Bioinformatics

VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots

1. Joachim Goedhart
2. Martijn S. Luijsterburg

Reviewed by eLife

A fully automated deep learning pipeline for high-throughput colony segmentation and classification

1. Sarah H. Carl
2. Lea Duempelmann
3. Yukiko Shimada
4. Marc Bühler

Reviewed by Review Commons

Analysis of RNA processing directly from spatial transcriptomics data reveals previously unknown regulation

1. Julia Olivieri
2. Julia Salzman

• Curated by eLife

  eLife assessment:

  This important study describes spatial RNA processing events by combining methods for single-cell transcriptomics data with spatial transcriptomics data. The evidence supporting the claims of the authors is solid, although the analysis could be further strengthened by including a broader range of samples as well as orthogonal validation either by experimental methods or simulated data. The work will be of general interest to researchers in the spatial transcriptomics field as well as researchers investigating alternative pre-mRNA processing across diverse tissues.

Reviewed by eLife

Deep Boosted Molecular Dynamics (DBMD): Accelerating molecular simulations with Gaussian boost potentials generated using probabilistic Bayesian deep neural network

1. Hung N. Do
2. Yinglong Miao

Reviewed by PREreview

miR2Trait: an integrated resource for investigating miRNA-disease associations

1. Poornima Babu
2. Ashok Palaniappan

Reviewed by PeerJ

Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies

1. Jason W. Shapiro
2. Catherine Putonti

Reviewed by PeerJ

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly

1. Maxime Borry
2. Alexander Hübner
3. Adam B. Rohrlach
4. Christina Warinner

Reviewed by PeerJ

Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data

1. Bharath Nair
2. Ismael Rodríguez Palomo
3. Bo Markussen
4. Carsten Wiuf
5. Sarah Fiddyment
6. Matthew James Collins

Reviewed by Peer Community in Archaeology

Using macromolecular electron densities to improve the enrichment of active compounds in virtual screening

1. Wenzhi Ma
2. Wei Zhang
3. Yuan Le
4. Xiaoxuan Shi
5. Qingbo Xu
6. Yang Xiao
7. Yueying Dou
8. Xiaoman Wang
9. Wenbiao Zhou
10. Wei Peng
11. Hongbo Zhang
12. Bo Huang

Reviewed by PREreview

IFF : Identifying key residues in intrinsically disordered regions of proteins using machine learning

1. Wen‐Lin Ho
2. Hsuan‐Cheng Huang
3. Jie‐rong Huang

Reviewed by PREreview