Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: biopython

https://packages.ecosyste.ms/registries/pypi.org/packages/biopython

Freely available tools for computational molecular biology.
58 versions
Latest release: almost 2 years ago
575 dependent packages
855,332 downloads last month

Papers Mentioning biopython 114

10.1371/journal.pgen.1009065
Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study
Cited by: 49
Author(s): Marco Galardini, Olivier Clermont, Agnès Baron, Bede P. Busby, Sara Dion, Sören Schubert, Pedro Beltrão, Erick Denamur
Software Mentions: 20
Published: about 4 years ago
10.1093/bioinformatics/bty149
NanoPack: visualizing and processing long-read sequencing data
Cited by: 1,423
Author(s): Wouter De Coster, Svenn D’Hert, Darrin T. Schultz, Marc Cruts, Christine Van Broeckhoven
Software Mentions: 18
Published: almost 7 years ago
10.1186/s13059-018-1563-5
CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis
Cited by: 27
Author(s): Vivien A.C. Schoonenberg, Mitchel A Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello, Daniel E. Bauer
Software Mentions: 12
Published: about 6 years ago
10.1186/s12859-018-2367-z
Biotite: a unifying open source computational biology framework in Python
Cited by: 54
Author(s): Patrick Kunzmann, Kay Hamacher
Software Mentions: 12
Published: about 6 years ago
10.1186/s12859-019-2706-8
svist4get: a simple visualization tool for genomic tracks from sequencing experiments
Cited by: 32
Author(s): Artyom A. Egorov, Ekaterina Sakharova, Aleksandra S. Anisimova, Sergey E. Dmitriev, Vadim N. Gladyshev, Ivan V. Kulakovskiy
Software Mentions: 11
Published: almost 6 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: over 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: over 3 years ago
10.1186/s12859-018-2287-y
miRge 2.0 for comprehensive analysis of microRNA sequencing data
Cited by: 54
Author(s): Yin Lu, Alexander S. Baras, Marc K. Halushka
Software Mentions: 9
Published: over 6 years ago
10.3389/fphys.2017.00354
Expression, Localization of SUMO-1, and Analyses of Potential SUMOylated Proteins in Bubalus bubalis Spermatozoa
Cited by: 4
Author(s): Rahim Dad Brohi, Li Wang, Najla Ben Hassine, Jiang Cao, Hira Sajjad Talpur, Di Wu, Chun–Jie Huang, Zia Ur Rehman, Dinesh Bhattarai, Li–Jun Huo
Software Mentions: 9
Published: over 7 years ago
10.7150/jgen.41196
crispRdesignR: A Versatile Guide RNA Design Package in R for CRISPR/Cas9 Applications
Cited by: 2
Author(s): Dylan Beeber, Frédéric J. J. Chain
Software Mentions: 9
Published: almost 5 years ago
10.1111/tpj.15190
Subgenome evolution in allotetraploid plants
Cited by: 19
Author(s): Matteo Schiavinato, Alexandrina Bodrug‐Schepers, Juliane C. Dohm, Heinz Himmelbauer
Software Mentions: 9
Published: almost 4 years ago
10.1371/journal.pcbi.1008605
Machine learning based CRISPR gRNA design for therapeutic exon skipping
Cited by: 5
Author(s): Wilson Louie, Max W. Shen, Zakir Tahiry, Sophia Zhang, Daniel Worstell, Christopher A. Cassa, Richard I. Sherwood, David K. Gifford
Software Mentions: 8
Published: almost 4 years ago
10.1186/s13072-021-00401-y
Evaluation of whole-genome DNA methylation sequencing library preparation protocols
Cited by: 18
Author(s): Jacob Morrison, Julie Koeman, Benjamin K. Johnson, Kelly K. Foy, Ian Beddows, Wanding Zhou, David Chesla, Larissa L. Rossell, Emily J. Siegwald, Marie Adams, Hui Shen
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pgen.1009324
Virus-derived variation in diverse human genomes
Cited by: 0
Author(s): Shohei Kojima, Anselmo Jiro Kamada, Nicholas F. Parrish
Software Mentions: 8
Published: over 3 years ago
10.7717/peerj.4925
Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data
Cited by: 166
Author(s): Jonathan M. Palmer, Michelle A. Jusino, Mark T. Banik, Daniel L. Lindner
Software Mentions: 8
Published: over 6 years ago
10.1186/s12864-017-4268-3
GHOST: global hepatitis outbreak and surveillance technology
Cited by: 32
Author(s): Atkinson G. Longmire, Seth Sims, Inna Rytsareva, David S. Campo, Pavel Skums, Zoya Dimitrova, Sumathi Ramachandran, Magdalena Medrzycki, Hong Thai, Lilia Ganova-Raeva, Yulin Lin, Lili Punkova, Amanda Sue, Massimo Mirabito, Silver Wang, Robin Tracy, Victor Bolet, Thom Sukalac, Chris Lynberg, Yury Khudyakov
Software Mentions: 7
Published: about 7 years ago
10.15252/msb.20198831
The impact of the genetic background on gene deletion phenotypes in <i>Saccharomyces cerevisiae</i>
Cited by: 40
Author(s): Marco Galardini, Bede P. Busby, Cristina Viéitez, Alistair S. Dunham, Athanasios Typas, Pedro Beltrão
Software Mentions: 7
Published: about 5 years ago
10.1371/journal.pone.0253411
PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences
Cited by: 12
Author(s): Bulat Faezov, Roland L. Dunbrack
Software Mentions: 7
Published: over 3 years ago
10.1371/journal.pone.0239381
Short k-mer abundance profiles yield robust machine learning features and accurate classifiers for RNA viruses
Cited by: 8
Author(s): Nafis Ul Alam, Umar Faruq Chowdhury
Software Mentions: 7
Published: over 4 years ago
10.12688/f1000research.14470.2
Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts
Cited by: 2
Author(s): Robert R. Butler, Pablo V. Gejman
Software Mentions: 7
Published: over 6 years ago
10.1186/s13059-018-1521-2
omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data
Cited by: 18
Author(s): Philipp Drewe-Boß, Hans-Hermann Wessels, Uwe Ohler
Software Mentions: 7
Published: about 6 years ago
10.1093/gigascience/gix129
Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags
Cited by: 15
Author(s): Xianfeng Chen, Stephen Johnson, Patricio Jeraldo, Junwen Wang, Nicholas Chia, Jean Pierre A. Kocher, Jun Chen
Software Mentions: 7
Published: about 7 years ago
10.1093/gigascience/giy023
The Scientific Filesystem
Cited by: 1
Author(s): Vanessa Sochat
Software Mentions: 7
Published: almost 7 years ago
10.1099/mgen.0.000211
PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level
Cited by: 35
Author(s): Guilhem Royer, Jean‐Winoc Decousser, Catherine Branger, Mathieu Dubois, Claudine Médigue, Erick Denamur, David Vallenet
Software Mentions: 6
Published: over 6 years ago
10.1371/journal.pone.0190279
pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment
Cited by: 12
Author(s): Sven Warris, N. Roshan N. Timal, Marcel Kempenaar, Arne M. Poortinga, Henri van de Geest, Ana Lucia Vărbănescu, Jan-Peter Nap
Software Mentions: 6
Published: almost 7 years ago
10.1186/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 3 years ago
10.1371/journal.pone.0239154
Assessing the low complexity of protein sequences via the low complexity triangle
Cited by: 4
Author(s): Pablo Mier, Miguel A. Andrade‐Navarro
Software Mentions: 6
Published: about 4 years ago
10.1371/journal.ppat.1009304
Distinct clonal lineages and within-host diversification shape invasive Staphylococcus epidermidis populations
Cited by: 39
Author(s): Anna Both, Jia-Bin Huang, Minyue Qi, Christian Lausmann, Samira Weißelberg, Henning Büttner, Susanne Lezius, Antonio Virgilio Failla, Coralie Martin, Marc Stegger, Thorsten Gehrke, Sharmin Baig, Mustafa Citak, Malik Alawi, Martin Aepfelbacher, Holger Rohde
Software Mentions: 6
Published: almost 4 years ago
10.1080/19490976.2020.1814120
Analysis of 16S rRNA genes reveals reduced Fusobacterial community diversity when translocating from saliva to GI sites
Cited by: 10
Author(s): Miles Richardson, Ji‐Chang Ren, Mara Roxana Rubinstein, Jamila A Taylor, Richard A. Friedman, Bo Shen, Yiping W. Han
Software Mentions: 6
Published: about 4 years ago
10.1186/s13059-018-1589-8
Enhancers in the Peril lincRNA locus regulate distant but not local genes
Cited by: 20
Author(s): Abigail F. Groff, A. Rasim Barutcu, Jordan P. Lewandowski, John L. Rinn
Software Mentions: 6
Published: about 6 years ago
10.1186/1471-2164-15-71
Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian
Cited by: 37
Author(s): Derek Stefanik, Tristan Lubinski, Brian R. Granger, Allyson L. Byrd, Adam M. Reitzel, Lukas DeFilippo, Allison Lorenc, John R. Finnerty
Software Mentions: 5
Published: almost 11 years ago
10.1186/1471-2164-15-966
A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants
Cited by: 29
Author(s): Johannes A. Hofberger, Beifei Zhou, Haibao Tang, Jonathan D. G. Jones, M. Eric Schranz
Software Mentions: 5
Published: about 10 years ago
10.7717/peerj.8356
Conserved novel ORFs in the mitochondrial genome of the ctenophore <i>Beroe forskalii</i>
Cited by: 14
Author(s): Darrin T. Schultz, Jordan M. Eizenga, Russell Corbett-Detig, Warren R. Francis, Lynne M. Christianson, Steven H. D. Haddock
Software Mentions: 5
Published: almost 5 years ago
10.1186/s12859-020-03730-z
SAPPHIRE: a neural network based classifier for σ70 promoter prediction in Pseudomonas
Cited by: 29
Author(s): Lucas Coppens, Rob Lavigne
Software Mentions: 5
Published: over 4 years ago
10.7717/peerj.3391
Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates
Cited by: 15
Author(s): Dariya K. Sydykova, Claus O. Wilke
Software Mentions: 5
Published: over 7 years ago
10.3390/plants9121794
Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development
Cited by: 15
Author(s): Ilya Kirov, Maxim Dudnikov, Pavel Merkulov, Andrey Shingaliev, Murad Omarov, Elizaveta Kolganova, Alexandra Sigaeva, Г. И. Карлов, A. A. Soloviev
Software Mentions: 5
Published: about 4 years ago
10.1186/1471-2164-15-141
Transcriptome sequencing of Atlantic salmon (Salmo salar L.) notochord prior to development of the vertebrae provides clues to regulation of positional fate, chordoblast lineage and mineralisation
Cited by: 40
Author(s): Wang Shou, Tomasz Furmanek, Harald Kryvi, Christel Krossøy, Geir K. Totland, Sindre Grotmol, Anna Wargelius
Software Mentions: 5
Published: almost 11 years ago
10.1093/gigascience/giaa008
GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms
Cited by: 77
Author(s): Patrick Browne, Tue Kjærgaard Nielsen, Witold Kot, Anni Aggerholm, M. Thomas P. Gilbert, Lara Puetz, Morten Rasmussen, Athanasios Zervas, Lars Hestbjerg Hansen
Software Mentions: 5
Published: almost 5 years ago
10.1080/23802359.2021.1966334
Aln2tbl: building a mitochondrial features table from a assembly alignment in fasta format
Cited by: 0
Author(s): Joan Pons, Juan José Ensenyat, Pere Rosselló Bover, M. Serra, Francesco Nardi
Software Mentions: 5
Published: over 3 years ago
10.1002/1878-0261.12138
<scp>APE</scp>1/Ref‐1 knockdown in pancreatic ductal adenocarcinoma – characterizing gene expression changes and identifying novel pathways using single‐cell <scp>RNA</scp> sequencing
Cited by: 26
Author(s): Fenil Shah, Emery Goossens, Nadia M. Atallah, Michelle Grimard, Mark R. Kelley, Melissa L. Fishel
Software Mentions: 5
Published: about 7 years ago
10.1093/bib/bbab055
RNA2HLA: HLA-based quality control of RNA-seq datasets
Cited by: 9
Author(s): Irina Chelysheva, Andrew J. Pollard, Daniel O’Connor
Software Mentions: 5
Published: almost 4 years ago
10.1038/s41598-020-66178-4
Comparison of lung microbiota between antineutrophil cytoplasmic antibody-associated vasculitis and sarcoidosis
Cited by: 5
Author(s): Shoichi Fukui, Shimpei Morimoto, Kunihiro Ichinose, Shota Nakashima, Hiroshi Ishimoto, Atsuko Hara, Tomoyuki Kakugawa, Noriho Sakamoto, Yoshika Tsuji, Toshiyuki Aramaki, Tomohiro Koga, Shin‐ya Kawashiri, Naoki Iwamoto, Mami Tamai, Hideki Nakamura, Tomoki Origuchi, Yukitaka Ueki, Shino Suzuki, Hiroshi Mukae, Atsushi Kawakami
Software Mentions: 5
Published: over 4 years ago
10.1186/s40168-019-0722-6
Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease
Cited by: 28
Author(s): Samuel S. Minot, Amy Willis
Software Mentions: 4
Published: over 5 years ago
10.3390/jof2010006
Proteomic Analysis of Pathogenic Fungi Reveals Highly Expressed Conserved Cell Wall Proteins
Cited by: 41
Author(s): Jackson Champer, James I. Ito, Karl V. Clemons, David A. Stevens, Markus Kalkum
Software Mentions: 4
Published: almost 9 years ago
10.1080/19490976.2021.1927635
Engraftment of strictly anaerobic oxygen-sensitive bacteria in irritable bowel syndrome patients following fecal microbiota transplantation does not improve symptoms
Cited by: 8
Author(s): Patrick Browne, Frederik Cold, Andreas Munk Petersen, Sofie Ingdam Halkjær, Alice Højer Christensen, Stig Günther, Lars Hestbjerg Hansen
Software Mentions: 4
Published: almost 4 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: over 4 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: almost 11 years ago
10.1128/mBio.01280-18
Evolution of the U.S. Biological Select Agent Rathayibacter toxicus
Cited by: 8
Author(s): Edward W. Davis, Javier F. Tabima, Alexandra J. Weisberg, Lucas Dantas Lopes, Michele S. Wiseman, Michael S. Wiseman, Tal Pupko, Michael S. Belcher, A. Sechler, Matt A. Tancos, Brenda K. Schroeder, Timothy Murray, Douglas G. Luster, William L. Schneider, Elizabeth E. Rogers, Fernando Dini Andreote, Niklaus J. Grünwald, M. L. Putnam, Jeff H. Chang
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pcbi.1006844
A new clustering and nomenclature for beta turns derived from high-resolution protein structures
Cited by: 50
Author(s): Maxim V. Shapovalov, Slobodan Vučetić, Roland L. Dunbrack
Software Mentions: 4
Published: almost 6 years ago
10.3390/ijms20205062
DockNmine, a Web Portal to Assemble and Analyse Virtual and Experimental Interaction Data
Cited by: 6
Author(s): Ennys Gheyouche, Romain Launay, Jean Lethiec, Antoine Labeeuw, Caroline Roze, Alan Amossé, Stéphane Teletchea
Software Mentions: 4
Published: about 5 years ago
10.1186/s12859-019-2864-8
Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity
Cited by: 18
Author(s): Neerja Thakkar, Chris Bailey‐Kellogg
Software Mentions: 4
Published: over 5 years ago
10.1128/mSystems.00731-19
Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries
Cited by: 113
Author(s): Matthew R. Olm, Alexander Crits-Christoph, Spencer Diamond, Adi Lavy, Paula B. Matheus Carnevali, Jillian F. Banfield
Software Mentions: 4
Published: almost 5 years ago
10.1016/j.xpro.2021.100505
Computational generation of proteins with predetermined three-dimensional shapes using ProteinSolver
Cited by: 6
Author(s): Alexey Strokach, David Becerra, Carles Corbi‐Verge, Albert Perez-Riba, Philip M. Kim
Software Mentions: 3
Published: over 3 years ago
10.1098/rspb.2016.2756
Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
Cited by: 46
Author(s): Ludovic Dutoit, Nagarjun Vijay, Carina F. Mugal, Christen M. Bossu, Reto Burri, Jochen B. W. Wolf, Hans Ellegren
Software Mentions: 3
Published: almost 8 years ago
10.7554/eLife.47301
Comment on 'Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi'
Cited by: 6
Author(s): Ben Auxier, Anna Bazzicalupo
Software Mentions: 3
Published: about 5 years ago
10.1371/journal.ppat.1005225
Non-Human Primates Harbor Diverse Mammalian and Avian Astroviruses Including Those Associated with Human Infections
Cited by: 63
Author(s): Erik A. Karlsson, Christopher T Small, Pamela Freiden, MM Feeroz, F. A. Matsen, San Sorn, Md. Rakib Hasan, David Wang, Lisa Jones‐Engel, Stacey Schultz‐Cherry
Software Mentions: 3
Published: about 9 years ago
10.1186/1471-2164-13-726
Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data
Cited by: 13
Author(s): Melissa M L Wong, Charles H. Cannon, R Wickneswari V Ratnam
Software Mentions: 3
Published: about 12 years ago
10.1371/journal.ppat.1004795
The Aspartate-Less Receiver (ALR) Domains: Distribution, Structure and Function
Cited by: 25
Author(s): Andrew J. Maule, David P. Wright, Joshua Weiner, Lu Han, Francis C. Peterson, Brian F. Volkman, N.R. Silvaggi, Andrew T. Ulijasz
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pcbi.1005775
Estimating time of HIV-1 infection from next-generation sequence diversity
Cited by: 44
Author(s): Vadim Puller, Richard A. Neher, Jan Albert
Software Mentions: 3
Published: about 7 years ago
10.1186/s12864-018-4701-2
Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes
Cited by: 22
Author(s): Daniel R. Bogema, Melinda L. Micallef, Mengmeng Liu, Matthew P. Padula, Steven P. Djordjevic, Aaron E. Darling, Cheryl Jenkins
Software Mentions: 3
Published: over 6 years ago
10.1186/s12859-019-3329-9
Automatic construction of metabolic models with enzyme constraints
Cited by: 56
Author(s): Pavlos Stephanos Bekiaris, Steffen Klamt
Software Mentions: 3
Published: almost 5 years ago
10.1371/journal.pone.0017429
NAViGaTing the Micronome – Using Multiple MicroRNA Prediction Databases to Identify Signalling Pathway-Associated MicroRNAs
Cited by: 194
Author(s): Elize A. Shirdel, Wing Xie, Tak W. Mak, Igor Jurišica
Software Mentions: 3
Published: almost 14 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/s12014-018-9188-y
Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization
Cited by: 37
Author(s): Melanie Christine Föll, Matthias Fahrner, Victor Oginga Oria, Markus Kühs, Martin L. Biniossek, Martin Werner, Peter Bronsert, Oliver Schilling
Software Mentions: 3
Published: almost 7 years ago
10.3897/CompCytogen.v12i4.31015
Pilot satellitome analysis of the model plant, Physcomitrella patens, revealed a transcribed and high-copy IGS related tandem repeat
Cited by: 20
Author(s): Ilya Kirov, Marina Gilyok, Andrey Knyazev, Igor Fesenko
Software Mentions: 3
Published: about 6 years ago
10.1038/s41598-019-53032-5
The β-oxidation pathway is downregulated during diapause termination in Calanus copepods
Cited by: 12
Author(s): Elise Skottene, Ann M. Tarrant, Anders J. Olsen, Dag Altin, Mari‐Ann Östensen, Bjørn Henrik Hansen, Marvin Choquet, Bjørn Munro Jenssen, Rolf Erik Olsen
Software Mentions: 3
Published: about 5 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
10.1038/s41598-018-36561-3
Uncovering secondary metabolite evolution and biosynthesis using gene cluster networks and genetic dereplication
Cited by: 30
Author(s): Sebastian Theobald, Tammi Camilla Vesth, Jakob Kræmmer Haar Rendsvig, Kristian Fog Nielsen, Robert Riley, Lucas M. Abreu, Asaf Salamov, Jens Christian Frisvad, Thomas Ostenfeld Larsen, Mikael Rørdam Andersen, Jakob Blæsbjerg Hoof
Software Mentions: 3
Published: about 6 years ago
10.1016/j.omtm.2021.03.024
CRISPAltRations: A validated cloud-based approach for interrogation of double-strand break repair mediated by CRISPR genome editing
Cited by: 17
Author(s): Gavin Kurgan, Rolf Turk, Heng Li, Nathan James Roberts, Garrett R. Rettig, Ashley M. Jacobi, Lauren Tso, Morgan Sturgeon, Massimo Mertens, Roel Noten, Kurt Florus, Mark A. Behlke, Yu Wang, Matthew McNeill
Software Mentions: 3
Published: over 3 years ago
10.3389/fgene.2017.00165
New Tools in Orthology Analysis: A Brief Review of Promising Perspectives
Cited by: 55
Author(s): Bruno Thiago de Lima Nichio, Jeroniza Nunes Marchaukoski, Roberto Tadeu Raittz
Software Mentions: 3
Published: about 7 years ago
10.3389/fpls.2019.00345
Cercis: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family
Cited by: 23
Author(s): Jacob S. Stai, Akhilesh Yadav, Carole Sinou, Anne Bruneau, Jeff J. Doyle, David Fernández-Baca, Steven B. Cannon
Software Mentions: 3
Published: over 5 years ago
10.7717/peerj.6995
ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data
Cited by: 72
Author(s): Andrew Low, Adam Koziol, Paul Manninger, Burton W. Blais, Catherine D. Carrillo
Software Mentions: 3
Published: over 5 years ago
10.1128/mSphere.00140-18
The <i>Lactobacillus</i> Bile Salt Hydrolase Repertoire Reveals Niche-Specific Adaptation
Cited by: 67
Author(s): Sarah O’Flaherty, Alexandra B. Crawley, Casey M. Theriot, Rodolphe Barrangou
Software Mentions: 2
Published: over 6 years ago
10.3390/v13091800
Variability in Codon Usage in Coronaviruses Is Mainly Driven by Mutational Bias and Selective Constraints on CpG Dinucleotide
Cited by: 6
Author(s): Josquin Daron, Ignacio G. Bravo
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0211043
Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE)
Cited by: 5
Author(s): Stéphane Teletchea, Hubert Santuz, Sylvain Léonard, Catherine Etchebest
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0025376
Putting into Practice Domain-Linear Motif Interaction Predictions for Exploration of Protein Networks
Cited by: 37
Author(s): Katja Luck, Sadek Fournane, Bruno Kieffer, Murielle Masson, Yves Nominé, Gilles Travé
Software Mentions: 2
Published: about 13 years ago
10.1016/j.csbj.2021.08.012
Computationally grafting an IgE epitope onto a scaffold: Implications for a pan anti-allergy vaccine design
Cited by: 1
Author(s): Sari Sabban
Software Mentions: 2
Published: almost 4 years ago
10.3389/fcimb.2018.00249
Incompatible Translation Drives a Convergent Evolution and Viral Attenuation During the Development of Live Attenuated Vaccine
Cited by: 12
Author(s): Xumin Ou, Mingshu Wang, Sai Mao, Jingyu Cao, Anchun Cheng, Dekang Zhu, Shun Chen, Renyong Jia, Mafeng Liu, Qiao Yang, Ying Wu, Xinxin Zhao, Shaqiu Zhang, Yunya Liu, Yanling Yu, Ling Zhang, Xiaoyue Chen, Maikel P. Peppelenbosch
Software Mentions: 2
Published: over 6 years ago
10.1186/1471-2105-15-292
Native structure-based modeling and simulation of biomolecular systems per mouse click
Cited by: 6
Author(s): Benjamin Lutz, Claude Sinner, S. Bozic, Ivan Kondov, Alexander Schug
Software Mentions: 2
Published: over 10 years ago
10.3389/fmicb.2017.01852
Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment
Cited by: 59
Author(s): Heidi Gumpert, Jessica Z. Kubicek-Sutherland, Andreas Porse, Nahid Karami, Christian Munck, Marius Linkevičius, Ingegerd Adlerberth, Agnes E. Wold, Dan I. Andersson, Morten Otto Alexander Sommer
Software Mentions: 2
Published: over 7 years ago
10.3389/fmicb.2013.00052
Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l
Cited by: 31
Author(s): Esther Singer, John F. Heidelberg, A. S. Dhillon, Katrina J. Edwards
Software Mentions: 2
Published: almost 12 years ago
10.3389/fpls.2018.01438
Respective Contributions of URT1 and HESO1 to the Uridylation of 5′ Fragments Produced From RISC-Cleaved mRNAs
Cited by: 16
Author(s): Hélène Zuber, Hélène Scheer, Anne-Caroline Joly, Dominique Gagliardi
Software Mentions: 2
Published: about 6 years ago
10.1093/g3journal/jkab250
orthofisher: a broadly applicable tool for automated gene identification and retrieval
Cited by: 10
Author(s): Jacob L. Steenwyk, Antonis Rokas
Software Mentions: 2
Published: over 3 years ago
10.3390/genes10120978
Artificial Intelligence (AI) in Rare Diseases: Is the Future Brighter?
Cited by: 58
Author(s): Sandra Brasil, Carlota Pascoal, Rita Francisco, Vanessa Ferreira, Paula A. Videira, Gonçalo Valadão
Software Mentions: 2
Published: about 5 years ago
10.1186/s12859-018-2376-y
MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes
Cited by: 87
Author(s): Juan Manuel Crescente, Diego Zavallo, Marcelo Helguera, Leonardo Sebastián Vanzetti
Software Mentions: 2
Published: about 6 years ago
10.1186/s13059-019-1909-7
Paragraph: a graph-based structural variant genotyper for short-read sequence data
Cited by: 92
Author(s): Sai Chen, Peter Krusche, Egor Dolzhenko, Rachel M. Sherman, Roman Petrovski, Felix Schlesinger, Melanie Kirsche, David Bentley, Michael C. Schatz, Fritz J. Sedlazeck, Michael A. Eberle
Software Mentions: 2
Published: about 5 years ago
10.1093/gbe/evaa127
Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence
Cited by: 12
Author(s): Karina Zile, Christophe Dessimoz, Yannick Wurm, Joanna Masel
Software Mentions: 2
Published: over 4 years ago
10.1093/gigascience/giaa161
Multiple origins of a frameshift insertion in a mitochondrial gene in birds and turtles
Cited by: 3
Author(s): Sergio Andreu‐Sánchez, Wanjun Chen, Josefin Stiller, Guojie Zhang
Software Mentions: 2
Published: almost 4 years ago
10.21203/rs.3.rs-80345/v1
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes
Cited by: 6
Author(s): Irwin Jungreis, Rachel Sealfon, M Kellis
Software Mentions: 2
Published: about 4 years ago
10.1038/s41598-021-97965-2
Biomolecular simulation based machine learning models accurately predict sites of tolerability to the unnatural amino acid acridonylalanine
Cited by: 4
Author(s): Sam Giannakoulias, Sumant R. Shringari, John J. Ferrie, E. James Petersson
Software Mentions: 2
Published: over 3 years ago
10.1093/synbio/ysaa030
Synthesis of libraries and multi-site mutagenesis using a PCR-derived, dU-containing template
Cited by: 0
Author(s): Gretchen Meinke, Nahide Dalda, Benjamin Brigham, Andrew Bohm
Software Mentions: 2
Published: almost 4 years ago
10.1128/mBio.00010-20
A Simple, Cost-Effective, and Robust Method for rRNA Depletion in RNA-Sequencing Studies
Cited by: 66
Author(s): Peter H. Culviner, Chantal K. Guegler, Michael T. Laub
Software Mentions: 2
Published: over 4 years ago
10.1186/s40168-020-00889-8
Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community
Cited by: 30
Author(s): Pratibha Panwar, Michelle A. Allen, Timothy J. Williams, Alyce M. Hancock, Sarah Brazendale, James Bevington, Simon Roux, David Páez-Espino, Stephen Nayfach, Maureen Berg, Frederik Schulz, I-Min A. Chen, Marcel Huntemann, Nicole Shapiro, Nikos C. Kyrpides, Tanja Woyke, Emiley A. Eloe‐Fadrosh, Ricardo Cavicchioli
Software Mentions: 2
Published: over 4 years ago
10.1038/s41396-020-0726-z
Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation
Cited by: 37
Author(s): Jorge Moura de Sousa, Amandine Nucci, Matthieu Haudiquet, Eduardo P. C. Rocha, Olaya Rendueles
Software Mentions: 2
Published: over 4 years ago
10.1186/1753-6561-8-S2-S7
Seeing the results of a mutation with a vertex weighted hierarchical graph
Cited by: 0
Author(s): Debra J. Knisley, Jeff Knisley
Software Mentions: 2
Published: over 10 years ago
10.1093/bib/bbaa206
Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes
Cited by: 19
Author(s): Eva S. Deutekom, Berend Snel, Teunis J. P. van Dam
Software Mentions: 2
Published: over 4 years ago
10.1002/cpmc.130
Programmable Gene Knockdown in Diverse Bacteria Using Mobile‐CRISPRi
Cited by: 4
Author(s): Amy B. Banta, Ryan D. Ward, Jennifer S. Tran, Emily E. Bacon, Joseph E. Peters
Software Mentions: 1
Published: about 4 years ago
10.1038/s41598-020-80814-z
Prediction of lithium response using genomic data
Cited by: 10
Author(s): William L. Stone, Abraham Nunes, Kazufumi Akiyama, Nirmala Akula, Raffaella Ardau, Jean Michel Aubry, Lena Backlund, Michael Bauer, Frank Bellivier, Pablo Cervantes, Hsi‐Chung Chen, Caterina Chillotti, Cristiana Cruceanu, Alexandre Dayer, Franziska Degenhardt, Maria Del Zompo, Andreas J. Forstner, Mark A. Frye, Janice M. Fullerton, Maria Grigoroiu-Serbǎnescu, Paul Grof, Ryota Hashimoto, Liping Hou, Esther Jiménez, Takeshi Kato, John R. Kelsoe, Sarah Kittel‐Schneider, Po-Hsiu Kuo, Ichiro Kusumi, Catharina Lavebratt, Mirko Manchia, Lina Martinsson, Manuel Mattheisen, Francis J. McMahon, Vincent Millischer, Philip B. Mitchell, Markus M. Nöthen, Claire O’Donovan, Norio Ozaki, Claudia Pisanu, Andreas Reif, Marcella Rietschel, Guy A. Rouleau, Janusz Rybakowski, Martin Schalling, Peter R. Schofield, Thomas G. Schulze, Giovanni Severino, Alessio Squassina, Julia Veeh, Eduard Vieta, Thomas Trappenberg, Martin Alda
Software Mentions: 1
Published: almost 4 years ago
10.1186/s12864-016-2616-3
Transcriptome and metabolome analysis in shoot and root of Valeriana fauriei
Cited by: 16
Author(s): Yun Ji Park, Xiaohua Li, Seung Jae Noh, Jae Kwang Kim, Soon Sung Lim, Nam Il Park, Soonok Kim, Yeon Bok Kim, Young Ock Kim, Sang Won Lee, Mariadhas Valan Arasu, Naif Abdullah Al‐Dhabi, Sang Un Park
Software Mentions: 1
Published: over 8 years ago
10.1093/ve/veaa044
Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains
Cited by: 5
Author(s): Charles Masembe, My V. T. Phan, David L. Robertson, Matthew Cotten
Software Mentions: 1
Published: over 4 years ago