Publications

Peer-reviewed publications, preprints and conference presentations by Natalia Gumińska, PhD.

Peer-reviewed articles and preprints. The complete and canonical record is on ORCID and Google Scholar.

Publications

2026

Poly(A) profiling for euglenozoans using Oxford Nanopore direct RNA sequencing, illustrated by the example of Euglena gracilis

First author

Book chapter

Nanopore

poly(A)

Euglenids

A protocol chapter taking the poly(A) tail workflow to organisms it was not designed for.

Gumińska N., Czarnocka-Cieciura A., Zakryś B., Milanowski R.

Methods in Molecular Biology, volume 3013

Protocol for efficient ribodepletion of Euglena gracilis RNA

First author

Book chapter

Method

Euglenids

Removing ribosomal RNA from an organism with no off-the-shelf kit.

Gumińska N., Hałakuc P., Zakryś B., Milanowski R.

Methods in Molecular Biology, volume 3014

rDNAmine: a new tool for the analysis of long repetitive sequences

Journal article

Software

Long reads

Long reads span repeat arrays that short reads collapse, which makes rDNA tractable again.

Czarnocka-Cieciura A., Gumińska N.

Yeast

2025

Polyadenylation landscape of in vivo long-term potentiation in the rat brain

First author

Journal article

Nanopore

poly(A)

Neuroscience

What happens to poly(A) tails in the hours after a memory is laid down.

Gumińska N., Pauzin F.P., Kuźniewska B., Miłek J., Wardaszka P., Krawczyk P.S., Mroczek S., Jeleń S., Pagenhart P.U., Bramham C.R., Dziembowski A., Dziembowska M.

RNA

Re-adenylation by TENT5A enhances efficacy of SARS-CoV-2 mRNA vaccines

Journal article

poly(A)

mRNA therapeutics

A cellular enzyme extends the tails of vaccine mRNA, and that extension tracks with how well the vaccine works.

Krawczyk P.S., Mazur M., Orzeł W., Gewartowska O., Jeleń S., Antczak W., Kasztelan K., Brouze A., Matylla-Kulińska K., Gumińska N., et al., Dziembowski A., Mroczek S.

Nature

Direct profiling of non-adenosines in poly(A) tails of endogenous and therapeutic mRNAs with Ninetails

First author

Journal article

Nanopore

poly(A)

Software

Deep learning

The ninetails paper. A convolutional network reads raw nanopore current and finds the residues in a poly(A) tail that are not adenosine.

Gumińska N., Matylla-Kulińska K., Krawczyk P.S., Maj M., Orzeł W., Mackiewicz Z., Brouze A., Mroczek S., Dziembowski A.

Nature Communications

Terminal nucleotidyltransferase Tent2 microRNA A-tailing enzyme regulates excitatory/inhibitory balance in the hippocampus

Journal article

poly(A)

Neuroscience

Tailing of microRNAs, and what it does to the balance of signalling in the hippocampus.

Wardaszka-Pianka P., Kuźniewska B., Gumińska N., Hojka-Osińska A., Puchalska M., Miłek J., Stawikowska A., Krawczyk P.S., Pauzin F.P., Wojtowicz T., Radwańska K., Bramham C.R., Dziembowski A., Dziembowska M.

RNA

Comprehensive analysis of poly(A) tails in mouse testes and ovaries using Nanopore direct RNA sequencing

Journal article

Nanopore

poly(A)

Dataset

A reference dataset of tail lengths across mouse germline tissue.

Czarnocka-Cieciura A., Brouze M., Gumińska N., Mroczek S., Gewartowska O., Krawczyk P.S., Dziembowski A.

Scientific Data

2024

Circular extrachromosomal DNA in Euglena gracilis under normal and stress conditions

First author

Journal article

Euglenids

Circular DNA

Which parts of the genome escape as circles, and whether stress changes the answer.

Gumińska N., Hałakuc P., Zakryś B., Milanowski R.

Protist

Efficient globin production during terminal erythropoiesis depends on the synergistic action of TENT5C poly(A) polymerase and LARP4/5

Preprint

poly(A)

Preprint. Tail extension as a throttle on how much haemoglobin a maturing red blood cell can make.

Mazur M., Gumińska N., Brouze A., Cysewski D., Mleczko-Sanecka K., Niklewicz M., Kusio-Kobiałka M., Dziembowski A.

bioRxiv (preprint, in review)

2022

TENT5 cytoplasmic noncanonical poly(A) polymerases regulate the innate immune response in animals

Journal article

poly(A)

Immunology

A family of tailing enzymes turns out to sit inside the innate immune response.

Liudkovska V., Krawczyk P.S., Brouze A., Gumińska N., Wegierski T., Cysewski D., Mackiewicz Z., Ewbank J.J., Drabikowski K., Mroczek S., Dziembowski A.

Science Advances

A long noncoding RNA promotes parasite differentiation in African trypanosomes

Journal article

RNA biology

Parasitology

A noncoding transcript acting as a switch in the trypanosome life cycle.

Guegan F., Rajan K.S., Bento F., Pinto-Neves D., Sequeira M., Gumińska N., Mroczek S., Dziembowski A., Cohen-Chalamish S., Doniger T., et al.

Science Advances

2021

Evaluation of V2 18S rDNA barcode marker and assessment of sample collection and DNA extraction methods for metabarcoding of autotrophic euglenids

First author

Journal article

Euglenids

Method

Which barcode region, and which extraction method, survive contact with pond water.

Gumińska N., Łukomska-Kowalczyk M., Chaber K., Zakryś B., Milanowski R.

Environmental Microbiology

A new type of circular RNA derived from nonconventional introns in nuclear genes of euglenids

First author

Journal article

Euglenids

RNA biology

Introns removed unconventionally leave behind circles nobody had catalogued.

Gumińska N., Zakryś B., Milanowski R.

Journal of Molecular Biology

2018

Order of removal of conventional and nonconventional introns from nuclear transcripts of Euglena gracilis

First author

Journal article

Euglenids

RNA biology

Splicing order is not arbitrary, and the two intron types are not removed in the same pass.

Gumińska N., Płecha M., Zakryś B., Milanowski R.

PLOS Genetics

Culture purification and DNA extraction procedures suitable for next-generation sequencing of euglenids

First author

Journal article

Euglenids

Method

Getting material clean enough out of a culture that a sequencer will accept it.

Gumińska N., Płecha M., Walkiewicz H., Hałakuc P., Zakryś B., Milanowski R.

Journal of Applied Phycology

2016

Intermediate introns in nuclear genes of euglenids – are they a distinct type?

Journal article

Euglenids

RNA biology

A third category of intron, or a continuum between the two already known.

Milanowski R., Gumińska N., Karnkowska A., Ishikawa T., Zakryś B.

BMC Evolutionary Biology

Conference presentations

Selected talks and posters. Awarded presentations are marked.

2025 · Poznań

Tracking poly(A) tail diversity with Ninetails: mixed tails from cells to mRNA therapies

2nd Polish RNA Meeting

2024 · Edinburgh

The polyadenylation landscape after in vivo long-term potentiation in the rat brain best poster

29th Annual Meeting of the RNA Society

2023 · Warsaw

Detection of non-adenosine residues within poly(A) tails using Oxford Nanopore direct RNA sequencing and deep learning best poster

1st Polish RNA Meeting

2023 · London

Ninetails: a comprehensive tool for investigation of non-adenosine residues within poly(A) tails from direct RNA sequencing data

London Calling (online)

2022 · online

Investigating the repertoire of nuclear-derived circular extrachromosomal DNAs in Euglena gracilis invited speaker

2nd Annual International Congress on Euglenoids

2022 · Boulder

Direct detection of non-adenosine nucleotides within poly(A) tails – a new tool for the analysis of post-transcriptional mRNA tailing best poster

27th Annual Meeting of the RNA Society

2019 · Rome

Assessment of V2 18S rDNA as a DNA barcode for phototrophic euglenids best poster

8th European Congress of Protistology

2017 · Prague

The order of intron removal during splicing of α-tubulin (tubA) pre-mRNA in Euglena gracilis

15th International Congress of Protistology (Holz-Conner Travel Award)

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