Prof. Dr. ŞEFİKA KUTLU ÜLGEN

Yayın Ağı

Makaleler 100

1. Exploring the Integrated Gut-Brain Metabolic Model for ADHD

Tas E., ÜLGEN Ş. K.

Biochemical Genetics , cilt.64, sa.3, ss.4091-4129, 2026 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

2. 3D bioprinted melanoma constructs reveal delivery-dependent efficacy of phytochemical-gold nanoparticle formulations

Kirac M. K., Bilge B., Ozdil C. C., TUĞCU T., ÜLGEN Ş. K.

Biomedical Materials (Bristol) , cilt.21, sa.3, 2026 (SCI-Expanded, Scopus)

3. Harnessing Phytochemicals for Brain Cancer Therapy: Insights Into Medulloblastoma and Glioblastoma Treatment

Ozbek I. I., Aktas M., Saybasili H., ÜLGEN Ş. K.

Phytochemical Analysis , cilt.37, sa.4, ss.507-535, 2026 (SCI-Expanded, Scopus)

4. Co-administration of phytochemicals and anti-melanoma drugs: Mechanisms, metastasis prevention, and regulatory challenges

Huner I. B., Kasim Kirac M., ÜLGEN Ş. K.

Pharmacological Research - Natural Products , cilt.10, 2026 (Scopus)

5. Exploring the role of gut microbiota in rheumatoid arthritis: the effects of diet and drug supplementation

Genc D. E., ÖZBEK Ö., ÜLGEN Ş. K.

BMC Rheumatology , cilt.9, sa.1, 2025 (ESCI, Scopus)

6. Community Modeling Reveals Disrupted Gut Microbial Secretion in Autism Associated With Redox and Neurometabolic Alterations

ESVAP E., ÜLGEN Ş. K.

Biotechnology Journal , cilt.20, sa.12, 2025 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

7. Predictive Modeling of Pharmacokinetic Drug–Drug and Herb–Drug Interactions in Oncology: Insights From PBPK Studies

TAŞ E. E., ÜLGEN Ş. K.

International Journal of Toxicology , cilt.44, sa.5, ss.424-440, 2025 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

8. Alterations in Gut Microbiota-Brain Axis in Major Depressive Disorder as Identified by Machine Learning

Oncu A. D., ÖZGÜR TÜRKMEN A., ÜLGEN Ş. K.

OMICS A Journal of Integrative Biology , cilt.29, sa.7, ss.309-319, 2025 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

9. Exploring Human Brain Metabolism via Genome-Scale Metabolic Modeling with Highlights on Multiple Sclerosis

Sertbas M., ÜLGEN Ş. K.

ACS Chemical Neuroscience , cilt.16, sa.7, ss.1346-1360, 2025 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

10. Genome-Scale Metabolic Modeling of Human Pancreas with Focus on Type 2 Diabetes

Sertbas M., ÜLGEN Ş. K.

OMICS A Journal of Integrative Biology , cilt.29, sa.4, ss.125-138, 2025 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

11. Advances in Physiologically Based Pharmacokinetic (PBPK) Modeling of Nanomaterials

ÖZBEK Ö., Genc D. E., ÜLGEN Ş. K.

ACS Pharmacology and Translational Science , cilt.7, sa.8, ss.2251-2279, 2024 (ESCI, Scopus) Sürdürülebilir Kalkınma

12. Applications of 3D Bioprinting Technology to Brain Cells and Brain Tumor Models: Special Emphasis to Glioblastoma

Ozbek I. I., Saybasili H., ÜLGEN Ş. K.

ACS Biomaterials Science and Engineering , cilt.10, sa.5, ss.2616-2635, 2024 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

13. Uncovering the Effect of SARS-CoV-2 on Liver Metabolism via Genome-Scale Metabolic Modeling for Reprogramming and Therapeutic Strategies

Sertbas M., ÜLGEN Ş. K.

ACS Omega , cilt.9, sa.13, ss.15535-15546, 2024 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

14. Exploring data-driven chemical SMILES tokenization approaches to identify key protein–ligand binding moieties

TEMİZER KESER A. B., ULUDOĞAN G., Özçelik R., Koulani T., Ozkirimli E., ÜLGEN Ş. K., et al.

Molecular Informatics , cilt.43, sa.3, 2024 (SCI-Expanded, Scopus)

15. Circadian clock crosstalks with autism

Yurdakul E., Barlas Y., ÜLGEN Ş. K.

Brain and Behavior , cilt.13, sa.12, 2023 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

16. Understanding the ADHD-Gut Axis by Metabolic Network Analysis

Taş E., ÜLGEN Ş. K.

Metabolites , cilt.13, sa.5, 2023 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

17. Neuroinflammation, Energy and Sphingolipid Metabolism Biomarkers Are Revealed by Metabolic Modeling of Autistic Brains

ESVAP E., ÜLGEN Ş. K.

Biomedicines , cilt.11, sa.2, 2023 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

18. Comprehensive genome-scale metabolic model of the human pathogen Cryptococcus neoformans: A platform for understanding pathogen metabolism and identifying new drug targets

Tezcan E. F., Demirtas Y., Çakar Z. P., ÜLGEN Ş. K.

Frontiers in Bioinformatics , cilt.3, 2023 (Scopus)

19. Identification of Therapeutic Targets for Medulloblastoma by Tissue-Specific Genome-Scale Metabolic Model

Ozbek I. I., ÜLGEN Ş. K.

Molecules , cilt.28, sa.2, 2023 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

20. Understanding HMF inhibition on yeast growth coupled with ethanol production for the improvement of bio-based industrial processes

Gencturk E., ÜLGEN Ş. K.

Process Biochemistry , cilt.121, ss.425-438, 2022 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

21. Exploiting pretrained biochemical language models for targeted drug design

ULUDOĞAN G., Ozkirimli E., ÜLGEN Ş. K., Karall N., ÖZGÜR TÜRKMEN A.

Bioinformatics , cilt.38, sa.2 S, 2022 (SCI-Expanded, Scopus)

22. Understanding the adaptive laboratory evolution of multiple stress-resistant yeast strains by genome-scale modeling

Çetin H., Çakar Z. P., ÜLGEN Ş. K.

Yeast , cilt.39, sa.8, ss.449-465, 2022 (SCI-Expanded, Scopus)

23. Understanding the Link between Inflammasome and Apoptosis through the Response of THP-1 Cells against Drugs Using DropletBased Microfluidics

Gencturk E., KASIM KIRAÇ M., Morova B., Kiraz A., ÜLGEN Ş. K.

ACS Omega , cilt.7, sa.19, ss.16323-16332, 2022 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

24. Carvacrol Enhances the Antimicrobial Potency of Berberine in Bacillus subtilis

Atas B., Aksoy C. S., Avci F. G., SAYAR N. A., ÜLGEN Ş. K., Ozkirimli E., et al.

Current Microbiology , cilt.79, sa.5, 2022 (SCI-Expanded, Scopus)

25. Real-Time Single-Cell Monitoring of Drug Effects Using Droplet-Based Microfluidic Technology: A Proof-of-Concept Study

KASIM KIRAÇ M., Gencturk E., ÜLGEN Ş. K.

OMICS A Journal of Integrative Biology , cilt.25, sa.10, ss.641-651, 2021 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

26. Advances in Genome-Scale Metabolic Modeling toward Microbial Community Analysis of the Human Microbiome

ESVAP E., ÜLGEN Ş. K.

ACS Synthetic Biology , cilt.10, sa.9, ss.2121-2137, 2021 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

27. Live Cell Imaging of Peptide Uptake Using a Microfluidic Platform

Yüce M., Ozkirimli E., SARIYAR AKBULUT B., ÜLGEN Ş. K.

International Journal of Peptide Research and Therapeutics , cilt.27, sa.3, ss.2003-2013, 2021 (SCI-Expanded, Scopus)

28. The Toxicity of Polystyrene-Based Nanoparticles in Saccharomyces cerevisiae Is Associated with Nanoparticle Charge and Uptake Mechanism

ÖZBEK Ö., ÜLGEN Ş. K., İLERİ ERCAN N.

Chemical Research in Toxicology , cilt.34, sa.4, ss.1055-1068, 2021 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

29. Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens

Sertbas M., ÜLGEN Ş. K.

Frontiers in Cell and Developmental Biology , cilt.8, 2020 (SCI-Expanded, Scopus)

30. Thermoplastic microfluidic bioreactors with integrated electrodes to study tumor treating fields on yeast cells

Gencturk E., ÜLGEN Ş. K., Mutlu S.

Biomicrofluidics , cilt.14, sa.3, 2020 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

31. Cell trapping microfluidic chip made of Cyclo olefin polymer enabling two concurrent cell biology experiments with long term durability

Gencturk E., Yurdakul E., Celik A. Y., Mutlu S., ÜLGEN Ş. K.

Biomedical Microdevices , cilt.22, sa.1, 2020 (SCI-Expanded, Scopus)

32. A drug repurposing and protein-protein interaction network study of ribosomopathies using yeast as a model system

Ertekin E., Gencturk E., KASIM KIRAÇ M., ÜLGEN Ş. K.

OMICS A Journal of Integrative Biology , cilt.24, sa.2, ss.96-109, 2020 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

33. Application of supercritical gel drying method on fabrication of mechanically improved and biologically safe three-component scaffold composed of graphene oxide/chitosan/hydroxyapatite and characterization studies

Yilmaz P., Öztürk Er E., BAKIRDERE S., ÜLGEN Ş. K., ÖZBEK B.

Journal of Materials Research and Technology , cilt.8, sa.6, ss.5201-5216, 2019 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

34. A low cost PS based microfluidic platform to investigate cell cycle towards developing a therapeutic strategy for cancer

Odabasi I. E., Gencturk E., Puza S., Mutlu S., ÜLGEN Ş. K.

Biomedical Microdevices , cilt.20, sa.3, 2018 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

35. Unlocking human brain metabolism by genome-scale and multiomics metabolic models: Relevance for neurology research, health, and disease

Sertbas M., ÜLGEN Ş. K.

OMICS A Journal of Integrative Biology , cilt.22, sa.7, ss.455-467, 2018 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

36. In silico identification of novel orthosteric inhibitors of sphingosine kinase 1 (SK1)

Bayraktar O., Ozkirimli E., ÜLGEN Ş. K.

Current Protein and Peptide Science , cilt.19, sa.5, ss.430-444, 2018 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

37. Investigation of novel pharmacological chaperones for Gaucher Disease

Yilmazer B., Yagci Z. B., Bakar E., Ozden B., ÜLGEN Ş. K., Ozkirimli E.

Journal of Molecular Graphics and Modelling , cilt.76, ss.364-378, 2017 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

38. Advances in microfluidic devices made from thermoplastics used in cell biology and analyses

Gencturk E., Mutlu S., ÜLGEN Ş. K.

Biomicrofluidics , cilt.11, sa.5, 2017 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

39. Sphingosine kinase 1 (SK1) allosteric inhibitors that target the dimerization site

Bayraktar O., Ozkirimli E., ÜLGEN Ş. K.

Computational Biology and Chemistry , cilt.69, ss.64-76, 2017 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

40. A review on wax printed microfluidic paper-based devices for international health

ALTUNDEMİR S., UĞUZ A. K., ÜLGEN Ş. K.

Biomicrofluidics , cilt.11, sa.4, 2017 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

41. Fabrication of cyclo olefin polymer microfluidic devices for trapping and culturing of yeast cells

Puza S., Gencturk E., Odabasi I. E., Iseri E., Mutlu S., ÜLGEN Ş. K.

Biomedical Microdevices , cilt.19, sa.2, 2017 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

42. Multiomics Approach to Novel Therapeutic Targets for Cancer and Aging-Related Diseases: Role of Sld7 in Yeast Aging Network

Dayan I. E., ARGA K. Y., ÜLGEN Ş. K.

OMICS A Journal of Integrative Biology , cilt.21, sa.2, ss.100-113, 2017 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

43. Comparative interactomics for virus–human protein–protein interactions: DNA viruses versus RNA viruses

Durmuş S., ÜLGEN Ş. K.

FEBS Open Bio , cilt.7, sa.1, ss.96-107, 2017 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

44. Screening applications in drug discovery based on microfluidic technology

Eribol P., UĞUZ A. K., ÜLGEN Ş. K.

Biomicrofluidics , cilt.10, sa.1, 2016 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

45. A systematic methodology for large scale compound screening: A case study on the discovery of novel S1PL inhibitors

Deniz U., Ozkirimli E., ÜLGEN Ş. K.

Journal of Molecular Graphics and Modelling , cilt.63, ss.110-124, 2016 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

46. Transcriptional remodeling in response to transfer upon carbon-limited or metformin-supplemented media in S. cerevisiae and its effect on chronological life span

Borklu-Yucel E., Eraslan S., ÜLGEN Ş. K.

Applied Microbiology and Biotechnology , cilt.99, sa.16, ss.6775-6789, 2015 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

47. Identification of potential Tpx inhibitors against pathogen-host interactions

Deniz U., ÜLGEN Ş. K., Ozkirimli E.

Computational Biology and Chemistry , cilt.58, ss.126-138, 2015 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

48. Aminopurine derivatives as putative SopE inhibitors

Ozbuyukkaya G., Ozkirimli Olmez E., ÜLGEN Ş. K.

Journal of Enzyme Inhibition and Medicinal Chemistry , cilt.29, sa.1, ss.137-145, 2014 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

49. The impact of medium acidity on the chronological life span of Saccharomyces cerevisiae - Lipids, signaling cascades, mitochondrial and vacuolar functions

YÜCEL E., Eraslan S., ÜLGEN Ş. K.

FEBS Journal , cilt.281, sa.4, ss.1281-1303, 2014 (SCI-Expanded, Scopus)

50. Targeting the Akt1 allosteric site to identify novel scaffolds through virtual screening

Yilmaz O. G., Olmez E. O., ÜLGEN Ş. K.

Computational Biology and Chemistry , cilt.48, ss.1-13, 2014 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

51. Systematic analysis of transcription-level effects of neurodegenerative diseases on human brain metabolism by a newly reconstructed brain-specific metabolic network

Sertbaş M., ÜLGEN Ş. K., Çakir T.

FEBS Open Bio , cilt.4, ss.542-553, 2014 (SCI-Expanded, Scopus)

52. Assessment of crosstalks between the Snf1 kinase complex and sphingolipid metabolism in S. cerevisiae via systems biology approaches

Borklu Yucel E., ÜLGEN Ş. K.

Molecular BioSystems , cilt.9, sa.11, ss.2914-2931, 2013 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

53. PHISTO: Pathogen-host interaction search tool

Durmuş Tekir S., Çakir T., Ardiç E., Sayilirbaş A. S., Konuk G., Konuk M., et al.

Bioinformatics , cilt.29, sa.10, ss.1357-1358, 2013 (SCI-Expanded, Scopus)

54. Systems biology of pathogen-host interaction: Networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era

Durmuş Tekir S. D., ÜLGEN Ş. K.

Biotechnology Journal , cilt.8, sa.1, ss.85-96, 2013 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

55. Infection strategies of bacterial and viral pathogens through pathogen-human protein-protein interactions

Tekir S. D., Çakir T., ÜLGEN Ş. K.

Frontiers in Microbiology , cilt.3, sa.FEB, 2012 (Scopus)

56. A network-based approach on elucidating the multi-faceted nature of chronological aging in S. cerevisiae

Borklu Yucel E., ÜLGEN Ş. K.

PLoS ONE , cilt.6, sa.12, 2011 (SCI-Expanded, Scopus)

57. Reconstruction and crosstalk of protein-protein interaction networks of Wnt and Hedgehog signaling in Drosophila melanogaster

Toku A. E., Tekir S. D., Özbayraktar F. B. K., ÜLGEN Ş. K.

Computational Biology and Chemistry , cilt.35, sa.5, ss.282-292, 2011 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

58. Crucial components in toll-like receptor signaling network as key regulators for immunological disorders

Özbabacan S. E. A., Tekir S. D., ÜLGEN Ş. K.

International Journal of Physical Sciences , cilt.6, sa.8, ss.2016-2026, 2011 (Scopus)

59. Stoichiometric network reconstruction and analysis of yeast sphingolipid metabolism incorporating different states of hydroxylation

Kavun Ozbayraktar F. B., ÜLGEN Ş. K.

BioSystems , cilt.104, sa.1, ss.63-75, 2011 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

60. Reconstruction of protein-protein interaction network of insulin signaling in Homo sapiens

Tekir S. D., Ümit P., Toku A. E., ÜLGEN Ş. K.

Journal of Biomedicine and Biotechnology , cilt.2010, 2010 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

61. Drug target identification in sphingolipid metabolism by computational systems biology tools: Metabolic control analysis and metabolic pathway analysis

Özbayraktar F. B. K., ÜLGEN Ş. K.

Journal of Biomedical Informatics , cilt.43, sa.4, ss.537-549, 2010 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

62. Molecular facets of sphingolipids: Mediators of diseases

Ozbayraktar F. B. K., ÜLGEN Ş. K.

Biotechnology Journal , cilt.4, sa.7, ss.1028-1041, 2009 (Scopus)

63. Drug targets for tumorigenesis: Insights from structural analysis of EGFR signaling network

Durmuş Tekir S., Yalçin Arga K., ÜLGEN Ş. K.

Journal of Biomedical Informatics , cilt.42, sa.2, ss.228-236, 2009 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

64. Integration of metabolic modeling and phenotypic data in evaluation and improvement of ethanol production using respiration-deficient mutants of Saccharomyces cerevisiae

Dikicioglu D., Pir P., ÖNSAN Z. İ., ÜLGEN Ş. K., Kirdar B., Oliver S. G.

Applied and Environmental Microbiology , cilt.74, sa.18, ss.5809-5816, 2008 (SCI-Expanded, Scopus)

65. Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae

Pir P., Kirdar B., Hayes A., ÖNSAN Z. İ., ÜLGEN Ş. K., Oliver S. G.

Yeast , cilt.25, sa.9, ss.661-672, 2008 (SCI-Expanded, Scopus)

66. Emerging roles for metabolic engineering - Understanding primitive and complex metabolic models and their relevance to healthy and diseased kidney podocytes

Altintas M. M., ÜLGEN Ş. K., Palmer-Toy D., Shih V. E., Kompala D. S., Reiser J.

Current Chemical Biology , cilt.2, sa.1, ss.68-82, 2008 (Scopus)

67. Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: Application to cerebral hypoxia

Çakir T., Alsan S., Saybaşili H., AKIN A., ÜLGEN Ş. K.

Theoretical Biology and Medical Modelling , cilt.4, 2007 (Scopus)

68. Understanding signaling in yeast: Insights from network analysis

ARGA K. Y., ÖNSAN Z. İ., Kirdar B., ÜLGEN Ş. K., Nielsen J.

Biotechnology and Bioengineering , cilt.97, sa.5, ss.1246-1258, 2007 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

69. Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae

Çakir T., Kirdar B., ÖNSAN Z. İ., ÜLGEN Ş. K., Nielsen J.

BMC Systems Biology , cilt.1, 2007 (Scopus)

70. Analysis of enzymopathies in the human red blood cells by constraint-based stoichiometric modeling approaches

Durmuş Tekir S., Çakir T., ÜLGEN Ş. K.

Computational Biology and Chemistry , cilt.30, sa.5, ss.327-338, 2006 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

71. Integration of metabolome data with metabolic networks reveals reporter reactions

Çakir T., Patil K. R., ÖNSAN Z. İ., ÜLGEN Ş. K., Kirdar B., Nielsen J.

Molecular Systems Biology , cilt.2, 2006 (SCI-Expanded, Scopus)

72. Annotation of unknown yeast ORFs by correlation analysis of microarray data and extensive literature searches

Pir P., ÜLGEN Ş. K., Hayes A., Önsan I., Kirdar B., Oliver S. G.

Yeast , cilt.23, sa.7, ss.553-571, 2006 (SCI-Expanded, Scopus)

73. Integrative investigation of metabolic and transcriptomic data

Pir P., Kirdar B., Hayes A., ÖNSAN Z. İ., ÜLGEN Ş. K., Oliver S. G.

BMC Bioinformatics , cilt.7, 2006 (SCI-Expanded, Scopus)

74. Bubble column reactors

Kantarci N., Borak F., ÜLGEN Ş. K.

Process Biochemistry , cilt.40, sa.7, ss.2263-2283, 2005 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

75. Modelling of calcium dynamics in brain energy metabolism and Alzheimer's disease

Tiveci S., AKIN A., Çakir T., Saybaşili H., ÜLGEN Ş. K.

Computational Biology and Chemistry , cilt.29, sa.2, ss.151-162, 2005 (Scopus) Sürdürülebilir Kalkınma

76. A study on hydrodynamics and heat transfer in a bubble column reactor with yeast and bacterial cell suspensions

Kantarci N., ÜLGEN Ş. K., Borak F.

Canadian Journal of Chemical Engineering , cilt.83, sa.4, ss.764-773, 2005 (SCI-Expanded, Scopus)

77. Flux analysis of recombinant Saccharomyces cerevisiae YPB-G utilizing starch for optimal ethanol production

Çakir T., ARGA K. Y., Altintaş M. M., ÜLGEN Ş. K.

Process Biochemistry , cilt.39, sa.12, ss.2097-2108, 2004 (Scopus) Sürdürülebilir Kalkınma

78. Transfer function approach in structured modeling of recombinant yeast utilizing starch

ARGA K. Y., Çakir T., Pir P., Özer N., Altintaş M. M., ÜLGEN Ş. K.

Process Biochemistry , cilt.39, sa.10, ss.1237-1248, 2004 (Scopus)

79. Metabolic Pathway Analysis of Yeast Strengthens the Bridge between Transcriptomics and Metabolic Networks

Çakir T., Kirdar B., ÜLGEN Ş. K.

Biotechnology and Bioengineering , cilt.86, sa.3, ss.251-260, 2004 (Scopus) Sürdürülebilir Kalkınma

80. Metabolic pathway analysis of enzyme-deficient human red blood cells

Çakir T., Tacer C. S., ÜLGEN Ş. K.

BioSystems , cilt.78, sa.1-3, ss.49-67, 2004 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

81. Modeling of the induced expression for high-level production of a foreign protein by recombinant E. coli under the control of the T7 phage promoter

TOKSOY ÖNER E., Kirdar B., ÖNSAN Z. İ., ÜLGEN Ş. K.

Process Biochemistry , cilt.39, sa.3, ss.315-323, 2003 (SCI-Expanded, Scopus)

82. Optimal substrate feeding policy for fed-batch cultures of S. cerevisiae expressing bifunctional fusion protein displaying amylolytic activities

Altintaş M. M., ÜLGEN Ş. K., Kirdar B., ÖNSAN Z. İ., Oliver S. G.

Enzyme and Microbial Technology , cilt.33, sa.2-3, ss.262-269, 2003 (SCI-Expanded, Scopus)

83. Improvement of ethanol production from starch by recombinant yeast through manipulation of environmental factors

Mete Altintaş M., ÜLGEN Ş. K., Kirdar B., ÖNSAN Z. İ., Oliver S. G.

Enzyme and Microbial Technology , cilt.31, sa.5, ss.640-647, 2002 (SCI-Expanded, Scopus)

84. Cybernetic modelling of growth and ethanol production in a recombinant Saccharomyces cerevisiae strain secreting a bifunctional fusion protein

Altintaş M., Kirdar B., ÖNSAN Z. İ., ÜLGEN Ş. K.

Process Biochemistry , cilt.37, sa.12, ss.1439-1445, 2002 (SCI-Expanded, Scopus)

85. Bioconversion of starch into ethanol by a recombinant Saccharomyces cerevisiae strain YPG-AB

ÜLGEN Ş. K., Saygili B., ÖNSAN Z. İ., Kirdar B.

Process Biochemistry , cilt.37, sa.10, ss.1157-1168, 2002 (SCI-Expanded, Scopus)

86. Recovery of antithrombin III from milk by expanded bed chromatography

Özyurt S., Kirdar B., ÜLGEN Ş. K.

Journal of Chromatography A , cilt.944, sa.1-2, ss.203-210, 2002 (SCI-Expanded, Scopus)

87. Modeling of TaqI endonuclease purification by HPLC

Düzenli M., ÜLGEN Ş. K.

Turkish Journal of Chemistry , cilt.26, sa.6, ss.877-887, 2002 (Scopus, TRDizin)

88. Recovery of actinorhodin from fermentation broth

Güzeltunç E., ÜLGEN Ş. K.

Journal of Chromatography A , cilt.914, sa.1-2, ss.67-76, 2001 (SCI-Expanded, Scopus)

89. A structured model for intracellular EcoRI endonuclease production by recombinant E. coli 294

Tamerler C., ÜLGEN Ş. K., Kirdar B., ÖNSAN Z. İ.

Process Biochemistry , cilt.36, sa.7, ss.621-627, 2001 (SCI-Expanded, Scopus)

90. Quantitative description of protein adsorption by frontal analysis

AVCI A. K., Çamurdan M. C., ÜLGEN Ş. K.

Process Biochemistry , cilt.36, sa.1-2, ss.141-148, 2000 (SCI-Expanded, Scopus)

91. The stability of enzymes after sonication

ÖZBEK B., ÜLGEN Ş. K.

Process Biochemistry , cilt.35, sa.9, ss.1037-1043, 2000 (Scopus)

92. Optimization of the mobile phase conditions for the purification of Taql endonuclease

Duzenli M., ÜLGEN Ş. K.

Chromatographia , cilt.52, sa.5-6, ss.377-380, 2000 (SCI-Expanded, Scopus)

93. Growth of Thermus aquaticus and its TaqI endonuclease production

Altintas M., ÜLGEN Ş. K.

Acta Biotechnologica , cilt.19, sa.1, ss.45-56, 1999 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

94. Purification of TaqI endonuclease from Thermus aquaticus

Altintaş M. M., Özer N., ÜLGEN Ş. K.

Journal of Chromatography A , cilt.828, sa.1-2, ss.373-381, 1998 (SCI-Expanded, Scopus)

95. Oxygen transfer and uptake in Streptomyces coelicolor A3(2) culture in a batch bioreactor

ÜLGEN Ş. K., Mavituna F.

Journal of Chemical Technology and Biotechnology , cilt.73, sa.3, ss.243-250, 1998 (Scopus)

96. Mathematical description of ethanol fermentation by immobilised Saccharomyces cerevisiae

Birol G., Doruker P., Kirdar B., ÖNSAN Z. İ., ÜLGEN Ş. K.

Process Biochemistry , cilt.33, sa.7, ss.763-771, 1998 (Scopus)

97. Analysis of protein adsorption to ion exchangers in a finite bath

Habbaba M. M., ÜLGEN Ş. K.

Journal of Chemical Technology and Biotechnology , cilt.69, sa.4, ss.405-414, 1997 (SCI-Expanded, Scopus)

98. Effect of inoculum type on actinorhodin production by Streptomyces coelicolor A3(2)

Elibol M., ÜLGEN Ş. K., Kamaruddin K., Mavituna F.

Biotechnology Letters , cilt.17, sa.6, ss.579-582, 1995 (Scopus)

99. Comparison of the activity of immobilised and freely suspended Streptomyces coelicolor A3(2)

ÜLGEN Ş. K., Mavituna F.

Applied Microbiology and Biotechnology , cilt.41, sa.2, ss.197-202, 1994 (Scopus)

100. Actinorhodin production by Streptomyces coelicolor A3(2): kinetic parameters related to growth, substrate uptake and production

ÜLGEN Ş. K., Mavituna F.

Applied Microbiology and Biotechnology , cilt.40, sa.4, ss.457-462, 1993 (Scopus)

Hakemli Bilimsel Toplantılarda Yayımlanmış Bildiriler 50

1. Uncovering Neuroinflammation and Metabolic Biomarkers in Autism Spectrum Disorder through Genome-scale Metabolic Modeling

ESVAP E., ÜLGEN Ş. K.

9th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2024), san diego, Amerika Birleşik Devletleri, 24 Ekim - 26 Aralık 2024, (Özet Bildiri)

2. Preliminary Studies on Flow Assisted Propagation of Fluorescent Microbeads in Microfluidic Channels for Molecular Communication Systems

Durmaz M. G., Dilmac A., Camli B., Gencturk E., Canbek Ozdil Z. C., PUSANE A. E., et al.

12th EAI International Conference on Bio-inspired Information and Communications Technologies, BICT 2020, Shanghai, Çin, 7 - 08 Temmuz 2020, cilt.329 LNICST, ss.294-302, (Tam Metin Bildiri)

3. Development of genome-scale metabolic model for Daphnia pulex

başıbüyük s., SERTBAŞ M., ÜLGEN Ş. K.

7th BAU Drug Design Conference, 19 - 21 Aralık 2019, (Özet Bildiri)

4. İnme Durumunda Beyin Metabolizmasının Sistem Biyolojisi Yaklaşımı ile İncelenmesi

SERTBAŞ M., ÜLGEN Ş. K.

VI Türk Tıp Dünyası Kurultayı, Türkiye, 01 Eylül 2019, (Özet Bildiri)

5. Application of Thermoplastic Microbioreactor to the Single Cell Study of Budding Yeast to Decipher the Effect of 5-Hydroxymethylfurfural on Growth

GENÇTÜRK E., yurdakul e., çelik a., MUTLU Ş., ÜLGEN Ş. K.

World Academy of Science, Engineering and Technology, 1 - 03 Temmuz 2019, (Tam Metin Bildiri)

6. Prostate CAncer

ÜLGEN Ş. K., ÖZKIRIMLI ÖLMEZ E., ESVAP E.

ICSB, 28 Ekim - 02 Kasım 2018, (Özet Bildiri)

7. Synthesis of Liposome-Polymeric NanoparticleHybrid Systems for Therapeutic Applications

ÖZBEK Ö., İLERİ ERCAN N., ÜLGEN Ş. K.

19th International Conference on Systems BiologyICSB 2018, 28 Ekim - 01 Kasım 2018, (Özet Bildiri)

8. ANALYSIS OF THE EFFECTS OF INHIBITOR DRUGS AGAINST RIBOSOME BIOGENESIS BY USING SELF-ORGANIZED MAPS

kasım m., GENÇTÜRK E., ÜLGEN Ş. K.

19th International Conference on Systems Biology im 2018, 28 Ekim - 01 Kasım 2018, (Özet Bildiri)

9. PLITOOL: Protein-Ligand Interactions Tool

ÖZTÜRK H., BÜYÜKÖZ B., YIRIK M. A., ERÇETİN E., ÖZGÜR TÜRKMEN A., ÖZKIRIMLI ÖLMEZ E., et al.

17TH EUROPEAN CONFERENCE ON COMPUTATIONAL BIOLOGY, Yunanistan, 8 - 12 Eylül 2018, (Özet Bildiri)

10. MAYADA RİBOZOM BİYOJENEZİNİ VE DNA SENTEZİNİ ARAŞTIRMAK ÜZERE DÜŞÜK MALİYETLİ TERMOPLASTİK MİKROAKIŞKAN AYGITLAR

GENÇTÜRK E., yurdakul e., celik a. y., MUTLU Ş., ÜLGEN Ş. K.

13. Ulusal Kimya Mühendisliği Kongresi, Türkiye, 3 - 06 Eylül 2018, (Özet Bildiri)

11. MAYADA RİBOZOM BİYOJENEZİNİ VE DNA SENTEZİNİ ARAŞTIRMAK ÜZERE DÜŞÜK MALİYETLİ TERMOPLASTİK MİKROAKIŞKAN AYGITLAR

ÜLGEN Ş. K., GENÇTÜRK E., MUTLU Ş.

UKMK 13, Türkiye, 3 - 06 Eylül 2018, (Özet Bildiri)

12. Toxicity Effect Investigation of Graphene Oxide Addition into a Three-Component Scaffold Composed of Hydroxyapatite-Graphene Oxide-Chitosan for Bone Tissue Engineering Applications

YILMAZ P., ÖZTÜRK ER E., BAKIRDERE S., ÜLGEN Ş. K., ÖZBEK B.

23rd International Congress of Chemical and Process Engineering (CHISA 2018), PRAGUE, Çek Cumhuriyeti, 25 - 29 Ağustos 2018, (Özet Bildiri)

13. Production and Characterization Studies of a Three-Component Scaffold Composed of Hydroxyapatite-Graphene Oxide-Chitosan for Bone Tissue EngineeringApplications

YILMAZ P., ÖZTÜRK E., BAKIRDERE S., ÜLGEN Ş. K., ÖZBEK B.

23th International Congress of Chemical and Process Engineering (CHISA2018), PRAGUE, Çek Cumhuriyeti, 25 - 29 Ağustos 2018, (Özet Bildiri)

14. A study on the effects of polystyrene latexnanoparticles on Saccharomyces Cerevisiae

ÖZBEK Ö., İLERİ ERCAN N., ÜLGEN Ş. K.

23rd International Congress of Chemical andProcess Engineering CHISA 2018, 25 - 29 Ağustos 2018, (Özet Bildiri)

15. Low cost thermoplastic microfluidic devices to investigate the ribosome biogenesis and DNA synthesis in yeast

GENÇTÜRK E., yurdakul e., celik a. y., MUTLU Ş., ÜLGEN Ş. K.

SELECTBIO Lab-on-a-Chip Microfluidics Europe 2018, 5 - 06 Haziran 2018, (Özet Bildiri)

16. Identification of Mutual and Specific Ligands Related to the Proteins in Sphingolipid and Inflammation Pathways Using a Data Mining and Network Modeling Approach

ESVAP E., ÜLGEN Ş. K., ÖZKIRIMLI ÖLMEZ E., YAĞCI Z. B.

GRC Glycolipid and Sphingolipid Biology, 11 - 16 Şubat 2018, (Özet Bildiri)

17. Investigation Of Cell Cycle Network Of Yeast Using Lab-On-A-Chip Platform

dayan i. e., GENÇTÜRK E., puza s., MUTLU Ş., ÜLGEN Ş. K.

3rd Microfluidics Congress, 4 - 05 Aralık 2017, (Özet Bildiri)

18. Ligand-centric Clustering of Proteins: A case-study on Sphingolipid Metabolic Pathway

ÖZTÜRK H., Yirik M. A., ÖZKIRIMLI ÖLMEZ E., ÖZGÜR TÜRKMEN A., ÜLGEN Ş. K.

5th International BAU Drug Design Congress, 19 - 21 Ekim 2017, (Özet Bildiri)

19. MOTILITY STUDIES BY USING MICROFLUIDIC TECHNOLOGY

YÜCE M., ÜLGEN Ş. K., ÖZKIRIMLI ÖLMEZ E., SARIYAR AKBULUT B.

5TH BAU DRUG DESIGN CONGRESS, İstanbul, Türkiye, 19 - 21 Ekim 2017, (Özet Bildiri)

20. Structural and Dynamical Analysis of Bacterial Neutral Sphingomyelinase

Yagci Z. B., ÖZKIRIMLI ÖLMEZ E., ÜLGEN Ş. K.

XII Sphingolipid Club Meeting, Trabia, İtalya, 7 - 10 Eylül 2017, (Özet Bildiri)

21. Understanding the Relationship among Immune System – Prostate Cancer – Sphingolipid Metabolism by Network Analysis

ESVAP E., ÜLGEN Ş. K., ÖZKIRIMLI ÖLMEZ E.

XII Sphingolipid Club Meeting, Trabia, İtalya, 7 - 10 Eylül 2017, (Özet Bildiri)

22. A novel methodology on distributed representations of proteins using their interacting ligands: A case-study on Sphingolipid Metabolic Pathway

ÖZTÜRK H., Yirik M. A., ÖZGÜR TÜRKMEN A., ÖZKIRIMLI ÖLMEZ E., ÜLGEN Ş. K.

25th Conference on Intelligent Systems for Molecular Biology (ISMB) and the 16th European Conference on Computational Biology ISMB/ECCB 2017, Prague, Çek Cumhuriyeti, 21 - 25 Temmuz 2017, (Özet Bildiri)

23. In The Light Of Pharmacological Chaperone Search For Metachromatic Leukodystrophy: Effects Of Mutations And pH On The Stability And Dynamics Of Arylsulfatase A

Eren A., ÖZKARA H. A., ÜLGEN Ş. K., ÖZKIRIMLI ÖLMEZ E.

3rd Neurological Disorders Summit, San-Francisco, Kostarika, 6 - 08 Ağustos 2017, (Özet Bildiri)

24. Pharmacological Chaperone Search For Lysosomal Storage Diseases

Eren A., ÖZKARA H. A., ÖZKIRIMLI ÖLMEZ E., ÜLGEN Ş. K.

9th international ceramide conference, Long Island, NY, Amerika Birleşik Devletleri, 1 - 05 Mayıs 2017, (Özet Bildiri)

25. Insights into Inactivity of Arylsulfatase A due to Two Novel Cases: W318C and E307KT391S, ICC9

Eren A., ÖZKARA H. A., ÖZKIRIMLI ÖLMEZ E., ÜLGEN Ş. K.

9th international ceramide conference, Long Island, NY, 1 - 05 Mayıs 2017, (Özet Bildiri)

26. Analysis of Sphingolipid Insulin Metabolisms

Yırık M. A., ÜLGEN Ş. K., ÖZKIRIMLI ÖLMEZ E.

4th Bau Drug Design, 13 - 15 Ekim 2016, (Özet Bildiri)

27. Sphingolipid protein interaction network as a drug target

ÜLGEN Ş. K.

4the International Drug Design Congress, 13 - 15 Ekim 2016, (Özet Bildiri)

28. Arylsulfatase A and Its Mutants In the light of Pharmacological Chaperone Search

eren A., ÖZKARA H. A., ÜLGEN Ş. K., ÖZKIRIMLI ÖLMEZ E.

4th Drug Design, 13 - 15 Ekim 2016, (Özet Bildiri)

29. yeast co culturing in 1nL microbioreactor system

üçpınar s., GENÇTÜRK E., İŞERİ E., MUTLU Ş., ÜLGEN Ş. K.

ICSB, Barcelona, İspanya, 16 - 20 Eylül 2016, (Özet Bildiri)

30. The dual role of sld7 in cell cycle and chronological aging in budding yeast

dayan i. e., arga k. y., ÜLGEN Ş. K.

ICSB, Barcelona, İspanya, 16 - 20 Eylül 2016, (Özet Bildiri)

31. Identification of the effect of mutations on the stability and function of arylsulphatase A

Eren A., ÖZKARA H. A., ÜLGEN Ş. K., ÖZKIRIMLI ÖLMEZ E.

EMBL, 31 Ağustos - 03 Eylül 2016, (Özet Bildiri)

32. FAbrication of microfluidic devices for yeast culturing

üçpınar s., GENÇTÜRK E., İŞERİ E., MUTLU Ş., ÜLGEN Ş. K.

EMBL, Heidelberg, Almanya, 24 - 26 Temmuz 2016, (Özet Bildiri)

33. TArgeting Arylsulphatase A Effect of Mutations on mechanism and Dynamics

Eren A., ÖZKARA H. A., ÜLGEN Ş. K., ÖZKIRIMLI ÖLMEZ E.

Gordon Research Conference: Glycolipids, 6 - 11 Mart 2016, (Özet Bildiri)

34. docking and molecular dynamics evaluations of potential S1PL inhibitors for neurodegerative disorder therapy

DENİZ U., ÖZKIRIMLI ÖLMEZ E., ÜLGEN Ş. K.

Gordon Research Conference: Glycolipids and Sphingolipids, 6 - 11 Mart 2016

35. in Silico identification of orthosteric and allosteric inhibitors of sphingosine kinase 1

bayraktar ö., ÖZKIRIMLI ÖLMEZ E., ÜLGEN Ş. K.

Gordon Research Conference: Glycolipids and Sphingolipids, 6 - 11 Mart 2016, (Özet Bildiri)

36. Fabrication of steel displacement amplifiers integrated to microfluidic channels

Iseri E., ÜLGEN Ş. K., YILMAZ Ç., Mutlu S.

29th IEEE International Conference on Micro Electro Mechanical Systems, MEMS 2016, Shanghai, Çin, 24 - 28 Ocak 2016, cilt.2016-February, ss.493-496, (Tam Metin Bildiri)

37. Understanding the function of Sld7 protein of yeast using a microfluidic system

GENÇTÜRK E., ÜLGEN Ş. K.

3rd Applied Synthetic Biology, 22 - 24 Şubat 2016, (Özet Bildiri)

38. Yeast culturing in 1 5 nL Microbioreactors

GENÇTÜRK E., ÜLGEN Ş. K.

3rd Applied Synthetic Biology in Europe, 22 - 24 Şubat 2016, (Özet Bildiri)

39. Investigation of SLD7 protein in 1 5nL Chambers of a Microchemostat

GENÇTÜRK E., MUTLU Ş., ÜLGEN Ş. K.

Microfluidics Congress, 20 - 21 Ekim 2015

40. Comparative Analysis of arylsulphatase A and its mutants

Eren A., Maral B., ÖZKARA H. A., ÜLGEN Ş. K., ÖZKIRIMLI ÖLMEZ E.

3rd BAU Drug Design Conference, 1 - 03 Ekim 2015

41. An integrated computational approach of virtual screening molecular docking and MD simulations for the discovery of S1PL inhibitors against inflammatory neurodegenerative disorders

DENİZ U., Elif O., ÜLGEN Ş. K.

3rd BAU Drug Design conference, 1 - 03 Ekim 2015

42. Computer aided discovery of Sphk1 inhibitors

Bayraktar Ö., ÖZKIRIMLI ÖLMEZ E., ÜLGEN Ş. K.

3rd BAU Drug Design Conference, 1 - 03 Ekim 2015, (Özet Bildiri)

43. Insights into the effects of the mutations of arylsulfatase A on its structure using MD simulations

maral b., Eren A., ÖZKARA H. A., ÜLGEN Ş. K., Elif Ö. O.

8th International Ceramide Conference, 6 - 10 Mayıs 2015

44. Reconstruction and Analysis of Yeast Sphingolipid Protein Interaction Network

ÜLGEN Ş. K.

8th International Ceramide Conference, 6 - 10 Mayıs 2015, (Özet Bildiri)

45. Discovery of novel S1PL inhibitors against multiple sclerosis disease

DENİZ U., Elif O. O., ÜLGEN Ş. K.

8th International Ceramide Conference, 6 - 10 Mayıs 2015

46. Macro to microfluidic channel integration using 3D printing for laminar flow investigation in a Y channel

İŞERİ E., Elif G., Meriç G., UĞUZ A. K., ÜLGEN Ş. K., Senol M.

25th Micromechanics and Microsystems Europe workshop, 1 - 03 Eylül 2014, (Tam Metin Bildiri)

47. PHISTO: A new web platform for pathogen-human interactions

Tekir S. D., Çakir T., Ardiç E., Karadeniz I., ÖZGÜR TÜRKMEN A., Sevilgen F. E., et al.

11th International Conference on Computational Methods in Systems Biology, CMSB 2013, Klosterneuburg, Avusturya, 22 - 24 Eylül 2013, cilt.8130 LNBI, ss.268-269, (Tam Metin Bildiri)