Evaluated articles

Mycobacterial Metabolic Model Development for Drug Target Identification

1. Bridget P. Bannerman
2. Alex Oarga
3. Jorge Júlvez

• Curated by GigaByte

  Editor’s Assessment

  This work has generated metabolic models for the human pathogens Mycobacterium leprae and Mycobacteroides abscessus, alongside a new computational tool that can be used to identify potential drug targets. The standardised genomic scale metabolic models have been developed using the systems biology community standards for quality control and evaluation of models. After providing more detail on reproducibility, comparative performance of the models, and reuse, these resources are now published and are available for reuse by the global scientific community via the GigaDB, Biomodels, and PatMeDB repositories.

  This assessment refers to version 1 of this preprint.

Reviewed by GigaByte

Genome assembly of the deep-sea coral Lophelia pertusa

1. Santiago Herrera
2. Erik E. Cordes

Reviewed by GigaByte

The first genome assembly of the amphibian nematode parasite ( Aplectana chamaeleonis )

1. Lei Han
2. Tianlu Liu
3. Fengping He
4. Zhijun Hou

Reviewed by GigaByte

PhysiCOOL: A generalized framework for model Calibration and Optimization Of modeLing projects

1. Inês G. Gonçalves
2. David A. Hormuth
3. Sandhya Prabhakaran
4. Caleb M. Phillips
5. José Manuel García-Aznar

Reviewed by GigaByte

Improvements to the Gulf Pipefish Syngnathus scovelli Genome

1. B Ramesh
2. CM Small
3. H Healey
4. B Johnson
5. E Barker
6. M Currey
7. S Bassham
8. M Myers
9. WA Cresko
10. AG Jones

Reviewed by GigaByte

Nanopore-based enrichment of antimicrobial resistance genes – a case-based study

1. Adrian Viehweger
2. Mike Marquet
3. Martin Hölzer
4. Nadine Dietze
5. Mathias W. Pletz
6. Christian Brandt

Reviewed by GigaByte

The first complete mitochondrial genome of Diadema antillarum (Diadematoida, Diadematidae)

1. Audrey J. Majeske
2. Alejandro J. Mercado Capote
3. Aleksey Komissarov
4. Anna Bogdanova
5. Nikolaos V. Schizas
6. Stephanie O. Castro Márquez
7. Kenneth Hilkert
8. Walter Wolfsberger
9. Tarás K. Oleksyk

Reviewed by GigaByte

PhysiPKPD: A pharmacokinetics and pharmacodynamics module for PhysiCell

1. Daniel Bergman
2. Lauren Marazzi
3. Mukti Chowkwale
4. Deepa Maheshvare M
5. Supriya Bidanta
6. Tarunendu Mapder
7. Jialun Li

Reviewed by GigaByte

A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research

1. Nataly Allasi Canales
2. Oscar A. Pérez-Escobar
3. Robyn F. Powell
4. Mats Töpel
5. Catherine Kidner
6. Mark Nesbitt
7. Carla Maldonado
8. Christopher J. Barnes
9. Nina Rønsted
10. Natalia A. S. Przelomska
11. Ilia J. Leitch
12. Alexandre Antonelli

Reviewed by GigaByte

svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data

1. Ruining Dong
2. Daniel Cameron
3. Justin Bedo
4. Anthony T. Papenfuss

Reviewed by GigaByte

A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)

1. Awais Khan
2. Sarah B. Carey
3. Alicia Serrano
4. Huiting Zhang
5. Heidi Hargarten
6. Haley Hale
7. Alex Harkess
8. Loren Honaas

Reviewed by GigaByte

Sex-based de novo transcriptome assemblies of the parasitoid wasp Encarsia suzannae, a host of the manipulative heritable symbiont Cardinium hertigii

1. Dylan L. Schultz
2. Evelyne Selberherr
3. Corinne M. Stouthamer
4. Matthew R. Doremus
5. Suzanne E. Kelly
6. Martha S. Hunter
7. Stephan Schmitz-Esser

Reviewed by GigaByte

The genome of a giant (trevally): Caranx ignobilis

1. Brandon D. Pickett
2. Jessica R. Glass
3. Timothy P. Johnson
4. Perry G. Ridge
5. John S. K. Kauwe

Reviewed by GigaByte

First De novo whole genome sequencing and assembly of mutant Dendrobium hybrid cultivar ‘Emma White’

1. Rubina Sherpa
2. Ramgopal Devadas
3. Penna Suprasanna
4. Sadashiv Narayan Bolbhat
5. Tukaram Dayaram Nikam

Reviewed by GigaByte

The genome of the mustard hill coral, Porites astreoides

1. Kevin H. Wong
2. Hollie M. Putnam

Reviewed by GigaByte

Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes

1. Akito Y. Kawahara
2. Caroline G. Storer
3. Amanda Markee
4. Jacqueline Heckenhauer
5. Ashlyn Powell
6. David Plotkin
7. Scott Hotaling
8. Timothy P. Cleland
9. Rebecca B. Dikow
10. Torsten Dikow
11. Ryoichi B. Kuranishi
12. Rebeccah Messcher
13. Steffen U. Pauls
14. Russell J. Stewart
15. Koji Tojo
16. Paul B. Frandsen

Reviewed by GigaByte

A chromosome-level genome assembly and annotation of the maize elite breeding line Dan340

1. Yikun Zhao
2. Yuancong Wang
3. De Ma
4. Guang Feng
5. Yongxue Huo
6. Zhihao Liu
7. Ling Zhou
8. Yunlong Zhang
9. Liwen Xu
10. Liang Wang
11. Han Zhao
12. Jiuran Zhao
13. Fengge Wang

Reviewed by GigaByte

The Lithuanian reference genome LT1 - a human de novo genome assembly with short and long read sequence and Hi-C data

1. Hui-Su Kim
2. Asta Blazyte
3. Sungwon Jeon
4. Changhan Yoon
5. Yeonkyung Kim
6. Changjae Kim
7. Dan Bolser
8. Ji-Hye Ahn
9. Jeremy S. Edwards
10. Jong Bhak

Reviewed by GigaByte

Annotation of Hox cluster and Hox cofactor genes in the Asian citrus psyllid, Diaphorina citri, reveals novel features

1. Teresa D. Shippy
2. Prashant S. Hosmani
3. Mirella Flores-Gonzalez
4. Lukas A. Mueller
5. Wayne B. Hunter
6. Susan J. Brown
7. Tom D’Elia
8. Surya Saha

Reviewed by GigaByte

Annotation of putative circadian rhythm-associated genes in Diaphorina citri (Hemiptera: Liviidae)

1. Max Reynolds
2. Lucas de Oliveira
3. Chad Vosburg
4. Thomson Paris
5. Crissy Massimino
6. Jordan Norus
7. Yasmin Ortiz
8. Michelle Espino
9. Nina Davis
10. Ron Masse
11. Alan Neiman
12. Rachel Holcomb
13. Kylie Gervais
14. Melissa Kemp
15. Maria Hoang
16. Teresa D. Shippy
17. Prashant S. Hosmani
18. Mirella Flores-Gonzalez
19. Kirsten Pelz-Stelinski
20. Jawwad A. Qureshi
21. Lukas A. Mueller
22. Wayne B. Hunter
23. Joshua B. Benoit
24. Susan J. Brown
25. Tom D’Elia
26. Surya Saha

Reviewed by GigaByte