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The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable.

Interface focus

Nickerson D, Atalag K, de Bono B, Geiger J, Goble C, Hollmann S, Lonien J, Müller W, Regierer B, Stanford NJ, Golebiewski M, Hunter P.
PMID: 27051515
Interface Focus. 2016 Apr 06;6(2):20150103. doi: 10.1098/rsfs.2015.0103.

Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability...

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Nickerson D, Atalag K, de Bono B, et al. The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. Interface Focus. 2016;6(2):20150103doi: 10.1098/rsfs.2015.0103.
Nickerson, D., Atalag, K., de Bono, B., Geiger, J., Goble, C., Hollmann, S., Lonien, J., Müller, W., Regierer, B., Stanford, N. J., Golebiewski, M., & Hunter, P. (2016). The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. Interface focus, 6(2), 20150103. https://doi.org/10.1098/rsfs.2015.0103
Nickerson, David, et al. "The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable." Interface focus vol. 6,2 (2016): 20150103. doi: https://doi.org/10.1098/rsfs.2015.0103
Nickerson D, Atalag K, de Bono B, Geiger J, Goble C, Hollmann S, Lonien J, Müller W, Regierer B, Stanford NJ, Golebiewski M, Hunter P. The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. Interface Focus. 2016 Apr 06;6(2):20150103. doi: 10.1098/rsfs.2015.0103. PMID: 27051515; PMCID: PMC4759754.
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The role of laparoscopy in the management of pediatric appendicitis: a survey of Polish pediatric surgeons.

Wideochirurgia i inne techniki maloinwazyjne = Videosurgery and other miniinvasive techniques

Golebiewski A, Czauderna P.
PMID: 25960800
Wideochir Inne Tech Maloinwazyjne. 2015 Apr;10(1):101-6. doi: 10.5114/wiitm.2014.47510. Epub 2014 Dec 04.

INTRODUCTION: Despite the increase in use of laparoscopic appendectomy (LA) in recent years, until now no nationwide survey on this issue has been performed in Poland.AIM: To determine current surgical practice patterns among Polish pediatric surgeons in the treatment...

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Golebiewski A, Czauderna P. The role of laparoscopy in the management of pediatric appendicitis: a survey of Polish pediatric surgeons. Wideochir Inne Tech Maloinwazyjne. 2014;10(1):101-6doi: 10.5114/wiitm.2014.47510.
Golebiewski, A., & Czauderna, P. (2015). The role of laparoscopy in the management of pediatric appendicitis: a survey of Polish pediatric surgeons. Wideochirurgia i inne techniki maloinwazyjne = Videosurgery and other miniinvasive techniques, 10(1), 101-6. https://doi.org/10.5114/wiitm.2014.47510
Golebiewski, Andrzej, and Czauderna, Piotr. "The role of laparoscopy in the management of pediatric appendicitis: a survey of Polish pediatric surgeons." Wideochirurgia i inne techniki maloinwazyjne = Videosurgery and other miniinvasive techniques vol. 10,1 (2015): 101-6. doi: https://doi.org/10.5114/wiitm.2014.47510
Golebiewski A, Czauderna P. The role of laparoscopy in the management of pediatric appendicitis: a survey of Polish pediatric surgeons. Wideochir Inne Tech Maloinwazyjne. 2015 Apr;10(1):101-6. doi: 10.5114/wiitm.2014.47510. Epub 2014 Dec 04. PMID: 25960800; PMCID: PMC4414095.
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The first case of human autochtonous subconjunctival dirofilariosis in Poland and MALT lymphoma as possible consequence of this parasitosis.

Infectious agents and cancer

Borkowski PK, Rymkiewicz G, Golebiewska J, Nestoros N, Romejko-Jarosinska J, Zarnowska-Prymek H, Masny A, Palucki J, Cielecka D.
PMID: 25589901
Infect Agent Cancer. 2015 Jan 07;10(1):1. doi: 10.1186/1750-9378-10-1. eCollection 2015.

The first case of human dirofilarosis in Poland was recorded in 2007. Until that time our country was free of Dirofilaria repens. Recent studies show that 21,4- 60% of dogs in Warsaw region harbour microfilariae, therefore it is becoming...

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Borkowski PK, Rymkiewicz G, Golebiewska J, et al. The first case of human autochtonous subconjunctival dirofilariosis in Poland and MALT lymphoma as possible consequence of this parasitosis. Infect Agent Cancer. 2015;10(1):1doi: 10.1186/1750-9378-10-1.
Borkowski, P. K., Rymkiewicz, G., Golebiewska, J., Nestoros, N., Romejko-Jarosinska, J., Zarnowska-Prymek, H., Masny, A., Palucki, J., & Cielecka, D. (2015). The first case of human autochtonous subconjunctival dirofilariosis in Poland and MALT lymphoma as possible consequence of this parasitosis. Infectious agents and cancer, 10(1), 1. https://doi.org/10.1186/1750-9378-10-1
Borkowski, Piotr K, et al. "The first case of human autochtonous subconjunctival dirofilariosis in Poland and MALT lymphoma as possible consequence of this parasitosis." Infectious agents and cancer vol. 10,1 (2015): 1. doi: https://doi.org/10.1186/1750-9378-10-1
Borkowski PK, Rymkiewicz G, Golebiewska J, Nestoros N, Romejko-Jarosinska J, Zarnowska-Prymek H, Masny A, Palucki J, Cielecka D. The first case of human autochtonous subconjunctival dirofilariosis in Poland and MALT lymphoma as possible consequence of this parasitosis. Infect Agent Cancer. 2015 Jan 07;10(1):1. doi: 10.1186/1750-9378-10-1. eCollection 2015. PMID: 25589901; PMCID: PMC4293813.
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Structural transformations of nitrogen adsorbed on graphite: Monte Carlo studies of spatial heterogeneity in multilayer system.

The Journal of chemical physics

Golebiowska M, Firlej L, Kuchta B, Fabianski R.
PMID: 19485471
J Chem Phys. 2009 May 28;130(20):204703. doi: 10.1063/1.3142529.

We present numerical Monte Carlo studies of nitrogen multilayers adsorbed on the basal plane of graphite. The analysis is focused on the system spatial heterogeneity and its influence on structures and phase transitions. The simulations have been carried out...

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Golebiowska M, Firlej L, Kuchta B, et al. Structural transformations of nitrogen adsorbed on graphite: Monte Carlo studies of spatial heterogeneity in multilayer system. J Chem Phys. 2009;130(20):204703doi: 10.1063/1.3142529.
Golebiowska, M., Firlej, L., Kuchta, B., & Fabianski, R. (2009). Structural transformations of nitrogen adsorbed on graphite: Monte Carlo studies of spatial heterogeneity in multilayer system. The Journal of chemical physics, 130(20), 204703. https://doi.org/10.1063/1.3142529
Golebiowska, M, et al. "Structural transformations of nitrogen adsorbed on graphite: Monte Carlo studies of spatial heterogeneity in multilayer system." The Journal of chemical physics vol. 130,20 (2009): 204703. doi: https://doi.org/10.1063/1.3142529
Golebiowska M, Firlej L, Kuchta B, Fabianski R. Structural transformations of nitrogen adsorbed on graphite: Monte Carlo studies of spatial heterogeneity in multilayer system. J Chem Phys. 2009 May 28;130(20):204703. doi: 10.1063/1.3142529. PMID: 19485471.
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Morphological and Functional Parameters in Patients with Tooth Wear before and after Treatment.

The open dentistry journal

Sierpinska T, Kuc J, Golebiewska M.
PMID: 23802024
Open Dent J. 2013 May 17;7:55-61. doi: 10.2174/1874210601307010055. Print 2013.

UNLABELLED: Advanced tooth wear often results in lost vertical dimension and impacts facial aesthetics. Complex restorative treatment can replace the lost tooth structure and improve functional occlusal and facial skeleton parameters.PURPOSE: The aim of the study is to assess...

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Sierpinska T, Kuc J, Golebiewska M. Morphological and Functional Parameters in Patients with Tooth Wear before and after Treatment. Open Dent J. 2013;7:55-61doi: 10.2174/1874210601307010055.
Sierpinska, T., Kuc, J., & Golebiewska, M. (2013). Morphological and Functional Parameters in Patients with Tooth Wear before and after Treatment. The open dentistry journal, 755-61. https://doi.org/10.2174/1874210601307010055
Sierpinska, Teresa, et al. "Morphological and Functional Parameters in Patients with Tooth Wear before and after Treatment." The open dentistry journal vol. 7 (2013): 55-61. doi: https://doi.org/10.2174/1874210601307010055
Sierpinska T, Kuc J, Golebiewska M. Morphological and Functional Parameters in Patients with Tooth Wear before and after Treatment. Open Dent J. 2013 May 17;7:55-61. doi: 10.2174/1874210601307010055. Print 2013. PMID: 23802024; PMCID: PMC3681002.
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Author Correction: Diversity of nectar amino acids in the Fritillaria (Liliaceae) genus: ecological and evolutionary implications.

Scientific reports

Roguz K, Bajguz A, Chmur M, Gołębiewska A, Roguz A, Zych M.
PMID: 31959863
Sci Rep. 2020 Jan 21;10(1):1184. doi: 10.1038/s41598-020-58145-w.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Roguz K, Bajguz A, Chmur M, et al. Author Correction: Diversity of nectar amino acids in the Fritillaria (Liliaceae) genus: ecological and evolutionary implications. Sci Rep. 2020;10(1):1184doi: 10.1038/s41598-020-58145-w.
Roguz, K., Bajguz, A., Chmur, M., Gołębiewska, A., Roguz, A., & Zych, M. (2020). Author Correction: Diversity of nectar amino acids in the Fritillaria (Liliaceae) genus: ecological and evolutionary implications. Scientific reports, 10(1), 1184. https://doi.org/10.1038/s41598-020-58145-w
Roguz, Katarzyna, et al. "Author Correction: Diversity of nectar amino acids in the Fritillaria (Liliaceae) genus: ecological and evolutionary implications." Scientific reports vol. 10,1 (2020): 1184. doi: https://doi.org/10.1038/s41598-020-58145-w
Roguz K, Bajguz A, Chmur M, Gołębiewska A, Roguz A, Zych M. Author Correction: Diversity of nectar amino acids in the Fritillaria (Liliaceae) genus: ecological and evolutionary implications. Sci Rep. 2020 Jan 21;10(1):1184. doi: 10.1038/s41598-020-58145-w. PMID: 31959863; PMCID: PMC6971005.
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A Novel Dopamine Transporter Inhibitor CE-123 Improves Cognitive Flexibility and Maintains Impulsivity in Healthy Male Rats.

Frontiers in behavioral neuroscience

Nikiforuk A, Kalaba P, Ilic M, Korz V, Dragačević V, Wackerlig J, Langer T, Höger H, Golebiowska J, Popik P, Lubec G.
PMID: 29230168
Front Behav Neurosci. 2017 Nov 27;11:222. doi: 10.3389/fnbeh.2017.00222. eCollection 2017.

Reduced cognitive abilities are often characterized by an impairment of flexibility, i.e., the ability to switch from learned rules or categories that were important in certain contexts to different new modalities that rule the task. Drugs targeting the dopamine...

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Nikiforuk A, Kalaba P, Ilic M, et al. A Novel Dopamine Transporter Inhibitor CE-123 Improves Cognitive Flexibility and Maintains Impulsivity in Healthy Male Rats. Front Behav Neurosci. 2017;11:222doi: 10.3389/fnbeh.2017.00222.
Nikiforuk, A., Kalaba, P., Ilic, M., Korz, V., Dragačević, V., Wackerlig, J., Langer, T., Höger, H., Golebiowska, J., Popik, P., & Lubec, G. (2017). A Novel Dopamine Transporter Inhibitor CE-123 Improves Cognitive Flexibility and Maintains Impulsivity in Healthy Male Rats. Frontiers in behavioral neuroscience, 11222. https://doi.org/10.3389/fnbeh.2017.00222
Nikiforuk, Agnieszka, et al. "A Novel Dopamine Transporter Inhibitor CE-123 Improves Cognitive Flexibility and Maintains Impulsivity in Healthy Male Rats." Frontiers in behavioral neuroscience vol. 11 (2017): 222. doi: https://doi.org/10.3389/fnbeh.2017.00222
Nikiforuk A, Kalaba P, Ilic M, Korz V, Dragačević V, Wackerlig J, Langer T, Höger H, Golebiowska J, Popik P, Lubec G. A Novel Dopamine Transporter Inhibitor CE-123 Improves Cognitive Flexibility and Maintains Impulsivity in Healthy Male Rats. Front Behav Neurosci. 2017 Nov 27;11:222. doi: 10.3389/fnbeh.2017.00222. eCollection 2017. PMID: 29230168; PMCID: PMC5711856.
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Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.

Methods in molecular biology (Clifton, N.J.)

Stanford NJ, Scharm M, Dobson PD, Golebiewski M, Hucka M, Kothamachu VB, Nickerson D, Owen S, Pahle J, Wittig U, Waltemath D, Goble C, Mendes P, Snoep J.
PMID: 31602618
Methods Mol Biol. 2019;2049:285-314. doi: 10.1007/978-1-4939-9736-7_17.

Computational systems biology involves integrating heterogeneous datasets in order to generate models. These models can assist with understanding and prediction of biological phenomena. Generating datasets and integrating them into models involves a wide range of scientific expertise. As a...

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Stanford NJ, Scharm M, Dobson PD, et al. Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. Methods Mol Biol. 2019;2049:285-314doi: 10.1007/978-1-4939-9736-7_17.
Stanford, N. J., Scharm, M., Dobson, P. D., Golebiewski, M., Hucka, M., Kothamachu, V. B., Nickerson, D., Owen, S., Pahle, J., Wittig, U., Waltemath, D., Goble, C., Mendes, P., & Snoep, J. (2019). Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. Methods in molecular biology (Clifton, N.J.), 2049285-314. https://doi.org/10.1007/978-1-4939-9736-7_17
Stanford, Natalie J, et al. "Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices." Methods in molecular biology (Clifton, N.J.) vol. 2049 (2019): 285-314. doi: https://doi.org/10.1007/978-1-4939-9736-7_17
Stanford NJ, Scharm M, Dobson PD, Golebiewski M, Hucka M, Kothamachu VB, Nickerson D, Owen S, Pahle J, Wittig U, Waltemath D, Goble C, Mendes P, Snoep J. Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. Methods Mol Biol. 2019;2049:285-314. doi: 10.1007/978-1-4939-9736-7_17. PMID: 31602618.
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Impact of Tetrazolium Ionic Liquid Thermal Decomposition in Solvothermal Reaction on the Remarkable Photocatalytic Properties of TiO.

Nanomaterials (Basel, Switzerland)

Paszkiewicz-Gawron M, Gołąbiewska A, Pancielejko A, Lisowski W, Zwara J, Paszkiewicz M, Zaleska-Medynska A, Łuczak J.
PMID: 31096544
Nanomaterials (Basel). 2019 May 15;9(5). doi: 10.3390/nano9050744.

Ionic liquids (ILs) could serve as a structuring agent, a solvent, or a source of dopant during solvothermal synthesis of semiconductors particles. To understand the role of IL during formation of TiO

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Paszkiewicz-Gawron M, Gołąbiewska A, Pancielejko A, et al. Impact of Tetrazolium Ionic Liquid Thermal Decomposition in Solvothermal Reaction on the Remarkable Photocatalytic Properties of TiO. Nanomaterials (Basel). 2019;9(5)doi: 10.3390/nano9050744.
Paszkiewicz-Gawron, M., Gołąbiewska, A., Pancielejko, A., Lisowski, W., Zwara, J., Paszkiewicz, M., Zaleska-Medynska, A., & Łuczak, J. (2019). Impact of Tetrazolium Ionic Liquid Thermal Decomposition in Solvothermal Reaction on the Remarkable Photocatalytic Properties of TiO. Nanomaterials (Basel, Switzerland), 9(5), . https://doi.org/10.3390/nano9050744
Paszkiewicz-Gawron, Marta, et al. "Impact of Tetrazolium Ionic Liquid Thermal Decomposition in Solvothermal Reaction on the Remarkable Photocatalytic Properties of TiO." Nanomaterials (Basel, Switzerland) vol. 9,5 (2019). doi: https://doi.org/10.3390/nano9050744
Paszkiewicz-Gawron M, Gołąbiewska A, Pancielejko A, Lisowski W, Zwara J, Paszkiewicz M, Zaleska-Medynska A, Łuczak J. Impact of Tetrazolium Ionic Liquid Thermal Decomposition in Solvothermal Reaction on the Remarkable Photocatalytic Properties of TiO. Nanomaterials (Basel). 2019 May 15;9(5). doi: 10.3390/nano9050744. PMID: 31096544; PMCID: PMC6567212.
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Rainbow Dash: Intuitiveness, interpretability and memorability of the rainbow color scheme in visualization.

IEEE transactions on visualization and computer graphics

Golebiowska I, Coltekin A.
PMID: 33151882
IEEE Trans Vis Comput Graph. 2020 Nov 05; doi: 10.1109/TVCG.2020.3035823. Epub 2020 Nov 05.

After demonstrating that rainbow colors are still commonly used in scientific publications, we comparatively evaluate the rainbow and sequential color schemes on choropleth and isarithmic maps in an empirical user study with 544 participants to examine if a) people...

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Golebiowska I, Coltekin A. Rainbow Dash: Intuitiveness, interpretability and memorability of the rainbow color scheme in visualization. IEEE Trans Vis Comput Graph. 2020;doi: 10.1109/TVCG.2020.3035823.
Golebiowska, I., & Coltekin, A. (2020). Rainbow Dash: Intuitiveness, interpretability and memorability of the rainbow color scheme in visualization. IEEE transactions on visualization and computer graphics, . https://doi.org/10.1109/TVCG.2020.3035823
Golebiowska, Izabela, and Coltekin, Arzu. "Rainbow Dash: Intuitiveness, interpretability and memorability of the rainbow color scheme in visualization." IEEE transactions on visualization and computer graphics vol. (2020). doi: https://doi.org/10.1109/TVCG.2020.3035823
Golebiowska I, Coltekin A. Rainbow Dash: Intuitiveness, interpretability and memorability of the rainbow color scheme in visualization. IEEE Trans Vis Comput Graph. 2020 Nov 05; doi: 10.1109/TVCG.2020.3035823. Epub 2020 Nov 05. PMID: 33151882.
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Temozolomide-Induced RNA Interactome Uncovers Novel LncRNA Regulatory Loops in Glioblastoma.

Cancers

Fritah S, Muller A, Jiang W, Mitra R, Sarmini M, Dieterle M, Golebiewska A, Ye T, Van Dyck E, Herold-Mende C, Zhao Z, Azuaje F, Niclou SP.
PMID: 32927769
Cancers (Basel). 2020 Sep 10;12(9). doi: 10.3390/cancers12092583.

Resistance to chemotherapy by temozolomide (TMZ) is a major cause of glioblastoma (GBM) recurrence. So far, attempts to characterize factors that contribute to TMZ sensitivity have largely focused on protein-coding genes, and failed to provide effective therapeutic targets. Long...

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Fritah S, Muller A, Jiang W, et al. Temozolomide-Induced RNA Interactome Uncovers Novel LncRNA Regulatory Loops in Glioblastoma. Cancers (Basel). 2020;12(9)doi: 10.3390/cancers12092583.
Fritah, S., Muller, A., Jiang, W., Mitra, R., Sarmini, M., Dieterle, M., Golebiewska, A., Ye, T., Van Dyck, E., Herold-Mende, C., Zhao, Z., Azuaje, F., & Niclou, S. P. (2020). Temozolomide-Induced RNA Interactome Uncovers Novel LncRNA Regulatory Loops in Glioblastoma. Cancers, 12(9), . https://doi.org/10.3390/cancers12092583
Fritah, Sabrina, et al. "Temozolomide-Induced RNA Interactome Uncovers Novel LncRNA Regulatory Loops in Glioblastoma." Cancers vol. 12,9 (2020). doi: https://doi.org/10.3390/cancers12092583
Fritah S, Muller A, Jiang W, Mitra R, Sarmini M, Dieterle M, Golebiewska A, Ye T, Van Dyck E, Herold-Mende C, Zhao Z, Azuaje F, Niclou SP. Temozolomide-Induced RNA Interactome Uncovers Novel LncRNA Regulatory Loops in Glioblastoma. Cancers (Basel). 2020 Sep 10;12(9). doi: 10.3390/cancers12092583. PMID: 32927769; PMCID: PMC7563839.
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Discovery and Pharmacokinetics of Sulfamides and Guanidines as Potent Human Arginase 1 Inhibitors.

ACS medicinal chemistry letters

Blaszczyk R, Brzezinska J, Dymek B, Stanczak PS, Mazurkiewicz M, Olczak J, Nowicka J, Dzwonek K, Zagozdzon A, Golab J, Golebiowski A.
PMID: 32292546
ACS Med Chem Lett. 2020 Mar 13;11(4):433-438. doi: 10.1021/acsmedchemlett.9b00508. eCollection 2020 Apr 09.

We designed and synthesized a series of arginase inhibitors as derivatives of the well-known 2-(

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Blaszczyk R, Brzezinska J, Dymek B, et al. Discovery and Pharmacokinetics of Sulfamides and Guanidines as Potent Human Arginase 1 Inhibitors. ACS Med Chem Lett. 2020;11(4):433-438doi: 10.1021/acsmedchemlett.9b00508.
Blaszczyk, R., Brzezinska, J., Dymek, B., Stanczak, P. S., Mazurkiewicz, M., Olczak, J., Nowicka, J., Dzwonek, K., Zagozdzon, A., Golab, J., & Golebiowski, A. (2020). Discovery and Pharmacokinetics of Sulfamides and Guanidines as Potent Human Arginase 1 Inhibitors. ACS medicinal chemistry letters, 11(4), 433-438. https://doi.org/10.1021/acsmedchemlett.9b00508
Blaszczyk, Roman, et al. "Discovery and Pharmacokinetics of Sulfamides and Guanidines as Potent Human Arginase 1 Inhibitors." ACS medicinal chemistry letters vol. 11,4 (2020): 433-438. doi: https://doi.org/10.1021/acsmedchemlett.9b00508
Blaszczyk R, Brzezinska J, Dymek B, Stanczak PS, Mazurkiewicz M, Olczak J, Nowicka J, Dzwonek K, Zagozdzon A, Golab J, Golebiowski A. Discovery and Pharmacokinetics of Sulfamides and Guanidines as Potent Human Arginase 1 Inhibitors. ACS Med Chem Lett. 2020 Mar 13;11(4):433-438. doi: 10.1021/acsmedchemlett.9b00508. eCollection 2020 Apr 09. PMID: 32292546; PMCID: PMC7153016.
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