pypi: py | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0021931

Real-Time PyMOL Visualization for Rosetta and PyRosetta
Cited by: 51
Author(s): Evan H. Baugh, Sergey Lyskov, Brian D. Weitzner, Jeffrey J. Gray
Software Mentions: 4
Published: over 13 years ago

Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol
Cited by: 22
Author(s): Maurício M. Zenker, Alexandre Specht, Vera G. Fonseca
Software Mentions: 4
Published: over 4 years ago

10.1038/s41597-020-0415-9

A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task
Cited by: 8
Author(s): Nand Chandravadia, Daan Liang, Andrea Gómez Palacio Schjetnan, April A Carlson, Maïlys C. M. Faraut, Jeffrey M. Chung, Chrystal M. Reed, Benjamin Dichter, Uri Maoz, Suneil K. Kalia, Taufik A. Valiante, Adam N. Mamelak, Ueli Rutishauser
Software Mentions: 4
Published: over 4 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: over 16 years ago

10.7717/peerj.2988

Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies
Cited by: 84
Author(s): Cédric Cabau, Frédéric Escudié, Anis Djari, Yann Guiguen, Julien Bobe, Christophe Klopp
Software Mentions: 4
Published: almost 8 years ago

10.1007/s00122-021-03798-y

Quantitative trait locus mapping combined with variant and transcriptome analyses identifies a cluster of gene candidates underlying the variation in leaf wax between upland and lowland switchgrass ecotypes
Cited by: 8
Author(s): Peng Qi, Thomas H. Pendergast, Alexander Johnson, Bochra Amina Bahri, So‐Yeon Choi, Ali Missaoui, Katrien M. Devos
Software Mentions: 4
Published: over 3 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: over 5 years ago

10.3390/molecules25245934

CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations
Cited by: 13
Author(s): Alessandro Marchetto, Zeineb Si Chaib, Claudia Rossi, Rui P. P. L. Ribeiro, Sergio Pantano, Giulia Rossetti, Alejandro Giorgetti
Software Mentions: 4
Published: almost 4 years ago

10.1093/molbev/msy023

RADpainter and fineRADstructure: Population Inference from RADseq Data
Cited by: 234
Author(s): Milan Malinsky, Emiliano Trucchi, Daniel J. Lawson, Daniel Falush
Software Mentions: 4
Published: almost 7 years ago

10.7717/peerj.6842

ERISNet: deep neural network for Sargassum detection along the coastline of the Mexican Caribbean
Cited by: 41
Author(s): Javier Arellano‐Verdejo, Hugo-Enrique Lazcano-Hernández, Nancy Cabañillas-Terán
Software Mentions: 4
Published: over 5 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: over 3 years ago

10.1016/j.devcel.2016.08.013

Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis
Cited by: 61
Author(s): Stefano Bencivenga, Antonio Serrano-Mislata, Maxwell S. Bush, Samantha Fox, Robert Sablowski
Software Mentions: 4
Published: about 8 years ago

10.1038/sdata.2018.55

Massively parallel recordings in macaque motor cortex during an instructed delayed reach-to-grasp task
Cited by: 41
Author(s): Thomas Brochier, Lyuba Zehl, Yaoyao Hao, Margaux Duret, Julia Sprenger, Michael Denker, Sonja Grün, Alexa Riehle
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-75984-9

Omics approaches for conservation biology research on the bivalve Chamelea gallina
Cited by: 8
Author(s): Federica Carducci, Maria Assunta Biscotti, Emiliano Trucchi, Maria Giuliani, Stefania Gorbi, Alessandro Coluccelli, Marco Barucca, Adriana Canapa
Software Mentions: 4
Published: about 4 years ago

10.1107/S2059798318001353

Gyreandgimble: a maximum-likelihood replacement for Patterson correlation refinement
Cited by: 13
Author(s): Airlie J. McCoy, Robert D. Oeffner, Claudia Millán, Massimo Sammito, Isabel Usón, Randy J. Read
Software Mentions: 4
Published: over 6 years ago

10.1007/s10278-018-0081-z

IoT in Radiology: Using Raspberry Pi to Automatically Log Telephone Calls in the Reading Room
Cited by: 9
Author(s): Po-Hao Chen, Nathan M. Cross
Software Mentions: 4
Published: over 6 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: about 5 years ago

10.3389/fgene.2020.566569

EAT-UpTF: Enrichment Analysis Tool for Upstream Transcription Factors of a Group of Plant Genes
Cited by: 4
Author(s): Sangrea Shim, Pil Joon Seo
Software Mentions: 4
Published: about 4 years ago

10.3390/microorganisms9081595

Habitats Are More Important Than Seasons in Shaping Soil Bacterial Communities on the Qinghai-Tibetan Plateau
Cited by: 7
Author(s): Rui Wang, Wei Miao, Jing Wang, Yongjun Lin
Software Mentions: 4
Published: over 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: almost 4 years ago

10.1038/sdata.2018.141

MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations
Cited by: 12
Author(s): Oriol Fornés, Marius Gheorghe, Phillip A. Richmond, David J. Arenillas, Wyeth W. Wasserman, Anthony Mathelier
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-020-6722-x

MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression
Cited by: 15
Author(s): Chin-Sheng Teng, Bing-Heng Wu, Ming‐Ren Yen, Pao‐Yang Chen
Software Mentions: 4
Published: over 4 years ago

10.1523/ENEURO.0524-20.2021

Sharing an Open Stimulation System for Auditory EEG Experiments Using Python, Raspberry Pi, and HifiBerry
Cited by: 1
Author(s): Alexandra Corneyllie, Fabien Perrin, Lizette Heine
Software Mentions: 4
Published: over 3 years ago

10.3390/e21101023

Teaching Ordinal Patterns to a Computer: Efficient Encoding Algorithms Based on the Lehmer Code
Cited by: 10
Author(s): Sebastian Berger, Andrii Kravtsiv, Gerhard Schneider, Denis Jordan
Software Mentions: 4
Published: about 5 years ago

10.3390/insects12070618

Genetic Screening to Identify Candidate Resistance Alleles to Cry1F Corn in Fall Armyworm Using Targeted Sequencing
Cited by: 10
Author(s): Katrina Schlum, Kurt Lamour, P. A. Tandy, Scott J. Emrich, Caroline Placidi De Bortoli, Tejas Rao, Diego M Viteri Dillon, Angela M. Linares‐Ramírez, Juan Luís Jurat-Fuentes
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-021-02483-z

Trycycler: consensus long-read assemblies for bacterial genomes
Cited by: 128
Author(s): Ryan R. Wick, Louise M. Judd, Louise Cerdeira, Jane Hawkey, Guillaume Méric, Ben Vezina, Kelly L. Wyres, Kathryn E. Holt
Software Mentions: 4
Published: about 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: almost 6 years ago

10.1371/journal.pone.0148028

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis
Cited by: 198
Author(s): Adam G. Clooney, Fiona Fouhy, Roy D. Sleator, Aisling O’ Driscoll, Catherine Stanton, Paul D. Cotter, Marcus J. Claesson
Software Mentions: 4
Published: almost 9 years ago

10.3389/fgene.2020.00736

DNA N6-Methyladenine Modification in Wild and Cultivated Soybeans Reveals Different Patterns in Nucleus and Cytoplasm
Cited by: 13
Author(s): Di Yuan, Jian-Feng Xing, Meiwei Luan, Kai-Kai Ji, Jun Guo, Shuang Xie, Yuanming Zhang
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0024982

SNPpy - Database Management for SNP Data from Genome Wide Association Studies
Cited by: 10
Author(s): Faheem Mitha, Herodotos Herodotou, Nedyalko Borisov, Chen Jiang, Josh Yoder, Kouros Owzar
Software Mentions: 4
Published: about 13 years ago

10.12688/f1000research.22400.2

Ribosome profiling of HEK293T cells overexpressing codon optimized coagulation factor IX
Cited by: 1
Author(s): Aikaterini Alexaki, Jacob Kames, Gaya Hettiarachchi, John C. Athey, Upendra Katneni, Ryan Hunt, Nobuko Hamasaki-Katagiri, David D. Holcomb, Michael DiCuccio, Haim Bar, Anton A. Komar, Chava Kimchi-Sarfaty
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0036852

Generalized DNA Barcode Design Based on Hamming Codes
Cited by: 82
Author(s): Leonid Bystrykh
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0108852

Expression, Purification, and Structural Insights for the Human Uric Acid Transporter, GLUT9, Using the Xenopus laevis Oocytes System
Cited by: 34
Author(s): Benjamin Clémençon, Benjamin P. Lüscher, Michael Fine, Marc Baumann, Daniel Surbek, Olivier Bonny, Matthias A. Hediger
Software Mentions: 4
Published: about 10 years ago

10.7554/eLife.19893

The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status
Cited by: 16
Author(s): Dongming Li, Ana Marie S. Palanca, So Youn Won, Lei Gao, Ying Feng, Ajay A. Vashisht, Li Liu, Yuanyuan Zhao, Xigang Liu, Xiuyun Wu, Shaofang Li, Brandon H. Le, Yun Ju Kim, Guodong Yang, Shengben Li, Jinyuan Liu, James A. Wohlschlegel, Hongwei Guo, Beixin Mo, Xuemei Chen, Julie A. Law
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pntd.0009597

Field evaluation of the gut microbiome composition of pre-school and school-aged children in Tha Song Yang, Thailand, following oral MDA for STH infections
Cited by: 8
Author(s): Katharina Stracke, Poom Adisakwattana, Suparat Phuanukoonnon, Tippayarat Yoonuan, Akkarin Poodeepiyasawat, Paron Dekumyoy, Kittipong Chaisiri, Alexandra Roth Schulze, Stephen Wilcox, Harin Karunajeewa, Rebecca J. Traub, Aaron R. Jex
Software Mentions: 4
Published: over 3 years ago

10.1186/s13568-019-0747-z

Dietary supplementation with fermented Mao-tai lees beneficially affects gut microbiota structure and function in pigs
Cited by: 18
Author(s): Huan Li, Huawei Li, Peifeng Xie, Zhihua Li, Yulong Yin, François Blachier, Xiangfeng Kong
Software Mentions: 4
Published: almost 6 years ago

10.1534/g3.115.023655

Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution
Cited by: 145
Author(s): John W. Davey, Mathieu Chouteau, Sarah L. Barker, Luana S. Maroja, Simon W. Baxter, Fraser Simpson, Richard M. Merrill, Mathieu Joron, James Mallet, Kanchon K. Dasmahapatra, Chris D. Jiggins
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-018-1539-5

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
Cited by: 41
Author(s): Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, Shadrielle M. G. Espiritu, Vincent Huang, Kristen K. Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi, Michael R. Kellen, Ken Chen, Thea Norman, Stephen H. Friend, Justin Guinney, Gustavo Stolovitzky, David Haussler, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros
Software Mentions: 4
Published: about 6 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: over 3 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: over 6 years ago

10.1107/S1600576715010092

TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits
Cited by: 70
Author(s): Irene Farabella, Daven Vasishtan, Agnel Praveen Joseph, Arun Prasad Pandurangan, Harpal Sahota, Maya Topf
Software Mentions: 4
Published: over 9 years ago

10.1155/2014/264519

A Bioinformatics Pipeline for the Analyses of Viral Escape Dynamics and Host Immune Responses during an Infection
Cited by: 6
Author(s): Preston Leung, Rowena A. Bull, Andrew R. Lloyd, Fabio Luciani
Software Mentions: 4
Published: almost 11 years ago

10.12688/f1000research.6924.1

The khmer software package: enabling efficient nucleotide sequence analysis
Cited by: 325
Author(s): Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar Boucher, Adam Caldwell, R.A. Cartwright, Amanda Charbonneau, Bede Constantinides, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan A. Fish, Leonor García-Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Rhys Kidd, David M. Lin, Justin Lippi, Tamer Mansour, Pamela McA'Nulty, McDonald Eric, Jessica E. Mizzi, Kevin Murray, Joshua R. Nahum, Kaben Nanlohy, Alexander J. Nederbragt, Humberto Ortíz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N. Russ, Erich M. Schwarz, Camille Scott, Josiah Seaman, Scott Sievert, Jared T. Simpson, Connor T. Skennerton, James Spencer, S. Ramakrishnan, Daniel Standage, James A. Stapleton, Susan R. Steinman, J.J. Stein, Benjamin A. Taylor, W. Trimble, Heather L. Wiencko, Michael J. Wright, Brian Wyss, Zhang Qingpeng, en zyme, C. Titus Brown
Software Mentions: 4
Published: about 9 years ago

10.3389/fgene.2020.00513

Estimating Conformational Traits in Dairy Cattle With DeepAPS: A Two-Step Deep Learning Automated Phenotyping and Segmentation Approach
Cited by: 13
Author(s): Jessica Nye, Laura M. Zingaretti, Miguel Pérez‐Enciso
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pcbi.1004008

A RESTful API for Accessing Microbial Community Data for MG-RAST
Cited by: 62
Author(s): Andreas Wilke, Jared Bischof, Travis Harrison, Tom Brettin, Mark D’Souza, Wolfgang Gerlach, Hunter Matthews, Tobias Paczian, Jared Wilkening, Elizabeth M. Glass, Narayan Desai, Folker Meyer
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12859-020-03764-3

Avian Immunome DB: an example of a user-friendly interface for extracting genetic information
Cited by: 8
Author(s): Ralf Mueller, Nicolai Mallig, Jacqueline Smith, Lél Eöery, Richard Kuo, Robert H. S. Kraus
Software Mentions: 3
Published: about 4 years ago

10.1186/s12896-018-0476-4

A highly parallel strategy for storage of digital information in living cells
Cited by: 10
Author(s): Azat Akhmetov, Andrew D. Ellington, Edward M. Marcotte
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pbio.1000574

Evidence of Activity-Specific, Radial Organization of Mitotic Chromosomes in Drosophila
Cited by: 26
Author(s): Yuri G. Strukov, Tuba Halise Sural, Mitzi I. Kuroda, John W. Sedat
Software Mentions: 3
Published: almost 14 years ago

10.6026/97320630015246

Insights into Molecular Interactions of human Wnt5b and Frizzled proteins for their role in teratogenicity
Cited by: 3
Author(s): Sween Dahiya, Vandana Saini, Pawan Kumar, Ajit Kumar
Software Mentions: 3
Published: over 5 years ago

10.3390/plants10081702

Species Delimitation and Conservation in Taxonomically Challenging Lineages: The Case of Two Clades of Capurodendron (Sapotaceae) in Madagascar
Cited by: 6
Author(s): Carlos G. Boluda, Camille Christe, Aina Randriarisoa, Laurent Gautier, Yamama Naciri
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-11-S12-S10

interPopula: a Python API to access the HapMap Project dataset
Cited by: 0
Author(s): Tiago Antão
Software Mentions: 3
Published: almost 14 years ago

10.1111/tpj.14747

Rapid identification of an Arabidopsis NLR gene as a candidate conferring susceptibility to Sclerotinia sclerotiorum using time‐resolved automated phenotyping
Cited by: 26
Author(s): Adelin Barbacci, Olivier Navaud, Malick Mbengue, Marielle Barascud, Laurence Godiard, Mehdi Khafif, Aline Lacaze, Sylvain Raffaele
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-020-03856-0

High quality genome assemblies of Mycoplasma bovis using a taxon-specific Bonito basecaller for MinION and Flongle long-read nanopore sequencing
Cited by: 33
Author(s): Nick Vereecke, Jade Bokma, Freddy Haesebrouck, Hans Nauwynck, Filip Boyen, Bart Pardon, Sebastiaan Theuns
Software Mentions: 3
Published: about 4 years ago

10.1186/s12870-020-02365-9

High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome
Cited by: 33
Author(s): Teng Wen, Mingwen Zhao, Ting Liu, Qiwei Huang, Jun Yuan, Qirong Shen
Software Mentions: 3
Published: over 4 years ago

10.1128/mBio.02376-18

Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments
Cited by: 38
Author(s): John Bird, Eric D. Tague, Laura Zinke, Jenna M. Schmidt, Andrew D. Steen, Brandi Kiel Reese, Ian P. G. Marshall, Gordon Webster, Andrew J. Weightman, Hector F. Castro, Shawn R. Campagna, Karen G. Lloyd
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.2676

Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)
Cited by: 10
Author(s): Matthew Z. DeMaere, Aaron E. Darling
Software Mentions: 3
Published: about 8 years ago

10.1128/mBio.00731-20

Differential Alphavirus Defective RNA Diversity between Intracellular and Extracellular Compartments Is Driven by Subgenomic Recombination Events
Cited by: 11
Author(s): Rose M. Langsjoen, Antonio E. Muruato, S. R. Kunkel, Elizabeth Jaworski, Andrew Routh
Software Mentions: 3
Published: about 4 years ago

10.7717/peerj.6785

Using Ipomoea aquatic as an environmental-friendly alternative to Elodea nuttallii for the aquaculture of Chinese mitten crab
Cited by: 6
Author(s): Linlin Shi, Meijuan Jin, Mingxing Shen, Lu ChangYing, Haihou Wang, Xingwei Zhou, Lijuan Mei, Shixue Yin
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.4174

Is there a link between aging and microbiome diversity in exceptional mammalian longevity?
Cited by: 26
Author(s): Graham M. Hughes, John Leech, Sébastien J. Puechmaille, Jose V. Lopez, Emma C. Teeling
Software Mentions: 3
Published: almost 7 years ago

10.3390/s18051312

Infrastructure for Integration of Legacy Electrical Equipment into a Smart-Grid Using Wireless Sensor Networks
Cited by: 21
Author(s): Paulo Régis C. de Araújo, Raimir Holanda Filho, Joel J. P. C. Rodrigues, João Paolo C. M. Oliveira, Stéphanie Alencar Braga
Software Mentions: 3
Published: over 6 years ago

10.1186/1751-0473-8-6

RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics
Cited by: 1
Author(s): Izawa Akiko, Jun Sese
Software Mentions: 3
Published: over 11 years ago

10.3389/fmicb.2015.01532

Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients
Cited by: 22
Author(s): Tom V. Joss, Catherine Burke, Bernard Hudson, Aaron E. Darling, Martin Forer, Dagmar Alber, Ian G. Charles, Nicholas W. Stow
Software Mentions: 3
Published: almost 9 years ago

10.1186/1742-5573-5-7

Methods for stratification of person-time and events – a prerequisite for Poisson regression and SIR estimation
Cited by: 70
Author(s): Klaus Rostgaard
Software Mentions: 3
Published: about 16 years ago

10.1038/s41598-021-90017-9

A python code for automatic construction of Fischer plots using proxy data
Cited by: 2
Author(s): Dayong Yang, Yongjian Huang, Zongyang Chen, Qinghua Huang, Yong’an Ren, Chengshan Wang
Software Mentions: 3
Published: over 3 years ago

10.3389/fnins.2018.00586

Analysis of Functional Connectivity and Oscillatory Power Using DICS: From Raw MEG Data to Group-Level Statistics in Python
Cited by: 22
Author(s): Marijn van Vliet, Mia Liljeström, Susanna Aro, Riitta Salmelin, Janne V. Kujala
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-80769-1

Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation
Cited by: 41
Author(s): Germano Heinzelmann, Michael K. Gilson
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41396-019-0468-y

Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert
Cited by: 50
Author(s): Gherman Uritskiy, Samantha Getsin, Adam Munn, Benito Gómez-Silva, Alfonso F. Dávila, B. Glass, James Taylor, Jocelyne DiRuggiero
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-020-03701-4

AdmixPipe: population analyses in Admixture for non-model organisms
Cited by: 17
Author(s): Steven M. Mussmann, Marlis R. Douglas, Tyler K. Chafin
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-48200-6

Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes
Cited by: 27
Author(s): Carlos Eduardo Posada-Perlaza, Adán Andrés Ramírez Rojas, Paola Porras, Boahemaa Adu-Oppong, Ana María Botero-Coy, Félix Hernández, Juan Manuel Anzola, Lorena Díaz, Gautam Dantas, Alejandro Reyes, María Mercedes Zambrano
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-48155-8

Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site
Cited by: 11
Author(s): Carsten Krichel, Christina Möckel, Oliver Schillinger, Pitter F. Huesgen, Heinrich Sticht, Birgit Strodel, Oliver H. Weiergräber, Dieter Willbold, Philipp Neudecker
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2017.02384

Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone
Cited by: 48
Author(s): Clara A. Fuchsman, Allan H. Devol, Jaclyn K. Saunders, Cedar McKay, Gabrielle Rocap
Software Mentions: 3
Published: almost 7 years ago

10.1038/s42003-021-02577-1

Machine learning-based real-time object locator/evaluator for cryo-EM data collection
Cited by: 19
Author(s): Koji Yonekura, Saori Maki-Yonekura, Hisashi Naitow, Tasuku Hamaguchi, Kiyotsugu Takaba
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2018.01402

Cholecystectomy Damages Aging-Associated Intestinal Microbiota Construction
Cited by: 47
Author(s): Wenxue Wang, Junfeng Wang, Julan Li, Peng Yan, Jimmy Yun, Ruyi Zhang, Wei Yue, Qiang Guo, Jiawei Geng
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-66791-3

Heritability and genome-wide association of swine gut microbiome features with growth and fatness parameters
Cited by: 43
Author(s): Matteo Bergamaschi, Christian Maltecca, Constantino Schillebeeckx, Nathan P. McNulty, Charles V. Schwab, Caleb M Shull, Justin Fix, Francesco Tiezzi
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-018-24775-4

A molecular dynamics simulation study decodes the Zika virus NS5 methyltransferase bound to SAH and RNA analogue
Cited by: 22
Author(s): Chih-Hung Chuang, Shean‐Jaw Chiou, Tian−Lu Cheng, Yeng‐Tseng Wang
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2018.00313

Simulation Modeling to Compare High-Throughput, Low-Iteration Optimization Strategies for Metabolic Engineering
Cited by: 1
Author(s): Stephen C. Heinsch, Siba R. Das, Michael J. Smanski
Software Mentions: 3
Published: over 6 years ago

10.1038/sdata.2019.2

Qresp, a tool for curating, discovering and exploring reproducible scientific papers
Cited by: 22
Author(s): Marco Govoni, Milson Munakami, Aditya Tanikanti, Jonathan H. Skone, Hakizumwami Birali Runesha, Federico Giberti, Juan Pablo, Giulia Galli
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-32040-x

The potential HLA Class I-restricted epitopes derived from LeIF and TSA of Leishmania donovani evoke anti-leishmania CD8+ T lymphocyte response
Cited by: 20
Author(s): Manas Ranjan Dikhit, Sushmita Das, Vijaya Mahantesh, Akhilesh Kumar, Ashish Kumar Singh, Budheswar Dehury, Ajaya Kumar Rout, Vahab Ali, Ganesh Chandra Sahoo, Roshan Kamal Topno, Krishna Pandey, Vidya Nand Rabi Das, Sanjiva Bimal, Pradeep Das
Software Mentions: 3
Published: about 6 years ago

10.1016/j.cell.2021.07.013

The genomic history of the Middle East
Cited by: 22
Author(s): Mohamed A. Almarri, Marc Haber, Reem A. Lootah, Pille Hallast, Saeed Al Turki, Hilary C. Martin, Yali Xue, Chris Tyler‐Smith
Software Mentions: 3
Published: about 3 years ago

10.1093/molbev/msz191

Contemporary Demographic Reconstruction Methods Are Robust to Genome Assembly Quality: A Case Study in Tasmanian Devils
Cited by: 68
Author(s): Austin H. Patton, Mark J. Margres, Amanda R. Stahlke, Sarah A. Hendricks, Kevin Lewallen, Rodrigo Hamede, Manuel Ruiz‐Aravena, Oliver A. Ryder, Hamish McCallum, Menna Lloyd Jones, Paul A. Hohenlohe, Andrew Storfer
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-019-3120-y

RNA 3D structure prediction guided by independent folding of homologous sequences
Cited by: 18
Author(s): Marcin Magnus, Kalli Kappel, Rhiju Das, Janusz M. Bujnicki
Software Mentions: 3
Published: about 5 years ago

10.1093/molbev/msaa224

CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets
Cited by: 12
Author(s): Connor D Harris, Ellis L. Torrance, Kasie Raymann, Louis‐Marie Bobay
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2019.01843

Stable Redox-Cycling Nitroxide Tempol Has Antifungal and Immune-Modulatory Properties
Cited by: 4
Author(s): Ava Hosseinzadeh, Marinos Stylianou, José Pedro Lopes, Daniel Curvello de Mendonça Müller, André Häggman, Sandra Holmberg, Christian Grumaz, Anders Johansson, Kai Sohn, Christoph Dieterich, Constantin F. Urban
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0167524

IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels
Cited by: 1
Author(s): Kota Kasahara, Kengo Kinoshita
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.ppat.1009226

The coronavirus proofreading exoribonuclease mediates extensive viral recombination
Cited by: 173
Author(s): Jennifer Gribble, Laura J. Stevens, Marco Agostini, Jordan Anderson-Daniels, James D. Chappell, Xiaotao Lu, Andrea J. Pruijssers, Andrew Routh, Mark R. Denison
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-015-0458-7

ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering
Cited by: 12
Author(s): Bie Verbist, Lieven Clement, Joke Reumers, Kim Thys, A. Vapirev, Willem Talloen, Yves Wetzels, Joris Meys, Jeroen Aerssens, Luc Bijnens, Olivier Thas
Software Mentions: 3
Published: over 9 years ago

10.3390/vaccines9070797

Bioinformatics Prediction of SARS-CoV-2 Epitopes as Vaccine Candidates for the Colombian Population
Cited by: 4
Author(s): Diana Montes-Grajales, Jesús Olívero-Verbel
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-016-1345-6

SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification
Cited by: 18
Author(s): João Victor de Araújo Oliveira, Fabrizio Costa, Rolf Backofen, Peter F. Stadler, Maria Emília M. T. Walter, Jana Hertel
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13321-017-0226-y

Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data
Cited by: 190
Author(s): Alexios Koutsoukas, Keith J. Monaghan, Xiaoli Li, Jun Huan
Software Mentions: 3
Published: over 7 years ago

10.1186/s40168-021-01081-2

A probiotic has differential effects on allergic airway inflammation in A/J and C57BL/6 mice and is correlated with the gut microbiome
Cited by: 12
Author(s): Mateus B. Casaro, Andrew Maltez Thomas, Erasmo Garcia Mendes, Claudio Fukumori, Willian R. Ribeiro, Fernando A. Oliveira, Amanda R. Crisma, Gilson Masahiro Murata, Bruna Bizzarro, Anderson Sá-Nunes, João Carlos Setúbal, Márcia Pinto Alves Mayer, Flaviano S. Martins, Angélica T. Vieira, Ana Tada Fonseca Brasil Antiorio, Wothan Tavares-de-Lima, Niels Olsen Saraiva Câmara, Rui Curi, Emmanuel Dias-Neto, Caroline M. Ferreira
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1008961

The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion
Cited by: 8
Author(s): Stefan L. Oliver, Yi Xing, Dong-Hua Chen, Sook Young Roh, Grigore Pintilie, David Bushnell, Marvin Sommer, Edward Yang, Andrea Carfı́, Wah Chiu, Ann M. Arvin
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0139654

lncRScan-SVM: A Tool for Predicting Long Non-Coding RNAs Using Support Vector Machine
Cited by: 86
Author(s): Lei Sun, Hui Liu, Lin Zhang, Jia Meng
Software Mentions: 3
Published: about 9 years ago

10.1038/s41438-020-00380-3

Enrichment of beneficial cucumber rhizosphere microbes mediated by organic acid secretion
Cited by: 46
Author(s): Teng Wen, Jun Yuan, Xiaoming He, Yue Lin, Qiwei Huang, Qirong Shen
Software Mentions: 3
Published: about 4 years ago

10.1002/hbm.24603

Exploring the impact of analysis software on task fMRI results
Cited by: 92
Author(s): Alexander Bowring, Camille Maumet, Thomas E. Nichols
Software Mentions: 3
Published: over 5 years ago

10.1099/mgen.0.000085

Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology
Cited by: 27
Author(s): Kim Judge, Martin Hunt, Sandra Reuter, Alan S. Tracey, Michael A. Quail, Julian Parkhill, Sharon J. Peacock
Software Mentions: 3
Published: about 8 years ago

10.1093/gigascience/giz043

Ultra-deep, long-read nanopore sequencing of mock microbial community standards
Cited by: 199
Author(s): Samuel M. Nicholls, Joshua Quick, Siu Wa Tang, Nicholas J. Loman
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-016-1380-3

ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons
Cited by: 24
Author(s): Giovanni Scala, Ornella Affinito, Domenico Palumbo, Ermanno Florio, Antonella Monticelli, Gennaro Miele, Lorenzo Chiariotti, Sérgio Cocozza
Software Mentions: 3
Published: almost 8 years ago

10.3390/ani11092677

Genomic Evidence for Rare Hybridization and Large Demographic Changes in the Evolutionary Histories of Four North American Dove Species
Cited by: 8
Author(s): Flor María Ávila Hernández, J. Brown, Marissa Kaminski, Michael Harvey, Philip Lavretsky
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0220813

DeepAuC: Joint deep learning and auction for congestion-aware caching in Named Data Networking
Cited by: 2
Author(s): Anselme Ndikumana, Saeed Ullah, Do Hyeon Kim, Choong Seon Hong
Software Mentions: 3
Published: over 5 years ago

10.1016/j.mex.2019.09.013

Low-cost automatic temperature monitoring system with alerts for laboratory rearing units
Cited by: 3
Author(s): François Rebaudo, Romain Benoist
Software Mentions: 3
Published: almost 6 years ago

Projects: pypi: py

Papers Mentioning py 403