pypi: matplotlib | Projects | Ecosyste.ms: Papers

10.1186/s12864-019-5624-2

ALFA: annotation landscape for aligned reads
Cited by: 9
Author(s): Mathieu Bahin, Benoît Noël, Valentine Murigneux, Charles Bernard, Leïla Bastianelli, Hervé Le Hir, Alice Lebreton, Auguste Genovesio
Software Mentions: 8
Published: over 5 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

10.3390/s21092964

Traffic Congestion Analysis Based on a Web-GIS and Data Mining of Traffic Events from Twitter
Cited by: 17
Author(s): Juan Salazar-Carrillo, Miguel Torres-Ruiz, Clodoveu A. Davis, Rolando Quintero, Marco Moreno-Ibarra, Giovanni Guzmán
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0216511

Modelling tick bite risk by combining random forests and count data regression models
Cited by: 10
Author(s): Irene Garcia‐Martí, R. Zurita-Milla, Arno Swart
Software Mentions: 8
Published: almost 5 years ago

10.26508/lsa.202101113

Statistical guidelines for quality control of next-generation sequencing techniques
Cited by: 1
Author(s): Maximilian Sprang, Matteo Krüger, Miguel A. Andrade‐Navarro, Jean-Fred Fontaine
Software Mentions: 8
Published: about 3 years ago

10.1371/journal.pntd.0008755

Combining natural language processing and metabarcoding to reveal pathogen-environment associations
Cited by: 2
Author(s): David Molik, DeAndre Tomlinson, Shane Davitt, Eric Lease Morgan, Matthew Sisk, Benjamin Roche, Natalie Meyers, Michael E. Pfrender
Software Mentions: 8
Published: over 3 years ago

10.7717/peerj.4925

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data
Cited by: 166
Author(s): Jonathan M. Palmer, Michelle A. Jusino, Mark T. Banik, Daniel L. Lindner
Software Mentions: 8
Published: over 6 years ago

10.3389/fninf.2014.00014

Machine learning for neuroimaging with scikit-learn
Cited by: 1,186
Author(s): A. Alexandre, Fabián Pedregosa, Michael Eickenberg, Philippe Gervais, Andreas Mueller, Jean Kossaifi, Alexandre Gramfort, Bertrand Thirion, Gaël Varoquaux
Software Mentions: 8
Published: almost 11 years ago

10.3390/cancers13071734

Role for the Histone Demethylase KDM4B in Rhabdomyosarcoma via CDK6 and CCNA2: Compensation by KDM4A and Apoptotic Response of Targeting Both KDM4B and KDM4A
Cited by: 5
Author(s): Zoë S. Walters, Ewa Aładowicz, Bárbara Villarejo-Balcells, Gary Nugent, Joanna Selfe, Paul D. Eve, Julian Blagg, Olivia W. Rossanese, Janet Shipley
Software Mentions: 8
Published: over 3 years ago

10.1107/S2059798319011471

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in <i>Phenix</i>
Cited by: 3,483
Author(s): Dorothée Liebschner, Pavel V. Afonine, Matthew L. Baker, G. Bunkóczi, V.B. Chen, Tristan I. Croll, Bradley J. Hintze, Li Wei Hung, Swati Jain, Airlie J. McCoy, Nigel W. Moriarty, Robert D. Oeffner, Billy K. Poon, Michael G. Prisant, R.J. Read, Jane S. Richardson, David C. Richardson, Massimo Sammito, Oleg Sobolev, Duncan H. Stockwell, Thomas C. Terwilliger, Alexandre Urzhumtsev, Lizbeth L. Videau, Christopher J. Williams, Paul D. Adams
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pone.0199239

Optimizing colormaps with consideration for color vision deficiency to enable accurate interpretation of scientific data
Cited by: 91
Author(s): Jamie Nuñez, Christopher R. Anderton, Ryan Renslow
Software Mentions: 8
Published: over 6 years ago

10.15252/msb.20199071

Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor
Cited by: 30
Author(s): Francisca Monteiro, Georg Hubmann, Vakil Takhaveev, Silke R. Vedelaar, Justin Norder, Johan Hekelaar, Joana Saldida, Athanasios Litsios, Hein J. Wijma, Alexander Schmidt, Matthias Heinemann
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pgen.1009386

Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus
Cited by: 39
Author(s): Thorsten Langner, Adeline Harant, Luis B. Gómez-Luciano, Ram-Krishna Shrestha, Angus Malmgren, Sergio M. Latorre, Hernán A. Burbano, Joe Win, Sophien Kamoun
Software Mentions: 8
Published: almost 4 years ago

10.3390/s20226666

Blood Stain Classification with Hyperspectral Imaging and Deep Neural Networks
Cited by: 18
Author(s): Kamil Książek, Michał Romaszewski, Przemysław Głomb, Bartosz Grabowski, Michał Cholewa
Software Mentions: 8
Published: about 4 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

10.3389/fmicb.2021.660920

Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages
Cited by: 28
Author(s): José Luis Maturana, Juan Pablo Cárdenas
Software Mentions: 8
Published: over 3 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: almost 10 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

10.1523/ENEURO.0415-20.2021

Real-Time Closed-Loop Feedback in Behavioral Time Scales Using DeepLabCut
Cited by: 17
Author(s): Keisuke Sehara, Paul Zimmer-Harwood, Matthew E. Larkum, Robert N. S. Sachdev
Software Mentions: 8
Published: almost 4 years ago

10.1007/s00216-021-03261-3

Need for speed: evaluation of dilute and shoot-mass spectrometry for accelerated metabolic phenotyping in bioprocess development
Cited by: 5
Author(s): Alexander M. Reiter, Laura Herbst, Wolfgang Wiechert, Marco Oldiges
Software Mentions: 7
Published: over 3 years ago

10.1186/s12918-016-0337-5

Quantifying differences in cell line population dynamics using CellPD
Cited by: 22
Author(s): Edwin F. Juarez, Roy Lau, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Edmond Jonckheere, David B. Agus, Shannon M. Mumenthaler, Paul Macklin
Software Mentions: 7
Published: about 8 years ago

10.1371/journal.pone.0250170

Introducing Point-of-Interest as an alternative to Area-of-Interest for fixation duration analysis
Cited by: 7
Author(s): Nak Won Rim, Kyoung Whan Choe, Coltan Scrivner, Marc G. Berman
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0218789

Jscatter, a program for evaluation and analysis of experimental data
Cited by: 23
Author(s): Ralf Biehl
Software Mentions: 7
Published: over 5 years ago

10.1186/1756-0500-5-360

LXtoo: an integrated live Linux distribution for the bioinformatics community
Cited by: 5
Author(s): Guangchuang Yu, Li-Gen Wang, Xiaohong Meng, Qing-Yu He
Software Mentions: 7
Published: over 12 years ago

10.1371/journal.pone.0237207

Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging
Cited by: 4
Author(s): Claudia Sala, Enrico Giampieri, Silvia Vitali, Paolo Garagnani, Daniel Remondini, Armando Bazzani, Claudio Franceschi, Gastone Castellani
Software Mentions: 7
Published: about 4 years ago

10.1186/s13321-019-0351-x

TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data
Cited by: 25
Author(s): Dominique Sydow, Andrea Morger, Maximilian Driller, Andrea Volkamer
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0239381

Short k-mer abundance profiles yield robust machine learning features and accurate classifiers for RNA viruses
Cited by: 8
Author(s): Nafis Ul Alam, Umar Faruq Chowdhury
Software Mentions: 7
Published: about 4 years ago

10.1186/s13073-019-0695-x

FIREVAT: finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures
Cited by: 7
Author(s): Hyunbin Kim, Andy Jinseok Lee, Jongkeun Lee, Hyonho Chun, Young Seok Ju, Dong Ho Hong
Software Mentions: 7
Published: almost 5 years ago

10.12688/f1000research.8452.2

The effects of an editor serving as one of the reviewers during the peer-review process
Cited by: 4
Author(s): Marco Giordan, Attila Csikász‐Nagy, Andy Collings, Federico Vaggi
Software Mentions: 7
Published: about 8 years ago

10.1371/journal.pone.0223141

Attenuation correction using 3D deep convolutional neural network for brain 18F-FDG PET/MR: Comparison with Atlas, ZTE and CT based attenuation correction
Cited by: 36
Author(s): Paul Blanc-Durand, Maya Khalifé, B. Sgard, Sandeep Kaushik, Marine Soret, Tiss Amal, Georges El Fakhri, Marie‐Odile Habert, Florian Wiesinger, Aurélie Kas
Software Mentions: 7
Published: about 5 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/fcell.2021.702046

Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous Trophoblast
Cited by: 17
Author(s): Robert Morey, Omar Farah, Sampada Kallol, Daniela F. Requena, Morgan Meads, Matteo Moretto-Zita, Francesca Soncin, Louise C. Laurent, Mana M. Parast
Software Mentions: 7
Published: about 3 years ago

10.1186/s13059-019-1699-y

CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics
Cited by: 56
Author(s): Chuner Guo, Wenjun Kong, Kenji Kamimoto, Guillermo C. Rivera-Gonzalez, Xue Yang, Yuhei Kirita, Samantha A. Morris
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pcbi.1006741

Spatial synchronization codes from coupled rate-phase neurons
Cited by: 19
Author(s): Joseph D. Monaco, Rose M. De Guzman, Hugh T. Blair, Kechen Zhang
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0230888

Site-specific machine learning predictive fertilization models for potato crops in Eastern Canada
Cited by: 13
Author(s): Zonlehoua Coulibali, Athyna N. Cambouris, Léon‐Étienne Parent
Software Mentions: 7
Published: over 4 years ago

10.1016/j.molcel.2021.03.013

Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression
Cited by: 17
Author(s): Amy Tresenrider, Kaitlin Morse, Victoria Jorgensen, Minghao Chia, Hanna Liao, Folkert J. van Werven, Elçin Ünal
Software Mentions: 7
Published: over 3 years ago

10.1021/acsomega.1c00991

Global Property Prediction: A Benchmark Study on Open-Source, Perovskite-like Datasets
Cited by: 5
Author(s): Felix Mayr, Alessio Gagliardi
Software Mentions: 7
Published: over 3 years ago

10.1186/gb-2011-12-6-r60

Metagenomic biomarker discovery and explanation
Cited by: 9,402
Author(s): Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S. Garrett, Curtis Huttenhower
Software Mentions: 7
Published: almost 14 years ago

10.7554/eLife.62161

Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones
Cited by: 18
Author(s): Nina Kirstein, Alexander Buschle, Xia Wu, Stefan Krebs, Helmut Blum, Elisabeth Kremmer, Ina Vorberg, Wolfgang Hammerschmidt, Laurent Lacroix, Olivier Hyrien, Benjamin Audit, Aloys Schepers
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.45403

The dynamic conformational landscape of the protein methyltransferase SETD8
Cited by: 37
Author(s): Shi Chen, Rafal Wiewiora, Fanwang Meng, Nicolas Babault, Anqi Ma, Wenyu Yu, Kun Qian, Hao Hu, Hua Zou, Junyi Wang, Shijie Fan, Gil Blum, Fábio Pittella Silva, Kyle A. Beauchamp, W. Tempel, Hualiang Jiang, Kaixian Chen, R.J. Skene, Y. George Zheng, Peter J. Brown, Jian Jin, Cheng Luo, John D. Chodera, Minkui Luo
Software Mentions: 7
Published: over 5 years ago

10.7554/eLife.62800

Mapping immune variation and var gene switching in naive hosts infected with Plasmodium falciparum
Cited by: 18
Author(s): Kathryn H. Milne, Alasdair Ivens, Adam J. Reid, Magda E. Lotkowska, Áine O’Toole, Geetha Sankaranarayanan, Diana Muñoz Sandoval, Wiebke Nahrendorf, Clément Regnault, Nick J. Edwards, Sarah E. Silk, Ruth Payne, Angela M. Minassian, Navin Venkatraman, Mandy Sanders, Adrian V. S. Hill, Michael P. Barrett, Matthew Berriman, Simon J. Draper, J. Alexandra Rowe, Philip J. Spence
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.31867

Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry
Cited by: 16
Author(s): Peter L. Freddolino, Jiping Yang, Amir Momen-Roknabadi, Saeed Tavazoie
Software Mentions: 7
Published: over 6 years ago

10.1016/j.csbj.2020.12.012

Virulence factor-related gut microbiota genes and immunoglobulin A levels as novel markers for machine learning-based classification of autism spectrum disorder
Cited by: 17
Author(s): Mingbang Wang, Ceymi Doenyas, Jing Wan, Shujuan Zeng, Chunquan Cai, Jiaxiu Zhou, Yanqing Liu, Yin Zhen, Wenhao Zhou
Software Mentions: 7
Published: almost 4 years ago

10.1016/j.dib.2021.106968

Dataset on structure and physical properties of stable diatomic systems based on van der Waals density functional method
Cited by: 2
Author(s): Kiyou Shibata, Eiki Suzuki, Teruyasu Mizoguchi
Software Mentions: 7
Published: over 3 years ago

10.1038/s42003-021-01785-z

Temporal hierarchy of intrinsic neural timescales converges with spatial core-periphery organization
Cited by: 42
Author(s): Mehrshad Golesorkhi, Javier Gómez‐Pilar, Shankar Tumati, Maia Fraser, Georg Northoff
Software Mentions: 7
Published: over 3 years ago

10.3389/fninf.2020.00024

Sammba-MRI: A Library for Processing SmAll-MaMmal BrAin MRI Data in Python
Cited by: 11
Author(s): Marina Célestine, Nachiket A. Nadkarni, Clément M. Garin, Salma Bougacha, Marc Dhénain
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0240573

Assessment of software methods for estimating protein-protein relative binding affinities
Cited by: 10
Author(s): Tawny R Gonzalez, Kyle Martin, Jonathan E. Barnes, Jagdish Suresh Patel, F. Marty Ytreberg
Software Mentions: 7
Published: almost 4 years ago

10.3389/fninf.2013.00010

The Virtual Brain: a simulator of primate brain network dynamics
Cited by: 296
Author(s): Paula Sanz-Leon, S. A. Knock, Michael Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor K. Jirsa
Software Mentions: 7
Published: almost 12 years ago

10.1186/s12864-021-07711-1

Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana
Cited by: 6
Author(s): Georg Back, Dirk Walther
Software Mentions: 7
Published: over 3 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

10.14814/phy2.14880

Animal blood in translational research: How to adjust animal blood viscosity to the human standard
Cited by: 6
Author(s): Paul Ecker, Andreas Sparer, Benjamin Lukitsch, Martin Elenkov, Monika Seltenhammer, Richard Crevenna, Margit Gfoehler, Michael Harasek, Ursula Windberger
Software Mentions: 7
Published: over 3 years ago

10.1038/s42003-021-02437-y

Neocortical inhibitory interneuron subtypes are differentially attuned to synchrony- and rate-coded information
Cited by: 3
Author(s): Luke Y. Prince, Matthew M Tran, Dorian Grey, Lydia Saad, Helen Chasiotis, Jeehyun Kwag, Michael Köhl, Blake A Richards
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.53281

Feedback inhibition and its control in an insect olfactory circuit
Cited by: 8
Author(s): Subhasis Ray, Zane Aldworth, Mark Stopfer
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-021-83784-y

Early risk assessment for COVID-19 patients from emergency department data using machine learning
Cited by: 57
Author(s): Stefan Heldt, Marcela P. Vizcaychipi, Sophie Peacock, Mattia Cinelli, Lachlan McLachlan, Fernando Andreotti, Stojan Jovanovic, Robert Dürichen, N. A. Lipunova, Robert A. Fletcher, Anne Hancock, Alex McCarthy, Richard A. Pointon, Alexander Brown, James Eaton, Roberto Liddi, Lucy Mackillop, Lionel Tarassenko, Rabia Khan
Software Mentions: 7
Published: almost 4 years ago

10.3389/fninf.2013.00045

The Design of SimpleITK
Cited by: 402
Author(s): Bradley Lowekamp, David T. Chen, Luis Ibáñez, Daniel J. Blezek
Software Mentions: 7
Published: almost 12 years ago

10.7717/peerj.2823

An extensive comparison of species-abundance distribution models
Cited by: 65
Author(s): Elita Baldridge, David J. Harris, Xiao Xiao, Ethan White
Software Mentions: 7
Published: almost 8 years ago

10.3389/fninf.2019.00059

PyParadigm—A Python Library to Build Screens in a Declarative Way
Cited by: 1
Author(s): Felix G. Knorr, Johannes Petzold, Michael Marxen
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-019-54700-2

Murine xenograft bioreactors for human immunopeptidome discovery
Cited by: 8
Author(s): James Heather, Paisley T. Myers, Feng Shi, Mohammad Ovais Aziz‐Zanjani, Keira E. Mahoney, Matthew Perez, Benjamin Morin, Christine Brittsan, Jeffrey Shabanowitz, Donald F. Hunt, Mark Cobbold
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pcbi.1009382

Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes
Cited by: 3
Author(s): Samantha N. Piekos, Sadhana Gaddam, Pranav Bhardwaj, Prashanth Radhakrishnan, Ramanathan V. Guha, Anthony E. Oro
Software Mentions: 7
Published: about 3 years ago

10.1038/s41598-018-22083-5

Chronic helminth infection burden differentially affects haematopoietic cell development while ageing selectively impairs adaptive responses to infection
Cited by: 14
Author(s): Simon A. Babayan, Amy Sinclair, Jessica Duprez, Colin Selman
Software Mentions: 7
Published: over 6 years ago

10.3389/fninf.2017.00044

SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales
Cited by: 13
Author(s): Martin Rueckl, Stephen C. Lenzi, Laura Moreno-Velasquez, Daniel Parthier, Dietmar Schmitz, Sten Ruediger, Friedrich W. Johenning
Software Mentions: 7
Published: over 7 years ago

10.1186/s12859-021-03986-z

MSIFinder: a python package for detecting MSI status using random forest classifier
Cited by: 6
Author(s): Tao Zhou, Libin Chen, Jing Guo, Mengmeng Zhang, Yanrui Zhang, Shanbo Cao, Li Feng, Haijun Wang
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-020-78777-2

Evolutionary design of optimal surface topographies for biomaterials
Cited by: 4
Author(s): Aliaksei Vasilevich, Aurélie Carlier, David A. Winkler, Shantanu Singh, Jan de Boer
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0118442

Active Degradation Explains the Distribution of Nuclear Proteins during Cellular Senescence
Cited by: 2
Author(s): Enrico Giampieri, Marco De Cecco, Daniel Remondini, John M. Sedivy, Gastone Castellani
Software Mentions: 7
Published: over 9 years ago

10.1038/s41598-017-02932-5

Transcriptomic analysis of short-fruit 1 (sf1) reveals new insights into the variation of fruit-related traits in Cucumis sativus
Cited by: 25
Author(s): Lina Wang, Chuanai Cao, Shuangshuang Zheng, Haiyang Zhang, Panjing Liu, Qian Ge, Jingrui Li, Zhonghai Ren
Software Mentions: 7
Published: over 7 years ago

10.1038/s41597-020-00760-3

Data-science ready, multisite, human diffusion MRI white-matter-tract statistics
Cited by: 9
Author(s): Garikoitz Lerma-Usabiaga, Pratik Mukherjee, Mike Perry, Brian A. Wandell
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-017-10853-6

The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages
Cited by: 39
Author(s): Elton J. R. Vasconcelos, Luis DaSilva, David S. Pires, Guilherme M. Lavezzo, Adriana S. A. Pereira, Murilo Sena Amaral, Sérgio Verjovski-Almeida
Software Mentions: 7
Published: about 7 years ago

10.1186/s12859-019-2796-3

rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics
Cited by: 15
Author(s): Jaume Bonet, Zander Harteveld, Fabian Sesterhenn, Andreas Scheck, Bruno E. Correia
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2021.641788

Successful ATAC-Seq From Snap-Frozen Equine Tissues
Cited by: 8
Author(s): Sichong Peng, Rebecca R. Bellone, Jessica L. Petersen, Theodore S. Kalbfleisch, Carrie J. Finno
Software Mentions: 7
Published: over 3 years ago

10.1107/S0907444913007051

<i>OpenStructure</i>: an integrated software framework for computational structural biology
Cited by: 82
Author(s): Marco Biasini, Tobias Schmidt, Stefan Bienert, Valerio Mariani, Gabriel Studer, Juergen Haas, Niklaus Johner, Andreas Schenk, Ansgar Philippsen, Torsten Schwede
Software Mentions: 7
Published: over 11 years ago

10.1371/journal.pone.0231824

Investigating the effect of dependence between conditions with Bayesian Linear Mixed Models for motif activity analysis
Cited by: 0
Author(s): Simone Lederer, Tom Heskes, Simon J. van Heeringen, Cornelis A. Albers
Software Mentions: 7
Published: over 4 years ago

10.1126/sciadv.abf7129

Endogenous variation in ventromedial prefrontal cortex state dynamics during naturalistic viewing reflects affective experience
Cited by: 55
Author(s): Luke J. Chang, Eshin Jolly, Jin Hyun Cheong, Kristina M. Rapuano, Nathan Greenstein, Pin-Hao A. Chen, Jeremy R. Manning
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-017-16050-9

Computational derivation of a molecular framework for hair follicle biology from disease genes
Cited by: 4
Author(s): Rachel K. Severin, Xinwei Li, Kun Qian, Andreas Mueller, Lynn Petukhova
Software Mentions: 7
Published: almost 7 years ago

10.3390/s21082852

Classification of Skin Disease Using Deep Learning Neural Networks with MobileNet V2 and LSTM
Cited by: 294
Author(s): Parvathaneni Naga Srinivasu, Jalluri Gnana SivaSai, Muhammad Fazal Ijaz, Akash Kumar Bhoi, Wonjoon Kim, James Jin Kang
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2105-14-38

FANTOM: Functional and taxonomic analysis of metagenomes
Cited by: 34
Author(s): Kemal Sanli, Fredrik Karlsson, Intawat Nookaew, Jens Nielsen
Software Mentions: 6
Published: almost 12 years ago

10.1371/journal.pone.0235159

Zooplankton biogeographic boundaries in the California Current System as determined from metabarcoding
Cited by: 13
Author(s): Kathleen J. Pitz, Jinchen Guo, Shannon B. Johnson, Tracy L. Campbell, Haibin Zhang, Robert C. Vrijenhoek, Francisco P. Chávez, Jonathan B. Geller
Software Mentions: 6
Published: over 4 years ago

10.1186/s13321-016-0180-0

Mapping the 3D structures of small molecule binding sites
Cited by: 13
Author(s): Joshua Meyers, Nathan Brown, Julian Blagg
Software Mentions: 6
Published: almost 8 years ago

10.1186/1471-2105-15-324

Polyphony: superposition independent methods for ensemble-based drug discovery
Cited by: 8
Author(s): William R. Pitt, Rinaldo W. Montalvão, Tom L. Blundell
Software Mentions: 6
Published: about 10 years ago

10.3758/s13428-020-01430-3

The Tobii Pro Spectrum: A useful tool for studying microsaccades?
Cited by: 7
Author(s): Maria Nyström, Diederick C Niehorster, Richard Andersson, Ignace T. C. Hooge
Software Mentions: 6
Published: over 4 years ago

10.3389/fncom.2014.00139

Diffusion approximation-based simulation of stochastic ion channels: which method to use?
Cited by: 8
Author(s): Danilo Pezo, Daniel Soudry, Patricio Orio
Software Mentions: 6
Published: about 10 years ago

10.3389/fncom.2018.00083

Task-Related Synaptic Changes Localized to Small Neuronal Population in Recurrent Neural Network Cortical Models
Cited by: 6
Author(s): Satoshi Kuroki, Takuya Isomura
Software Mentions: 6
Published: about 6 years ago

10.3389/fgene.2021.674783

Gene Loss, Pseudogenization in Plastomes of Genus Allium (Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions
Cited by: 8
Author(s): Victoria A. Scobeyeva, Ilya V. Artyushin, A.A. Krinitsina, Nikitin Pavel, Antipin Mi, Sergei V. Kuptsov, Maxim S. Belenikin, Denis O. Omelchenko, Maria D. Logacheva, Е. А. Коноров, Andrei E. Samoilov, Anna S. Speranskaya
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1005950

HaSAPPy: A tool for candidate identification in pooled forward genetic screens of haploid mammalian cells
Cited by: 9
Author(s): Giulio Di Minin, Andreas Postlmayr, Anton Wutz
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12859-015-0759-x

CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data
Cited by: 36
Author(s): Mark‐Anthony Bray, Anne E. Carpenter
Software Mentions: 6
Published: about 9 years ago

10.1371/journal.pone.0257535

Recalibrating expectations about effect size: A multi-method survey of effect sizes in the ABCD study
Cited by: 60
Author(s): Max M. Owens, Alexandra Potter, Courtland S. Hyatt, Matthew D. Albaugh, Wesley K. Thompson, Terry L. Jernigan, Dekang Yuan, Sage Hahn, Nicholas Allgaier, Hugh Garavan
Software Mentions: 6
Published: about 3 years ago

10.3389/fcell.2021.562908

FOntCell: Fusion of Ontologies of Cells
Cited by: 0
Author(s): Javier Cabau-Laporta, Alex M. Ascensión, Mikel Arrospide-Elgarresta, Daniela Gerovska, Marcos J. Araúzo‐Bravo
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12870-017-1070-y

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions
Cited by: 12
Author(s): Martin Schmidt, Michiel Van Bel, Magdalena Wołoszyńska, Bram Slabbinck, Cindy Martens, Marc De Block, Frederik Coppens, Mieke Van Lijsebettens
Software Mentions: 6
Published: over 7 years ago

10.1016/j.jbc.2021.100804

Droplet and fibril formation of the functional amyloid Orb2
Cited by: 8
Author(s): Kidist Ashami, Alexander S. Falk, Connor Hurd, Samridhi Garg, Silvia A. Cervantes, Anoop Rawat, Ansgar B. Siemer
Software Mentions: 6
Published: over 3 years ago

10.3390/v12080891

Viral Metagenomic Profiling of Croatian Bat Population Reveals Sample and Habitat Dependent Diversity
Cited by: 17
Author(s): Ivana Šimić, Tomaž Mark Zorec, Ivana Lojkić, Nina Krešić, Mario Poljak, Florence Cliquet, Evelyne Picard-Meyer, Marine Wasniewski, Vida Zrnčić, Anđela Čukušić, Tomislav Bedeković
Software Mentions: 6
Published: over 4 years ago

10.12688/f1000research.11905.2

Virtual-screening workflow tutorials and prospective results from the Teach-Discover-Treat competition 2014 against malaria
Cited by: 5
Author(s): Sereina Riniker, Gregory A. Landrum, Floriane Montanari, Santiago D. Villalba, Julie Maier, Johanna M. Jansen, W. Patrick Walters, Anang A. Shelat
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12859-021-04339-6

Predicting chemotherapy response using a variational autoencoder approach
Cited by: 7
Author(s): Qi Wei, Stephen A. Ramsey
Software Mentions: 6
Published: about 3 years ago

10.1186/s13059-020-02099-9

Contiguous and stochastic CHH methylation patterns of plant DRM2 and CMT2 revealed by single-read methylome analysis
Cited by: 11
Author(s): Keith D. Harris, Assaf Zemach
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0240802

OrganoidTracker: Efficient cell tracking using machine learning and manual error correction
Cited by: 32
Author(s): Rutger Nico Ulbe Kok, Laetitia Hebert, Guizela Huelsz-Prince, Yvonne J. Goos, Xuan Zheng, Katarzyna Bożek, Greg J. Stephens, Sander J. Tans, Jeroen S. van Zon
Software Mentions: 6
Published: about 4 years ago

10.1186/s12920-016-0164-y

Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease
Cited by: 84
Author(s): Alexandra Dumitriu, Javad Golji, Adam Labadorf, Benbo Gao, Thomas G. Beach, Richard H. Myers, Kenneth A. Longo, Jeanne C. Latourelle
Software Mentions: 6
Published: almost 9 years ago

10.1186/s13072-021-00411-w

Sensitivity of cohesin–chromatin association to high-salt treatment corroborates non-topological mode of loop extrusion
Cited by: 4
Author(s): Arkadiy K. Golov, Anastasia V. Golova, А. В. Гаврилов, Sergey V. Razin
Software Mentions: 6
Published: over 3 years ago

10.1186/s12920-019-0581-9

The caudate nucleus undergoes dramatic and unique transcriptional changes in human prodromal Huntington’s disease brain
Cited by: 26
Author(s): Filisia Agus, Diego Crespo, Richard H. Myers, Adam Labadorf
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0113838

The Connectome Visualization Utility: Software for Visualization of Human Brain Networks
Cited by: 29
Author(s): Roan A. LaPlante, Linda Douw, Wei Tang, Steven M. Stufflebeam
Software Mentions: 6
Published: almost 10 years ago

10.1074/mcp.O117.068122

Prediction of Protein Complexes in Trypanosoma brucei by Protein Correlation Profiling Mass Spectrometry and Machine Learning
Cited by: 23
Author(s): Thomas W. M. Crozier, Michele Tinti, Mark Larance, Angus I. Lamond, Michael A. J. Ferguson
Software Mentions: 6
Published: almost 7 years ago

10.1001/jamanetworkopen.2021.8075

Assessment of Overuse of Medical Tests and Treatments at US Hospitals Using Medicare Claims
Cited by: 21
Author(s): Kelsey Chalmers, Philip E. Smith, Judith A. Garber, Valérie Gopinath, Shannon Brownlee, Allen D. Schwartz, Adam G Elshaug, Vikas Saini
Software Mentions: 6
Published: over 3 years ago

10.1093/molbev/msz214

The Genetic Background Modulates the Evolution of Fluoroquinolone-Resistance in Mycobacterium tuberculosis
Cited by: 29
Author(s): Rhastin A D Castro, Amanda Ross, Lujeko Kamwela, Miriam Reinhard, Chloé Loiseau, Julia Feldmann, Sònia Borrell, Andrej Trauner, Sébastien Gagneux
Software Mentions: 6
Published: about 5 years ago

Projects: pypi: matplotlib

Papers Mentioning matplotlib 1,045