Bioinformatics

GTalign: spatial index-driven protein structure alignment, superposition, and search

1. Mindaugas Margelevičius

Reviewed by Arcadia Science

Robust virtual staining of landmark organelles

1. Ziwen Liu
2. Eduardo Hirata-Miyasaki
3. Soorya Pradeep
4. Johanna Rahm
5. Christian Foley
6. Talon Chandler
7. Ivan Ivanov
8. Hunter Woosley
9. Tiger Lao
10. Akilandeswari Balasubramanian
11. Rita Marreiros
12. Chad Liu
13. Manu Leonetti
14. Ranen Aviner
15. Carolina Arias
16. Adrian Jacobo
17. Shalin B. Mehta

Reviewed by Arcadia Science

Prediction of Anti‐Freezing Proteins From Their Evolutionary Profile

1. Nishant Kumar
2. Shubham Choudhury
3. Nisha Bajiya
4. Sumeet Patiyal
5. Gajendra P. S. Raghava

Reviewed by Arcadia Science

PSAURON: a tool for assessing protein annotation across a broad range of species

1. Markus J Sommer
2. Aleksey V Zimin
3. Steven L Salzberg

Reviewed by Arcadia Science

Combining DNA and protein alignments to improve genome annotation with LiftOn

1. Kuan-Hao Chao
2. Jakob M. Heinz
3. Celine Hoh
4. Alan Mao
5. Alaina Shumate
6. Mihaela Pertea
7. Steven L. Salzberg

Reviewed by Arcadia Science

Accurate prediction of CDR-H3 loop structures of antibodies with deep learning

1. Hedi Chen
2. Xiaoyu Fan
3. Shuqian Zhu
4. Yuchan Pei
5. Xiaochun Zhang
6. Xiaonan Zhang
7. Lihang Liu
8. Feng Qian
9. Boxue Tian

• Curated by eLife

  eLife assessment

  This paper presents H3-OPT, a deep learning method that effectively combines existing techniques for the prediction of antibody structure. This work, supported by convincing experiments for validation, is important because the method can aid in the design of antibodies, which are key tools in many research and industrial applications.

Reviewed by eLife

Heterogeneous folding landscapes and predetermined breaking points within a protein family

1. Sebastian Pechmann

Reviewed by PREreview

Topological Structures in the Space of Treatment-Naïve Patients with Chronic Lymphocytic Leukemia

1. Reginald L. McGee
2. Jake Reed
3. Caitlin E. Coombes
4. Carmen D. Herling
5. Michael J. Keating
6. Lynne V. Abruzzo
7. Kevin R. Coombes

Reviewed by Arcadia Science

Inferring Single-Cell RNA Kinetics from Various Biological Priors

1. Yanshuo Chen
2. Zhengmian Hu
3. Ke Ni
4. Site Feng
5. Wei Chen
6. Heng Huang

Reviewed by Arcadia Science

IPEV: identification of prokaryotic and eukaryotic virus-derived sequences in virome using deep learning

1. Hengchuang Yin
2. Shufang Wu
3. Jie Tan
4. Qian Guo
5. Mo Li
6. Jinyuan Guo
7. Yaqi Wang
8. Xiaoqing Jiang
9. Huaiqiu Zhu

Reviewed by GigaScience