Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data von Jiang, Lingjing, Haiminen, Niina, Carrieri, Anna‐Paola, Huang, Shi, Vázquez‐Baeza, Yoshiki, Parida, Laxmi, Kim, Ho‐Cheol, Swafford, Austin D., Knight, Rob, Natarajan, Loki

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Human Skin, Oral, and Gut Microbiomes Predict Chronological Age von Huang, Shi, Haiminen, Niina, Carrieri, Anna-Paola, Hu, Rebecca, Jiang, Lingjing, Parida, Laxmi, Russell, Baylee, Allaband, Celeste, Zarrinpar, Amir, Vázquez-Baeza, Yoshiki, Belda-Ferre, Pedro, Zhou, Hongwei, Kim, Ho-Cheol, Swafford, Austin D, Knight, Rob, Xu, Zhenjiang Zech

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Combining explainable machine learning, demographic and multi-omic data to inform precision medicine strategies for inflammatory bowel disease von Gardiner, Laura-Jayne, Carrieri, Anna Paola, Bingham, Karen, Macluskie, Graeme, Bunton, David, McNeil, Marian, Pyzer-Knapp, Edward O

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Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences von Carrieri, Anna Paola, Haiminen, Niina, Maudsley-Barton, Sean, Gardiner, Laura-Jayne, Murphy, Barry, Mayes, Andrew E., Paterson, Sarah, Grimshaw, Sally, Winn, Martyn, Shand, Cameron, Hadjidoukas, Panagiotis, Rowe, Will P. M., Hawkins, Stacy, MacGuire-Flanagan, Ashley, Tazzioli, Jane, Kenny, John G., Parida, Laxmi, Hoptroff, Michael, Pyzer-Knapp, Edward O.

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SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment von Marotz, Clarisse, Belda-Ferre, Pedro, Ali, Farhana, Das, Promi, Huang, Shi, Cantrell, Kalen, Jiang, Lingjing, Martino, Cameron, Diner, Rachel E., Rahman, Gibraan, McDonald, Daniel, Armstrong, George, Kodera, Sho, Donato, Sonya, Ecklu-Mensah, Gertrude, Gottel, Neil, Salas Garcia, Mariana C., Chiang, Leslie Y., Salido, Rodolfo A., Shaffer, Justin P., Bryant, Mac Kenzie, Sanders, Karenina, Humphrey, Greg, Ackermann, Gail, Haiminen, Niina, Beck, Kristen L., Kim, Ho-Cheol, Carrieri, Anna Paola, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Torriani, Francesca J., Knight, Rob, Gilbert, Jack, Sweeney, Daniel A., Allard, Sarah M.

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Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production von Beck, Kristen L, Haiminen, Niina, Agarwal, Akshay, Carrieri, Anna Paola, Madgwick, Matthew, Kelly, Jennifer, Pylro, Victor, Kawas, Ban, Wiedmann, Martin, Ganda, Erika

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DGCNN approach links metagenome-derived taxon and functional information providing insight into global soil organic carbon von Gardiner, Laura-Jayne, Marshall, Matthew, Reusch, Katharina, Dearden, Chris, Birmingham, Mark, Carrieri, Anna Paola, Pyzer-Knapp, Edward O., Krishna, Ritesh, Neal, Andrew L.

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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets von Cantrell, Kalen, Fedarko, Marcus W, Rahman, Gibraan, McDonald, Daniel, Yang, Yimeng, Zaw, Thant, Gonzalez, Antonio, Janssen, Stefan, Estaki, Mehrbod, Haiminen, Niina, Beck, Kristen L, Zhu, Qiyun, Sayyari, Erfan, Morton, James T, Armstrong, George, Tripathi, Anupriya, Gauglitz, Julia M, Marotz, Clarisse, Matteson, Nathaniel L, Martino, Cameron, Sanders, Jon G, Carrieri, Anna Paola, Song, Se Jin, Swafford, Austin D, Dorrestein, Pieter C, Andersen, Kristian G, Parida, Laxmi, Kim, Ho-Cheol, Vázquez-Baeza, Yoshiki, Knight, Rob

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Streaming histogram sketching for rapid microbiome analytics von Rowe, Will Pm, Carrieri, Anna Paola, Alcon-Giner, Cristina, Caim, Shabhonam, Shaw, Alex, Sim, Kathleen, Kroll, J Simon, Hall, Lindsay J, Pyzer-Knapp, Edward O, Winn, Martyn D

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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets von Cantrell, Kalen, Fedarko, Marcus W., Rahman, Gibraan, McDonald, Daniel, Yang, Yimeng, Zaw, Thant, Gonzalez, Antonio, Janssen, Stefan, Estaki, Mehrbod, Haiminen, Niina, Beck, Kristen L., Zhu, Qiyun, Sayyari, Erfan, Morton, James T., Armstrong, George, Tripathi, Anupriya, Gauglitz, Julia M., Marotz, Clarisse, Matteson, Nathaniel L., Martino, Cameron, Sanders, Jon G., Carrieri, Anna Paola, Song, Se Jin, Swafford, Austin D., Dorrestein, Pieter C., Andersen, Kristian G., Parida, Laxmi, Kim, Ho-Cheol, Vázquez-Baeza, Yoshiki, Knight, Rob

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Challenges in benchmarking metagenomic profilers von Sun, Zheng, Huang, Shi, Zhang, Meng, Zhu, Qiyun, Haiminen, Niina, Carrieri, Anna Paola, Vázquez-Baeza, Yoshiki, Parida, Laxmi, Kim, Ho-Cheol, Knight, Rob, Liu, Yang-Yu

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Fixed-parameter algorithms for scaffold filling von Bulteau, Laurent, Carrieri, Anna Paola, Dondi, Riccardo

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Sampling ARG of multiple populations under complex configurations of subdivision and admixture von Carrieri, Anna Paola, Utro, Filippo, Parida, Laxmi

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Using human in vitro transcriptome analysis to build trustworthy machine learning models for prediction of animal drug toxicity von Gardiner, Laura-Jayne, Carrieri, Anna Paola, Wilshaw, Jenny, Checkley, Stephen, Pyzer-Knapp, Edward O., Krishna, Ritesh

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Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes von Armstrong, George, Cantrell, Kalen, Huang, Shi, McDonald, Daniel, Haiminen, Niina, Carrieri, Anna Paola, Zhu, Qiyun, Gonzalez, Antonio, McGrath, Imran, Beck, Kristen L, Hakim, Daniel, Havulinna, Aki S, Méric, Guillaume, Niiranen, Teemu, Lahti, Leo, Salomaa, Veikko, Jain, Mohit, Inouye, Michael, Swafford, Austin D, Kim, Ho-Cheol, Parida, Laxmi, Vázquez-Baeza, Yoshiki, Knight, Rob

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AutoXAI4Omics: an automated explainable AI tool for omics and tabular data von Strudwick, James, Gardiner, Laura-Jayne, Denning-James, Kate, Haiminen, Niina, Evans, Ashley, Kelly, Jennifer, Madgwick, Matthew, Utro, Filippo, Seabolt, Ed, Gibson, Christopher, Bedi, Bharat, Clayton, Daniel, Howell, Ciaron, Parida, Laxmi, Carrieri, Anna Paola

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Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function von Gardiner, Laura-Jayne, Rusholme-Pilcher, Rachel, Colmer, Josh, Rees, Hannah, Crescente, Juan Manuel, Carrieri, Anna Paola, Duncan, Susan, Pyzer-Knapp, Edward O., Krishna, Ritesh, Hall, Anthony

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A colored graph approach to perfect phylogeny with persistent characters von Bonizzoni, Paola, Carrieri, Anna Paola, Della Vedova, Gianluca, Rizzi, Raffaella, Trucco, Gabriella

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Host Phenotype Prediction from Differentially Abundant Microbes Using RoDEO von Carrieri, Anna Paola, Haiminen, Niina, Parida, Laxmi

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Explaining evolution via constrained persistent perfect phylogeny von Bonizzoni, Paola, Carrieri, Anna Paola, Della Vedova, Gianluca, Trucco, Gabriella

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