pypi: numpy | Projects | Ecosyste.ms: Papers

10.1007/s12551-018-0489-1

Hi-C analysis: from data generation to integration
Cited by: 62
Author(s): Koustav Pal, Mattia Forcato, Francesco Ferrari
Software Mentions: 8
Published: almost 6 years ago

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

10.3390/biom10060878

High-Throughput Identification of Adapters in Single-Read Sequencing Data
Cited by: 3
Author(s): Asan M. S. H. Mohideen, Steinar Johansen, Igor Babiak
Software Mentions: 8
Published: over 4 years ago

10.7717/peerj.10670

Digital Cell Sorter (DCS): a cell type identification, anomaly detection, and Hopfield landscapes toolkit for single-cell transcriptomics
Cited by: 8
Author(s): Sergii Domanskyi, Alex Hakansson, T. J. Bertus, Giovanni Paternostro, Carlo Piermarocchi
Software Mentions: 8
Published: almost 4 years ago

10.1186/s13072-021-00401-y

Evaluation of whole-genome DNA methylation sequencing library preparation protocols
Cited by: 18
Author(s): Jacob Morrison, Julie Koeman, Benjamin K. Johnson, Kelly K. Foy, Ian Beddows, Wanding Zhou, David Chesla, Larissa L. Rossell, Emily J. Siegwald, Marie Adams, Hui Shen
Software Mentions: 8
Published: over 3 years ago

10.3390/plants10050840

Development of an Image Analysis Pipeline to Estimate Sphagnum Colony Density in the Field
Cited by: 1
Author(s): Willem Q. M. van de Koot, Larissa J. J. van Vliet, Wei‐Lun Chen, John Doonan, Cândida Nibau
Software Mentions: 8
Published: over 3 years ago

10.1186/s12859-021-04275-5

VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments
Cited by: 2
Author(s): Yingbo Cui, Zihang Wang, Johannes Köster, Xiangke Liao, Shaoliang Peng, Tao Tang, Chun Huang, Chi Yang
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.42448

Respiratory syncytial virus co-opts host mitochondrial function to favour infectious virus production
Cited by: 40
Author(s): Mengjie Hu, Keith E. Schulze, Reena Ghildyal, Darren C. Henstridge, Jacek L. Kolanowski, Elizabeth J. New, Yuning Hong, Alan Hsu, Philip M. Hansbro, Peter Wark, Marie A. Bogoyevitch, David A. Jans
Software Mentions: 8
Published: over 5 years ago

10.1093/bioinformatics/btaa093

Methplotlib: analysis of modified nucleotides from nanopore sequencing
Cited by: 22
Author(s): Wouter De Coster, Endre Bakken Stovner, Mojca Stražišar
Software Mentions: 8
Published: almost 5 years ago

10.7554/eLife.47859

Persistent epigenetic memory impedes rescue of the telomeric phenotype in human ICF iPSCs following DNMT3B correction
Cited by: 15
Author(s): Shir Toubiana, Miriam Gagliardi, Mariarosaria Papa, Roberta Manco, Maty Tzukerman, Maria R. Matarazzo, Sara Selig
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pcbi.1007696

The SONATA data format for efficient description of large-scale network models
Cited by: 26
Author(s): Kael Dai, Juan Hernando, Yazan N. Billeh, Sergey L. Gratiy, Judit Planas, Andrew P. Davison, Salvador Dura‐Bernal, Padraig Gleeson, Adrien Devresse, Benjamin Dichter, Michael Gevaert, James G. King, Werner A. H. Van Geit, Arseny V. Povolotsky, Eilif Müller, Jean-Denis Courcol, Anton Arkhipov
Software Mentions: 8
Published: over 4 years ago

10.7554/eLife.64000

TRex, a fast multi-animal tracking system with markerless identification, and 2D estimation of posture and visual fields
Cited by: 108
Author(s): Tristan Walter, Iain D. Couzin
Software Mentions: 8
Published: over 3 years ago

10.7717/peerj.2674

jicbioimage: a tool for automated and reproducible bioimage analysis
Cited by: 6
Author(s): Tjelvar S. G. Olsson, Matthew Hartley
Software Mentions: 8
Published: about 8 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

10.1016/j.patter.2021.100270

ACSNI: An unsupervised machine-learning tool for prediction of tissue-specific pathway components using gene expression profiles
Cited by: 1
Author(s): Chinedu Anthony Anene, Faraz Khan, Findlay Bewicke-Copley, Eleni Maniati, Jun Wang
Software Mentions: 8
Published: over 3 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

10.3389/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

10.1186/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

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

10.3390/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

10.1371/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

10.3389/fninf.2021.659005

PyGeNN: A Python Library for GPU-Enhanced Neural Networks
Cited by: 23
Author(s): James C. Knight, A. B. Комиссаров, Thomas Nowotny
Software Mentions: 8
Published: over 3 years ago

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.molcel.2020.06.002

Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates
Cited by: 41
Author(s): Tomasz W. Turowski, Elisabeth Petfalski, Benjamin D. Goddard, Sarah L. French, Aleksandra Helwak, David Tollervey
Software Mentions: 8
Published: over 4 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

10.1099/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/s13321-018-0270-2

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions
Cited by: 86
Author(s): Jie Dong, Zhi‐Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Aiping Lu, Alex F. Chen, Dong‐Sheng Cao
Software Mentions: 8
Published: over 6 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

10.3389/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

10.1371/journal.pcbi.1008488

On the NF-Y regulome as in ENCODE (2019)
Cited by: 4
Author(s): Mirko Ronzio, Andrea Bernardini, Giulio Pavesi, Roberto Mantovani, Diletta Dolfini
Software Mentions: 8
Published: almost 4 years ago

10.1186/s13059-015-0831-x

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
Cited by: 1,430
Author(s): Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Éric Viara, Chong Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot
Software Mentions: 7
Published: almost 9 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

10.1371/journal.pcbi.1004896

Deep Neural Networks as a Computational Model for Human Shape Sensitivity
Cited by: 263
Author(s): Jonas Kubilius, Stefania Bracci, Hans Op de Beeck
Software Mentions: 7
Published: over 8 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

10.1093/g3journal/jkaa036

Visualizing population structure with variational autoencoders
Cited by: 44
Author(s): C. J. Battey, Gabrielle C. Coffing, Andrew D. Kern
Software Mentions: 7
Published: almost 4 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

10.1186/s13059-019-1868-z

MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms
Cited by: 9
Author(s): Minji Kim, Meizhen Zheng, Simon Zhongyuan Tian, Byoungkoo Lee, Jeffrey H. Chuang, Yijun Ruan
Software Mentions: 7
Published: almost 5 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

10.5334/jors.319

CMakeCatchTemplate: A C++ template project
Cited by: 1
Author(s): Thomas Dowrick, Mian Ahmed, Stephen A. Thompson, James Hetherington, Jonathan Cooper, Matthew J. Clarkson
Software Mentions: 7
Published: almost 4 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

10.3390/jpm11060582

Body Mass Index and Birth Weight Improve Polygenic Risk Score for Type 2 Diabetes
Cited by: 11
Author(s): Avigail Moldovan, Yedael Y. Waldman, Nadav Brandes, Michal Linial
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pcbi.1003706

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue
Cited by: 54
Author(s): Fredrik Karlsson, Intawat Nookaew, Jens Nielsen
Software Mentions: 7
Published: over 10 years ago

10.3389/fneur.2021.580440

Machine Learning Models on ADC Features to Assess Brain Changes of Children With Pierre Robin Sequence
Cited by: 0
Author(s): Ying Wang, Feng Yang, Meijiao Zhu, Ming Yang
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

10.1186/s13550-020-00671-9

18F-FDG PET and DCE kinetic modeling and their correlations in primary NSCLC: first voxel-wise correlative analysis of human simultaneous [18F]FDG PET-MRI data
Cited by: 6
Author(s): Florent L. Besson, Brice Fernandez, Sylvain Faure, Olaf Mercier, Andrei Seferian, Xavier Mignard, Sacha Mussot, C. Le Péchoux, Caroline Caramella, Angela Botticella, Antonin Lévy, Florence Parent, Sophie Bulifon, David Montani, Délphine Mitilian, Élie Fadel, David Planchard, Benjamin Besse, Maria-Rosa Ghigna-Bellinzoni, Claude Comtat, Vincent Lebon, Emmanuel Durand
Software Mentions: 7
Published: over 4 years ago

10.12688/f1000research.27395.2

GeNePy3D: a quantitative geometry python toolbox for bioimaging
Cited by: 1
Author(s): Minh-Son Phan, Anatole Chessel
Software Mentions: 7
Published: over 3 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

10.1128/mSystems.00811-21

Separation of Donor and Recipient Microbial Diversity Allows Determination of Taxonomic and Functional Features of Gut Microbiota Restructuring following Fecal Transplantation
Cited by: 4
Author(s): Evgenii I. Olekhnovich, A. B. Ivanov, Vladimir Ulyantsev, Elena Ilina
Software Mentions: 7
Published: about 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

10.7717/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

10.1186/s12859-021-03984-1

PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies
Cited by: 6
Author(s): Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal K. Das, Paweł Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska, Dariusz Plewczynski
Software Mentions: 7
Published: almost 4 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

10.1371/journal.pcbi.1008551

DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles
Cited by: 39
Author(s): Giulio Tesei, João M. Martins, Micha B. A. Kunze, Yong Wang, Ramón Crehuet, Kresten Lindorff‐Larsen
Software Mentions: 7
Published: almost 4 years ago

10.1128/mBio.03221-19

A Master Regulator of Bacteroides thetaiotaomicron Gut Colonization Controls Carbohydrate Utilization and an Alternative Protein Synthesis Factor
Cited by: 24
Author(s): Guy E. Townsend, Weiwei Han, Nathan D. Schwalm, Xinyu Hong, Natasha A. Bencivenga-Barry, Andrew L. Goodman, Eduardo A. Groisman
Software Mentions: 7
Published: over 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.644

Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
Cited by: 73
Author(s): Olga Golosova, Ross Henderson, Yuriy Vaskin, Andrei Gabrielian, German Grekhov, Vijayaraj Nagarajan, Andrew J. Oler, Mariam Quiñones, Darrell E. Hurt, Mikhail Fursov, Yentram Huyen
Software Mentions: 7
Published: about 10 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

10.7554/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

10.1186/s12859-015-0608-y

affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling
Cited by: 3
Author(s): Carles Hernandez‐Ferrer, Inés Quintela, Katharina Danielski, Ángel Carracedo, Luis A. Pérez‐Jurado, Juan R. González
Software Mentions: 7
Published: over 9 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

10.1016/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

10.1371/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

10.1371/journal.pone.0253411

PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences
Cited by: 12
Author(s): Bulat Faezov, Roland L. Dunbrack
Software Mentions: 7
Published: over 3 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

10.3390/s21041072

A Do-It-Yourself Hyperspectral Imager Brought to Practice with Open-Source Python
Cited by: 8
Author(s): Kimmo A. Riihiaho, Matti A. Eskelinen, Ilkka Pölönen
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12864-017-4268-3

GHOST: global hepatitis outbreak and surveillance technology
Cited by: 32
Author(s): Atkinson G. Longmire, Seth Sims, Inna Rytsareva, David S. Campo, Pavel Skums, Zoya Dimitrova, Sumathi Ramachandran, Magdalena Medrzycki, Hong Thai, Lilia Ganova-Raeva, Yulin Lin, Lili Punkova, Amanda Sue, Massimo Mirabito, Silver Wang, Robin Tracy, Victor Bolet, Thom Sukalac, Chris Lynberg, Yury Khudyakov
Software Mentions: 7
Published: almost 7 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

10.1038/s41598-020-58601-7

Nationwide prediction of type 2 diabetes comorbidities
Cited by: 27
Author(s): Piotr Dworzyński, Martin Aasbrenn, Klaus Rostgaard, Mads Melbye, Thomas Alexander Gerds, Henrik Hjalgrim, Tune H. Pers
Software Mentions: 7
Published: almost 5 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/s41598-017-16050-9

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

10.1371/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.pgen.1009303

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

10.1371/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

10.1186/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

10.1007/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

10.1038/s41598-020-71805-1

Northstar enables automatic classification of known and novel cell types from tumor samples
Cited by: 8
Author(s): Fabio Zanini, Bojk A. Berghuis, Robert C. Jones, Benedetta Nicolis di Robilant, Rachel Yuan Nong, Jeffrey A. Norton, Michael F. Clarke, Stephen R. Quake
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

10.3389/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

10.1371/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

10.1016/j.mec.2019.e00089

Impact framework: A python package for writing data analysis workflows to interpret microbial physiology
Cited by: 4
Author(s): Naveen Venayak, Kaushik Raj, Radhakrishnan Mahadevan
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0209231

Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents
Cited by: 11
Author(s): Christopher Cheleuitte-Nieves, Christopher A. Gulvik, John R. McQuiston, Ben W. Humrighouse, Melissa Bell, Aaron Villarma, Vincent A. Fischetti, Lars F. Westblade, Neil S Lipman
Software Mentions: 7
Published: almost 6 years ago

10.1093/gigascience/gix129

Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags
Cited by: 15
Author(s): Xianfeng Chen, Stephen Johnson, Patricio Jeraldo, Junwen Wang, Nicholas Chia, Jean Pierre A. Kocher, Jun Chen
Software Mentions: 7
Published: almost 7 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

10.14814/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

10.7554/eLife.13503

A Mammalian enhancer trap resource for discovering and manipulating neuronal cell types
Cited by: 50
Author(s): Yasuyuki Shima, Ken Sugino, Chris M. Hempel, Masami Shima, Praveen Taneja, James B. Bullis, Sonam Mehta, Carlos Lois, Sacha B. Nelson
Software Mentions: 7
Published: over 8 years ago

10.1093/genetics/iyab014

Split-wrmScarlet and split-sfGFP: tools for faster, easier fluorescent labeling of endogenous proteins in <i>Caenorhabditis elegans</i>
Cited by: 13
Author(s): Jérôme Goudeau, Catherine S. Sharp, Jonathan S. Paw, Laura Savy, Manuel D. Leonetti, Andrew G. York, Dustin L. Updike, Cynthia Kenyon, Maria Ingaramo
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pcbi.1008978

scHiCTools: A computational toolbox for analyzing single-cell Hi-C data
Cited by: 9
Author(s): Xinjun Li, Fan Feng, Hongxi Pu, Wai Yan Leung, Jie Liu
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0203725

An open-source software analysis package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs)
Cited by: 15
Author(s): Björn Harink, Huy Nguyen, Kurt S. Thorn, Polly M. Fordyce
Software Mentions: 6
Published: over 5 years ago

10.1007/s00429-021-02358-w

Dissecting whole-brain conduction delays through MRI microstructural measures
Cited by: 6
Author(s): Matteo Mancini, Qiyuan Tian, Qiuyun Fan, Mara Cercignani, Susie Y. Huang
Software Mentions: 6
Published: over 3 years ago

10.3389/fbioe.2020.00453

Experimental and Model-Based Analysis to Optimize Microalgal Biomass Productivity in a Pilot-Scale Tubular Photobioreactor
Cited by: 15
Author(s): Tobias Weise, Claudia Grewe, Michael Pfaff
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0190279

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment
Cited by: 12
Author(s): Sven Warris, N. Roshan N. Timal, Marcel Kempenaar, Arne M. Poortinga, Henri van de Geest, Ana Lucia Vărbănescu, Jan-Peter Nap
Software Mentions: 6
Published: almost 7 years ago

10.3390/genes12071067

Total Genotype Score Modelling of Polygenic Endurance-Power Profiles in Lithuanian Elite Athletes
Cited by: 6
Author(s): Erinija Pranckevičienė, Valentina Ginevičienė, Audronė Jakaitienė, Laimonas Januska, Algirdas Utkus
Software Mentions: 6
Published: over 3 years ago

10.1186/s12859-018-2477-7

pyHIVE, a health-related image visualization and engineering system using Python
Cited by: 5
Author(s): Ruochi Zhang, Ruxing Zhao, Xinyang Zhao, Di Wu, Weiwei Zheng, Xin Feng, Fengfeng Zhou
Software Mentions: 6
Published: almost 6 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

10.1371/journal.pcbi.1007973

XDream: Finding preferred stimuli for visual neurons using generative networks and gradient-free optimization
Cited by: 9
Author(s): Will Xiao, Gabriel Kreiman
Software Mentions: 6
Published: over 4 years ago

10.3389/fcell.2019.00141

Single Cell Imaging of Nuclear Architecture Changes
Cited by: 17
Author(s): Rikke Morrish, Michael Hermes, Jeremy Metz, Edwin M. Stone, Stefano Pagliara, Richard Chahwan, Francesca Palombo
Software Mentions: 6
Published: over 5 years ago

10.3390/genes12030396

SMITER—A Python Library for the Simulation of LC-MS/MS Experiments
Cited by: 6
Author(s): Manuel Kösters, Johannes Leufken, Sebastian A. Leidel
Software Mentions: 6
Published: over 3 years ago

10.15252/emmm.202013257

Urinary proteome profiling for stratifying patients with familial Parkinson’s disease
Cited by: 66
Author(s): Sebastian Virreira Winter, Özge Karayel, Mike Strauss, Shalini Padmanabhan, Matthew Surface, Kalpana Merchant, Matthias Mann
Software Mentions: 6
Published: almost 4 years ago

Projects: pypi: numpy

Papers Mentioning numpy 832