Polecane publikacje

Spis publikacji do wybranych przedmiotów kursu – materiały polecane przez wykładowców Omics Data Science
Pełną listę zajęć można znaleźć tutaj.

Wprowadzenie do analizy danych wysokoprzepustowych

  • Quantum computing in bioinformatics: a systematic review mapping

    Katarzyna Nałęcz-Charkiewicz, Kamil Charkiewicz, Robert M. Nowak

    Briefings in Bioinformatics, 2024, 25(5), bbae391

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  • Algorithm for DNA sequence assembly by quantum annealing

    Katarzyna Nałęcz-Charkiewicz & Robert M. Nowak

    BMC Bioinformatics (2022) 23:122

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  • CNVind: an open source cloud‐based pipeline for rare CNVs detection in whole exome sequencing data based on the depth of coverage

    Wiktor Kuśmirek & Robert M. Nowak

    BMC Bioinformatics 23, Article number: 85 (2022)

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  • Forecasting SARS-CoV-2 epidemic dynamic in Poland with the pDyn agent-based mode

    Karol Niedzielewski, K. , Bartczuk, R. a b, Natalia Bielczyk, N.,…, Górski, Ł. … et al.

    Epidemics. 2024 Nov 12:49:100801

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  • A pre-registered short-term forecasting study of COVID-19 in Germany and Poland during the second wave

    Bracher, J., Wolffram, D., Deuschel, J.,… Górski, Ł. (ICM-agent Model), … et al.

    Nature Communications 12, Article number: 5173 (2021)

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  • Algorithms and Architectures for Parallel Processing

    Shadi Ibrahim , Kim-Kwang Raymond Choo , Zheng Yan , Witold Pedrycz

    ICA3PP 2017, Helsinki, Finland, August 21–23, 2017 Proceedings

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Praktyczne wykorzystanie analiz wysokoprzepustowych

  • Comprehensive analysis of the REST transcription factor regulatory networks in IDH mutant and IDH wild-type glioma cell lines and tumors

    Perycz, M., Dabrowski, M.J., Jardanowska-Kotuniak, M.,…, Wojtas, B., et al.

    Acta Neuropathologica Communications 12, Article number: 72 (2024)

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  • Regulatory networks driving expression of genes critical for glioblastoma are controlled by the transcription factor c-Jun and the pre-existing epigenetic modifcations

    Roura, AJ., Szadkowska, P., Poleszak, K., Wojtas, B., et al.

    Clinical Epigenetics 15, Article number: 29 (2023)

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  • Targeted sequencing of cancer-related genes reveals a recurrent TOP2A variant which affects DNA binding and coincides with global transcriptional changes in glioblastoma

    Gielniewski, B., Poleszak, K., Roura, A-J,…, Wojtas, B., et al.

    International Journal of Cancer. 2023;153(5):1003‐1015

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  • Identification of the immune gene expression signature associated with recurrence of high-grade gliomas

    Roura AJ, Gielniewski B, Pilanc P, Szadkowska P, Maleszewska M, Krol SK, Czepko R, Kaspera W, Wojtas B., Kaminska B.

    Journal of Molecular Medicine (2021) 99:241–255

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  • Determinants of the microbiome spatial variability in chronic rhinosinusitis

    Szaleniec J, Bezshapkin V, Krawczyk A, Kopera K, Zapala B, Gosiewski T, Kosciolek T.

    Rhinology 62: 1, 119 – 126, 2024

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  • Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method

    Maranga M, Szczerbiak P, Bezshapkin V, Gligorijevic V, Chandler C, Bonneau R, Xavier RJ, Vatanen T, Kosciolek T.

    mSystems 8:e01178-22 (2023)

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  • Treatment With Multi-Species Probiotics Changes the Functions, Not the Composition of Gut Microbiota in Postmenopausal Women With Obesity: A Randomized, Double-Blind, Placebo-Controlled Study

    Kaczmarczyk M, Szulińska M, Łoniewski I, Kręgielska-Narożna M, Skonieczna-Żydecka K, Kosciolek T, Bezshapkin V, Bogdański P.

    Front. Cell. Infect. Microbiol. 12:815798 (2022)

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  • QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

    Estaki M, Jiang L, Bokulich NA, McDonald D, González A, Kosciolek T, et al.

    Current Protocols in Bioinformatics, 70, e100 (2020)

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  • Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

    Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Kosciolek T, et al.

    Nat Biotechnol. 2019 August; 37(8): 852–857

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  • Qiita: rapid, web-enabled microbiome meta-analysis

    Gonzalez, A., Navas-Molina, J.A., Kosciolek, T. et al.

    Nat Methods. 2018 October ; 15(10): 796–798

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  • A communal catalogue reveals Earth’s multiscale microbial diversity

    Thompson, L., Sanders, J., McDonald, D., …, Kosciolek, T. et al.

    Nature 551, pages457–463 (2017)

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