Anna Ochab-Marcinek

Anna Ochab-Marcinek, Ph.D. (Dr. hab.)

Dioscuri Centre for Physics and Chemistry of Bacteria, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland

Google Scholar - ORCID - ResearcherID

CV - Programming - Experience with Scientific Tools and Software - GitHub - Research - Publications - COVID-19 - Patents - Grants - Popular Science - Tablet for a Person with a Mobility Impairment (PL) - Contact

CV

CV (PDF)

Programming

Currently working on software development for automated detection of bacteria in microscopic images using machine learning and image analysis libraries. The project also includes non-standard methods of Point Spread Function deconvolution from the microscopic image.

Previously, I worked on programming projects for numerical modeling of stochastic systems in biophysics and biochemistry: gene expression, cancer growth.

Also, I worked on an epidemiological data analysis project during the COVID-19 pandemic. The project included web scraping, image recognition, and calculation of statistics (see COVID-19 and GitHub).

Experience

Knowledge of

Exposure to

Software development tools

Experience with scientific tools and software

GitHub

Research

Publications

  1. J. Jędrak, M. Rubin, A. Ochab-Marcinek, Generalization of Powell’s results to population out of steady state, Physical Review E 108 (2), 024405 (2023) [arxiv preprint]
  2. J. Jędrak, A. Ochab-Marcinek, Contributions to the ‘noise floor’ in gene expression in a population of dividing cells, Scientific Reports, 10, 13533 (2020)
  3. J. Jędrak, M. Kwiatkowski, A. Ochab-Marcinek , Exactly solvable model of gene expression in proliferating bacterial cell population with stochastic protein bursts and protein partitioning, Phys. Rev. E, 99 (2019) 042416 [arxiv preprint]
  4. A. Ochab-Marcinek, J. Jędrak, M. Tabaka, Hill kinetics as a noise filter: The role of transcription factor autoregulation in gene cascades, Phys. Chem. Chem. Phys., 2017, 19, 22580-22591
  5. G. Angulo, J. Jędrak, A. Ochab-Marcinek, P. Pasitsuparoad, C. Radzewicz, P. Wnuk, A. Rosspeintner, How good is the generalized Langevin equation to describe the dynamics of photo-induced electron transfer in fluid solution? , J. Chem. Phys. 146 (2017) 244505 [arxiv preprint]
  6. J. Jędrak, A. Ochab-Marcinek, Influence of gene copy number on self-regulated gene expression, J. Theor. Biol., 408 (2016) 222 [arxiv preprint]
  7. J. Jędrak, A. Ochab-Marcinek, Time-dependent solutions for a stochastic model of gene expression with molecule production in the form of a compound Poisson process, Phys. Rev. E 94 (3) (2016) 032401 [arxiv preprint]
  8. T. Kalwarczyk, K. Sozanski, A. Ochab-Marcinek, J. Szymanski, M. Tabaka, S. Hou, R. Hołyst, Motion of nanoprobes in complex liquids within the framework of the length-scale dependent viscosity model, 2015, Advances in Colloid and Interface Science, 2015, 223, 55-63.
  9. A. Ochab-Marcinek, M. Tabaka, Transcriptional leakage versus noise: A simple mechanism of conversion between binary and graded response in autoregulated genes, Phys. Rev. E, 2015, 91(1), 012704 [arxiv preprint]
  10. K. Sozanski, A. Wisniewska, T. Piasecki, K. Waszczuk, A. Ochab-Marcinek, T. Gotszalk,R. Hołyst, Depletion Layer in Polymer Solutions at an Interface Oscillating at the Subnano-to Submicrometer Scale, Soft Matter 2014, 10, 7762-7768
  11. T.K.Piskorz, A. Ochab-Marcinek, A Universal Model of Restricted Diffusion for Fluorescence Correlation Spectroscopy, J. Phys. Chem. B, 2014, 118 (18), 4906–4912
  12. A. Lewandrowska, A. Majcher, A. Ochab-Marcinek, M. Tabaka, R. Hołyst, Taylor Dispersion Analysis in Coiled Capillaries at High Flow Rates, Anal. Chem., 2013, 85 (8), 4051–4056
  13. A. Ochab-Marcinek, S.A. Wieczorek, N. Ziębacz, R. Hołyst, The effect of depletion layer on diffusion of nanoparticles in solutions of flexible and polydisperse polymers , Soft Matter 2012, 8, 11173-11179
  14. A. Ochab-Marcinek, R. Hołyst, Scale-dependent diffusion of spheres in solutions of flexible and rigid polymers: mean square displacement and autocorrelation function for FCS and DLS measurements , Soft Matter 2011, 7, 7366-7374
  15. A. Ochab-Marcinek, M. Tabaka, Bimodal gene expression in noncooperative regulatory systems , PNAS 107(51) (2010) 22096-22101
  16. A. Ochab-Marcinek, Extrinsic noise passing through a Michaelis-Menten reaction: A universal response of a genetic switch, J. Theor. Biol. 263(4) (2010) 510-520 [arxiv preprint]
  17. A. Ochab-Marcinek, E. Gudowska-Nowak, E. Nasonova, S. Ritter, Modelling radiation-induced cell cycle delays, Rad. Env. Biophys. 48(4) (2009) 361 [arxiv preprint]
  18. A. Ochab-Marcinek, G. Schmid, I. Goychuk, P. Hanggi, Noise-assisted spike propagation in myelinated neurons, Phys. Rev. E 79, 011904 (2009) [arxiv preprint]
  19. A. Fiasconaro, A. Ochab-Marcinek, B. Spagnolo, E. Gudowska-Nowak, Monitoring noise-resonant effects in cancer growth influenced by external fluctuations and periodic treatment, Eur. Phys. J. B 65, 435-442 (2008) [arxiv preprint]
  20. Anna Ochab-Marcinek, Predicting the asymmetric response of a genetic switch to noise, J. Theor. Biol. 254 (2008) 37-44 [arxiv preprint]
  21. B. Spagnolo, A.A. Dubkov, A.L. Pankratov, E.V. Pankratova, A. Fiasconaro, A. Ochab-Marcinek Lifetime of Metastable States and Suppression of Noise in Interdisciplinary Physical Models. Acta Physica Polonica B 38(5) 2007, 1925.
  22. Anna Ochab-Marcinek, Alessandro Fiasconaro, Ewa Gudowska-Nowak, Bernardo Spagnolo, Coexistence of resonant activation and noise-enhanced stability in a model of tumor-host interaction: Statistics of extinction times. Acta Physica Polonica B 37(5) 2006, 1651.
  23. Alessandro Fiasconaro, Bernardo Spagnolo, Anna Ochab-Marcinek, Ewa Gudowska- Nowak, Co-occurrence of resonant activation and noise-enhanced stability in a model of cancer growth in the presence of immune response. Physical Review E 74, 041904 (2006)
    [arxiv preprint]
  24. Anna Ochab-Marcinek: Transient pattern formation in a stochastic model of cancer growth, Fluctuation and Noise Letters 5(2) (2005) L331
    [arxiv preprint]
  25. Anna Ochab-Marcinek: Pattern formation in a stochastic model of cancer growth , Acta Physica Polonica B 36(6) (2005) 1963
    [arxiv preprint]
  26. Anna Ochab-Marcinek, Ewa Gudowska-Nowak: Population growth and control in stochastic models of cancer development, Physica A, 343 (2004) 557-572
    [arxiv preprint]

COVID-19 Advisory Team to the President of the Polish Academy of Sciences

From June 30, 2020 to December 31, 2022, I was a member of the interdisciplinary COVID-19 Advisory Team attached to the President of the Polish Academy of Sciences. Our task was to monitor the course of the COVID-19 epidemic in Poland, analyze and predict its possible scenarios, and make recommendations. We also established contacts with similar teams in other countries in order to exchange experiences.

Our position papers

Archive of my epidemiological data analyses. See also GitHub.

Non-peer-reviewed publications

  1. J. Duszyński, A. Afelt, A. Ochab-Marcinek, R. Owczuk, K. Pyrć, M. Rosińska, A. Rychard, T. Smiatacz, Zrozumieć COVID-19, ACADEMIA - magazyn Polskiej Akademii Nauk 4 (64) 2020 pp. 1-80, DOI:10.24425/academiaPAN.2020.136169

  2. J. Duszyński, A. Afelt, A. Ochab-Marcinek, R. Owczuk, K. Pyrć, M. Rosińska, A. Rychard, T. Smiatacz, Understanding COVID-19, ACADEMIA - The magazine of the Polish Academy of Sciences 4 (68) 2020 pp. 1-80, DOI:10.24425/academiaPAS.2020.136172

  3. J. Duszyński, A. Afelt, M. Kossowska, A. Ochab-Marcinek, R. Owczuk, W. Paczos, A. Plater-Zyberk, K. Pyrć, M. Rosińska, A. Rychard, T. Smiatacz, Kroniki Pandemii: lata 2020-2021, ACADEMIA - magazyn Polskiej Akademii Nauk 4(68) 2021 pp. 1-118, DOI:10.24425/academiaPAN.2021.140621

  4. J. Duszyński, A. Afelt, M. Kossowska, A. Ochab-Marcinek, R. Owczuk, W. Paczos, A. Plater-Zyberk, K. Pyrć, M. Rosińska, A. Rychard, T. Smiatacz, Chronicles of a Pandemic, ACADEMIA - The magazine of the Polish Academy of Sciences 4(72) 2021 pp. 1-120

Patents

Grants

Anna Ochab-Marcinek, Porządek z przypadku, Academia, magazine of the Polish Academy of Sciences, 4/11(28)
Radio interview [Polish]: Wieczór Odkrywców, Polskie Radio 1, 9.7.2011
Radio interview [Polish]: Radiowa Akademia Nauk, Radio TOK FM, 2.3.2011

Popular science articles for Tygodnik Powszechny weekly:

Popular science blogs

Contact

E-mail: ochab@ichf.edu.pl

Phone: +48 22 343 2171

Office: Dioscuri Centre, Building 9

Mailing address:

Institute of Physical Chemistry

Polish Academy of Sciences

ul. Kasprzaka 44/52

01-224 Warsaw

Poland