Laboratory of Bioinformatics

Dr. hab. Anna Philips, prof. IBCH PAS

Head of Laboratory

aphilips@ibch.poznan.pl
ext. 1647

Research Projects

Keywords

NGS
WGS
RNA-seq
DE
Metagenomics
Transcriptomics
SNP
CNV
PCA

Offer

NGS:

Analysis of differential gene expression
Analysis of differential expression of transcripts (alternative splicing)
Assembly of transcriptomes ab initio (based on genome) and de novo (without genome sequence) and their annotation
Identification of new genes and splicing forms
Analysis of non-coding RNAs (miRNA, piRNA, circRNA ect.)
Identification of miRNA target sequences
SNP identification
CNV identification
Analysis of WGS, exons (Exome-Seq) and selected genes (targeted sequencing)
De novo assembly of genomes and their annotation
Metagenomics analyses

Other:

Data mining
Statistical analyses
Analysis of biological data in Python and Bioconductor (R language)

Equipment

Computers with high computing power
Computing cluster

Research activity

Predicting response to immunotherapy in melanoma using metabolic signatures of intestinal fungi - SONATA 21
Polish Microbiome Map - NCRD
"Airborne microbiome - characterization of microorganisms inhabiting particulate matter of urban areas and their impact on human health" - OPUS 21

Selected publications

1: Machowska M, Szostak N, Tire A, Wegorek W, Suszynska M, Kajdasz A, Galka- Marciniak P, Philips A, Kozlowski P. miRNA gene mutations commonly disrupt the proper functioning of miRNA genes. Sci Adv. 2026 Feb 20;12(8):eaea6079. doi: 10.1126/sciadv.aea6079. Epub 2026 Feb 18.

2: Szóstak N, Kozłowski P, Zuo T, Philips A. The role of gut mycobiome in responses to cancer immunotherapy. Gut Microbes. 2025 Dec 31;17(1):2571433. doi: 10.1080/19490976.2025.2571433. Epub 2025 Oct 29.

3: Galka-Marciniak P, Urbanek-Trzeciak MO, Kuznicki D, Szostak N, Tire A, Nawrocka-Muszynska PM, Chojnacka K, Suszynska M, Klonowska K, Czubak K, Machowska M, Philips A, Maksin K, Susok L, Sand M, Rys J, Jura J, Ratajska M, Dams-Kozlowska H, Kowalewski J, Lewandowska MA, Kozlowski P. Whole-miRNome sequencing: a panel for the targeted sequencing of all human miRNA genes. Nucleic Acids Res. 2025 Aug 27;53(16):gkaf812. doi: 10.1093/nar/gkaf812.

4: Su R, Wen W, Jin Y, Cao Z, Feng Z, Chen J, Lu Y, Zhou G, Dong C, Gao S, Li X, Zhang H, Chao K, Lan P, Wu X, Philips A, Li K, Gao X, Zhang F, Zuo T. Dietary whey protein protects against Crohn's disease by orchestrating cross-kingdom interaction between the gut phageome and bacteriome. Gut. 2025 Jul 7;74(8):1246-1260. doi: 10.1136/gutjnl-2024-334516.

5: Huang Z, Liu Y, Philips A, Zhang F, Zuo T. Varied prevalence and asymptomatic carriage of Cryptococcus gattii in the gut of Chinese populations. Lancet Microbe. 2025 Jul;6(7):101086. doi: 10.1016/j.lanmic.2025.101086. Epub 2025 Feb 6.

6: Feng Z, Burgermeister E, Philips A, Zuo T, Wen W. The gut virome in association with the bacteriome in gastrointestinal diseases and beyond: roles, mechanisms, and clinical applications. Precis Clin Med. 2025 May 28;8(2):pbaf010. doi: 10.1093/pcmedi/pbaf010

7: Wu Y, Cheng R, Lin H, Li L, Jia Y, Philips A, Zuo T, Zhang H. Gut virome and its implications in the pathogenesis and therapeutics of inflammatory bowel disease. BMC Med. 2025 Mar 26;23(1):183. doi: 10.1186/s12916-025-04016-y.

8: Szóstak N, Budnik M, Tomela K, Handschuh L, Samelak-Czajka A, Pietrzak B, Schmidt M, Kaczmarek M, Galus Ł, Mackiewicz J, Mackiewicz A, Kozlowski P, Philips A. Exploring correlations between gut mycobiome and lymphocytes in melanoma patients undergoing anti-PD-1 therapy. Cancer Immunol Immunother. 2025 Feb 25;74(4):110. doi: 10.1007/s00262-024-03918-9.

9: Szóstak N, Handschuh L, Samelak-Czajka A, Tomela K, Pietrzak B, Schmidt M, Galus Ł, Mackiewicz J, Mackiewicz A, Kozlowski P, Philips A. Gut Mycobiota Dysbiosis Is Associated with Melanoma and Response to Anti-PD-1 Therapy. Cancer Immunol Res. 2024 Apr 2;12(4):427-439. doi: 10.1158/2326-6066.CIR-23-0592.

10: Suszynska M, Machowska M, Fraszczyk E, Michalczyk M, Philips A, Galka- Marciniak P, Kozlowski P. CMC: Cancer miRNA Census - a list of cancer-related miRNA genes. Nucleic Acids Res. 2024 Feb 28;52(4):1628-1644. doi: 10.1093/nar/gkae017.

11: Szóstak N, Handschuh L, Samelak-Czajka A, Tomela K, Schmidt M, Pruss Ł, Milanowska-Zabel K, Kozlowski P, Philips A. Host Factors Associated with Gut Mycobiome Structure. mSystems. 2023 Apr 27;8(2):e0098622. doi: 10.1128/msystems.00986-22. Epub 2023 Feb 14.

12: Szóstak N, Figlerowicz M, Philips A. The emerging role of the gut mycobiome in liver diseases. Gut Microbes. 2023 Jan-Dec;15(1):2211922. doi: 10.1080/19490976.2023.2211922.

13: Szóstak N, Szymanek A, Havránek J, Tomela K, Rakoczy M, Samelak-Czajka A, Schmidt M, Figlerowicz M, Majta J, Milanowska-Zabel K, Handschuh L, Philips A. The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling. Sci Rep. 2022 May 19;12(1):8470. doi: 10.1038/s41598-022-12037-3.

14: Makowska N, Philips A, Dabert M, Nowis K, Trzebny A, Koczura R, Mokracka J. Metagenomic analysis of β-lactamase and carbapenemase genes in the wastewater resistome. Water Res. 2020 Mar 1;170:115277. doi: 10.1016/j.watres.2019.115277. Epub 2019 Nov 7.

15: Philips A, Stolarek I, Kuczkowska B, Juras A, Handschuh L, Piontek J, Kozlowski P, Figlerowicz M. Comprehensive analysis of microorganisms accompanying human archaeological remains. Gigascience. 2017 Jul 1;6(7):1-13. doi: 10.1093/gigascience/gix044.

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