bioRxiv/medRxiv TRiP Review Activity

37 Reviews — EMBO Press — Bioinformatics

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The value of genotype-specific reference for transcriptome analyses
Guo, W., Coulter, M., Waugh, R., Zhang, R.
10.1101/2021.09.14.460213 — Posted: 2021-09-15 — Discussion: 2023-05-14  EMBO Press
New algorithms for accurate and efficient de-novo genome assembly from long DNA sequencing reads
Gonzalez-Garcia, L. N., Guevara-Barrientos, D., Lozano-Arce, D., Gil, J., Diaz-Riano, J., Duarte, E., Andrade, G., Bojaca, J. C., Hoyos, M. C., Chavarro, C., Guayazan, N., Chica, L. A., Buitrago Acosta, M. C., Bautista, E., Trujillo, M., Duitama, J.
10.1101/2022.08.30.505891 — Posted: 2022-09-01 — Discussion: 2023-03-09  EMBO Press
Comparative analysis of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing
Liu, J., Tran, V., Vemuri, V. N. P., Byrne, A., Borja, M., Agarwal, S., Wang, R., Awayan, K., Murti, A., Taychameekiatchai, A., Wang, B., Emanuel, G., He, J., Haliburton, J., Pisco, A. O., Neff, N.
10.1101/2022.03.04.483068 — Posted: 2022-03-07 — Discussion: 2023-01-19  EMBO Press
CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq
Cuomo, A. S., Heinen, T., Vagiaki, D., Horta, D., Marioni, J., Stegle, O.
10.1101/2021.09.01.458524 — Posted: 2021-09-02 — Discussion: 2022-11-21  EMBO Press
Transposable elements as sensors of SARS-CoV-2 infection
Sorek, M., Meshorer, E., Schlesinger, S.
10.1101/2021.02.25.432821 — Posted: 2021-02-25 — Discussion: 2022-11-21  EMBO Press
Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations
Kiani, K., Sanford, E. M., Goyal, Y., Raj, A.
10.1101/2022.02.03.478981 — Posted: 2022-02-03 — Discussion: 2022-11-21  EMBO Press
Resolution of the curse of dimensionality in single-cell RNA sequencing data analysis
Imoto, Y., Nakamura, T., Escolar, E. G., Yoshiwaki, M., Kojima, Y., Yabuta, Y., Katou, Y., Yamamoto, T., Hiraoka, Y., Saitou, M.
10.1101/2022.05.02.490246 — Posted: 2022-05-02 — Discussion: 2022-08-19  EMBO Press
Cell-to-cell and type-to-type heterogeneity of signaling networks: Insights from the crowd
Gabor, A., Tognetti, M., Driessen, A., Tanevski, J., Guo, B., Cao, W., Shen, H., Yu, T., Chung, V., Single Cell Signaling in Breast Cancer DREAM Consortium, , Bodenmiller, B., Saez-Rodriguez, J.
10.1101/2021.03.23.436603 — Posted: 2021-03-23 — Discussion: 2021-11-30  EMBO Press
OrtSuite - from genomes to prediction of microbial interactions within targeted ecosystem processes
Saraiva, J. P., Bartholomäus, A., Kallies, R., Gomes, M., Fleming Bicalho, M. V., Vogt, C., Chatzinotas, A., Stadler, P. F., Dias, O., Nunes da Rocha, U.
10.1101/2021.06.04.447094 — Posted: 2021-06-07 — Discussion: 2021-10-27  EMBO Press
On the Relation of Gene Essentiality to Intron Structure: A Computational and Deep Learning Approach
Schonfeld, E., Vendrow, E., Vendrow, J., Schonfeld, E.
10.1101/2020.03.31.019125 — Posted: 2020-04-01 — Discussion: 2021-05-19  EMBO Press

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