pypi: py | Projects | Ecosyste.ms: Papers

10.3389/fninf.2013.00052

A framework for streamlining research workflow in neuroscience and psychology
Cited by: 12
Author(s): Jonas Kubilius
Software Mentions: 25
Published: over 10 years ago

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments
Cited by: 102
Author(s): Christopher Jackson, Dayanne M. Castro, Giuseppe-Antonio Saldi, Richard Bonneau, David Gresham
Software Mentions: 20
Published: over 4 years ago

10.1111/eva.13246

Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest
Cited by: 11
Author(s): Djampa Kozlowski, Rahim Hassanaly‐Goulamhoussen, Martine Da Rocha, Georgios Koutsovoulos, Marc Bailly‐Bechet, Étienne Danchin
Software Mentions: 15
Published: about 3 years ago

10.1007/s00401-021-02343-x

Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy body diseases
Cited by: 23
Author(s): Rahel Feleke, Regina H. Reynolds, Amy M. Smith, Bension S. Tilley, Sarah A. Gagliano Taliun, John Hardy, Paul M. Matthews, Steve Gentleman, David R. Owen, Michael R. Johnson, Prashant K. Srivastava, Mina Ryten
Software Mentions: 14
Published: almost 3 years ago

10.3389/fmicb.2021.713523

Dispersal Limitation Plays Stronger Role in the Community Assembly of Fungi Relative to Bacteria in Rhizosphere Across the Arable Area of Medicinal Plant
Cited by: 15
Author(s): Guozhuang Zhang, Guangfei Wei, Fang Wei, Zhongjian Chen, Min He, Shuo Jiao, Yong Wang, Lixin Dong, Shilin Chen
Software Mentions: 13
Published: almost 3 years ago

10.1371/journal.pone.0243241

CoMA – an intuitive and user-friendly pipeline for amplicon-sequencing data analysis
Cited by: 15
Author(s): Sebastian Hupfauf, Mohammad Etemadi, Marina Fernández-Delgado Juárez, María Gómez-Brandòn, Heribert Insam, Sabine Marie Podmirseg
Software Mentions: 13
Published: over 3 years ago

10.12688/f1000research.12874.2

Measuring evolutionary rates of proteins in a structural context
Cited by: 5
Author(s): Dariya K. Sydykova, Benjamin R. Jack, Scott R. Spielman, Claus O. Wilke
Software Mentions: 12
Published: over 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: over 4 years ago

10.1186/s13059-020-02070-8

The regulatory landscape of early maize inflorescence development
Cited by: 28
Author(s): Rajiv Krishna Parvathaneni, Edoardo Bertolini, Md. Shamimuzzaman, Daniel Vera, Pei Yau Lung, Brian R. Rice, Jinfeng Zhang, Patrick J. Brown, Alexander E. Lipka, Hank W. Bass, Andrea L. Eveland
Software Mentions: 12
Published: almost 4 years ago

10.3389/fgene.2021.640242

A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects
Cited by: 7
Author(s): Dustin Miller, Stephen R. Piccolo
Software Mentions: 11
Published: about 3 years ago

10.12688/f1000research.18458.2

3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
Cited by: 15
Author(s): Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev, Ivo L. Hofacker
Software Mentions: 11
Published: about 5 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: almost 3 years ago

10.1093/molbev/msaa218

Few Fixed Variants between Trophic Specialist Pupfish Species Reveal CandidateCis-Regulatory Alleles Underlying Rapid Craniofacial Divergence
Cited by: 16
Author(s): Joseph A. McGirr, Christopher H. Martin
Software Mentions: 10
Published: over 3 years ago

10.7554/eLife.44494

NetPyNE, a tool for data-driven multiscale modeling of brain circuits
Cited by: 101
Author(s): Salvador Dura‐Bernal, Benjamin A. Suter, Padraig Gleeson, Matteo Carandini, Adrián Quintana, Facundo Rodriguez, David J. Kedziora, George L. Chadderdon, Cliff C. Kerr, Samuel A. Neymotin, Robert A. McDougal, Michael L. Hines, Gordon M. Shepherd, William W. Lytton
Software Mentions: 10
Published: about 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: over 4 years ago

10.7554/eLife.65088

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Cited by: 604
Author(s): Francesco Beghini, Lauren J. McIver, Aitor Blanco-Míguez, Léonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Paolo Manghi, Matthias Scholz, Andrew Maltez Thomas, Mireia Vallès-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A. Franzosa, Nicola Segata
Software Mentions: 10
Published: about 3 years ago

10.1016/j.devcel.2018.01.022

Innate Immune Response and Off-Target Mis-splicing Are Common Morpholino-Induced Side Effects in Xenopus
Cited by: 40
Author(s): George E. Gentsch, Thomas Spruce, Rita S. Monteiro, Nick Owens, Stephen R. Martin, James C. Smith
Software Mentions: 10
Published: about 6 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: over 10 years ago

10.1002/advs.201901850

Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta
Cited by: 29
Author(s): Zhe Liang, Yuke Geng, Changmian Ji, Hongwu Du, Chui Eng Wong, Qian Zhang, Ye Zhang, Pingxian Zhang, Adeel Riaz, Sadaruddin Chachar, Yike Ding, Jing Wen, Yun-Wen Wu, Mingcheng Wang, Hongkun Zheng, Yanmin Wu, Viktor Demko, Lisha Shen, Han Xiao, Pengpeng Zhang, Xiaofeng Gu, Hao Yu
Software Mentions: 10
Published: over 4 years ago

10.3389/fninf.2020.00027

NWB Query Engines: Tools to Search Data Stored in Neurodata Without Borders Format
Cited by: 2
Author(s): Petr Ježek, Jeffery L. Teeters, Friedrich T. Sommer
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.69431

Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2
Cited by: 18
Author(s): Elektra Kantzari Robinson, Pratibha Jagannatha, Sergio Covarrubias, Matthew Cattle, Valeriya Smaliy, Rojin Safavi, Barbara Shapleigh, Robin Abu-Shumays, Miten Jain, Suzanne M. Cloonan, Mark Akeson, Angela N. Brooks
Software Mentions: 9
Published: almost 3 years ago

10.1038/s42003-018-0199-z

Improved reference genome for the domestic horse increases assembly contiguity and composition
Cited by: 137
Author(s): Theodore S. Kalbfleisch, Edward S. Rice, Michael S. DePriest, Brian P. Walenz, Matthew S. Hestand, Joris Vermeesch, Brendan O’Connell, Ian T. Fiddes, Alisa O. Vershinina, Nedda F. Saremi, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone, Molly E. McCue, Samantha A. Brooks, Ernest Bailey, Ludovic Orlando, Edward Green, Donald C. Miller, Douglas F. Antczak, James N. MacLeod
Software Mentions: 9
Published: over 5 years ago

10.1007/s11306-018-1356-6

A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository
Cited by: 8
Author(s): Andrey Smelter, Hunter N. B. Moseley
Software Mentions: 9
Published: about 6 years ago

10.12688/f1000research.15824.3

sPop: Age-structured discrete-time population dynamics model in C, Python, and R
Cited by: 3
Author(s): Kamil Erguler
Software Mentions: 9
Published: over 3 years ago

10.1186/1472-6807-9-27

PTools: an opensource molecular docking library
Cited by: 34
Author(s): Adrien Saladin, Sébastien Fiorucci, Pierre Poulain, Chantal Prévost, Martin Zacharias
Software Mentions: 9
Published: about 15 years ago

10.1371/journal.pbio.3001365

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
Cited by: 34
Author(s): Alexander K. Tice, David Žihala, Tomáš Pánek, Robert E. Jones, Eric D. Salomaki, Serafim Nenarokov, Fabien Burki, Marek Eliáš, Laura Eme, Andrew J. Roger, Antonis Rokas, Xing‐Xing Shen, Jürgen F. H. Strassert, Martin Kolísko, Matthew W. Brown
Software Mentions: 9
Published: almost 3 years ago

10.1371/journal.pcbi.1008223

Causal network inference from gene transcriptional time-series response to glucocorticoids
Cited by: 15
Author(s): Jonathan Lu, Bianca Dumitrascu, Ian C. McDowell, Brian Jo, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Timothy E. Reddy, Barbara E. Engelhardt
Software Mentions: 9
Published: over 3 years ago

10.3389/fmicb.2021.649517

Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST
Cited by: 15
Author(s): Carlus Deneke, Laura Uelze, Holger Brendebach, Simon H. Tausch, Burkhard Malorny
Software Mentions: 9
Published: almost 3 years ago

10.3390/molecules24213987

Mechanism of Action of Non-Synonymous Single Nucleotide Variations Associated with α-Carbonic Anhydrase II Deficiency
Cited by: 19
Author(s): Taremekedzwa Allan Sanyanga, Bilal Nizami, Özlem Tastan Bishop
Software Mentions: 8
Published: over 4 years ago

10.1128/mSystems.00174-16

Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China
Cited by: 89
Author(s): Bin Ma, Zhongmin Dai, Haizhen Wang, Melissa Dsouza, Xingmei Liu, Yan He, Jianjun Wu, Jorge L. Mazza Rodrigues, Jack A. Gilbert, Philip C. Brookes, Jianming Xu
Software Mentions: 8
Published: about 7 years ago

10.1186/s12859-017-1580-5

A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank
Cited by: 8
Author(s): Andrey Smelter, Morgan Astra, Hunter N. B. Moseley
Software Mentions: 8
Published: about 7 years ago

10.1186/s12864-020-07123-7

Illuminating the dark side of the human transcriptome with long read transcript sequencing
Cited by: 76
Author(s): Richard Kuo, Yuanyuan Cheng, Runxuan Zhang, John W. Brown, Jacqueline Smith, Alan Archibald, David W. Burt
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0000737

ADaCGH: A Parallelized Web-Based Application and R Package for the Analysis of aCGH Data
Cited by: 26
Author(s): Ramón Díaz‐Uriarte, Oscar M. Rueda
Software Mentions: 8
Published: almost 17 years ago

10.3389/fmicb.2017.02624

Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica
Cited by: 15
Author(s): Juan G. Abarca, Ibrahim Zuñiga, Gilmary Ortiz-Morales, Armando Lugo, Mariel Viquez-Cervilla, Natalia Rodríguez-Hernández, Frances Vázquez-Sánchez, Catalina Murillo‐Cruz, Ernesto A. Torres-Rivera, Adrián A. Pinto‐Tomás, Filipa Godoy-Vitorino
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.58615

GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background
Cited by: 67
Author(s): Nasa Sinnott-Armstrong, Sahin Naqvi, Manuel A. Rivas, Jonathan K. Pritchard
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0227434

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing
Cited by: 237
Author(s): Andrei Prodan, Valentina Tremaroli, Harald Brolin, Aeilko H. Zwinderman, Max Nieuwdorp, Evgeni Levin
Software Mentions: 7
Published: over 4 years ago

10.3389/fninf.2014.00023

CyNEST: a maintainable Cython-based interface for the NEST simulator
Cited by: 22
Author(s): Yury V. Zaytsev, Abigail Morrison
Software Mentions: 7
Published: about 10 years ago

10.7554/eLife.47994

DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning
Cited by: 304
Author(s): Jacob M. Graving, Daniel H. Chae, Hemal Naik, Liang Li, Benjamin Koger, Blair R. Costelloe, Iain D. Couzin
Software Mentions: 7
Published: over 4 years ago

10.1002/aps3.11280

Affordable remote monitoring of plant growth in facilities using Raspberry Pi computers
Cited by: 25
Author(s): Brandin Grindstaff, Makenzie E. Mabry, Paul D. Blischak, Micheal Quinn, J. Chris Pires
Software Mentions: 7
Published: almost 5 years ago

10.7554/eLife.55794

Intra-species differences in population size shape life history and genome evolution
Cited by: 31
Author(s): David Willemsen, Rongfeng Cui, Martin Reichard, Dario Riccardo Valenzano
Software Mentions: 7
Published: over 3 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

10.1177/1176934319843130

OSTRFPD: Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer
Cited by: 1
Author(s): Vivek Bhakta Mathema, Arjen M. Dondorp, Mallika Imwong
Software Mentions: 7
Published: over 5 years ago

10.7554/eLife.63194

Evolutionary dynamics of transposable elements in bdelloid rotifers
Cited by: 21
Author(s): Reuben W. Nowell, Christopher G. Wilson, Pedro Almeida, Philipp H. Schiffer, Diego Fontaneto, Lutz Becks, Fernando Rodríguez, Irina R. Arkhipova, Timothy G. Barraclough
Software Mentions: 7
Published: over 3 years ago

10.3390/metabo11030163

The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository
Cited by: 10
Author(s): Christian D. Powell, Hunter N. B. Moseley
Software Mentions: 7
Published: about 3 years ago

10.1371/journal.pgen.1008662

Discovery of novel hepatocyte eQTLs in African Americans
Cited by: 19
Author(s): Yi Zhong, Tanima De, Cristina Alárcon, C. Sehwan Park, Bianca Lec, Minoli Perera
Software Mentions: 7
Published: about 4 years ago

10.3389/fpls.2020.582422

Phylogenomics of the Andean Tetraploid Clade of the American Amaryllidaceae (Subfamily Amaryllidoideae): Unlocking a Polyploid Generic Radiation Abetted by Continental Geodynamics
Cited by: 7
Author(s): Alan W. Meerow, Elliot M. Gardner, Kyoko Nakamura
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

10.1186/s12864-020-6748-0

Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches
Cited by: 19
Author(s): Vladislav V. Babenko, Oleg V. Podgorny, Valentin A. Manuvera, Artem S. Kasianov, Alexander I. Manolov, Ekaterina N. Grafskaia, Dmitriy A. Shirokov, Alexey S. Kurdyumov, D. V. Vinogradov, Anastasia S. Nikitina, Sergey I. Kovalchuk, Nikolay Anikanov, Ivan Butenko, Olga Pobeguts, Daria Matyushkina, Daria V. Rakitina, Elena S. Kostryukova, Victor G. Zgoda, I. P. Baskova, В. М. Трухан, Mikhail S. Gelfand, Vadim M. Govorun, Helgi B. Schiöth, В. Н. Лазарев
Software Mentions: 6
Published: about 4 years ago

10.1186/s12859-021-04309-y

airpg: automatically accessing the inverted repeats of archived plastid genomes
Cited by: 2
Author(s): Tilman Mehl, Michael Gruenstaeudl
Software Mentions: 6
Published: over 2 years ago

10.3389/fmicb.2015.00277

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust
Cited by: 44
Author(s): Ulisses Nunes da Rocha, Hinsby Cadillo‐Quiroz, Ulaş Karaöz, Lara Rajeev, Niels Klitgord, Sean Dunn, Viet Truong, Mayra Buenrostro, Benjamin P. Bowen, Ferrán García-Pichel, Aindrila Mukhopadhyay, Trent Northen, Eoin L. Brodie
Software Mentions: 6
Published: about 9 years ago

10.3390/vision3040055

Development of Open-source Software and Gaze Data Repositories for Performance Evaluation of Eye Tracking Systems
Cited by: 0
Author(s): Anuradha Kar, Peter Corcoran
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pbio.3000241

Islands of retroelements are major components of Drosophila centromeres
Cited by: 117
Author(s): Ching-Ho Chang, Ankita Chavan, Jason Palladino, Xiaolu Wei, Nuno M. C. Martins, Bryce Santinello, Chin-Chi Chen, Jelena Erceg, Brian J. Beliveau, Chao-ting Wu, Amanda M. Larracuente, Barbara G. Mellone
Software Mentions: 6
Published: about 5 years ago

10.1186/s12864-021-07656-5

Species and population specific gene expression in blood transcriptomes of marine turtles
Cited by: 8
Author(s): Shreya M. Banerjee, Jamie Adkins Stoll, Camryn D. Allen, Jennifer M. Lynch, Heather Harris, Lauren Kenyon, Richard E. Connon, Eleanor J. Sterling, Eugênia Naro‐Maciel, Kathryn M. McFadden, Margaret M. Lamont, James Benge, Nadia B. Fernández, Jeffrey A. Seminoff, Scott R. Benson, Rebecca L. Lewison, Tomoharu Eguchi, Tammy M. Summers, Jessy R. Hapdei, Marc Rice, Summer L. Martin, T. Todd Jones, Peter H. Dutton, George H. Balazs, Lisa M. Komoroske
Software Mentions: 6
Published: about 3 years ago

10.1038/s41598-020-69791-5

Dynamical gene regulatory networks are tuned by transcriptional autoregulation with microRNA feedback
Cited by: 11
Author(s): Thomas G Minchington, Sam Griffiths‐Jones, Nancy Papalopulu
Software Mentions: 6
Published: almost 4 years ago

10.1038/s41598-020-78101-y

Meta-analysis of viscosity of aqueous deep eutectic solvents and their components
Cited by: 26
Author(s): Gudrun Gygli, Xinmeng Xu, Jürgen Pleiss
Software Mentions: 6
Published: over 3 years ago

10.3390/s18020539

A COTS-Based Portable System to Conduct Accurate Substance Concentration Measurements
Cited by: 9
Author(s): Juan Aznar-Poveda, José Antonio López-Pastor, Toribio F. Otero
Software Mentions: 6
Published: over 6 years ago

10.1093/gbe/evab069

Synteny-Based Genome Assembly for 16 Species of Heliconius Butterflies, and an Assessment of Structural Variation across the Genus
Cited by: 13
Author(s): Fernando Seixas, Nathaniel B. Edelman, James Mallet
Software Mentions: 6
Published: about 3 years ago

10.3390/s19194283

IoMT Platform for Pervasive Healthcare Data Aggregation, Processing, and Sharing Based on OneM2M and OpenEHR
Cited by: 62
Author(s): Jesús Noel Suárez Rubí, Paulo Roberto de Lira Gondim
Software Mentions: 6
Published: over 4 years ago

10.3389/fninf.2014.00024

BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs
Cited by: 67
Author(s): Anders Eklund, Paul Dufort, Mattias Villani, Stephen M. LaConte
Software Mentions: 5
Published: about 10 years ago

10.1186/s12915-017-0412-4

Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution
Cited by: 96
Author(s): Damien J. Lightfoot, David E. Jarvis, Thiruvarangan Ramaraj, R. Lee, Eric N. Jellen, Peter J. Maughan
Software Mentions: 5
Published: over 6 years ago

10.3389/fninf.2013.00040

pySPACE—a signal processing and classification environment in Python
Cited by: 31
Author(s): Mario Michael Krell, Sirko Straube, Anett Seeland, Hendrik Wöhrle, Johannes Teiwes, Jan Hendrik Metzen, Elsa Andrea Kirchner, Frank Kirchner
Software Mentions: 5
Published: over 11 years ago

10.3389/fninf.2018.00050

Automatically Selecting a Suitable Integration Scheme for Systems of Differential Equations in Neuron Models
Cited by: 8
Author(s): Inga Blundell, Dimitri Plotnikov, Jochen Martin Eppler, Abigail Morrison
Software Mentions: 5
Published: over 5 years ago

10.3389/fninf.2014.00076

Limits to high-speed simulations of spiking neural networks using general-purpose computers
Cited by: 50
Author(s): Friedemann Zenke, Wulfram Gerstner
Software Mentions: 5
Published: over 9 years ago

10.3389/fmicb.2019.02142

Particle-Associated Microbial Community in a Subtropical Lake During Thermal Mixing and Phytoplankton Succession
Cited by: 17
Author(s): Schweitzer-Natan Orna, Maya Ofek‐Lalzar, Daniel Sher, Assaf Sukenik
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2016.00772

Molecular Evidence for Metabolically Active Bacteria in the Atmosphere
Cited by: 72
Author(s): Ann M. Klein, Brendan J. M. Bohannan, Daniel A. Jaffe, David A. Levin, Jessica L. Green
Software Mentions: 5
Published: almost 8 years ago

10.7554/eLife.57492

Alternative polyadenylation mediates genetic regulation of gene expression
Cited by: 33
Author(s): Briana E Mittleman, Sebastian Pott, Shane Warland, Teng Zeng, Zepeng Mu, Mayher Kaur, Yoav Gilad, Yang Li
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.59404

Massively multiplex single-molecule oligonucleosome footprinting
Cited by: 41
Author(s): Nour J. Abdulhay, Christopher A. McNally, Laura J Hsieh, Sivakanthan Kasinathan, Aidan M. Keith, Laurel S Estes, Mehran Karimzadeh, Jason G. Underwood, Hani Goodarzi, Geeta J. Narlikar, Vijay Ramani
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2016.01221

Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales
Cited by: 23
Author(s): John Bird, Brett J. Baker, Alexander J. Probst, Mircea Podar, Karen G. Lloyd
Software Mentions: 5
Published: almost 8 years ago

10.1128/mSystems.00084-18

Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities
Cited by: 33
Author(s): Ashley R. Coenen, Joshua S. Weitz
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0215054

Numerical simulations for the Toda lattices Hamiltonian system: Higher order symplectic illustrative perspective
Cited by: 1
Author(s): Asif Mushtaq, Amna Noreen, Muhammad Farooq
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0232456

Investigation of the human nasal microbiome in persons with long- and short-term exposure to methicillin-resistant Staphylococcus aureus and other bacteria from the pig farm environment
Cited by: 10
Author(s): Zohorul Islam, Thor Bech Johannesen, Berit Lilje, Tinna Ravnholt Urth, Anders Rhod Larsen, Øystein Angen, Jesper Larsen
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-020-6769-8

High-resolution profile of transcriptomes reveals a role of alternative splicing for modulating response to nitrogen in maize
Cited by: 20
Author(s): Yuancong Wang, Jing Xu, Min Ge, Lei Ning, Meng-Mei Hu, Han Zhao
Software Mentions: 5
Published: about 4 years ago

10.3389/fmicb.2020.00308

Characterization of the Gut Microbiota of the Antarctic Heart Urchin (Spatangoida) Abatus agassizii
Cited by: 13
Author(s): Guillaume Schwob, Léa Cabrol, Élie Poulin, Julieta Orlando
Software Mentions: 5
Published: about 4 years ago

10.1186/s13029-016-0057-7

TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data
Cited by: 12
Author(s): Lindsay V. Clark, Erik J. Sacks
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41597-019-0103-9

Multitask learning and benchmarking with clinical time series data
Cited by: 414
Author(s): Hrayr Harutyunyan, Hrant Khachatrian, David C. Kale, Greg Ver Steeg, Aram Galstyan
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-018-36840-z

Identification of candidate neoantigens produced by fusion transcripts in human osteosarcomas
Cited by: 28
Author(s): Susan K. Rathe, Flavia E. Popescu, James E. Johnson, Adrienne L. Watson, Tracy A. Marko, Branden S. Moriarity, John R. Ohlfest, David A. Largaespada
Software Mentions: 5
Published: over 5 years ago

10.3390/insects11110783

Colony-Level Effects of Amygdalin on Honeybees and Their Microbes
Cited by: 5
Author(s): James P. Tauber, Cansu Özge Tozkar, Ryan S. Schwarz, Dawn Lopez, Rebecca E. Irwin, Lynn S. Adler, Jay D. Evans
Software Mentions: 5
Published: over 3 years ago

10.1038/sdata.2015.55

A multi-source dataset of urban life in the city of Milan and the Province of Trentino
Cited by: 203
Author(s): Gianni Barlacchi, Marco De Nadai, R. Larcher, Antonio Casella, Cristiana Chitic, Giovanni Luca Torrisi, Fabrizio Antonelli, Alessandro Vespignani, Alex Pentland, Bruno Lepri
Software Mentions: 5
Published: over 8 years ago

10.1002/ece3.5538

Old divergence and restricted gene flow between torrent duck ( Merganetta armata ) subspecies in the Central and Southern Andes
Cited by: 2
Author(s): Luis Alza, Philip Lavretsky, Jeffrey L. Peters, Gerardo Cerón, Matthew J. Smith, Cecilia Kopuchian, Andrea A. Astié, Kevin G. McCracken
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pcbi.1004668

A Quick Introduction to Version Control with Git and GitHub
Cited by: 97
Author(s): John Blischak, Emily Davenport, Gregory V. Wilson
Software Mentions: 5
Published: over 8 years ago

10.1186/s13059-019-1858-1

Evaluating nanopore sequencing data processing pipelines for structural variation identification
Cited by: 30
Author(s): Anbo Zhou, Timothy Lin, Jinchuan Xing
Software Mentions: 5
Published: over 4 years ago

10.7717/peerj.11827

Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei
Cited by: 12
Author(s): Estefanía Garibay‐Valdez, Francesco Cicala, Marcel Martínez‐Porchas, Ricardo Gómez-Reyes, Francisco Vargas‐Albores, Teresa Gollas‐Galván, Luis Rafael Martínez‐Córdova, Kadiya Calderón
Software Mentions: 5
Published: almost 3 years ago

10.1186/s13059-021-02283-5

Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase
Cited by: 24
Author(s): Vahid Akbari, Jean-Michel Garant, Kieran O’Neill, Pawan Pandoh, Richard A. Moore, Marco A. Marra, Martin Hirst, Steven J.M. Jones
Software Mentions: 5
Published: about 3 years ago

10.12688/f1000research.11022.3

Picopore: A tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality
Cited by: 3
Author(s): Scott Gigante
Software Mentions: 5
Published: over 6 years ago

10.3389/fvets.2019.00260

A Microbiomic Analysis of a Pasture-Raised Broiler Flock Elucidates Foodborne Pathogen Ecology Along the Farm-To-Fork Continuum
Cited by: 16
Author(s): Michael J. Rothrock, Aude Locatelli, Kristina M. Feye, Andrew J Caudill, Jean Guard, Kelli L. Hiett, Steven C. Ricke
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0210347

EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA
Cited by: 6
Author(s): Michael Gruenstaeudl, Yannick Hartmaring
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1005510

Good enough practices in scientific computing
Cited by: 240
Author(s): Greg Wilson, Jenny Bryan, Karen Cranston, Justin Kitzes, Alexander J. Nederbragt, Tracy K. Teal
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pcbi.1009285

ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A pipeline for sample-specific computational modeling of electrical stimulation of peripheral nerves
Cited by: 26
Author(s): Eric D. Musselman, Jake E. Cariello, Warren M. Grill, Nicole A. Pelot
Software Mentions: 4
Published: over 2 years ago

10.1038/s42003-021-02373-x

Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzus persicae
Cited by: 48
Author(s): Kumar Saurabh Singh, Erick M. G. Cordeiro, Bartlomiej J. Troczka, Adam Pym, Joanna Mackisack, Thomas C. Mathers, Ana Duarte, Fabrice Legeai, Stéphanie Robin, Pablo Bielza, Hannah J. Burrack, Kamel Charaabi, I. Denholm, Christian C. Figueroa, Richard H. ffrench‐Constant, Georg Jander, John T. Margaritopoulos, Emanuele Mazzoni, Ralf Nauen, Claudio C. Ramı́rez, Guangwei Ren, Ilona Stepanyan, Paul A Umina, Нина Владимировна Воронова, John Vontas, Martin S. Williamson, Alex C. C. Wilson, Xiwu Gao, Young‐Nam Youn, Christoph Zimmer, Jean‐Christophe Simon, Alex Hayward, Chris Bass
Software Mentions: 4
Published: almost 3 years ago

10.3758/s13428-019-01226-0

SMITE: A toolbox for creating Psychophysics Toolbox and PsychoPy experiments with SMI eye trackers
Cited by: 5
Author(s): Diederick C Niehorster, Maria Nyström
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2105-15-44

The HTS barcode checkerpipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data
Cited by: 19
Author(s): Youri Lammers, Tamara Peelen, Rutger A. Vos, Barbara Gravendeel
Software Mentions: 4
Published: over 10 years ago

10.1016/j.celrep.2019.02.012

Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control
Cited by: 56
Author(s): Lee Davidson, Laura Francis, Ross A. Cordiner, Joshua D. Eaton, Chris Estell, Sara Macías, Javier F. Cáceres, Steven West
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-018-2485-7

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies
Cited by: 590
Author(s): Michael J. Roach, Simon A. Schmidt, Anthony R. Borneman
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2018.01188

Canola Root–Associated Microbiomes in the Canadian Prairies
Cited by: 67
Author(s): Chih Ying Lay, Terrence H. Bell, Chantal Hamel, K. Neil Harker, Ramona M. Mohr, Charles W. Greer, Étienne Yergeau, Marc St‐Arnaud
Software Mentions: 4
Published: almost 6 years ago

10.3390/plants10050863

Genetic Diversity of Stratiotes aloides L. (Hydrocharitaceae) Stands across Europe
Cited by: 1
Author(s): Barbara Turner, Steffen Hameister, Andreas Hudler, Karl‐Georg Bernhardt
Software Mentions: 4
Published: about 3 years ago

10.1186/1752-153X-2-5

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit
Cited by: 297
Author(s): Noel M. O’Boyle, Chris Morley, Geoffrey Hutchison
Software Mentions: 4
Published: about 16 years ago

10.3390/plants8100377

Association Mapping Between Candidate Gene SNP and Production and Oil Quality Traits in Interspecific Oil Palm Hybrids
Cited by: 7
Author(s): Maider Astorkia, M. Rodríguez Hernández, Stéphanie Bocs, Emma Lopez de Armentia, Ana Herrán, Kevin Ponce, Olga León, Shone Morales, Nathalie Quezada, Francisco Orellana, Fahmi Wendra, Zulhermana Sembiring, Dwi Asmono, Enrique Ritter
Software Mentions: 4
Published: over 4 years ago

10.3389/fphar.2021.634047

Discovering Potential RNA Dependent RNA Polymerase Inhibitors as Prospective Drugs Against COVID-19: An in silico Approach
Cited by: 16
Author(s): Satabdi Saha, Rajat Nandi, Poonam Vishwakarma, Amresh Prakash, Diwakar Kumar
Software Mentions: 4
Published: about 3 years ago

10.3389/fgene.2020.585746

Profiling of H3K27Ac Reveals the Influence of Asthma on the Epigenome of the Airway Epithelium
Cited by: 7
Author(s): Peter McErlean, A. Paul Kelly, Jaideep Dhariwal, Max Kirtland, Julie Watson, Ismael Ranz, Janet L. Smith, Alka Saxena, David J. Cousins, Antoon van Oosterhout, Roberto Solari, Michael R. Edwards, Sebastian L. Johnston, Paul Lavender
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0209246

A modular and customizable open-source package for quantum voltage standards operation and control
Cited by: 1
Author(s): Paolo Durandetto, A. Sosso
Software Mentions: 4
Published: over 5 years ago

Projects: pypi: py

Papers Mentioning py 403