pypi: matplotlib | Projects | Ecosyste.ms: Papers

10.1038/s41598-019-46549-2

Using weather radar to monitor the number, timing and directions of flying-foxes emerging from their roosts
Cited by: 12
Author(s): Jessica Meade, Rodney van der Ree, Phillip M. Stepanian, David A. Westcott, Justin A. Welbergen
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1006184

Interplay of multiple pathways and activity-dependent rules in STDP
Cited by: 8
Author(s): Gaëtan Vignoud, Laurent Venance, Jonathan Touboul
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-021-87644-7

A deep learning model for the classification of indeterminate lung carcinoma in biopsy whole slide images
Cited by: 19
Author(s): Fahdi Kanavati, Gouji Toyokawa, Seiya Momosaki, Hiroaki Takeoka, Masaki Okamoto, Koji Yamazaki, Sadanori Takeo, Osamu Iizuka, Masayuki Tsuneki
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1005220

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist
Cited by: 63
Author(s): Brian Drawert, Andreas Hellander, Benjamin B. Bales, Debjani Banerjee, Giovanni Bellesia, Bernie J. Daigle, Geoffrey Douglas, M. Gu, Anand Gupta, Stefan Hellander, Christopher B. Horuk, Dibyendu Nath, Aviral Takkar, Sheng Wu, Per Lötstedt, Chandra Krintz, Linda R. Petzold
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-019-50228-7

Transcriptomic analysis reveals new hippocampal gene networks induced by prolactin
Cited by: 17
Author(s): Erika Alejandra Cabrera-Reyes, América Vanoye-Carlo, Mauricio Rodríguez-Dorantes, Edgar Ricardo Vázquez-Martínez, Nadia Alejandra Rivero-Segura, Omar Collazo-Navarrete, Marco Cerbón
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-51489-y

NMR-based metabolic profiling and comparison of Japanese persimmon cultivars
Cited by: 9
Author(s): Shinsei Ryu, Tsuyoshi Muramatsu, Kazuo Furihata, Feifei Wei, Masanori Koda, Takuya Miyakawa, Masaru Tanokura
Software Mentions: 3
Published: about 5 years ago

10.3390/antibiotics9080447

Characterization of Clinical MRSA Isolates from Northern Spain and Assessment of Their Susceptibility to Phage-Derived Antimicrobials
Cited by: 11
Author(s): Marina Salas, Maciej Wernecki, Lucía Fernández, Beatriz Menéndez Iglesias, Diana Gutiérrez, Azucena L. Alvarez, Laura García, Elisabeth Prieto, Pilar Garcı́a, Ana Rodrı́guez
Software Mentions: 3
Published: over 4 years ago

10.26508/lsa.201800278

A network of human functional gene interactions from knockout fitness screens in cancer cells
Cited by: 79
Author(s): Eiru Kim, Merve Dede, Walter F. Lenoir, Gang Wang, Sanjana Srinivasan, Medina Colic, Traver Hart
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2021.660002

Whole-Genome Analysis of Mycobacterium avium subsp. paratuberculosis IS900Insertions Reveals Strain Type-Specific Modalities
Cited by: 6
Author(s): Cyril Condé, Marian Price-Carter, Thierry Cochard, Maxime Branger, Karen Stevenson, Richard J. Whittington, John P. Bannantine, Franck Biet
Software Mentions: 3
Published: over 3 years ago

10.1016/j.bpj.2016.06.028

Modeling Functional Motions of Biological Systems by Customized Natural Moves
Cited by: 6
Author(s): Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Péter Mináry
Software Mentions: 3
Published: over 8 years ago

10.3389/fpls.2018.00841

Editing of Chloroplast rps14 by PPR Editing Factor EMB2261 Is Essential for Arabidopsis Development
Cited by: 16
Author(s): Yueming K. Sun, Bernard Gutmann, Aaron Yap, Peter Kindgren, Ian Small
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2019.00466

Phylogenetic Analyses and GAGA-Motif Binding Studies of BBR/BPC Proteins Lend to Clues in GAGA-Motif Recognition and a Regulatory Role in Brassinosteroid Signaling
Cited by: 34
Author(s): Marius L. Theune, Ulrich Bloss, Luise H. Brand, Friederike Ladwig, Dierk Wanke
Software Mentions: 3
Published: over 5 years ago

10.3390/ijerph18052713

A Real-Time Artificial Intelligence-Assisted System to Predict Weaning from Ventilator Immediately after Lung Resection Surgery
Cited by: 18
Author(s): Ying-Jen Chang, Kuo‐Chuan Hung, Li‐Kai Wang, Chia-Hung Yu, Chao-Kun Chen, Hung-Tze Tay, Jhi-Joung Wang, Chia‐Jung Chen
Software Mentions: 3
Published: over 3 years ago

10.1107/S2059798321003740

Are the St John's wort Hyp-1 superstructures different?
Cited by: 0
Author(s): Jeffrey J. Lovelace, Gloria E. O. Borgstahl
Software Mentions: 3
Published: over 3 years ago

10.3390/life11060554

Protein Secondary Structure Affects Glycan Clustering in Native Mass Spectrometry
Cited by: 7
Author(s): Hao Yan, Julia Lockhauserbäumer, Gergő Péter Szekeres, Álvaro Mallagaray, Robert Creutznacher, Stefan Taube, Thomas Peters, Kevin Pagel, Charlotte Uetrecht
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-60768-y

Complex approach for analysis of snake venom α-neurotoxins binding to HAP, the high-affinity peptide
Cited by: 9
Author(s): Denis S. Kudryavtsev, Valentin М. Tabakmakher, Gleb S. Budylin, N. S. Egorova, Roman G. Efremov, Igor A. Ivanov, Svetlana Yu. Belukhina, Artjom V. Jegorov, Igor E. Kasheverov, Elena V. Kryukova, Irina V. Shelukhina, Evgeny A. Shirshin, Nadezhda G. Zhdanova, Maxim N. Zhmak, Victor I. Tsetlin
Software Mentions: 3
Published: almost 5 years ago

10.1152/jn.00201.2021

Within-cycle instantaneous frequency profiles report oscillatory waveform dynamics
Cited by: 21
Author(s): Andrew Quinn, Vítor Lopes‐dos‐Santos, Norden E. Huang, Wei Kuang Liang, Juan C-H., Jia-Rong Yeh, Anna C. Nobre, David Dupret, Mark W. Woolrich
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0113516

Breaking an Epigenetic Chromatin Switch: Curious Features of Hysteresis in Saccharomyces cerevisiae Telomeric Silencing
Cited by: 8
Author(s): Vijayalakshmi H. Nagaraj, Swagatam Mukhopadhyay, Adel Dayarian, Anirvan M. Sengupta
Software Mentions: 3
Published: almost 10 years ago

10.2196/26139

Use of Multiprognostic Index Domain Scores, Clinical Data, and Machine Learning to Improve 12-Month Mortality Risk Prediction in Older Hospitalized Patients: Prospective Cohort Study
Cited by: 9
Author(s): Richard Woodman, Kimberley Bryant, Michael J. Sorich, Alberto Pilotto, Arduino A. Mangoni
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2021.651461

Exploring the Antibiotic Resistance Burden in Livestock, Livestock Handlers and Their Non-Livestock Handling Contacts: A One Health Perspective
Cited by: 13
Author(s): Rachel A. Hickman, Thongpan Leangapichart, Kamonwan Lunha, Jatesada Jiwakanon, Sunpetch Angkititrakul, Ulf Magnusson, Marianne Sunde, Josef D. Järhult
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-76012-6

Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris)
Cited by: 4
Author(s): Maria Joào Ramos, João L. Coito, David Faísca-Silva, Jorge Cunha, Maria Manuela Ribeiro Costa, Sara Amâncio, Margarida Rocheta
Software Mentions: 3
Published: about 4 years ago

10.2196/23229

A Biofeedback App for Migraine: Development and Usability Study
Cited by: 7
Author(s): Sigrid Hegna Ingvaldsen, Erling Tronvik, Eiliv Brenner, Ingunn Winnberg, Alexander Olsen, Gøril Bruvik Gravdahl, Anker Stubberud
Software Mentions: 3
Published: over 3 years ago

10.1186/s12862-021-01782-0

An interplay of resource availability, population size and mutation rate potentiates the evolution of metabolic signaling
Cited by: 1
Author(s): Bhaskar Kumawat, Ramray Bhat
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-71535-4

Sylvian fissure development is linked to differential genetic expression in the pre-folded brain
Cited by: 10
Author(s): Arka N. Mallela, Hansen Deng, Alyssa K. Brisbin, Alan Bush, Ezequiel Goldschmidt
Software Mentions: 3
Published: over 4 years ago

10.1107/S2052252518012149

Photocage-initiated time-resolved solution X-ray scattering investigation of protein dimerization
Cited by: 25
Author(s): Inokentijs Josts, Stephan Niebling, Yunyun Gao, Matteo Levantino, Henning Tidow, Diana C. F. Monteiro
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.64776

HIV-1 uncoating by release of viral cDNA from capsid-like structures in the nucleus of infected cells
Cited by: 59
Author(s): Thorsten G. Müller, Vojtěch Žíla, Kyra Peters, Sandra Schifferdecker, Mia Stanić, Bojana Lucic, Vibor Laketa, Marina Lušić, Bárbara Müller, Hans‐Georg Kräusslich
Software Mentions: 3
Published: over 3 years ago

10.3389/fpsyg.2014.01390

Jointly structuring triadic spaces of meaning and action: book sharing from 3 months on
Cited by: 62
Author(s): Nicole Rossmanith, Alan Costall, Andreas Reichelt, Beatriz López, Vasudevi Reddy
Software Mentions: 3
Published: almost 10 years ago

10.1107/S2052252518012058

Unwarping GISAXS data
Cited by: 12
Author(s): Jiliang Liu, Kevin G. Yager
Software Mentions: 3
Published: about 6 years ago

10.12688/f1000research.15841.2

The signs of adaptive mutations identified in the chloroplast genome of the algae endosymbiont of Baikal sponge.
Cited by: 1
Author(s): Sergey Feranchuk, Natalia Belkova, Lubov Chernogor, Ulyana Potapova, С. И. Беликов
Software Mentions: 3
Published: over 4 years ago

10.3389/fpubh.2017.00301

Dynamic Regimes of El Niño Southern Oscillation and Influenza Pandemic Timing
Cited by: 5
Author(s): Oluleke Oluwole
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0248537

Effects of phytonutrient-supplemented diets on the intestinal microbiota of Cyprinus carpio
Cited by: 7
Author(s): Milán Fehér, Péter Fauszt, Emese Tolnai, Gábor Fidler, Georgina Pesti-Asbóth, Anikó Stágel, István Szűcs, Sándor Bíró, Judit Remenyik, Melinda Paholcsek, László Stündl
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-7-194

Mining gene expression data by interpreting principal components
Cited by: 61
Author(s): J. Roden, Brandon King, Diane Trout, A Mortazavi, B Wold, Christopher E. Hart
Software Mentions: 3
Published: over 18 years ago

10.1128/mSystems.00689-20

Single-Inclusion Kinetics of Chlamydia trachomatis Development
Cited by: 12
Author(s): Travis J Chiarelli, Nicole A. Grieshaber, Anders Omsland, Christopher H. Remien, Scott S. Grieshaber
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0096814

Advancing Bag-of-Visual-Words Representations for Lesion Classification in Retinal Images
Cited by: 69
Author(s): Ramon Pires, Herbert F. Jelinek, Jacques Wainer, Eduardo Valle, Anderson Rocha
Software Mentions: 3
Published: over 10 years ago

10.1523/ENEURO.0122-21.2021

MEYE: Web App for Translational and Real-Time Pupillometry
Cited by: 9
Author(s): Raffaele Mazziotti, Fabio Carrara, Aurelia Viglione, Leonardo Lupori, Luca Lo Verde, Alessandro Benedetto, Giulia Ricci, Giulia Sagona, Giuseppe Amato, Tommaso Pizzorusso
Software Mentions: 3
Published: over 3 years ago

10.1128/mSystems.00350-20

CRISPR-CBEI: a Designing and Analyzing Tool Kit for Cytosine Base Editor-Mediated Gene Inactivation
Cited by: 16
Author(s): Haopeng Yu, Zhaowei Wu, Xiangdan Chen, Quanjiang Ji, Shiheng Tao
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-020-06858-7

An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells
Cited by: 6
Author(s): Henning Onsbring, Alexander K. Tice, Brandon T. Barton, Matthew W. Brown, Thijs J. G. Ettema
Software Mentions: 3
Published: over 4 years ago

10.1128/mSystems.00635-19

Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs
Cited by: 12
Author(s): Julia M. Gauglitz, James T. Morton, Anupriya Tripathi, Shalisa Hansen, Michele Gaffney, Carolina S. Carpenter, Kelly C. Weldon, Riya Shah, Amy Parampil, Andrea Fidgett, Austin D. Swafford, Rob Knight, Pieter C. Dorrestein
Software Mentions: 3
Published: over 4 years ago

10.1098/rsif.2020.0556

Nonlinear phenomena in models of the circadian clock
Cited by: 10
Author(s): Inge van Soest, Marta del Olmo, Christoph Schmal, Hanspeter Herzel
Software Mentions: 3
Published: over 4 years ago

10.3390/genes9020104

Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models
Cited by: 69
Author(s): Aeriel D. Belk, Zhenjiang Zech Xu, David Carter, Aaron M. Lynne, Sibyl R. Bucheli, Rob Knight, Jessica L. Metcalf
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pbio.3000814

Ratiometric quorum sensing governs the trade-off between bacterial vertical and horizontal antibiotic resistance propagation
Cited by: 4
Author(s): Alvaro Banderas, Arthur Carcano, Elisa Sia, Shuang Li, Ariel B. Lindner
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-018-5360-z

Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes
Cited by: 37
Author(s): Boas Pucker, Samuel F. Brockington
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0174635

Improving HybrID: How to best combine indirect and direct encoding in evolutionary algorithms
Cited by: 7
Author(s): Lucas Helms, Jeff Clune
Software Mentions: 3
Published: over 7 years ago

10.3390/genes10020098

A Hybrid Clustering Algorithm for Identifying Cell Types from Single-Cell RNA-Seq Data
Cited by: 14
Author(s): Xiaoshu Zhu, Hongdong Li, Yunpei Xu, Lei Guo, Fang‐Xiang Wu, Guihua Duan, Jianxin Wang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12859-021-04405-z

Identification, visualization, statistical analysis and mathematical modeling of high-feedback loops in gene regulatory networks
Cited by: 9
Author(s): Benjamin Nordick, Tian Hong
Software Mentions: 3
Published: about 3 years ago

10.3390/genes12020186

VIRMOTIF: A User-Friendly Tool for Viral Sequence Analysis
Cited by: 17
Author(s): Pedram Rajaei, Khadijeh Jahanian, Amin Beheshti, Shahab S. Band, Abdollah Dehzangi, Hamid Alinejad‐Rokny
Software Mentions: 3
Published: almost 4 years ago

10.3390/diagnostics11081398

Colon Tissues Classification and Localization in Whole Slide Images Using Deep Learning
Cited by: 12
Author(s): Pushpanjali Gupta, Yen‐Lin Huang, Prasan Kumar Sahoo, Jeng-Fu You, Sum-Fu Chiang, Djeane Debora Onthoni, Yih‐Jong Chern, Kuo-Yu Chao, Jy-Ming Chiang, Chien-Yuh Yeh, Wen‐Sy Tsai
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0166532

Accuracy and Reliability of the Kinect Version 2 for Clinical Measurement of Motor Function
Cited by: 177
Author(s): Karen Otte, Bastian Kayser, Sebastian Mansow-Model, Julius Verrel, Friedemann Paul, Alexander U. Brandt, Tanja Schmitz‐Hübsch
Software Mentions: 3
Published: about 8 years ago

10.3389/fninf.2015.00023

Pycortex: an interactive surface visualizer for fMRI
Cited by: 98
Author(s): James Gao, Alexander G. Huth, Mark D. Lescroart, Jack L. Gallant
Software Mentions: 3
Published: about 9 years ago

10.1186/s12859-019-3187-5

Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks
Cited by: 51
Author(s): Attayeb Mohsen, Jonguk Park, Yi‐An Chen, Hitoshi Kawashima, Kenji Mizuguchi
Software Mentions: 3
Published: about 5 years ago

10.1186/s13007-020-00639-9

A data workflow to support plant breeding decisions from a terrestrial field-based high-throughput plant phenotyping system
Cited by: 5
Author(s): A. E. Thompson, Kelly R. Thorp, Matthew M. Conley, Michael Roybal, David C. Moller, Jacob C. Long
Software Mentions: 3
Published: over 4 years ago

10.1111/pbi.13097

Immunogenicity of plant‐produced porcine circovirus‐like particles in mice
Cited by: 11
Author(s): Cornelius J. Gunter, Guy L. Regnard, Edward P. Rybicki, Inga I. Hitzeroth
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-015-0767-1

HiCPlotter integrates genomic data with interaction matrices
Cited by: 149
Author(s): Kadir C. Akdemir, Lynda Chin
Software Mentions: 3
Published: about 9 years ago

10.1016/j.dcn.2019.100630

BOLD signal variability and complexity in children and adolescents with and without autism spectrum disorder
Cited by: 35
Author(s): Amanda Easson, Anthony R. McIntosh
Software Mentions: 3
Published: over 5 years ago

10.1007/s00259-021-05326-y

Real-time intraoperative glioma diagnosis using fluorescence imaging and deep convolutional neural networks
Cited by: 16
Author(s): Biluo Shen, Zhe Zhang, Xiaojing Shi, Chuanxiang Cao, Zeyu Zhang, Zhenhua Hu, Nan Ji, Jie Tian
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj-cs.389

FNG-IE: an improved graph-based method for keyword extraction from scholarly big-data
Cited by: 5
Author(s): Noman Tahir, Muhammad Asif, Shahbaz Ahmad, Muhammad Sheraz Arshad Malik, Hanan Aljuaid, Muhammad Arif Butt, Mobashar Rehman
Software Mentions: 3
Published: over 3 years ago

10.3389/fninf.2013.00034

Integrated workflows for spiking neuronal network simulations
Cited by: 9
Author(s): Ján Antolík, Andrew P. Davison
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-016-3132-1

The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress
Cited by: 31
Author(s): Amine Namouchi, Marta Gómez-Muñoz, Stephan A. Frye, Line Victoria Moen, Torbjørn Rognes, Tone Tønjum, Seetha V. Balasingham
Software Mentions: 3
Published: about 8 years ago

10.3389/fninf.2013.00036

Hardware-accelerated interactive data visualization for neuroscience in Python
Cited by: 33
Author(s): Cyrille Rossant, Kenneth D. Harris
Software Mentions: 3
Published: almost 12 years ago

10.3390/toxins13080555

The Allosteric Activation of α7 nAChR by α-Conotoxin MrIC Is Modified by Mutations at the Vestibular Site
Cited by: 5
Author(s): Alican Gulsevin, Roger L. Papke, Clare Stokes, Hue N. T. Tran, Aihua Jin, Irina Vetter, Jens Meiler
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2019.02894

SampPick: Selection of a Cohort of Subjects Matching a Population HLA Distribution
Cited by: 6
Author(s): Joseph R. McGill, Osman N. Yogurtcu, Daniela Verthelyi, Hong Yang, Zuben E. Sauna
Software Mentions: 3
Published: almost 5 years ago

10.7717/peerj.824

CauseMap: fast inference of causality from complex time series
Cited by: 14
Author(s): M. Cyrus Maher, Ryan D. Hernández
Software Mentions: 3
Published: over 9 years ago

10.7717/peerj.8783

Meta-SourceTracker: application of Bayesian source tracking to shotgun metagenomics
Cited by: 36
Author(s): Jordan McGhee, Nick Rawson, Barbara Bailey, Antonio Fernández-Guerra, Laura Sisk-Hackworth, Scott T. Kelley
Software Mentions: 3
Published: over 4 years ago

10.1186/s13073-021-00847-5

Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients
Cited by: 80
Author(s): Yanqun Wang, Daxi Wang, Lu Zhang, Wanying Sun, Zhaoyong Zhang, Weijun Chen, Airu Zhu, Yongbo Huang, Fei Xiao, Jinxiu Yao, Mian Gan, Fang Li, Ling Luo, Xiaofang Huang, Yanjun Zhang, Sook‐San Wong, Xinyi Cheng, Jingkai Ji, Zhihua Ou, Mao Xiao, Min Li, Jiandong Li, Peng Ren, Ziqing Deng, Zhong Huang, Xun Xu, Tie Song, Chris Ka Pun Mok, Malik Peiris, Nanshan Zhong, Jingxian Zhao, Yimin Li, Junhua Li, Jincun Zhao
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13073-021-00935-6

Distinct signatures of codon and codon pair usage in 32 primary tumor types in the novel database CancerCoCoPUTs for cancer-specific codon usage
Cited by: 4
Author(s): Douglas Meyer, Jacob Kames, Haim Bar, Anton A. Komar, Aikaterini Alexaki, Juan C. Ibla, Ryan Hunt, Luis V. Santana‐Quintero, Anton Golikov, Michael DiCuccio, Chava Kimchi-Sarfaty
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj.5745

The BackMAP Python module: how a simpler Ramachandran number can simplify the life of a protein simulator
Cited by: 2
Author(s): Ranjan V. Mannige
Software Mentions: 3
Published: about 6 years ago

10.12688/f1000research.8251.2

pyGeno: A Python package for precision medicine and proteogenomics
Cited by: 6
Author(s): Tariq Daouda, Claude Perreault, Sébastien Lemieux
Software Mentions: 3
Published: over 8 years ago

10.1093/gigascience/giy064

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants
Cited by: 27
Author(s): Jonathan R Belyeu, Thomas J. Nicholas, Brent S. Pedersen, Thomas A Sasani, James M Havrilla, Stephanie N. Kravitz, Megan E Conway, Brian K. Lohman, Aaron R. Quinlan, Ryan M. Layer
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giz015

Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations
Cited by: 22
Author(s): Kang Kang, Basti Bergdahl, Daniel Machado, Laura Dato, Ting-Li Han, Jun Li, Silas G. Villas‐Bôas, Markus J. Herrgård, Jochen Förster, Gianni Panagiotou
Software Mentions: 3
Published: almost 6 years ago

10.1093/gigascience/giz138

Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)
Cited by: 64
Author(s): Gareth Linsmith, Stéphane Rombauts, Sara Montanari, Cecilia Deng, Jean‐Marc Celton, Philippe Guérif, Chang Liu, Rolf Lohaus, Jason D. Zurn, Alessandro Cestaro, Nahla V. Bassil, Linda V. Bakker, Elio Schijlen, Susan E. Gardiner, Yves Lespinasse, Charles‐Eric Durel, Riccardo Velasco, David B. Neale, David Chagné, Yves Van de Peer, Michela Troggio, Luca Bianco
Software Mentions: 3
Published: about 5 years ago

10.1186/s12866-021-02228-9

Genomic analysis of group B Streptococcus from milk demonstrates the need for improved biosecurity: a cross-sectional study of pastoralist camels in Kenya
Cited by: 3
Author(s): Dinah Seligsohn, Chiara Crestani, Taya Forde, Erika Chenais, Ruth N. Zadoks
Software Mentions: 3
Published: over 3 years ago

10.1093/gigascience/giaa159

Genome diversity in Ukraine
Cited by: 7
Author(s): Tarás K. Oleksyk, Walter Wolfsberger, Alexandra M. Weber, Khrystyna Shchubelka, О.T. Oleksyk, Olga Levchuk, Alla Patrus, Nelya Lazar, Stephanie O Castro-Marquez, Yaroslava Hasynets, Patricia Boldyzhar, Mikhailo Neymet, Alina Urbanovych, Viktoriya Stakhovska, Kateryna Malyar, Svitlana Chervyakova, Olena Podoroha, Natalia Kovalchuk, Juan L. Rodríguez-Flores, Weichen Zhou, Sarah Medley, Fabia U. Battistuzzi, Ryan Liu, Yong Hou, Siru Chen, Huanming Yang, Meredith Yeager, Michael Dean, Ryan E. Mills, Volodymyr Smolanka
Software Mentions: 3
Published: almost 4 years ago

10.1136/gutjnl-2018-317071

Fine needle aspirates comprehensively sample intrahepatic immunity
Cited by: 60
Author(s): Upkar S. Gill, Laura J. Pallett, Niclas Thomas, Alice R. Burton, Amit A. Patel, Simon Yona, Patrick Kennedy, Mala K. Maini
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.50568

Antagonistic regulation by insulin-like peptide and activin ensures the elaboration of appropriate dendritic field sizes of amacrine neurons
Cited by: 17
Author(s): Jiangnan Luo, Chun-Yuan Ting, Yan Li, Philip G. McQueen, Te‐Yu Lin, Chao‐Ping Hsu, Chi-Hon Lee
Software Mentions: 3
Published: over 4 years ago

10.1021/acs.jpcb.1c01281

Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR
Cited by: 13
Author(s): Sarah-Beth T. A. Amos, Thomas C. Schwarz, Jiye Shi, Benjamin P. Cossins, Terry Baker, Richard J. K. Taylor, Robert Konrat, Mark S. P. Sansom
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj.996

NxRepair: error correction inde novosequence assembly using Nextera mate pairs
Cited by: 20
Author(s): Rebecca R. Murphy, Jared O’Connell, A.J. Cox, Ole Schulz-Trieglaff
Software Mentions: 3
Published: over 9 years ago

10.1093/sysbio/syy063

Full Bayesian Comparative Phylogeography from Genomic Data
Cited by: 37
Author(s): Jamie R. Oaks
Software Mentions: 3
Published: about 6 years ago

10.1186/s12866-021-02281-4

Putative mobilized colistin resistance genes in the human gut microbiome
Cited by: 5
Author(s): Bruno de Bezerril Andrade, Tobias Goris, Haithem Afli, Felipe H. Coutinho, Alberto M. R. Dávila, Rafael R. C. Cuadrat
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0206193

Loose social organisation of AB strain zebrafish groups in a two-patch environment
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Author(s): Axel Séguret, Bertrand Collignon, Léo Cazenille, Yohann Chemtob, José Halloy
Software Mentions: 3
Published: almost 6 years ago

10.7717/peerj.11428

Comparative transcriptome profiling of a resistant vs susceptible bread wheat (Triticum aestivum L.) cultivar in response to water deficit and cold stress
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Author(s): Dmitrii K. Konstantinov, У. С. Зубаирова, Anton A. Ermakov, А. В. Дорошков
Software Mentions: 3
Published: over 3 years ago

10.1172/jci.insight.145704

Identification of a series of hair-cell MET channel blockers that protect against aminoglycoside-induced ototoxicity
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Author(s): Emma J. Kenyon, Nerissa K. Kirkwood, Siân R. Kitcher, Richard J. Goodyear, Marco Derudas, Daire Cantillon, Sarah Baxendale, Antonio de la Vega de León, Virginia N. Mahieu, Richard T. Osgood, Charlotte Donald Wilson, James C. Bull, Simon J. Waddell, Tanya T. Whitfield, Simon E. Ward, Corné J. Kros, Guy P. Richardson
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2202-13-S1-P176

Multiscale modeling with GENESIS 3, using the G-shell and Python
Cited by: 1
Author(s): Antony Rodríguez, Hugo Cornelis, David Beeman, James M. Bower
Software Mentions: 3
Published: over 12 years ago

10.1107/S1600576717015229

Hierarchical clustering for multiple-crystal macromolecular crystallography experiments: the ccCluster program
Cited by: 33
Author(s): Gianluca Santoni, U. Zander, Christoph Mueller-Dieckmann, Gordon A. Leonard, А. Н. Попов
Software Mentions: 3
Published: about 7 years ago

10.1186/s12859-018-2289-9

PRS-on-Spark (PRSoS): a novel, efficient and flexible approach for generating polygenic risk scores
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Author(s): Lawrence M. Chen, Nelson Yao, Elika Garg, Yuecai Zhu, Thao T. T. Nguyen, Irina Pokhvisneva, Shantala A. Hari Dass, Eva Unternäehrer, Hélène Gaudreau, Marie Forest, Lisa M. McEwen, Julia L. MacIsaac, Michæl S. Kobor, Celia Greenwood, Patrícia Pelufo Silveira, Michael J. Meaney, Kieran J. O’Donnell
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.54812

CB1-receptor-mediated inhibitory LTD triggers presynaptic remodeling via protein synthesis and ubiquitination
Cited by: 16
Author(s): Hannah R. Monday, Mathieu Bourdenx, Bryen A. Jordan, Pablo E. Castillo
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0215337

FluoroCellTrack: An algorithm for automated analysis of high-throughput droplet microfluidic data
Cited by: 22
Author(s): Manibarathi Vaithiyanathan, Nora Safa, Adam T. Melvin
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.5453

Raritas: a program for counting high diversity categorical data with highly unequal abundances
Cited by: 1
Author(s): David Lazarus, Johan Renaudie, Dorina Lenz, Patrick Diver, Jens Klump
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0167356

A Novel Microfluidic Assay for Rapid Phenotypic Antibiotic Susceptibility Testing of Bacteria Detected in Clinical Blood Cultures
Cited by: 33
Author(s): Christer Malmberg, Pikkei Yuen, Johanna Spaak, Otto Cars, Thomas Tängdén, Pernilla Lagerbäck
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0171212

Morphogene adsorption as a Turing instability regulator: Theoretical analysis and possible applications in multicellular embryonic systems
Cited by: 12
Author(s): Alexey M. Nesterenko, Maxim Kuznetsov, Daria D. Korotkova, Andrey G. Zaraisky
Software Mentions: 3
Published: almost 8 years ago

10.1016/j.dib.2020.105736

Dataset for supporting a modular autoinduction device for control of gene expression in Bacillus subtilis
Cited by: 3
Author(s): Graciely Gomes Corrêa, Milca Rachel da Costa Ribeiro Lins, Bruna Fernandes Silva, Gabriela Barbosa de Paiva, Vitória Fernanda Bertolazzi Zocca, Nathan Vinícius Ribeiro, Flávio Pereira Picheli, Matthias Mack, Danielle Biscaro Pedrolli
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-019-2865-7

SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation
Cited by: 11
Author(s): Nathan Ungerleider, Erik K. Flemington
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.36953

Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates
Cited by: 96
Author(s): Benjamin Mattes, Yonglong Dang, Gediminas Greicius, Lilian T. Kaufmann, Benedikt Prunsche, Jakob Rosenbauer, Johannes Stegmaier, Ralf Mikut, Suat Özbek, G. Ulrich Nienhaus, Alexander Schug, David M. Virshup, Steffen Scholpp
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pntd.0006524

Vector competence of Aedes aegypti, Culex tarsalis, and Culex quinquefasciatus from California for Zika virus
Cited by: 43
Author(s): Bradley J. Main, Jay Nicholson, Olivia C. Winokur, Cody Steiner, Kasen K. Riemersma, Jackson B. Stuart, Ryan Takeshita, Michelle O. Krasnec, Christopher M. Barker, Lark L. Coffey
Software Mentions: 3
Published: over 6 years ago

10.1186/s13072-018-0177-1

Individual retrotransposon integrants are differentially controlled by KZFP/KAP1-dependent histone methylation, DNA methylation and TET-mediated hydroxymethylation in naïve embryonic stem cells
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Author(s): Andrea Coluccio, Gabriela Ecco, Julien Duc, Sandra Offner, Priscilla Turelli, Didier Trono
Software Mentions: 3
Published: almost 7 years ago

10.3390/cancers12061593

Sex-Specific Differences in Primary CNS Lymphoma
Cited by: 2
Author(s): Thomas Roetzer, Julia Furtner, Johanna Gesperger, Lukas Seebrecht, Dave Bandke, Martina Brada, Tanisa Brandner-Kokalj, Astrid Grams, Johannes Haybaeck, Melitta Kitzwoegerer, Stefan Leber, Franz Marhold, Patrizia Moser, Camillo Sherif, Johannes Trenkler, Julia Judith Unterluggauer, Serge Weis, Franz Wuertz, Johannes A. Hainfellner, Georg Langs, Karl-Heinz Nenning, Adelheid Wöehrer
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1005940

The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors
Cited by: 91
Author(s): Nicola Wiechens, Vijender Singh, Triantafyllos Gkikopoulos, Pietà Schofield, Sónia Rocha, Tom Owen-Hughes
Software Mentions: 3
Published: over 8 years ago

10.3390/plants9111548

RNA-Seq Time Series of Vitis vinifera Bud Development Reveals Correlation of Expression Patterns with the Local Temperature Profile
Cited by: 6
Author(s): Boas Pucker, Anna Schwandner, Sarah Becker, Ludger Hausmann, Prisca Viehöver, Reinhard Töpfer, Bernd Weißhaar, Daniela Holtgräwe
Software Mentions: 2
Published: about 4 years ago

10.3389/fchem.2019.00211

The Effect of Cofactor Binding on the Conformational Plasticity of the Biological Receptors in Artificial Metalloenzymes: The Case Study of LmrR
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Author(s): Lur Alonso‐Cotchico, Jaime Rodríguez-Guerra Pedregal, Agustı́ Lledós, Jean‐Didier Maréchal
Software Mentions: 2
Published: over 5 years ago

10.3389/fncom.2017.00021

Feature Detection in Visual Cortex during Different Functional States
Cited by: 1
Author(s): Pavel M. Esir, Alexander Simonov, Misha Tsodyks
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0145199

Genetic Mapping of Novel Loci Affecting Canine Blood Phenotypes
Cited by: 9
Author(s): Mary H. White, Jessica J. Hayward, Tracy Stokol, Adam R. Boyko
Software Mentions: 2
Published: almost 9 years ago

Projects: pypi: matplotlib

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