pypi: BESST | Projects | Ecosyste.ms: Papers

10.1007/s10126-021-10033-8

Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions
Cited by: 5
Author(s): Magnus Alm Rosenblad, Anna Abramova, Ulrika Lind, Pall I. Olason, Stefania Giacomello, Björn Nystedt, Anders Blomberg
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-020-06784-8

The nuclear and mitochondrial genomes of Frieseomelitta varia – a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste
Cited by: 13
Author(s): Flávia Cristina de Paula Freitas, A. P. Lourenço, Francis Morais Franco Nunes, Alexandre Rossi Paschoal, Fabiano Carlos Pinto de Abreu, Fábio O. Barbin, Luana Bataglia, Carlos Antônio Mendes Cardoso-Júnior, Mário Sérgio Cervoni, Saura R. Silva, Fernanda Dalarmi, Marco Antônio Del Lama, Thiago S. Depintor, Kátia Maria Ferreira, Paula Salles Gória, Michael C. Jaskot, Denyse Cavalcante Lago, Danielle Luna˗Lucena, Lívia Maria Rosatto Moda, Leonardo Penteado Nascimento, Matheus Pedrino, Franciene Rabiço Oliveira, Fernanda C. Sanches, Douglas Elias Santos, Carolina G. Santos, Joseana Vieira, Angel Roberto Barchuk, Klaus Hartfelder, Zilá Luz Paulino Simões, M. M. G. Bitondi, Daniel Guariz Pinheiro
Software Mentions: 5
Published: over 4 years ago

10.1038/s42003-020-01382-6

Adaptation by copy number variation increases insecticide resistance in the fall armyworm
Cited by: 40
Author(s): Sylvie Gimenez, Heba Abdelgaffar, Gaëlle Le Goff, Frédérique Hilliou, Carlos A. Blanco, Sabine Hänniger, Anthony Bretaudeau, Fabrice Legeai, Nicolas Nègre, Juan Luís Jurat-Fuentes, Emmanuelle d’Alençon, Kiwoong Nam
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-018-4750-6

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen
Cited by: 124
Author(s): Lamprinos Frantzeskakis, Barbara Kracher, Stefan Kusch, Makoto Yoshikawa-Maekawa, Saskia Bauer, Carsten Pedersen, Pietro D. Spanu, Takaki Maekawa, Paul Schulze‐Lefert, Ralph Panstruga
Software Mentions: 5
Published: over 6 years ago

10.1093/dnares/dsz002

A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants
Cited by: 32
Author(s): Asuka Arimoto, Koki Nishitsuji, Yoshimi Higa, Nana Arakaki, Kanako Hisata, Chuya Shinzato, Noriyuki Satoh, Eiichi Shoguchi
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-019-5752-8

New insights from Opisthorchis felineus genome: update on genomics of the epidemiologically important liver flukes
Cited by: 25
Author(s): Nikita I. Ershov, В. А. Мордвинов, Egor Prokhortchouk, Maria Y. Pakharukova, Konstantin Gunbin, Kirill Ustyantsev, Mikhail A. Genaev, А. Г. Блинов, Alexander Mazur, Eugenia Boulygina, Svetlana Tsygankova, Ekaterina Khrameeva, Nikolay Chekanov, Guangyi Fan, An Xiao, He Zhang, Xun Xu, Huanming Yang, Victor Solovyev, Simon Ming‐Yuen Lee, Xin Liu, D. A. Afonnikov, K. G. Skryabin
Software Mentions: 4
Published: over 5 years ago

10.1186/s12862-020-01715-3

Positive selection alone is sufficient for whole genome differentiation at the early stage of speciation process in the fall armyworm
Cited by: 17
Author(s): Kiwoong Nam, Sandra Nhim, Stéphanie Robin, Anthony Bretaudeau, Nicolas Nègre, Emmanuelle d’Alençon
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-016-0969-x

MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data
Cited by: 11
Author(s): Mohammed‐Amin Madoui, Carole Dossat, Léo d'Agata, Jan van Oeveren, Edwin van der Vossen, Jean‐Marc Aury
Software Mentions: 4
Published: over 8 years ago

10.1128/mSystems.00038-17

Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions
Cited by: 23
Author(s): Valerie Hubalek, Moritz Buck, BoonFei Tan, Julia M. Foght, Annelie Wendeberg, David Berry, Stefan Bertilsson, Alexander Eiler
Software Mentions: 3
Published: about 7 years ago

10.1093/gigascience/giz111

Genomic evidence of neo-sex chromosomes in the eastern yellow robin
Cited by: 32
Author(s): Han Ming Gan, Stephanie Falk, Hernán E. Morales, Christopher M. Austin, Paul Sunnucks, Alexandra Pavlova
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-018-4567-3

P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
Cited by: 38
Author(s): Bai-Han Zhu, Jun Xiao, Wei Xue, Gui-Cai Xu, Mingyuan Sun, Jiong-Tang Li
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2105-15-281

BESST - Efficient scaffolding of large fragmented assemblies
Cited by: 136
Author(s): Kristoffer Sahlin, Francesco Vezzi, Björn Nystedt, Joakim Lundeberg, Lars Arvestad
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-018-4743-5

Distinctive characters of Nostoc genomes in cyanolichens
Cited by: 30
Author(s): Andrey Gagunashvili, Ólafur S. Andrésson
Software Mentions: 3
Published: over 6 years ago

10.1093/gbe/evaa063

An Annotated Chromosome-Level Reference Genome of the Red-Eared Slider Turtle (Trachemys scripta elegans)
Cited by: 23
Author(s): W. Brian Simison, James F. Parham, Theodore J. Papenfuss, Athena Lam, James Henderson
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-019-1899-5

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools
Cited by: 166
Author(s): Cécile Monat, Sudharsan Padmarasu, Thomas Lux, Thomas Wicker, Heidrun Gundlach, Axel Himmelbach, Jennifer Ens, Chengdao Li, Gary J. Muehlbauer, Alan H. Schulman, Robbie Waugh, Ilka Braumann, Curtis Pozniak, Uwe Scholz, Klaus Mayer, Manuel Spannagl, Nils Stein, Martin Mascher
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12859-018-2425-6

Tigmint: correcting assembly errors using linked reads from large molecules
Cited by: 86
Author(s): Shaun D. Jackman, Lauren Coombe, Justin Chu, René L. Warren, Ben Vandervalk, Sarah Yeo, Zhen‐Zhen Xue, Hamid Mohamadi, Jöerg Bohlmann, Steven J.M. Jones, İnanç Birol
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2020.01100

Characterization of a Novel Functional Trimeric Catechol 1,2-Dioxygenase From a Pseudomonas stutzeri Isolated From the Gulf of Mexico
Cited by: 16
Author(s): Julieta Rodríguez-Salazar, Arisbeth G Almeida-Juarez, Katya Ornelas-Ocampo, Sofía Millán-López, Enrique Raga-Carbajal, José Luis Rodríguez-Mejía, Luis Felipe Muriel-Millán, Elizabeth Ernestina Godoy-Lozano, Nancy Rivera-Gómez, E. Rudiño-Piñera, Liliana Pardo-López
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-16-S14-S2

Exact approaches for scaffolding
Cited by: 22
Author(s): Mathias Weller, Annie Château, Rodolphe Giroudeau
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-018-19430-x

Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)
Cited by: 9
Author(s): Iria Fernandez‐Silva, James Henderson, Luiz A. Rocha, W. Brian Simison
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-019-6337-2

LRScaf: improving draft genomes using long noisy reads
Cited by: 47
Author(s): Xingran Liao, Shigang Wu, Alun Li, Fengli Zhao, Feng Hu, Lulu Ding, Jue Ruan
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13059-016-0951-y

OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees
Cited by: 65
Author(s): Song Gao, Denis Bertrand, Burton K. Chia, Niranjan Nagarajan
Software Mentions: 2
Published: over 8 years ago

10.1186/s12859-018-2570-y

Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)
Cited by: 38
Author(s): Dmitry A. Kuzmin, Sergey Feranchuk, Vadim V. Sharov, Alexander N. Cybin, Stepan V. Makolov, Yuliya A. Putintseva, Н. В. Орешкова, Konstantin V. Krutovsky
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-018-4466-7

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes
Cited by: 11
Author(s): Yoann Anselmetti, Wandrille Duchemin, Éric Tannier, Cédric Chauve, Sèverine Bérard
Software Mentions: 2
Published: over 6 years ago

10.1093/molbev/msaa240

Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits
Cited by: 48
Author(s): Cheng Sun, Jiaxing Huang, Yun Wang, Xiaomeng Zhao, Long Su, Gregg W.C. Thomas, Mengya Zhao, Xingtan Zhang, Irwin Jungreis, M Kellis, Saverio Vicario, Igor V. Sharakhov, Semen M. Bondarenko, Martin Hasselmann, Chang N. Kim, Benedict Paten, Luca Penso-Dolfin, Li Wang, Yuxiao Chang, Qiang Gao, Ling Ma, Lina Ma, Zhang Zhang, Hongbo Zhang, Hua-Hao Zhang, Livio Ruzzante, Hugh M. Robertson, Yihui Zhu, Yanjie Liu, Huipeng Yang, Lele Ding, Quangui Wang, Dongna Ma, Weilin Xu, Cheng Liang, Michael W. Itgen, Lauren Mee, Gang Cui, Ze Zhang, Ben M. Sadd, Matthew W. Hahn, Sarah Schaack, Seth M. Barribeau, Paul H. Williams, Robert M. Waterhouse, Rachel Lockridge Mueller
Software Mentions: 2
Published: about 4 years ago

10.1002/ece3.7611

The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat
Cited by: 5
Author(s): Changyi Xiao, Jingjin Li, Tingting Xie, Jianhai Chen, Sijia Zhang, Salma Hassan Elaksher, Jun Fan, Yaoxin Jiang, Lu Zhang, Wei Zhang, Yue Xiang, Zhenyang Wu, Shuhong Zhao, Xiaoyong Du
Software Mentions: 2
Published: over 3 years ago

10.1093/gigascience/giz023

A draft nuclear-genome assembly of the acoel flatworm<i>Praesagittifera naikaiensis</i>
Cited by: 15
Author(s): Asuka Arimoto, Tomoe Hikosaka-Katayama, Akira Hikosaka, Kunifumi Tagawa, Toyoshige Inoue, Tomoyuki Ueki, Masa‐aki Yoshida, Miyuki Kanda, Eiichi Shoguchi, Kanako Hisata, Noriyuki Satoh
Software Mentions: 2
Published: over 5 years ago

10.1038/sdata.2018.69

The draft genome sequence of cork oak
Cited by: 78
Author(s): António Marcos Ramos, Ana Usié, Pedro Barbosa, Pedro M. Barros, Tiago Capote, Inês Chaves, Fernanda Simões, Isabel A. Abreu, Isabel Carrasquinho, Carlos Faro, Joana Bagoin Guimarães, Diogo Mendonça, Filomena Nóbrega, L. Rodrigues, Nelson J. M. Saibo, Maria Carolina Varela, Conceição Egas, José Matos, Celia María Gonzalo Miguel, M. Margarida Oliveira, Cândido Pinto Ricardo, Sónia Gonçalves
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-50978-4

Improvement of the Pacific bluefin tuna (Thunnus orientalis) reference genome and development of male-specific DNA markers
Cited by: 28
Author(s): Ayako Suda, Issei Nishiki, Yoshiaki Iwasaki, Aiko Matsuura, Tetsuya Akita, Nobuaki Suzuki, Atushi Fujiwara
Software Mentions: 2
Published: about 5 years ago

10.3389/fpsyg.2021.680959

Recognition Characteristics of Facial and Bodily Expressions: Evidence From ERPs
Cited by: 0
Author(s): Xiaoxiao Li
Software Mentions: 1
Published: over 3 years ago

10.1534/g3.117.300429

The End of a 60-year Riddle: Identification and Genomic Characterization of an Iridovirus, the Causative Agent of White Fat Cell Disease in Zooplankton
Cited by: 11
Author(s): Elena R. Toenshoff, Peter D. Fields, Yann Bourgeois, Dieter Ebert
Software Mentions: 1
Published: over 6 years ago

10.3390/genes12060847

Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome
Cited by: 18
Author(s): Vidhya Jagannathan, Christophe Hitte, Jeffrey M. Kidd, Patrick Masterson, Terence Murphy, Sarah B. Emery, Brian W. Davis, R. Buckley, Liu Yan-hu, Xiangquan Zhang, Tosso Leeb, Yaping Zhang, Elaine A. Ostrander, Wang Guo-dong
Software Mentions: 1
Published: over 3 years ago

10.3389/fgene.2020.00201

A Giant Genome for a Giant Crayfish (Cherax quadricarinatus) With Insights Into cox1 Pseudogenes in Decapod Genomes
Cited by: 21
Author(s): Mun Hua Tan, Han Ming Gan, Yin Peng Lee, Frédéric Grandjean, Laurence J. Croft, Christopher M. Austin
Software Mentions: 1
Published: over 4 years ago

10.1111/eva.12178

A field guide to whole‐genome sequencing, assembly and annotation
Cited by: 278
Author(s): Robert Ekblom, Jochen B. W. Wolf
Software Mentions: 1
Published: over 10 years ago

10.5964/ejop.v15i3.1633

Predictive attentional bias modification induces stimulus-evoked attentional bias for threat
Cited by: 8
Author(s): Thomas Gladwin, Martin Möbius, Eni S. Becker
Software Mentions: 1
Published: about 5 years ago

10.1186/s12859-019-3114-9

SLR: a scaffolding algorithm based on long reads and contig classification
Cited by: 15
Author(s): Junwei Liu, Mengna Lyu, Ranran Chen, Xiaohong Zhang, Huimin Luo, CH Yan
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-020-07061-4

Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome
Cited by: 38
Author(s): Yuliya A. Putintseva, Eugeniya I. Bondar, Evgeniy Simonov, Vadim V. Sharov, Н. В. Орешкова, Dmitry A. Kuzmin, Yu. M. Konstantinov, В. Н. Шмаков, V.I. Belkov, Michael G. Sadovsky, Olivier Keech, Konstantin V. Krutovsky
Software Mentions: 1
Published: about 4 years ago

10.3390/insects12070652

Genome Sequence of the Asian Honeybee in Pakistan Sheds Light on Its Phylogenetic Relationship with Other Honeybees
Cited by: 2
Author(s): Huachun Tan, M. Naeem, Ali Husnain, Muhammad Taimoor Shakeel, Haiou Kuang, Ze Zhang, Cheng Sun
Software Mentions: 1
Published: over 3 years ago

10.3906/biy-1805-42

Evaluation of genome scaffolding tools using pooled clone sequencing
Cited by: 0
Author(s): Elif Dal, Can Alkan
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-15-439

Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools
Cited by: 6
Author(s): Andrey Alexeyenko, Björn Nystedt, Francesco Vezzi, Ellen Sherwood, Rosa Ye, Bjarne Knudsen, Martin Simonsen, Benjamín L. Turner, Pieter J. de Jong, Chun-Ta Wu, Joakim Lundeberg
Software Mentions: 1
Published: over 10 years ago

10.3389/fmicb.2021.713702

Paenarthrobacter sp. GOM3 Is a Novel Marine Species With Monoaromatic Degradation Relevance
Cited by: 7
Author(s): Jaime Rosas-Díaz, Alejandra Escobar‐Zepeda, Libertad Adaya, Jorge Rojas-Vargas, Diego Humberto Cuervo-Amaya, Ayixón Sánchez-Reyes, Liliana Pardo-López
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2019.01445

ABC Transporter Genes Show Upregulated Expression in Drug-Resistant Clinical Isolates of Candida auris: A Genome-Wide Characterization of ATP-Binding Cassette (ABC) Transporter Genes
Cited by: 48
Author(s): Mohd Wasi, Nitesh Khandelwal, Alexander J. Moorhouse, Remya Nair, Poonam Vishwakarma, Gustavo Bravo Ruiz, Zoe K. Ross, Alexander Lorenz, Shivaprakash M Rudramurthy, Arunaloke Chakrabarti, Andrew M. Lynn, Alok K. Mondal, Neil A. R. Gow, Rajendra Prasad
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2021.695700

Draft Genome of the Mirrorwing Flyingfish (Hirundichthys speculiger)
Cited by: 1
Author(s): Pengwei Xu, Chenxi Zhao, Xinxin You, Fan Yang, Jieming Chen, Zhiqiang Ruan, Ruobo Gu, Junmin Xu, Chao Bian, Qiong Shi
Software Mentions: 1
Published: over 3 years ago

Projects: pypi: BESST

Papers Mentioning BESST 42