Anna Paola Carrieri  Anna Paola Carrieri photo         

contact information

Manager & Senior Research Scientist
IBM Research Laboratory, UK



Efficient computation of Faiths phylogenetic diversity with applications in characterizing microbiomes
George W Armstrong, Kalen Cantrell, Shi Huang, Daniel McDonald, Niina Haiminen, Anna Paola Carrieri, Qiyun Zhu, Antonio Gonzalez, Imran McGrath, Kristen Beck, Daniel Hakim, Aki S Havulinna, Guillaume Meric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Mohit Jain, Michael Inouye, Austin D Swafford, Ho-Cheol Kim, Laxmi Parida, Yoshiki Vazquez-Baeza, Rob Knight
Genome Research, Cold Spring Harbor Laboratory, 2021
Abstract   phylogenetic diversity, alpha diversity, metric, phylogenetic tree, metagenomics, diversity, scale, data mining, computation, biology

Combining explainable machine learning, demographic and multi-omic data to identify precision medicine strategies for inflammatory bowel disease
Gardiner L, Carrieri Ap, Bingham K, Macluskie G, Bunton D, McNeil M, Pyzer-Knapp Eo
medRxiv, Cold Spring Harbor Laboratory Press, 2021
Abstract   precision medicine, disease, inflammatory bowel disease, efficacy, drug, ulcerative colitis, omics, transcriptome, medicine, machine learning, artificial intelligence

Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function
Gardiner L, Rusholme-Pilcher R, Colmer J, Rees H, Crescente Jm, Carrieri Ap, Duncan S, Pyzer-Knapp Eo, Krishna R, Halll A
bioRxiv, Cold Spring Harbor Laboratory, 2021
Abstract   circadian clock, circadian rhythm, expression, function, identification, machine learning, computer science, artificial intelligence, circadian regulation, experimental work, model interpretation

Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
Anna Paola Carrieri, Niina Haiminen, Sean Maudsley-Barton, Laura-Jayne Gardiner, Barry Murphy, Andrew Mayes, Sarah Paterson, Sally Grimshaw, Martyn Winn, Cameron Shand, Panagiotis Hadjidoukas, Will Rowe, Stacy Hawkins, Ashley MacGuire-Flanagan, Jane Tazzioli, John Kenny, Laxmi Parida, Michael Hoptroff, Edward O Pyzer-Knapp
Scientific Reports 11(4565), 2021
Abstract   Blog:

SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment
C. Marotz, P. Belda-Ferre, F. Ali, P. Das, K. Cantrell, L. Jiang, C. Martino, R. E. Diner, G. Rahman, D. McDonald, G. Armstrong, S. Kodera, S. Donato, G. Ecklu-Mensah, N. Gottel M. C. Salas Garcia, L. Y. Chiang, R. A. Salido, J. P. Shaffer, M. K. Bryant, K. Sanders, G. Humphrey, G. Ackerman, N. Haiminen, K. L. Beck, H-C. Kim, A. P. Carrieri, L. Parida, Y. Vazquez-Baeza, F. J. Torriani, R. Knight, J. Gilbert, D. A. Sweeney, S. M. Allard
Microbiome 9(132), 2021
Abstract   Learn more:

Multi-omics profiling of Earths biomes reveals that microbial and metabolite composition are shaped by the environment
Shaffer Jp, Nothias L, Nothias L, Thompson Lr, Thompson Lr, Sanders Jg, Salido Ra, Couvillion Sp, Brejnrod Ad, Huang S, Lejzerowicz F, Lutz Hl, Zhu Q, Martino C, Morton Jt, Karthikeyan S, Nothias-Esposito M, Nothias-Esposito M, Duhrkop K, Bocker S, Kim H, Aksenov Aa, Aksenov Aa, Bittremieux W, Bittremieux W, Bittremieux W, Minich Jj, Marotz C, Bryant Mm, Sanders K, Schwartz T, Humphrey G, Vasquez-Baeza Y, Tripathi A, Tripathi A, Parida L, Carrieri Ap, Haiminen N, Beck Kl, Das P, Gonzalez A, McDonald D, Kars
bioRxiv, Cold Spring Harbor Laboratory, 2021
Abstract   metabolome, metagenomics, metabolite, microbiome, genome, computational biology, biome, biology, profiling, multi omics

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
Kalen Cantrell, Marcus W. Fedarko, Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Stefan Janssen, Mehrbod Estaki, Niina Haiminen, Kristen L. Beck, Qiyun Zhu, Erfan Sayyari, James T. Morton, George Armstrong, Anupriya Tripathi, Julia M. Gauglitz, Clarisse Marotz, Nathaniel L. Matteson, Cameron Martino, Jon G. Sanders, Anna Paola Carrieri, Se Jin Song, Austin D. Swafford, Pieter C. Dorrestein, Pieter C. Dorrestein, Kristian G. Andersen, Laxmi Parida, Ho Cheol Kim, Yoshiki Vazquez-B
mSystems 6(2), American Society for Microbiology, 2021
Abstract   context, tree, data structure, workflow, data science, scalability, ordination, computer science, microbiome, scale

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data
Lingjing Jiang, Niina Haiminen, Anna-Paola Carrieri, Shi Huang, Yoshiki Vazquez-Baeza, Laxmi Parida, Ho-Cheol Kim, Austin D. Swafford, Rob Knight, Loki Natarajan
Biometrics, 2021
Abstract   CMI blog:

Challenges in benchmarking metagenomic profilers
Zheng Sun, Shi Huang, Meng Zhang, Qiyun Zhu, Niina Haiminen, Anna-Paola Carrieri, Yoshiki Vazquez-Baeza, Laxmi Parida, Ho-Cheol Kim, Rob Knight, Yang-Yu Liu
Nature Methods, 2021
Abstract   CMI blog:


Human Skin, Oral, and Gut Microbiomes Predict Chronological Age
Shi Huang, Niina Haiminen, Anna-Paola Carrieri, Rebecca Hu, Lingjing Jiang, Laxmi Parida, Baylee Russell, Celeste Allaband, Amir Zarrinpar, Yoshiki V\'azquez-Baeza, Pedro Belda-Ferre, Hongwei Zhou, Ho-Cheol Kim, Austin D. Swafford, Rob Knight, Zhenjiang Zech Xu
mSystems 5(1), American Society for Microbiology Journals, 2020


Combining human cell line transcriptome analysis and Bayesian inference to build trustworthy machine learning models for prediction of animal toxicity in drug development
Laura-Jayne Gardiner, Anna Paola Carrieri, Jenny Wilshaw, Stephen Checkley, Edward O Pyzer-Knapp, Ritesh Krishna
arXiv preprint arXiv:1911.04374, 2019
Abstract   trustworthiness, model selection, machine learning, genomics, gaussian process, drug discovery, drug development, biology, bayesian probability, bayesian inference, artificial intelligence

A Fast Machine Learning Workflow for Rapid Phenotype Prediction from Whole Shotgun Metagenomes
Anna Paola Carrieri, Will P. M. Rowe, Martyn D. Winn, Edward O. Pyzer-Knapp
Proceedings of the AAAI Conference on Artificial Intelligence, pp. 9434-9439, 2019
Abstract   workflow, terabyte, shotgun, precision agriculture, microbiome, metagenomics, machine learning, computer science, cloud computing, big data, artificial intelligence

Streaming histogram sketching for rapid microbiome analytics
WP Rowe, Anna Paola Carrieri, Cristina Alcon-Giner, Shabhonam Caim, Alex Shaw, Kathleen Sim, J Simon Kroll, Lindsay Hall, Edward O Pyzer-Knapp, Martyn D Winn
Microbiome, 40, BioMed Central, 2019


Accelerating molecular discovery through data and physical sciences: Applications to peptide-membrane interactions
Flaviu Cipcigan, Anna Paola Carrieri, Edward O Pyzer-Knapp, Ritesh Krishna, Ya-Wen Hsiao, Martyn Winn, Maxim G Ryadnov, Colin Edge, Glenn Martyna, Jason Crain
The Journal of chemical physics, 2018


A colored graph approach to the perfect phylogeny with persistent characters
Bonizzoni P., Carrieri A.P., Della Vedova G., Trucco, G.
Theoretical Computer Science658, 60-73, 2017

Host phenotype prediction from differentially abundant microbes using RoDEO
A.P. Carrieri*, N. Haiminen*, L. Parida
In: Bracciali A., Caravagna G., Gilbert D., Tagliaferri R. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics, Lecture Notes in Computer Science, pp. 27-41, Springer, 2017

Species-Driven Persistent Phylogeny
Bonizzoni, P., Carrieri, A. P., Della Vedova, G., Rizzi, R., Trucco, G.
Fundamenta Informaticae 154(1-4), 47-63, IOS Press, 2017


Dimension reduction of metagenome data using RoDEO improves phenotype prediction
Carrieri A.P., Haiminen N., Parida L.
In: Computational Intelligence Methods for Bioinformatics and Biostatistics, Proc. 13th International Meeting CIBB, Bracciali A., Gilbert D., MacKenzie G. (Eds.), pp. 51-56, 2016


Fixed-parameter algorithms for scaffold filling
Bulteau, L., Carrieri, A. P., Dondi, R.
Theoretical Computer Science, pp. 72-83, Elsevier, 2015

Topological Signatures for Population Admixture
Parida L., Utro F., Yorukoglu D., Carrieri A.P., David Kuhn D., Basu S.
In: Research in Computational Molecular Biology, RECOMB 2015, Lecture Notes in Computer Science, Teresa M. Przytycka (Ed.), pp. 261-275, Springer


Algorithms for the Constrained Perfect Phylogeny with Persistent Characters
Bonizzoni, P., Carrieri, A. P., Della Vedova, G., Trucco, G.
arXiv preprint arXiv:1405.7497, 2014

SimRA: Rapid & Accurate Simulation of Populations based on Random-Graph Models of ARG
Carrieri A.P., Parida L.
Poster: RECOMB-CG, Cold Spring Harbor (NY) , 2014

Fixed-Parameter Algorithms for Scaffold Filling
Bulteau, L., Carrieri, A.P., Dondi, R.
In: Proc. Third International Symposium on Combinatorial Optimization, ISCO 2014, Lisbon, Portugal, Lecture Notes in Computer Science, P. Fouilhoux, L. E. Neves Gouveia, A. Ridha Mahjoub, V. T. Paschos (Eds), pp. 137-148, Springer

Explaining Evolution via Constrained Persistent Perfect Phylogeny
Bonizzoni P., Carrieri A.P., Della Vedova G., Trucco G.
BMC Genomics 15(6), 2014


When and how the perfect phylogeny model explains evolution
Bonizzoni, P., Carrieri, A. P., Della Vedova, G., Dondi, R., Przytycka, T. M.
Discrete and Topological Models in Molecular Biology, Jonoska N., Saito M. (Eds), pp. 67-83, Springer, 2013


An in-silico framework for comparing and validating transcripts predicted from single and paired-end reads
Beretta S., Bonizzoni P., Carrieri A.P., Della Vedova G., Pirola Y., Pesole G., Picardi E., Rizzi R.
Poster: Next Generation Sequencing Workshop, Bari (Italy) , 2012