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138 Reviews — eLife — Bioinformatics

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GENIUS: GEnome traNsformatIon and spatial representation of mUltiomicS data
Sokac, M., Dyrskjot Andersen, L., Haibe-Kains, B., Aerts, H. J. W. L., Juul Birkbak, N.
10.1101/2023.02.09.525144 — Posted: 2023-02-10 — Discussion: 2023-08-09  eLife
Analysis of RNA processing directly from spatial transcriptomics data reveals previously unknown regulation
Olivieri, J. E., Salzman, J.
10.1101/2023.03.13.532412 — Posted: 2023-03-14 — Discussion: 2023-07-10  eLife
Expanding the stdpopsim species catalog, and lessons learned forrealistic genome simulations
Lauterbur, M. E., Cavassim, M. I. A., Gladstein, A. L., Gower, G., Pope, N. S., Tsambos, G., Adrion, J., Belsare, S., Biddanda, A., Caudill, V., Cury, J., Echevarria, I., Haller, B. C., Hasan, A. R., Huang, X., Iasi, L. N. M., Noskova, E., Obsteter, J., Pavinato, V. A. C., Pearson, A., Peede, D., Perez, M. F., Rodrigues, M. F., Smith, C. C. R., Spence, J. P., Teterina, A., Tittes, S., Unneberg, P., Vazquez, J. M., Waples, R. K., Wohns, A. W., Wong, Y., Baumdicker, F., Cartwright, R. A., Gorjanc, G., Gutenkunst, R. N., Kelleher, J., Kern, A. D., Ragsdale, A. P., Ralph, P. L., Schrider, D. R., G
10.1101/2022.10.29.514266 — Posted: 2022-10-31 — Discussion: 2023-05-22  eLife
A novel in silico method employs chemical and protein similarity algorithms to accurately identify chemical transformations in the human gut microbiome
Bustion, A. E., Agrawal, A., Turnbaugh, P. J., Pollard, K. S.
10.1101/2022.08.02.502504 — Posted: 2022-08-04 — Discussion: 2023-03-29  eLife
Interrogating the Precancerous Evolution of Pathway Dysfunction in Lung Squamous Cell Carcinoma Using XTABLE
Roberts, M., Ogden, J., Hossain, A. S. M. M., Kerr, A., Dive, C., Beane, J., Lopez-Garcia, C.
10.1101/2022.05.06.490640 — Posted: 2022-05-06 — Discussion: 2023-03-14  eLife
Learning the differences: a transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity
Bravi, B., Di Gioacchino, A., Fernandez-de-Cossio-Diaz, J., Walczak, A. M., Mora, T., Cocco, S., Monasson, R.
10.1101/2022.12.06.519259 — Posted: 2022-12-09 — Discussion: 2023-02-19  eLife
ProteInfer: deep networks for protein functional inference
Sanderson, T., Bileschi, M. L., Belanger, D., Colwell, L.
10.1101/2021.09.20.461077 — Posted: 2021-09-23 — Discussion: 2023-02-08  eLife
CriSNPr: a single interface for the curated and de-novo design of gRNAs for CRISPR diagnostics using diverse Cas systems
Chakraborty, D., Ansari, A. H., Kumar, M., Sarkar, S., Maiti, S.
10.1101/2022.02.17.479653 — Posted: 2022-02-17 — Discussion: 2023-01-25  eLife
Network-based multi-omics integration reveals metabolic risk profile within treated HIV-infection
Mikaeloff, F., Gelpi, M., Benfeitas, R., Knudsen, A. D., Vestad, B., Hogh, J., Hov, J., Benfield, T., Murray, D., Giske, C. G., Mardinoglu, A., Troseid, M., Poulsen, S. D., Neogi, U.
10.1101/2022.06.08.495246 — Posted: 2022-06-13 — Discussion: 2023-01-04  eLife
Decoding rRNA Sequences for Improved Metagenomics in Sylvatic Mosquito Species
Koh, C., Frangeul, L., Blanc, H., Ngoagouni, C., Boyer, S., Dussart, P., Grau, N., Girod, R., Duchemin, J.-B., Saleh, M. C.
10.1101/2022.02.01.478639 — Posted: 2022-02-03 — Discussion: 2022-12-30  eLife

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