bioRxiv/medRxiv TRiP Review Activity

37 Reviews — EMBO Press — Bioinformatics

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DICE: Fast and Accurate Distance-Based Reconstruction of Single-Cell Copy Number Phylogenies
Weiner, S., Bansal, M. S.
10.1101/2024.06.03.597037 — Posted: 2024-06-04 — Discussion: 2025-05-20  EMBO Press
A highly scalable approach to topic modelling in single-cell data by approximate pseudobulk projection
Subedi, S., Sumida, T. S., Park, Y.
10.1101/2024.02.21.581497 — Posted: 2024-02-23 — Discussion: 2024-09-10  EMBO Press
RedRibbon: A new rank-rank hypergeometric overlap pipeline to compare gene and transcript expression signatures
Piron, A., Szymczak, F., Alvelos, M. I., Defrance, M., Lenaerts, T., Eizirik, D. L., Cnop, M.
10.1101/2022.08.31.505818 — Posted: 2022-09-02 — Discussion: 2024-08-01  EMBO Press
Detecting Cell Contact-dependent Gene Expression from Spatial Transcriptomics Data
Kim, H., Lövkvist, C., Martin, P. C. N., Kim, J., Won, K. J.
10.1101/2022.02.16.480673 — Posted: 2022-02-19 — Discussion: 2023-12-12  EMBO Press
Dimensionality reduction methods for extracting functional networks from large-scale CRISPR screens
Hassan, A. Z., Ward, H. N., Rahman, M., Billmann, M., Lee, Y., Myers, C. L.
10.1101/2023.02.22.529573 — Posted: 2023-02-22 — Discussion: 2023-11-21  EMBO Press
Accurate genotype-based demultiplexing of single cell RNA sequencing samples from non-human animals
Cardiello, J. F., Joven Araus, A., Giatrellis, S., Simon, A., Leigh, N. D.
10.1101/2022.09.22.508993 — Posted: 2022-09-23 — Discussion: 2023-06-29  EMBO Press
Updated benchmarking of variant effect predictors using deep mutational scanning
Livesey, B. J., Marsh, J. A.
10.1101/2022.11.19.517196 — Posted: 2022-11-22 — Discussion: 2023-06-27  EMBO Press
Gapless provides combined scaffolding, gap filling and assembly correction with long reads
Schmeing, S., Robinson, M. D.
10.1101/2022.03.08.483466 — Posted: 2022-03-09 — Discussion: 2023-05-26  EMBO Press
Exploratory Meta-Analysis of Hypoxic Transcriptomes Using a Precise Transcript Reference Sequence Set
Ono, Y., Bono, H.
10.1101/2022.05.01.489280 — Posted: 2022-05-01 — Discussion: 2023-05-26  EMBO Press
Transcription factor expression is the main determinant of variability in gene co-activity
van Duin, L., Krautz, R., Rennie, S., Andersson, R.
10.1101/2022.10.11.511770 — Posted: 2022-10-14 — Discussion: 2023-05-24  EMBO Press

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