Publications

Computational Genomics Group

International Centre for Translational Eye Research

Institute of Physical Chemistry, Polish Academy of Sciences

All publications

Distinct mouse models of Stargardt disease display differences in pharmacological targeting of ceramides and inflammatory responses

Proceedings of the National Academy of Sciences 120, e2314698120 (2023)

34

Stress resilience-enhancing drugs preserve tissue structure and function in degenerating retina via phosphodiesterase inhibition

Proceedings of the National Academy of Sciences 120, e2221045120 (2023)

33

Tim-3 adapter protein Bat3 acts as an endogenous regulator of tolerogenic dendritic cell function

Science Immunology 7, DOI: 10.1126/sciimmunol.abm0631 (2022)

Cycling cancer persister cells arise from lineages with distinct programs

Nature 596, 576-582 (2021)

28

TIM-3 restrains anti-tumour immunity by regulating inflammasome activation

Nature 595, 101–106 (2021)

27

Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells

Nature 586, 769–775 (2020)

26

Inhibition of ceramide accumulation in AdipoR1–/– mice increases photoreceptor survival and improves vision

JCI insight 7, e156301 (2022)

30

Blood and immune development in human fetal bone marrow and Down syndrome

Nature 598, 327-331 (2021)

29

spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content

Nature Communications 14, 4768 (2023)

32

31

Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq

Nature Methods 17, 793–798 (2020)

25

Integrated scRNA-Seq identifies human postnatal thymus seeding progenitors and regulatory dynamics of differentiating immature thymocytes

Immunity 52, 1088–1104 (2020)

24

Transcriptional atlas of intestinal immune cells reveals that neuropeptide α-CGRP modulates group 2 innate lymphoid cell responses

Immunity 51, 696–708 (2019)

23

A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia

Cell 177, 1–18 (2019)

Decoding human fetal liver haematopoiesis

Nature 574, 365-371 (2019)

22

A cellular taxonomy of the bone marrow stroma in homeostasis and leukemia

Cell 177, 1–18 (2019)

21

Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming

Cell 176, 928–943 (2019)

20

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

Nature Genetics 50, 1140-1150 (2018)

19

Enforcement of developmental lineage specificity by transcription factor Oct1

eLife 6, e20937 (2017)

18

Hill kinetics as a noise filter: the role of transcription factor autoregulation in gene cascades

Phys. Chem. Chem. Phys 19, 22580-22591 (2017)

17

The hinge region strengthens the nonspecific interaction between lac-repressor and DNA: a computer simulation study

PLoS ONE 11, e0152002 (2016)

16

Method for the analysis of contribution of sliding and hopping to a facilitated diffusion of DNA-binding protein: application to in vivo data

Phys. Rev. E 92, 022721 (2015)

15

Transcriptional leakage versus noise: a simple mechanism of conversion between binary and graded response in autoregulated genes

Phys. Rev. E 91, 012704 (2015)

14

Small crowders slow down Kinesin-1 stepping by hindering motor domain diffusion

Phys. Rev. Lett. 115, 218102 (2015)

13

Motion of nanoprobes in complex liquids within the framework of the length-scale dependent viscosity model

Adv. Colloid Interface Sci. 223, 55 (2015)

12

Quantitative influence of macromolecular crowding on gene regulation kinetics

Nucleic Acids Res. 42, 727-738 (2014)

11

The effect of macromolecular crowding on mobility of biomolecules, association kinetics and gene expression in living cells

Front. Phys. 2, 54 (2014)

10

A flexible fluorescence correlation spectroscopy based method for quantification of the DNA double labeling efficiency with precision control

Laser Phys. Lett. 11, 085602 (2014)

9

Implications of macromolecular crowding for protein-protein association kinetics in cytoplasm of living cells

Soft Matter 9, 4386-4389 (2013)

8

Taylor dispersion analysis in coiled capillary at high flow rates

Anal. Chem. 85, 4051-4056 (2013)

7

Biologistics–diffusion coefficients for complete proteome of Escherichia coli

Bioinformatics 28, 2971-2978 (2012)

6

Characterization of Caulobacter crescentus FtsZ protein using dynamic light scattering

J. Biol. Chem. 287, 23878-23886 (2012)

5

Bimodal gene expression in noncooperative regulatory systems

PNAS 107, 22096-22101 (2010)

4

Binary and graded evolution in time in a simple model of gene induction

Phys. Rev. E 82, 052902 (2010)

3

Scaling form of viscosity at all length-scales in poly(ethylene glycol) solutions studied by fluorescence correlation spectroscopy and capillary electrophoresis

Phys. Chem. Chem. Phys. 11, 9025-9032 (2009)

2

Accurate genetic switch in Escherichia coli: novel mechanism of regulation by corepressor

J. Mol. Biol. 377, 1002-1014 (2008)

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