Updated list of publications: Google Scholar

1) C.S.D. Palma, N. Allen, M. Basevicius, H. Do, K. Li, D.J. Haller, A. Konovalova, O. Igoshin (2025). Modeling σE biochemical network reveals context-dependent feedback control and kinetic constraints in the envelope stress response. bioRxiv. DOI: 10.1101/2025.10.22.683963

3) Y. Zhang, C.S.D. Palma, Z. Chen, B. Zarazua-Osorio, M. Fujita, O. Igoshin (2025). Biophysical modeling reveals the transcriptional regulatory mechanism of Spo0A, the master regulator in starving Bacillus subtilis. mSystems, 10(5), e00072-25. DOI: 10.1128/msystems.00072-25

4) R. Jagadeesan, C.S.D. Palma*, S. Dash*, I. Baptista*, V. Chauhan, J. Mäkelä, A.S. Ribeiro (2025). Dynamics of bacterial operons during genome-wide stresses is influenced by premature terminations and internal promoters. Science Advances, 11(20), eadl3570. DOI: 10.1126/sciadv.adl3570 . *Equal contributions.

5) V.A. Gobbo, P. Turkki, C.S.D. Palma, V. Parihar, E. Vernè, S. Spriano, A.S. Ribeiro, V.P. Hytönen, J. Massera (2023). Surface modification of silicate, borosilicate, and phosphate bioactive glasses to improve/control protein adsorption: Part II. Ceramics International, 49(8), 12856–12865. DOI: 10.1016/j.ceramint.2022.12.157

6) C.S.D. Palma*, S. Dash*, I.S.C. Baptista, M.N.M. Bahrudeen, B.L.B. Almeida, V. Chauhan, R. Jagadeesan, A.S. Ribeiro (2022). Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli. Nucleic Acids Research, 50(15), 8512–8528. DOI: 10.1093/nar/gkac643 . *Equal contributions.

7) B.L.B. Almeida, M.N.M. Bahrudeen*, V. Chauhan*, S. Dash*, V. Kandavalli, A. Häkkinen, J. Lloyd-Price, C.S.D. Palma, I.S.C. Baptista, A. Gupta, J. Kesseli, E. Dufour, O.P. Smolander, M. Nykter, P. Auvinen, H.T. Jacobs, S.M.D. Oliveira, A.S. Ribeiro (2022). The transcription factor network of E. coli steers global responses to shifts in RNAP concentration. Nucleic Acids Research, 50(12), 6801–6819. DOI: 10.1093/nar/gkac540 . *Equal contributions.

8) I.S.C. Baptista*, V. Kandavalli*, V. Chauhan, M. Bahurudeen, B.L.B. Almeida, C.S.D. Palma, S. Dash, A.S. Ribeiro (2022). A general model of the dynamics of genes with dual σ factor preference. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1865(3), 194812. DOI: 10.1016/j.bbagrm.2022.194812 . *Equal contributions.

9) V. Chauhan*, M.N.M. Bahrudeen*, C.S.D. Palma, I. Baptista, B.L.B. Almeida, S. Dash, V. Kandavalli, A.S. Ribeiro (2022). Analytical kinetic model of native tandem promoters in E. coli. PLOS Computational Biology, 18(1), e1009824. DOI: 10.1371/journal.pcbi.1009824 . *Equal contributions.

10) N.B. Hyunh, C.S.D. Palma, R. Rahikainen, A. Mishra, L. Azizi, E. Verne, S. Ferraris, V.P. Hytönen, A.S. Ribeiro, J. Massera (2021). Surface modified phosphate glasses for controlled protein adsorption. ACS Biomaterials Science and Engineering, 7(9), 4483–4493. DOI: 10.1021/acsbiomaterials.1c00735

11) C.S.D. Palma, V. Kandavalli, M.N.M. Bahrudeen, M. Minoia, V. Chauhan, S. Dash, A.S. Ribeiro (2020). Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1863(5), 194515. DOI: 10.1016/j.bbagrm.2020.194515

12) M.N.M. Bahrudeen*, V. Chauhan*, C.S.D. Palma, S.M.D. Oliveira, V. Kandavalli, A.S. Ribeiro (2019). Estimating RNA numbers in single cells by RNA fluorescent tagging and flow cytometry. Journal of Microbiological Methods, 166, 105745. DOI: 10.1016/j.mimet.2019.105745 . *Equal contributions.

13) N.S.M. Goncalves, S. Startceva, C.S.D. Palma, M. Bahrudeen, S.M.D. Oliveira, A.S. Ribeiro (2018). Temperature-dependence of the single-cell variability in the kinetics of transcription activation in Escherichia coli. Physical Biology, 15(2). DOI: 10.1088/1478-3975/aa9ddf

Scientific Conferences

Talks

1) C.S.D. Palma, N. Allen, M. Basevicius, H. Do, K. Li, D.J. Haller, A. Konovalova, O. Igoshin (2026). Modeling σE biochemical network reveals context-dependent feedback control and kinetic constraints in the envelope stress response. APS Global Physics Summit, American Physical Society, March 16–20, Denver, Colorado, USA. Virtual participation.

2) C.S.D. Palma*, D. Haller*, J. Tabor, O. Igoshin (2024). Temporal dynamics of Spo0A control the B. subtilis cell fate decision of entering starvation or biofilm formation. APS March Meeting 2024, American Physical Society, March 3–8, Minneapolis, Minnesota, USA. Virtual participation. *Equal contributions.

3) C.S.D. Palma, S. Dash, I.S.C. Baptista, B.L.B. Almeida, M.N.M. Bahrudeen, V. Chauhan, R. Jagadeesan, A.S. Ribeiro (2022). Alterações no superenrolamento do DNA controlam a rápida repressão de vários genes da Escherichia coli durante um choque frio. International Congress of Microbiology in Portuguese Language (Microbiologia 2022), October 17–19. Virtual.

4) V. Chauhan, M.N.M. Bahrudeen, C.S.D. Palma, I. Baptista, B. Almeida, S. Dash, A.S. Ribeiro (2021). A study of native tandem promoters of E. coli and their use in synthetic circuits. Congress of Microbiology and Biotechnology (Microbiotec21), November 23–26, Lisbon, Portugal. Virtual.

5) C.S.D. Palma, S. Dash, M.N.M. Bahrudeen, B. Almeida, I. Baptista, V. Chauhan, A.S. Ribeiro (2021). Single-cell statistics of protein numbers following temperature downshifts in Escherichia coli. Single-Molecule Bacteriology Online Symposium, Biochemical Society, July 21. Virtual.

6) B.L.B. Almeida, M.N.M. Bahrudeen, V. Chauhan, C.S.D. Palma, I. Baptista, S. Dash, V. Kandavalli, A.S. Ribeiro (2021). Information entropy of single gene expression during genome-wide perturbations. Entropy 2021: The Scientific Tool of the 21st Century, May 5–7. Virtual.

7) B. Almeida*, I. Baptista*, C.S.D. Palma*, V. Kandavalli, M.N.M. Bahrudeen, V. Chauhan, S. Dash, A.S. Ribeiro (2019). Genome-wide responses of Escherichia coli to changing RNA polymerase concentrations. Congress of Microbiology and Biotechnology (MicroBiotech 19), December 5–7, Coimbra, Portugal. *Equal contributions.

8) V. Chauhan, C.S.D. Palma, A.S. Ribeiro (2018). Stochastic modeling and inference of temperature-dependent transcription supercoiling dynamics. 11th European Conference on Mathematical and Theoretical Biology (ECMTB 2018), July 23–27, Lisbon, Portugal.

9) C.S.D. Palma, V. Chauhan, A.S. Ribeiro (2018). Using stochastic modeling and analytical estimation to determine the dynamics of promoters supercoiled states. 5th International Conference on Complex Dynamical Systems in Life Sciences: Modeling and Analysis (5th ICCDS 2018), May 10–12, Aveiro, Portugal.

Posters

1) D.J. Haller, C.S.D. Palma, S.M. Castillo-Hair, K. Yang, O. Igoshin, J. Tabor (2025). Unraveling the role of Spo0A dynamics in B. subtilis cell fate determination through optogenetics. Synthetic Biology: Engineering, Evolution & Design (SEED), June 23–26, The Westin Galleria Houston, Houston, Texas, USA.

2) Y. Zhang, C.S.D. Palma, Z. Chen, B. Zarazua-Osorio, M. Fujita, O. Igoshin (2025). Biophysical modeling reveals the transcriptional regulatory mechanism of Spo0A, the master regulator in starving Bacillus subtilis. Rice Bioengineering Retreat, April 4, Helix Park Life Science Complex, Houston, Texas, USA.

3) C.S.D. Palma, O. Igoshin (2025). Regulation of σE in E. coli during transitioning from stress to non-stress conditions. Rice Bioengineering Retreat, April 4, Helix Park Life Science Complex, Houston, Texas, USA.

4) C.S.D. Palma, D. Haller, J. Tabor, O. Igoshin (2024). Spo0A~P oscillatory dynamics are the primary cause for biofilm matrix deactivation. Rice Synthetic Biology Retreat, October 14–15, Galveston, Texas, USA.

5) C.S.D. Palma*, D. Haller*, J. Tabor, O. Igoshin (2024). Spo0A~P oscillatory dynamics are the primary cause for biofilm matrix deactivation. Gordon Research Conference – Microbial Stress Response, July 14–19, Mount Holyoke College, South Hadley, Massachusetts, USA. *Equal contributions.

6) Y. Zhang, C.S.D. Palma, M. Fujita, O. Igoshin (2024). Understanding the mechanism of master regulator Spo0A using a biophysical model. Rice University Bioscience Research Collaborative Symposium, February 8–9, Galveston, Texas, USA.

7) C.S.D. Palma, D. Haller, J. Tabor, O. Igoshin (2024). Dissecting B. subtilis gene regulatory networks via optogenetics and mathematical modeling. Rice University Bioscience Research Collaborative Symposium, February 8–9, Galveston, Texas, USA.

8) Y. Zhang, C.S.D. Palma, M. Fujita, O. Igoshin (2023). Understanding the mechanism of master regulator Spo0A using a biophysical model. International Physics of Living Systems Annual Meeting (PoLS), August 1–4, Georgia Institute of Technology, Atlanta, Georgia, USA.

9) M. Gill, C.S.D. Palma, O. Igoshin (2023). Alternative σ-factor pulse dynamics in response to stress stimulus. IBB Summer Undergraduate Research Symposium, July 28, Rice University, Texas, USA.

10) C.S.D. Palma, S. Dash, I.S.C. Baptista, M.N.M. Bahrudeen, B.L.B. Almeida, V. Chauhan, R. Jagadeesan, A.S. Ribeiro (2022). Changes in DNA supercoiling contribute to the triggering of the short-term, cold shock transcriptional program of E. coli. Major Ideas in Quantitative Microbial Physiology, June 13–15, Copenhagen, Denmark.

11) I.S.C. Baptista*, V. Kandavalli*, V. Chauhan, M. Bahurudeen, B. Almeida, C.S.D. Palma, A.S. Ribeiro (2021). Accurate modeling of promoters with multiple σ factor preferences. 14th Great Lakes Bioinformatics Conference (GLBIO2021), May 10–13. Virtual. *Equal contributions.

12) C.S.D. Palma, M.N.M. Bahrudeen, V. Chauhan, I. Baptista, S. Dash, B. Almeida, A.S. Ribeiro (2020). Regulatory mechanisms of the dynamics of closely spaced promoters in E. coli. 1st International BioDesign Research Conference (IBDRC2020), December 1–18. Virtual. DOI: 10.12236/ibdrc2020-a-0045 . Best Poster Award, 3rd Prize.

13) S. Dash, C.S.D. Palma, I. Baptista, A.S. Ribeiro (2020). Single cell, over-time protein numbers of cold shock repressed genes in Escherichia coli. EMBL Conference: From Functional Genomics to Systems Biology, November 16–19, Heidelberg, Germany. Virtual.

14) A.S. Ribeiro, C.S.D. Palma, B.A. Eales, F.G. Biddle (2018). Symmetry breaking and the emergence of individuality in random paw choices and procedural learning in mice. 2018 Champalimaud Research Symposium, October 23–26, Lisbon, Portugal.

15) C.S.D. Palma, A.S. Ribeiro (2018). Kinetics of promoter locking due to positive supercoiling buildup. 84th Harden Conference: Single-Molecule Bacteriology, September 9–12, Lady Margaret Hall, Oxford, UK.