pypi: scipy | Projects | Ecosyste.ms: Papers

10.1016/j.isci.2021.102762

NANOS2 is a sequence-specific mRNA-binding protein that promotes transcript degradation in spermatogonial stem cells
Cited by: 9
Author(s): Azzurra Codino, Tomasz W. Turowski, Louie N. van de Lagemaat, Ivayla Ivanova, Andrea Tavosanis, Christian Much, Tania Auchynnikava, Lina Vasiliauskaitė, Marcos Morgan, Juri Rappsilber, Robin Allshire, Kamil R. Kranc, David Tollervey, Dónal O’Carroll
Software Mentions: 8
Published: almost 3 years ago

10.1371/journal.pcbi.1005727

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
Cited by: 40
Author(s): Kevin Murray, Christfried Webers, Cheng Soon Ong, Justin O. Borevitz, Norman Warthmann
Software Mentions: 8
Published: over 6 years ago

10.7554/eLife.68312

A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma
Cited by: 12
Author(s): Dayana C Farhat, Matthew W. Bowler, Guillaume Communie, Dominique Pontier, Lucid Belmudes, Caroline Mas, Charlotte Corrao, Yohann Couté, Alexandre Bougdour, Thierry Lagrange, Mohamed‐Ali Hakimi, Christopher Swale
Software Mentions: 8
Published: almost 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: almost 5 years ago

10.1371/journal.pcbi.1007832

Flux-based hierarchical organization of Escherichia coli’s metabolic network
Cited by: 2
Author(s): Semidán Robaina-Estévez, Zoran Nikoloski
Software Mentions: 8
Published: about 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: over 3 years ago

10.1371/journal.pcbi.1008605

Machine learning based CRISPR gRNA design for therapeutic exon skipping
Cited by: 5
Author(s): Wilson Louie, Max W. Shen, Zakir Tahiry, Sophia Zhang, Daniel Worstell, Christopher A. Cassa, Richard I. Sherwood, David K. Gifford
Software Mentions: 8
Published: over 3 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: over 4 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: almost 3 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: over 5 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: over 3 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: 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: about 3 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: almost 7 years ago

10.3390/cells9020458

Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites
Cited by: 25
Author(s): Karl Frey, Boas Pucker
Software Mentions: 7
Published: over 4 years ago

10.3389/fninf.2019.00014

Visbrain: A Multi-Purpose GPU-Accelerated Open-Source Suite for Multimodal Brain Data Visualization
Cited by: 44
Author(s): Etienne Combrisson, Raphaël Vallat, Christian O’Reilly, Mainak Jas, Annalisa Pascarella, Anne-Lise Saive, Thomas Thiery, David Meunier, Dmitrii Altukhov, Tarek Lajnef, Perrine Ruby, Aymeric Guillot, Karim Jerbi
Software Mentions: 7
Published: about 5 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: over 3 years ago

10.1038/s41598-020-78180-x

Personalized quantification of facial normality: a machine learning approach
Cited by: 6
Author(s): Osman Boyaci, Erchin Serpedin, Mitchell A. Stotland
Software Mentions: 7
Published: over 3 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: almost 7 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: over 3 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: almost 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: 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: over 6 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: over 4 years ago

10.1371/journal.pcbi.1006644

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types
Cited by: 35
Author(s): Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuñiga, Jared T. Broddrick, Karsten Zengler, Jaehyung Kim
Software Mentions: 7
Published: over 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: over 7 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: about 8 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: almost 5 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: almost 9 years ago

10.1172/jci.insight.148035

Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells
Cited by: 7
Author(s): Ruoyi Jiang, Hailong Meng, Khadir Raddassi, Ira Fleming, Kenneth B. Hoehn, Kenneth R. Dardick, Alexia A. Belperron, Ruth R. Montgomery, Alex K. Shalek, David A. Hafler, Steven H. Kleinstein, Linda K. Bockenstedt
Software Mentions: 7
Published: almost 3 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: over 6 years ago

10.3390/e23060657

Variational Quantum Chemistry Programs in JaqalPaq
Cited by: 2
Author(s): Oliver G. Maupin, Andrew David Baczewski, Peter J. Love, Andrew J. Landahl
Software Mentions: 7
Published: almost 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: 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: almost 3 years ago

10.1186/s12864-019-5924-6

A catalog of CasX genome editing sites in common model organisms
Cited by: 4
Author(s): Elisha D.O. Roberson
Software Mentions: 7
Published: almost 5 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: almost 3 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: over 4 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: 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: over 8 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: almost 3 years ago

10.7554/eLife.68265

Spectral signature and behavioral consequence of spontaneous shifts of pupil-linked arousal in human
Cited by: 21
Author(s): Ella Podvalny, Leana E King, Biyu J. He
Software Mentions: 7
Published: over 2 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: about 8 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: about 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: about 4 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: about 6 years ago

10.3389/fnins.2018.00727

Teaching Computational Reproducibility for Neuroimaging
Cited by: 15
Author(s): K. Jarrod Millman, Matthew Brett, Ross Barnowski, Jean‐Baptiste Poline
Software Mentions: 7
Published: over 5 years ago

10.1128/mSystems.00269-18

Calour: an Interactive, Microbe-Centric Analysis Tool
Cited by: 24
Author(s): Zhenjiang Zech Xu, Amir Almasi‐Hashiani, Jon G. Sanders, Quanyin Zhu, James T. Morton, Molly C. Bletz, Anupriya Tripathi, Shi Huang, Daniel McDonald, Lingjing Jiang, Rob Knight
Software Mentions: 6
Published: about 5 years ago

10.3389/fninf.2014.00022

SCoT: a Python toolbox for EEG source connectivity
Cited by: 21
Author(s): Martin Billinger, Clemens Brunner, Gernot Müller-Putz
Software Mentions: 6
Published: about 10 years ago

10.1186/s13029-015-0042-6

PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols
Cited by: 3
Author(s): Alexandros Kanterakis, Joël Kuiper, George Potamias, Morris A. Swertz
Software Mentions: 6
Published: over 8 years ago

10.1016/j.str.2015.12.011

The Role of the Membrane in the Structure and Biophysical Robustness of the Dengue Virion Envelope
Cited by: 79
Author(s): Tyler Reddy, Mark S. P. Sansom
Software Mentions: 6
Published: about 8 years ago

10.1038/s42003-021-02181-3

Multiparametric biophysical profiling of red blood cells in malaria infection
Cited by: 9
Author(s): Shreya Deshmukh, Bikash Shakya, Anna Chen, Naside Gözde Durmus, Bryan Greenhouse, Elizabeth S. Egan, Utkan Demirci
Software Mentions: 6
Published: almost 3 years ago

10.3389/fninf.2014.00034

Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages
Cited by: 45
Author(s): Juan Nunez-Iglesias, Ryan Kennedy, Stephen M. Plaza, Anirban Chakraborty, William T. Katz
Software Mentions: 6
Published: about 10 years ago

10.1186/1751-0473-3-10

Flow: Statistics, visualization and informatics for flow cytometry
Cited by: 11
Author(s): Jacob Frelinger, Thomas B. Kepler, Cliburn Chan
Software Mentions: 6
Published: almost 16 years ago

10.1371/journal.pgen.1007276

Argonaute2 and LaminB modulate gene expression by controlling chromatin topology
Cited by: 19
Author(s): Ezequiel Názer, Ryan Dale, Madoka Chinen, Behram Radmanesh, Elissa P. Lei
Software Mentions: 6
Published: about 6 years ago

10.1093/bioinformatics/btt080

eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows
Cited by: 43
Author(s): Patrick Kiefer, Uwe Schmitt, Julia A. Vorholt
Software Mentions: 6
Published: over 11 years ago

10.3389/fninf.2017.00021

Reproducible Large-Scale Neuroimaging Studies with the OpenMOLE Workflow Management System
Cited by: 8
Author(s): Jonathan Passerat–Palmbach, Romain Reuillon, Mathieu Leclaire, Antonios Makropoulos, Emma C. Robinson, Sarah Parisot, Daniel Rueckert
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pbio.3001146

Anesthetics fragment hippocampal network activity, alter spine dynamics, and affect memory consolidation
Cited by: 26
Author(s): Yang Wei, Mattia Chini, Jastyn A. Pöpplau, A. Formozov, Alexander Dieter, Patrick Piechocinski, Cynthia Rais, Fabio Morellini, Olaf Sporns, Ileana L. Hanganu‐Opatz, J. Simon Wiegert
Software Mentions: 6
Published: about 3 years ago

10.3390/cells10020235

A Multimodal Platform for Simultaneous T-cell Imaging, Defined Activation, and Mechanobiological Characterization
Cited by: 4
Author(s): Martin Fölser, Viktoria Motsch, René Platzer, Johannes B. Huppa, Gerhard J. Schütz
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: over 5 years ago

10.3390/s21134550

Evaluation of Open-Source and Pre-Trained Deep Convolutional Neural Networks Suitable for Player Detection and Motion Analysis in Squash
Cited by: 3
Author(s): Christopher Brumann, Markus Kukuk, Claus Reinsberger
Software Mentions: 6
Published: almost 3 years ago

10.3390/s20092546

Mind Wandering in a Multimodal Reading Setting: Behavior Analysis & Automatic Detection Using Eye-Tracking and an EDA Sensor
Cited by: 19
Author(s): Iuliia Brishtel, Anam Ahmad Khan, Thomas Schmidt, Tilman Dingler, Shoya Ishimaru, Andreas Dengel
Software Mentions: 6
Published: about 4 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: over 11 years ago

10.3390/s20133647

Comparing Person-Specific and Independent Models on Subject-Dependent and Independent Human Activity Recognition Performance
Cited by: 4
Author(s): Sebastian Scheurer, Salvatore Tedesco, Brendan O’Flynn, Kenneth N. Brown
Software Mentions: 6
Published: almost 4 years ago

10.1016/j.celrep.2018.10.073

Microanatomic Distribution of Myeloid Heme Oxygenase-1 Protects against Free Radical-Mediated Immunopathology in Human Tuberculosis
Cited by: 29
Author(s): Krishna C. Chinta, Md. Aejazur Rahman, Vikram Saini, Joel N. Glasgow, Vineel P. Reddy, Jeremie M. Lever, Shepherd Nhamoyebonde, Alasdair Leslie, Ryan M. Wells, Amie M. Traylor, Rajhmun Madansein, Gene P. Siegal, Veena B. Antony, Jessy Deshane, Gordon Wells, Kievershen Nargan, James F. George, Pratistadevi K. Ramdial, Anupam Agarwal, Adrie J. C. Steyn
Software Mentions: 6
Published: over 5 years ago

10.3390/s20205947

A Pattern-Recognition-Based Ensemble Data Imputation Framework for Sensors from Building Energy Systems
Cited by: 7
Author(s): Liang Zhang
Software Mentions: 6
Published: over 3 years ago

10.1186/s12870-020-02756-y

Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus
Cited by: 8
Author(s): Armin Scheben, Anita A. Severn‐Ellis, Dhwani A. Patel, Aneeta Pradhan, S.J. Rae, Jacqueline Batley, David Edwards
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-94105-8

Sublinear domination and core–periphery networks
Cited by: 1
Author(s): Marios Papachristou
Software Mentions: 6
Published: almost 3 years ago

10.3389/fninf.2018.00075

VIOLA—A Multi-Purpose and Web-Based Visualization Tool for Neuronal-Network Simulation Output
Cited by: 12
Author(s): Johanna Senk, Corto Carde, Espen Hagen, Torsten Kuhlen, Markus Diesmann, Benjamin Weyers
Software Mentions: 6
Published: over 5 years ago

10.15252/msb.20199146

Mammalian gene expression variability is explained by underlying cell state
Cited by: 85
Author(s): Robert T. Foreman, Roy Wollman
Software Mentions: 6
Published: over 4 years ago

10.2196/28265

Correlation of Population SARS-CoV-2 Cycle Threshold Values to Local Disease Dynamics: Exploratory Observational Study
Cited by: 18
Author(s): Chak Foon Tso, Anurag Garikipati, Abigail Green‐Saxena, Qingqing Mao, Ritankar Das
Software Mentions: 6
Published: almost 3 years ago

10.3389/fimmu.2018.02342

Supplemented Alkaline Phosphatase Supports the Immune Response in Patients Undergoing Cardiac Surgery: Clinical and Computational Evidence
Cited by: 18
Author(s): Alva Presbitero, Emiliano Mancini, Ruud Brands, Valeria V. Krzhizhanovskaya, Peter M. A. Sloot
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-63036-1

Hierarchical clustering of MS/MS spectra from the firefly metabolome identifies new lucibufagin compounds
Cited by: 12
Author(s): C. J. Rawlinson, Darcy A. B. Jones, S. Rakshit, Shiv Meka, Caroline S. Moffat, Paula Moolhuijzen
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-019-39866-z

Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions
Cited by: 10
Author(s): Adrian I. Campos-González, Julio A. Freyre-González
Software Mentions: 6
Published: about 5 years ago

10.3389/fnhum.2019.00348

EEG-Based Classification of Internally- and Externally-Directed Attention in an Augmented Reality Paradigm
Cited by: 34
Author(s): Lisa-Marie Vortmann, Felix Kroll, Felix Putze
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-019-55777-5

Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties
Cited by: 7
Author(s): Viktor Ahlberg Gagnér, Ida Lundholm, María-José García-Bonete, Helena Rodilla, Ran Friedman, Vitali Zhaunerchyk, Gleb Bourenkov, Thomas R. Schneider, Jan Stake, Gergely Katona
Software Mentions: 6
Published: over 4 years ago

10.1016/j.ssmph.2020.100687

Application of machine learning to understand child marriage in India
Cited by: 9
Author(s): Anita Raj, Nabamallika Dehingia, Abhishek Singh, Lotus McDougal, Julian McAuley
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-017-15695-w

Objective quantification of nanoscale protein distributions
Cited by: 15
Author(s): Miklos Szoboszlay, Tekla Kirizs, Zoltán Nusser
Software Mentions: 6
Published: over 6 years ago

10.3389/fgene.2020.00238

Detection and Comparative Analysis of Methylomic Biomarkers of Rheumatoid Arthritis
Cited by: 4
Author(s): Xin Feng, Xubing Hao, Ruoyao Shi, Zhiqiang Xia, Lan Huang, Qiong Yu, Fengfeng Zhou
Software Mentions: 6
Published: about 4 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: over 6 years ago

10.3389/fimmu.2021.707830

In-Depth Profiling of T-Cell Responsiveness to Commonly Recognized CMV Antigens in Older People Reveals Important Sex Differences
Cited by: 6
Author(s): Bernhard Reus, Stefano Caserta, Martin Larsen, George W. Morrow, Aalia Bano, Michael Hallensleben, Chakravarthi Rajkumar, Alejandra Pera, Florian Kern
Software Mentions: 6
Published: almost 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: over 4 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: about 4 years ago

10.1186/s40168-020-00822-z

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios
Cited by: 69
Author(s): Lucas Palma Perez Braga, Aymé Spor, Witold Kot, Marie-Christine Breuil, Lars H. Hansen, João Carlos Setúbal, Laurent Philippot
Software Mentions: 6
Published: about 4 years ago

10.1186/s12859-019-3320-5

DynaVenn: web-based computation of the most significant overlap between ordered sets
Cited by: 14
Author(s): Jérémy Amand, Tobias Fehlmann, Christina Backes, Andreas Keller
Software Mentions: 6
Published: over 4 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: over 5 years ago

10.1186/s12864-021-07974-8

SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data
Cited by: 8
Author(s): N M Prashant, Nawaf Alomran, Yu Chen, Hongyu Liu, Pavlos Bousounis, Mercedeh Movassagh, Nathan Edwards, Anélia Horvath
Software Mentions: 6
Published: over 2 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: about 3 years ago

10.1002/1878-0261.12786

Allele‐specific proximal promoter hypomethylation of the telomerase reverse transcriptase gene (<i>TERT</i>) associates with <i>TERT</i> expression in multiple cancers
Cited by: 20
Author(s): Teisha J. Rowland, Andrew J. Bonham, Thomas R. Cech
Software Mentions: 6
Published: over 3 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: over 9 years ago

10.1007/s11306-020-1640-0

Migrating from partial least squares discriminant analysis to artificial neural networks: a comparison of functionally equivalent visualisation and feature contribution tools using jupyter notebooks
Cited by: 32
Author(s): Kevin Mendez, David Broadhurst, Stacey N. Reinke
Software Mentions: 6
Published: over 4 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: almost 4 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: almost 3 years ago

10.1371/journal.ppat.1009029

Drivers of within-host genetic diversity in acute infections of viruses
Cited by: 22
Author(s): Maoz Gelbart, Sheri Harari, Ya’ara Ben-Ari, Talia Kustin, Dana Wolf, Michal Mandelboim, Orna Mor, Pleuni S. Pennings, Adi Stern
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-017-3630-9

Interferon signaling in ascites-associated macrophages is linked to a favorable clinical outcome in a subgroup of ovarian carcinoma patients
Cited by: 42
Author(s): Till Adhikary, Annika Wortmann, Florian Finkernagel, Sonja Lieber, Andrea Nist, Thorsten Stiewe, Uwe Wagner, Sabine Müller‐Brüsselbach, Silke Reinartz, Rolf Müller
Software Mentions: 6
Published: about 7 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: almost 4 years ago

10.3390/md17020081

Predicting Blood–Brain Barrier Permeability of Marine-Derived Kinase Inhibitors Using Ensemble Classifiers Reveals Potential Hits for Neurodegenerative Disorders
Cited by: 28
Author(s): Fabien Plisson, Andrew M. Piggott
Software Mentions: 6
Published: over 5 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: almost 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: about 6 years ago

10.1186/s13550-020-00744-9

Repeatability of two semi-automatic artificial intelligence approaches for tumor segmentation in PET
Cited by: 12
Author(s): Elisabeth Pfaehler, Liesbet Mesotten, Gem Kramer, Michiel Thomeer, Karolien Vanhove, Johan de Jong, Peter Adriaensens, Otto S. Hoekstra, Ronald Boellaard
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1007553

Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes
Cited by: 18
Author(s): David Moi, Laurent Kilchoer, Pablo S. Aguilar, Christophe Dessimoz
Software Mentions: 6
Published: almost 4 years ago

Projects: pypi: scipy

Papers Mentioning scipy 1,071