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: scikit-allel

https://packages.ecosyste.ms/registries/pypi.org/packages/scikit-allel

A Python package for exploring and analysing genetic variation data.
62 versions
Latest release: about 1 year ago
13 dependent packages
12,406 downloads last month

Papers Mentioning scikit-allel 23

10.7554/eLife.60474

The effect of hybridization on transposable element accumulation in an undomesticated fungal species
Cited by: 26
Author(s): Mathieu Hénault, Souhir Marsit, Guillaume Charron, Christian R. Landry
Software Mentions: 12
Published: about 4 years ago

10.1093/molbev/msaa128

Evolution of the Insecticide Target Rdl in African Anopheles Is Driven by Interspecific and Interkaryotypic Introgression
Cited by: 25
Author(s): Xavier Grau‐Bové, Sean Tomlinson, Andrias O. O’Reilly, Nicholas J. Harding, Alistair Miles, Dominic Kwiatkowski, Martin Donnelly, David Weetman
Software Mentions: 12
Published: over 4 years ago

10.1371/journal.pgen.1009253

Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus
Cited by: 22
Author(s): Xavier Grau‐Bové, Eric R. Lucas, Dimitra Pipini, Emily J. Rippon, Arjèn Emiel van 't Hof, Constant Edi, Samuel Dadzie, Alexander Egyir-Yawson, John Essandoh, Joseph Chabi, Luc Djogbénou, Nicholas J. Harding, Alistair Miles, Dominic P. Kwiatkowski, Martin J. Donnelly, David Weetman
Software Mentions: 8
Published: almost 4 years ago

10.1093/g3journal/jkaa036

Visualizing population structure with variational autoencoders
Cited by: 44
Author(s): C. J. Battey, Gabrielle C. Coffing, Andrew D. Kern
Software Mentions: 7
Published: almost 4 years ago

10.1093/molbev/msz154

Ancient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome Parasites
Cited by: 51
Author(s): Roy N. Platt, Marina McDew-White, Winka Le Clec’h, Frédéric D. Chevalier, Fiona Allan, Aidan M. Emery, Amadou Garba, Amina Amadou Hamidou, M. Shaali, Joanne P. Webster, David Rollinson, Bonnie L. Webster, Timothy J. Anderson
Software Mentions: 7
Published: over 5 years ago

10.1016/j.xplc.2020.100105

Maintenance of Species Differences in Closely Related Tetraploid Parasitic Euphrasia (Orobanchaceae) on an Isolated Island
Cited by: 20
Author(s): Hannes Becher, Brown Mr, Gavin Powell, Chris Metherell, Nick Riddiford, Alex D. Twyford
Software Mentions: 4
Published: about 4 years ago

10.1093/molbev/msaa259

Discovery of Ongoing Selective Sweeps within<i>Anopheles</i>Mosquito Populations Using Deep Learning
Cited by: 22
Author(s): Alexander T. Xue, Daniel R. Schrider, Andrew D. Kern, Alessandra della Torre, Andrew D. Kern, Beniamino Caputo, Bilali Kabula, Bradley J. White, Charles Godfray, Constant Edi, Craig S. Wilding, Dan Neafsey, Daniel R. Schrider, David J. Conway, David Weetman, Diégo Ayala, Dominic Kwiatkowski, Igor V. Sharakhov, Janet Midega, Jianchu Xu, João Pinto, John Essandoh, Johnson Matowo, Ken Vernick, Luc Djogbénou, Mamadou B. Coulibaly, Mara Lawniczak, Martin Donnelly, Matthew W. Hahn, Michaël C. Fontaine, Michelle M. Riehle, Nora J. Besansky, Omar E. Cornejo, Robert S. McCann, Sam O’Loughlin, Vincent Robert, Alexander T. Xue, Alistair Miles, Chris S. Clarkson, C. J. Battey, Cody Champion, Frédéric Labbé, Giordano Bottà, Jeffrey R. Adrion, Joel T. Nelson, Nick Harding, Thomas J. Wang, Scott T. Small, Seth Redmond, Tiago Antão
Software Mentions: 4
Published: about 4 years ago

10.3390/insects12020097

Anopheles gambiae Genome Conservation as a Resource for Rational Gene Drive Target Site Selection
Cited by: 8
Author(s): Nace Kranjc, Andrea Crisanti, Tony Nolan, Federica Bernardini
Software Mentions: 4
Published: almost 4 years ago

10.1534/genetics.120.303253

Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes
Cited by: 38
Author(s): Peter L. Ralph, Kevin R. Thornton, Jerome Kelleher
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pgen.1007279

Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens
Cited by: 74
Author(s): Lyndal Henden, Stuart Lee, Ivo Müeller, Alyssa E. Barry, Melanie Bahlo
Software Mentions: 3
Published: over 6 years ago

10.1038/s41396-020-0655-x

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow
Cited by: 38
Author(s): Alexander Crits-Christoph, Matthew R. Olm, Spencer Diamond, Keith Bouma‐Gregson, Jillian F. Banfield
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.54507

Predicting geographic location from genetic variation with deep neural networks
Cited by: 57
Author(s): C. J. Battey, Peter L. Ralph, Andrew D. Kern
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pbio.3000391

Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
Cited by: 97
Author(s): Sean Stankowski, Madeline A. Chase, Allison M. Fuiten, Murillo F. Rodrigues, Peter L. Ralph, Matthew A. Streisfeld
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2020.00781

MicroHapDB: A Portable and Extensible Database of All Published Microhaplotype Marker and Frequency Data
Cited by: 11
Author(s): Daniel Standage, Rebecca Mitchell
Software Mentions: 2
Published: over 4 years ago

10.3389/fpls.2020.00701

BRIDGE – A Visual Analytics Web Tool for Barley Genebank Genomics
Cited by: 27
Author(s): Patrick König, Sebastian Beier, Martín Basterrechea, Danuta Schüler, Daniel Arend, Martin Mascher, Nils Stein, Uwe Scholz, Matthias Lange
Software Mentions: 2
Published: over 4 years ago

10.3390/insects11100693

High-Throughput Genotyping of Common Chromosomal Inversions in the Afrotropical Malaria Mosquito Anopheles Funestus
Cited by: 7
Author(s): Martin Lukindu, R. Rebecca Love, Moussa W. Guelbeogo, Scott T. Small, Melissa Stephens, Nathan R. Campbell, N’Falé Sagnon, Carlo Costantini, Nora J. Besansky
Software Mentions: 2
Published: about 4 years ago

10.1038/s42003-019-0717-7

Transcontinental dispersal of Anopheles gambiae occurred from West African origin via serial founder events
Cited by: 11
Author(s): Hanno Schmidt, Lee Y, Travis C. Collier, Mark J. Hanemaaijer, Oscar D. Kirstein, A. Ouledi, Mbanga Muleba, Douglas E. Norris, Montgomery Slatkin, Anthony J. Cornel, Gregory C. Lanzaro
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12936-021-03757-4

Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii
Cited by: 4
Author(s): Martin G. Wagah, Petra Korlević, Christopher S. Clarkson, Alistair Miles, Mara K. N. Lawniczak, Alex Makunin
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1009095

Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe)
Cited by: 50
Author(s): Thomas C. Nelson, Angela Stathos, Daniel D. Vanderpool, Findley R. Finseth, Yao‐Wu Yuan, Lila Fishman
Software Mentions: 1
Published: over 3 years ago

10.1038/s42003-021-02168-0

The origin of island populations of the African malaria mosquito, Anopheles coluzzii
Cited by: 6
Author(s): Melina Campos, Mark J. Hanemaaijer, Hans Gripkey, Travis C. Collier, Lee Y, Anthony J. Cornel, João Pinto, Diégo Ayala, Herodes Rompão, Gregory C. Lanzaro
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-019-5586-4

Genome-wide divergence among invasive populations of Aedes aegypti in California
Cited by: 41
Author(s): Lee Y, Hanno Schmidt, Travis C. Collier, William R. Conner, Mark J. Hanemaaijer, Montgomery Slatkin, John M. Marshall, Joanna C. Chiu, Chelsea T. Smartt, Gregory C. Lanzaro, F. S. Mulligan, Anthony J. Cornel
Software Mentions: 1
Published: over 5 years ago

10.12688/f1000research.13807.2

Mitochondrial genomes of Anopheles arabiensis, An. gambiae and An. coluzzii show no clear species division
Cited by: 8
Author(s): Mark J. Hanemaaijer, Parker D. Houston, Travis C. Collier, L. C. Norris, Abdrahamane Fofana, Gregory C. Lanzaro, Anthony J. Cornel, Lee Y
Software Mentions: 1
Published: over 5 years ago

10.1093/g3journal/jkab086

Ultra-conserved sequences in the genomes of highly diverse Anopheles mosquitoes, with implications for malaria vector control
Cited by: 2
Author(s): Samantha OʼLoughlin, Annie J Forster, Silke Fuchs, Tania Dottorini, Tony Nolan, Andrea Crisanti, Austin Burt
Software Mentions: 1
Published: over 3 years ago