Bioinformatics

Bashing irreproducibility with shournal

1. Tycho Kirchner
2. Konstantin Riege
3. Steve Hoffmann

Reviewed by Arcadia Science

The necessity of considering enzymes as compartments in constraint-based genome-scale metabolic models

1. Xue Yang
2. Zhitao Mao
3. Jianfeng Huang
4. Ruoyu Wang
5. Huaming Dong
6. Yanfei Zhang
7. Hongwu Ma

Reviewed by PREreview

MetaCerberus: distributed highly parallelized scalable HMM-based implementation for robust functional annotation across the tree of life

1. Jose L. Figueroa
2. Eliza Dhungel
3. Cory R. Brouwer
4. Richard Allen White

Reviewed by Arcadia Science

Metaphor - A workflow for streamlined assembly and binning of metagenomes

1. Vinícius W. Salazar
2. Babak Shaban
3. Maria del Mar Quiroga
4. Robert Turnbull
5. Edoardo Tescari
6. Vanessa Rossetto Marcelino
7. Heroen Verbruggen
8. Kim-Anh Lê Cao

Reviewed by GigaScience

Hetnet connectivity search provides rapid insights into how two biomedical entities are related

1. Daniel S. Himmelstein
2. Michael Zietz
3. Vincent Rubinetti
4. Kyle Kloster
5. Benjamin J. Heil
6. Faisal Alquaddoomi
7. Dongbo Hu
8. David N. Nicholson
9. Yun Hao
10. Blair D. Sullivan
11. Michael W. Nagle
12. Casey S. Greene

Reviewed by GigaScience

SODAR: managing multi-omics study data and metadata

1. Mikko Nieminen
2. Oliver Stolpe
3. Mathias Kuhring
4. January Weiner
5. Patrick Pett
6. Dieter Beule
7. Manuel Holtgrewe

Reviewed by GigaScience

MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction

1. Wenhuan Zeng
2. Anupam Gautam
3. Daniel H. Huson

Reviewed by GigaScience

Structure-based learning to model complex protein-DNA interactions and transcription-factor co-operativity in cis -regulatory elements

1. O Fornes
2. A Meseguer
3. J Aguirre-Plans
4. P Gohl
5. PM Bota
6. R Molina-Fernández
7. J Bonet
8. AC Hernandez
9. F Pegenaute
10. O Gallego
11. N Fernandez-Fuentes
12. B Oliva

• Curated by eLife

  eLife assessment

  This valuable study describes the development of a new structure-based learning approach to predict transcription binding specificity and its application in the modeling of regulatory complexes in cis-regulatory modules. The authors developed a structure-based learning approach to predict TF binding features and model the regulatory complex(es) in cis-regulatory modules, integrating experimental knowledge of structures of TF-DNA complexes and high-throughput TF-DNA interactions. The validation presented by the authors is currently incomplete, with a large variability in the performance of the method on the different TF families tested.

Reviewed by eLife

Similarity metric learning on perturbational datasets improves functional identification of perturbations

1. Ian Smith
2. Petr Smirnov
3. Benjamin Haibe-Kains

Reviewed by preLights

Inter-species association mapping links splice site evolution to METTL16 and SNRNP27K

1. Matthew T Parker
2. Sebastian M Fica
3. Geoffrey J Barton
4. Gordon G Simpson

Reviewed by Review Commons