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Discovering plasmids in metagenomes based on genetic architecture

Yu, M. K., Fogarty, E. C., Eren, A. M.

10.1101/2020.11.01.361691 — Posted: 2020-11-01 — Discussion: 2025-02-25

Pervasive selective sweeps across human gut microbiomes

Garud, N., Wolff, R.

10.1101/2023.12.22.573162 — Posted: 2023-12-23 — Discussion: 2025-02-25

mEnrich-seq: Methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome

Cao, L., Kong, Y., Fan, Y., Ni, M., Tourancheau, A., Ksiezarek, M., Mead, E. A., Koo, T., Gitman, M. R., Zhang, X.-S., Fang, G.

10.1101/2022.11.07.515285 — Posted: 2022-11-08 — Discussion: 2025-02-25

SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs)

Pan, S., Zhu, C., Zhao, X.-M., Coelho, L. P.

10.1101/2021.08.16.456517 — Posted: 2021-08-16 — Discussion: 2025-02-25

Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut.

Bohmann, N., Wilmanski, T., Levy, L., Lampe, J., Gurry, T., Rappaport, N., Diener, C., Gibbons, S. M.

10.1101/2023.02.28.530516 — Posted: 2023-03-01 — Discussion: 2025-02-25

Gut microbial genes are associated with neurocognition and brain development in healthy children

Bonham, K. S., Bruchhage, M. M. K., Rowland, S., Volpe, L., Dyer, K., RESONANCE Consortium, , D'Sa, V., Huttenhower, C., Deoni, S., Klepac-Ceraj, V.

10.1101/2020.02.13.944181 — Posted: 2020-02-14 — Discussion: 2025-02-25

Time of Sample Collection Critical for Microbiome Replicability

Allaband, C., Lingaraju, A., Ramos, S. F., Kumar, T., Javaheri, H., Tiu, M. D., Machado, A. C. D., Richter, R. A., Elijah, E., Haddad, G. G., Leone, V. A., Dorrestein, P. C., Knight, R., Zarrinpar, A.

10.1101/2022.10.26.513817 — Posted: 2022-10-28 — Discussion: 2025-02-25

Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria is Governed by a Global Transcriptional Regulator NagR

Arzamasov, A. A., Nakajima, A., Sakanaka, M., Ojima, M. N., Katayama, T., Rodionov, D. A., Osterman, A. L.

10.1101/2022.04.06.487429 — Posted: 2022-04-07 — Discussion: 2025-02-25

LotuS2: An ultrafast and highly accurate tool for amplicon sequencing analysis

Ozkurt, E., Fritscher, J., Soranzo, N., Ng, D. Y. K., Davey, R. P., Bahram, M., Hildebrand, F.

10.1101/2021.12.24.474111 — Posted: 2021-12-24 — Discussion: 2025-02-25

Expanding the human gut microbiome atlas of Africa

Maghini, D. G., Oduaran, O. H., Wirbel, J., Ingasia Olubayo, L. A., Smyth, N., Mathema, T., Belger, C. W., Agongo, G., Boua, P. R., Choma, S. S., Gomez-Olive, F. X., Kisiangani, I., Mashaba, G. R., Micklesfield, L., Mohamed, S. F., Nonterah, E. A., Norris, S., Sorgho, H., Tollman, S., Wafawanaka, F., Tluway, F., Ramsay, M., Bhatt, A. S., Hazelhurst, S.

10.1101/2024.03.13.584859 — Posted: 2024-03-14 — Discussion: 2025-02-25