of the molecular circadian clockwork in the Madeira cockroach
Cited by: 3
Author(s): Achim Werckenthin, Jannik Huber, Thordis Arnold, Susanne Koziarek, Marcus J. A. Plath, Jenny Aino Plath, Olaf Stursberg, Hanspeter Herzel, Monika Stengl
Software Mentions: 9
Published: over 4 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 8 years ago

10.1371/journal.pcbi.1008364

pyTFM: A tool for traction force and monolayer stress microscopy
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Author(s): Andreas Bauer, Magdalena Přechová, Lena Fischer, Ingo Thievessen, Martin Gregor, Ben Fabry
Software Mentions: 9
Published: over 3 years ago

10.3390/s19122772

Extracting Value from Industrial Alarms and Events: A Data-Driven Approach Based on Exploratory Data Analysis
Cited by: 16
Author(s): Aguinaldo Bezerra, Ivanovitch Silva, Luiz Affonso Guedes, Diego R. C. Silva, Gustavo Bezerra Paz Leitão, Kaku Saito
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0078009

Frequency Response and Gap Tuning for Nonlinear Electrical Oscillator Networks
Cited by: 0
Author(s): Harish S. Bhat, Garnet J. Vaz
Software Mentions: 9
Published: about 11 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: almost 5 years ago

10.1371/journal.pcbi.1008126

Ten simple rules to power drug discovery with data science
Cited by: 10
Author(s): Enrico Ferrero, Sophie Brachat, Jeremy L. Jenkins, Philippe Marc, Peter Skewes-Cox, Robert C. Altshuler, Caroline Gubser Keller, Audrey Kauffmann, Erik K Sassaman, Jason M. Laramie, Birgit Schoeberl, Mark Borowsky, Nikolaus Stiefl
Software Mentions: 9
Published: about 4 years ago

10.3389/fninf.2013.00026

Spyke Viewer: a flexible and extensible platform for electrophysiological data analysis
Cited by: 15
Author(s): Robert Pröpper, Klaus Obermayer
Software Mentions: 9
Published: almost 12 years ago

10.1371/journal.pcbi.1008223

Causal network inference from gene transcriptional time-series response to glucocorticoids
Cited by: 15
Author(s): Jonathan Lu, Bianca Dumitrascu, Ian C. McDowell, Brian Jo, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Timothy E. Reddy, Barbara E. Engelhardt
Software Mentions: 9
Published: almost 4 years ago

10.15252/msb.20209819

Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration
Cited by: 17
Author(s): Nader Morshed, William T. Ralvenius, Alexi Nott, L. Ashley Watson, Felicia H. Rodriguez, Leyla Anne Akay, Brian A. Joughin, Ping‐Chieh Pao, Jay Penney, Lauren M. LaRocque, Diego Mastroeni, Li Huei Tsai, Forest M. White
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12859-014-0408-9

Kiwi: a tool for integration and visualization of network topology and gene-set analysis
Cited by: 12
Author(s): Leif Väremo, Francesco Gatto, Jens Nielsen
Software Mentions: 9
Published: almost 10 years ago

10.3389/fphys.2017.00354

Expression, Localization of SUMO-1, and Analyses of Potential SUMOylated Proteins in Bubalus bubalis Spermatozoa
Cited by: 4
Author(s): Rahim Dad Brohi, Li Wang, Najla Ben Hassine, Jiang Cao, Hira Sajjad Talpur, Di Wu, Chun–Jie Huang, Zia Ur Rehman, Dinesh Bhattarai, Li–Jun Huo
Software Mentions: 9
Published: over 7 years ago

10.3389/fmed.2021.640515

Performance of Different Diagnostic PD-L1 Clones in Head and Neck Squamous Cell Carcinoma
Cited by: 13
Author(s): Julika Ribbat‐Idel, Frederick A. Dressler, Rosemarie Krupar, Christian Watermann, F. Paulsen, Patrick Kuppler, Luise Klapper, Anne Offermann, Barbara Wollenberg, Dirk Rades, Simon Laban, Markus Reischl, Karl‐Ludwig Bruchhage, Christian Idel, Sven Perner
Software Mentions: 9
Published: over 3 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 3 years ago

10.1038/s41598-021-81773-9

Verifying explainability of a deep learning tissue classifier trained on RNA-seq data
Cited by: 26
Author(s): Melvyn Yap, Rebecca L. Johnston, Helena Foley, Samual MacDonald, Olga Kondrashova, Khoa Tran, Kátia Nones, Lambros T. Koufariotis, Cameron Bean, John V. Pearson, Maciej Trzaskowski, Nicola Waddell
Software Mentions: 9
Published: almost 4 years ago

10.1371/journal.pbio.3001341

Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain
Cited by: 3
Author(s): Shaina Lu, Cantin Ortiz, Daniel Fürth, Stephan Fischer, Konstantinos Meletis, Anthony M. Zador, Jesse Gillis
Software Mentions: 8
Published: over 3 years ago

10.3389/fcell.2021.702741

Wnt Signaling Induces Asymmetric Dynamics in the Actomyosin Cortex of the C. elegans Endomesodermal Precursor Cell
Cited by: 4
Author(s): Francesca Caroti, Wim Thiels, Michiel Vanslambrouck, Rob Jelier
Software Mentions: 8
Published: about 3 years ago

10.1007/s10278-017-0037-8

SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research
Cited by: 239
Author(s): Ziv Yaniv, Bradley Lowekamp, Hans J. Johnson, Richard Beare
Software Mentions: 8
Published: almost 7 years ago

10.1002/pmic.201400377

Open source libraries and frameworks for biological data visualisation: A guide for developers
Cited by: 37
Author(s): Rui Wang, Yasset Perez‐Riverol, Henning Hermjakob, Juan Antonio Vizcaíno
Software Mentions: 8
Published: over 9 years ago

10.1016/j.ymeth.2015.07.012

Construction of an instant structured illumination microscope
Cited by: 30
Author(s): Alistair Curd, Alexa Cleasby, Katarzyna Makowska, Andrew G. York, Hari Shroff, Michelle Peckham
Software Mentions: 8
Published: about 9 years ago

10.1099/mgen.0.000168

Correlation between bacterial G+C content, genome size and the G+C content of associated plasmids and bacteriophages
Cited by: 73
Author(s): Apostolos Almpanis, Martin Swain, Derek Gatherer, Neil McEwan
Software Mentions: 8
Published: over 6 years ago

10.1186/s12870-019-1693-2

A k-mer grammar analysis to uncover maize regulatory architecture
Cited by: 32
Author(s): Maria Katherine Mejía‐Guerra, Edward S. Buckler
Software Mentions: 8
Published: over 5 years ago

10.3389/fgene.2021.602196

AI Aided Design of Epitope-Based Vaccine for the Induction of Cellular Immune Responses Against SARS-CoV-2
Cited by: 4
Author(s): Giovanni Mazzocco, Iga Niemiec, Alexander Myronov, Piotr Skoczylas, Jan Kaczmarczyk, Anna Sanecka-Duin, Katarzyna Gruba, Paulina Król, Michał Drwal, Marian Szczepanik, Krzysztof Pyrć, Piotr Stępniak
Software Mentions: 8
Published: over 3 years ago

10.1186/s12859-016-1003-z

Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations
Cited by: 26
Author(s): Niklaus Johner, Daniel Harries, George Khelashvili
Software Mentions: 8
Published: over 8 years ago

Projects: pypi: matplotlib

Papers Mentioning matplotlib 1,045