pypi: numpy | Projects | Ecosyste.ms: Papers

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

10.1038/s41396-020-00814-9

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

10.1093/gigascience/giaa026

ShinyLearner: A containerized benchmarking tool for machine-learning classification of tabular data
Cited by: 13
Author(s): Stephen R. Piccolo, Terry J. Lee, Erica Suh, Kimball T Hill
Software Mentions: 21
Published: over 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

10.1186/s13059-020-02100-5

Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data
Cited by: 56
Author(s): Nikolaus Fortelny, Christoph Bock
Software Mentions: 20
Published: over 4 years ago

10.3390/ijms21186652

Identification of Gastritis Subtypes by Convolutional Neuronal Networks on Histological Images of Antrum and Corpus Biopsies
Cited by: 15
Author(s): Georg Steinbuß, Katharina Kriegsmann, Mark Kriegsmann
Software Mentions: 19
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/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

10.1186/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: almost 4 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

10.1186/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

10.1371/journal.pgen.1008405

Causal relationships between obesity and the leading causes of death in women and men
Cited by: 106
Author(s): Jenny C Censin, Sanne A.E. Peters, Jonas Bovijn, Teresa Ferreira, Sara L. Pulit, Reedik Mägi, Anubha Mahajan, Michael V Holmes, Cecilia M. Lindgren
Software Mentions: 14
Published: about 5 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

10.1186/s13059-021-02349-4

PEPPRO: quality control and processing of nascent RNA profiling data
Cited by: 14
Author(s): Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin, Nathan C. Sheffield
Software Mentions: 14
Published: over 3 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

10.12688/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

10.3389/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

10.1371/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

10.3390/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

10.1186/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

10.1128/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/s12859-020-03774-1

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

10.1186/s13321-020-00455-2

spyrmsd: symmetry-corrected RMSD calculations in Python
Cited by: 23
Author(s): Rocco Meli, Philip C. Biggin
Software Mentions: 13
Published: about 4 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: almost 4 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

10.1371/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

10.7554/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/ani11072131

Predicting Subclinical Ketosis in Dairy Cows Using Machine Learning Techniques
Cited by: 7
Author(s): Alicja Satoła, Edyta Bauer
Software Mentions: 12
Published: over 3 years ago

10.1128/mSystems.00903-19

manta: a Clustering Algorithm for Weighted Ecological Networks
Cited by: 7
Author(s): Lisa Röttjers, Karoline Faust
Software Mentions: 12
Published: almost 5 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

10.1371/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: almost 5 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

10.7717/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

10.1016/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

10.1371/journal.pcbi.1009136

Multidimensional analysis and detection of informative features in human brain white matter
Cited by: 14
Author(s): Adam Richie-Halford, Jason D. Yeatman, Noah Simon, Ariel Rokem
Software Mentions: 12
Published: over 3 years ago

10.3389/fonc.2021.625207

MYCN Drives a Tumor Immunosuppressive Environment Which Impacts Survival in Neuroblastoma
Cited by: 18
Author(s): Salvatore Raieli, Daniele Di Renzo, Silvia Lampis, Camilla Amadesi, Luca Montemurro, Andrea Pession, Patrizia Hrelia, Matthias Fischer, Roberto Tonelli
Software Mentions: 12
Published: over 3 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

10.1186/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.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: over 3 years ago

10.3389/fmicb.2019.01770

Gut Microbiota as an Objective Measurement for Auxiliary Diagnosis of Insomnia Disorder
Cited by: 55
Author(s): Bingdong Liu, Win Lin, Shujie Chen, Ting Xiang, Yifan Yang, Yulong Yin, Guohuan Xu, Zhihong Liu, Li Liu, Jiyang Pan, Liwei Xie
Software Mentions: 11
Published: over 5 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

10.1107/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

10.3390/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: almost 5 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

10.1186/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

10.3390/nu12020302

The Role of Glycemic Index and Glycemic Load in the Development of Real-Time Postprandial Glycemic Response Prediction Models for Patients with Gestational Diabetes
Cited by: 14
Author(s): Evgenii Pustozerov, Aleksandra Tkachuk, Elena Vasukova, А. В. Дронова, Ekaterina S. Shilova, Anna D. Anopova, Faina Piven, Tatiana Pervunina, Elena Vasilieva, Elena Grineva, Polina Popova
Software Mentions: 11
Published: almost 5 years ago

10.1038/s41598-021-82043-4

PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
Cited by: 10
Author(s): Pablo Acera Mateos, Renzo F. Balboa, Simon Easteal, Eduardo Eyras, Hardip R. Patel
Software Mentions: 11
Published: almost 4 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: almost 7 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

10.3389/fmolb.2019.00025

Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations
Cited by: 22
Author(s): Dalibor Trapl, Izabela Horvacanin, Václav Mareška, Furkan Özçelik, Gözde Ünal, Vojtěch Spiwok
Software Mentions: 11
Published: over 5 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

10.1016/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

10.1029/2019EA001004

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

10.7554/eLife.67490

Non-linear dimensionality reduction on extracellular waveforms reveals cell type diversity in premotor cortex
Cited by: 27
Author(s): Eric Lee, Hymavathy Balasubramanian, Alexandra Tsolias, Stephanie Udochukwu Anakwe, Maria Medalla, Krishna V. Shenoy, Chandramouli Chandrasekaran
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

10.3389/fnins.2019.00494

Automated, Efficient, and Accelerated Knowledge Modeling of the Cognitive Neuroimaging Literature Using the ATHENA Toolkit
Cited by: 6
Author(s): Michael C. Riedel, Taylor Salo, Jason Hays, Matthew D. Turner, Matthew T. Sutherland, Jessica A. Turner, Angela R. Laird
Software Mentions: 10
Published: over 5 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

10.1038/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

10.3389/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

10.1002/pro.3299

Automating tasks in protein structure determination with the clipper python module
Cited by: 6
Author(s): Stuart McNicholas, Tristan I. Croll, Tom Burnley, Colin M. Palmer, Soon Wen Hoh, Huw T. Jenkins, E.J. Dodson, Kevin Cowtan, Jon Agirre
Software Mentions: 10
Published: about 7 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

10.3389/fninf.2019.00018

Draculab: A Python Simulator for Firing Rate Neural Networks With Delayed Adaptive Connections
Cited by: 3
Author(s): Sergio Verduzco-Flores, Erik De Schutter
Software Mentions: 10
Published: over 5 years ago

10.1186/s12920-019-0628-y

A deep neural network approach to predicting clinical outcomes of neuroblastoma patients
Cited by: 14
Author(s): Léon-Charles Tranchevent, Francisco Azuaje, Jagath C. Rajapakse
Software Mentions: 10
Published: almost 5 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

10.1016/j.cell.2021.07.017

Whole-body integration of gene expression and single-cell morphology
Cited by: 59
Author(s): Hernando Vergara, Constantin Pape, Kimberly Meechan, Valentyna Zinchenko, Christel Genoud, Adrian Wanner, Kevin Nzumbi Mutemi, Benjamin Titze, Rachel Templin, Paola Bertucci, Oleg Simakov, Wiebke Dürichen, Pedro Machado, Emily L. Savage, Lothar Schermelleh, Yannick Schwab, Rainer W. Friedrich, Anna Kreshuk, Christian Tischer, Detlev Arendt
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: about 4 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

10.1186/s12864-015-2250-5

Leveraging global gene expression patterns to predict expression of unmeasured genes
Cited by: 3
Author(s): James Rudd, René A. Zelaya, Eugene Demidenko, Ellen L. Goode, Casey S. Greene, Jennifer A. Doherty
Software Mentions: 10
Published: almost 9 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

10.12688/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

10.3390/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

10.3389/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: over 3 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

10.1099/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

10.1186/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

10.1186/s40168-021-01054-5

A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere
Cited by: 39
Author(s): Robyn J. Wright, Rafael Bosch, Morgan G. I. Langille, Matthew I. Gibson, Joseph Alexander Christie-Oleza
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pcbi.1008982

Predicting mean ribosome load for 5’UTR of any length using deep learning
Cited by: 14
Author(s): Alexander Karollus, Žiga Avsec, Julien Gagneur
Software Mentions: 9
Published: over 3 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

10.1111/tpj.15190

Subgenome evolution in allotetraploid plants
Cited by: 19
Author(s): Matteo Schiavinato, Alexandrina Bodrug‐Schepers, Juliane C. Dohm, Heinz Himmelbauer
Software Mentions: 9
Published: over 3 years ago

10.1186/s12859-021-04093-9

Machine learning predicts nucleosome binding modes of transcription factors
Cited by: 1
Author(s): K C Kishan, Sridevi K. Subramanya, Rui Li, Feng Cui
Software Mentions: 9
Published: over 3 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/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.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

10.3389/fninf.2017.00046

Software for Brain Network Simulations: A Comparative Study
Cited by: 42
Author(s): Ruben A. Tikidji-Hamburyan, Vikram K. Narayana, Zeki Bozkuş, Tarek El‐Ghazawi
Software Mentions: 9
Published: over 7 years ago

10.1186/s12911-021-01459-0

Transformers-sklearn: a toolkit for medical language understanding with transformer-based models
Cited by: 14
Author(s): Feihong Yang, Xuwen Wang, Hetong Ma, Jiao Li
Software Mentions: 9
Published: over 3 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.pgen.1009773

Transcriptional progression during meiotic prophase I reveals sex-specific features and X chromosome dynamics in human fetal female germline
Cited by: 7
Author(s): Xueying Fan, Ioannis Moustakas, Vanessa Torrens-Juaneda, Qijing Lei, Geert Hamer, Leoni A. Louwé, Gonneke S. K. Pilgram, Károly Szuhai, Roberto Matorras, Cristina Eguizábal, Lucette van der Westerlaken, Hailiang Mei, Susana M. Chuva de Sousa Lopes
Software Mentions: 9
Published: about 3 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

10.3390/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: about 5 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

10.1172/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

10.15252/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/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.pcbi.1008364

pyTFM: A tool for traction force and monolayer stress microscopy
Cited by: 19
Author(s): Andreas Bauer, Magdalena Přechová, Lena Fischer, Ingo Thievessen, Martin Gregor, Ben Fabry
Software Mentions: 9
Published: over 3 years ago

10.3389/fcimb.2020.00137

Microbiotyping the Sinonasal Microbiome
Cited by: 15
Author(s): Ahmed Bassiouni, S. Paramasivan, Arron Shiffer, Matthew R. Dillon, Emily K. Cope, Clare Cooksley, Mahnaz Ramezanpour, Sophia Moraitis, Mohammad Javed Ali, Benjamin S. Bleier, Claudio Callejas, Marjolein Cornet, Richard Douglas, Daniel Lorena Dutra, Christos Georgalas, Richard J. Harvey, Peter H. Hwang, Amber U. Luong, Rodney J. Schlosser, Pongsakorn Tantilipikorn, Marc A. Tewfik, Sarah Vreugde, Peter John Wormald, J. Gregory Caporaso, Alkis James Psaltis
Software Mentions: 9
Published: over 4 years ago

10.1186/s13059-020-02165-2

iMOKA: k-mer based software to analyze large collections of sequencing data
Cited by: 6
Author(s): Claudio Lorenzi, Sylvain Barriere, Jean-Philippe Villemin, Laureline Dejardin Bretones, Alban Mancheron, William Ritchie
Software Mentions: 9
Published: about 4 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

10.1186/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

10.3389/fneur.2021.681140

Using Base-ml to Learn Classification of Common Vestibular Disorders on DizzyReg Registry Data
Cited by: 3
Author(s): Gerome Vivar, Ralf Strobl, Eva Grill, Nassir Navab, Andreas Zwergal, Seyed-Ahmad Ahmadi
Software Mentions: 9
Published: over 3 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

Projects: pypi: numpy

Papers Mentioning numpy 832