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122 Reviews — eLife — Bioinformatics

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A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture
Andradi-Brown, C., Wichers-Misterek, J. S., von Thien, H., Höppner, Y. D., Scholz, J. A. M., Smedegaard Hansson, H., Filtenborg Hocke, E., Gilberger, T. W., Duffy, M., Lavstsen, T., Baum, J., Otto, T. D., Cunnington, A. J., Bachmann, A.
10.1101/2023.03.21.533599 — Posted: 2023-03-24 — Discussion: 2023-12-18  eLife
The reprogrammed mouse heart phosphoproteome in response to the chronic stress of markedly high cardiac-specific adenylyl cyclase type 8 overexpression
Qu, J.-H., Chakir, K., Tarasov, K. V., Riordon, D. R., Perino, M. G., Silvester, A. J., Lakatta, E. G.
10.1101/2022.04.29.488779 — Posted: 2022-05-01 — Discussion: 2023-11-22  eLife
Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models
Vezina, B., Watts, S. C., Hawkey, J., Cooper, H. B., Judd, L. M., Jenney, A., Monk, J. M., Holt, K. E., Wyres, K. L.
10.1101/2023.02.26.530115 — Posted: 2023-02-27 — Discussion: 2023-09-19  eLife
ModCRE: a structure homology-modeling approach to predict TF binding in cis-regulatory elements
Fornes, O., Meseguer, A., Aguirre-Plans, J., GOHL, P., Mireia-Bota, P., MOLINA-FERNANDEZ, R., BONET, J., CHINCHILLA, A., PEGENAUTE, F., Gallego, O., Fernandez-Fuentes, N., Oliva, B.
10.1101/2022.04.17.488557 — Posted: 2022-04-17 — Discussion: 2023-08-21  eLife
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

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