I. Kavakli

发表

IVT-seq reveals extreme bias in RNA sequencing

Michael B. Black, R. Irizarry, Hannah Dueck, 2014, Genome Biology.

MerR and ChrR mediate blue light induced photo-oxidative stress response at the transcriptional level in Vibrio cholerae

I. Kavakli, Mehmet Tardu, S. Bulut, 2017, Scientific Reports.

Oncogenic K-Ras4B Dimerization Enhances Downstream Mitogen-activated Protein Kinase Signaling

R. Nussinov, Chung-Jung Tsai, O. Keskin, 2020, Journal of Molecular Biology.

A Magnetically Actuated Resonant Mass Sensor With Integrated Optical Readout

B. E. Alaca, I. Kavakli, H. Urey, 2008, IEEE Photonics Technology Letters.

Machine Learning Helps Identify CHRONO as a Circadian Clock Component

John B. Hogenesch, Julie E. Baggs, Ron C. Anafi, 2014, PLoS biology.

Investigation of Real-Time Photorepair Activity on DNA via Surface Plasmon Resonance

R. Kizilel, I. Kavakli, S. Azizoglu, 2012, PloS one.

Cryptochrome deletion in p53 mutant mice enhances apoptotic and anti-tumorigenic responses to UV damage at the transcriptome level

Ayse Derya Cavga, O. Keskin, A. Gursoy, 2019, Functional & Integrative Genomics.

IVT-seq reveals extreme bias in RNA sequencing

Michael B. Black, R. Irizarry, Hannah Dueck, 2014, Genome Biology.

Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism.

Aziz Sancar, Aalim M Weljie, Anthony O. Olarerin-George, 2017, Cell metabolism.

Perovskite‐Based Optoelectronic Biointerfaces for Non‐Bias‐Assisted Photostimulation of Cells

S. B. Srivastava, I. Kavakli, M. M. Aria, 2019, Advanced Materials Interfaces.

Band Alignment Engineers Faradaic and Capacitive Photostimulation of Neurons Without Surface Modification

S. B. Srivastava, I. Kavakli, M. M. Aria, 2019, Physical Review Applied.

Reduced Glucose Sensation Can Increase the Fitness of Saccharomyces cerevisiae Lacking Mitochondrial DNA

I. Kavakli, Mehmet Tardu, Cory D. Dunn, 2015, bioRxiv.

Reduced Glucose Sensation Can Increase the Fitness of Saccharomyces cerevisiae Lacking Mitochondrial DNA

I. Kavakli, Mehmet Tardu, Cory D. Dunn, 2015, bioRxiv.

The Rop GTPase switch turns on polar growth in pollen

Zhenbiao Yang, I. Kavakli, T. Okita, 2000 .

Enhancement of the lipid productivity and fatty acid methyl ester profile of Chlorella vulgaris by two rounds of mutagenesis.

I. Kavakli, C. Erkey, Ehsan Sarayloo, 2018, Bioresource technology.

Differential requirement for centriolar satellites in cilium formation among different vertebrate cells

I. Kavakli, J. Andersen, Ezgi Odabasi, 2018, bioRxiv.

Glu-370 in the large subunit influences the substrate binding, allosteric, and heat stability properties of potato ADP-glucose pyrophosphorylase.

I. Kavakli, Seref Gul, I. Baris, 2016, Plant science : an international journal of experimental plant biology.

Glu-370 in the Large Subunit Influences the Substrate Binding, Allosteric, and Heat Stability Properties of Potato ADP-glucose Pyrophosphorylase

I. Kavakli, Seref Gul, I. Baris, 2016, bioRxiv.

Enhanced heterotetrameric assembly of potato ADP-glucose pyrophosphorylase using reverse genetics.

I. Kavakli, G. Cevahir, A. B. Seferoğlu, 2014, Plant & cell physiology.

Transcriptional regulation of the ADP-glucose pyrophosphorylase isoforms in the leaf and the stem under long and short photoperiod in lentil.

I. Kavakli, Isil Tulum, I. Baris, 2013, Plant science : an international journal of experimental plant biology.

Enhanced turnover of transitory starch by expression of up-regulated ADP-glucose pyrophosphorylases in

I. Kavakli, T. Okita, G. Edwards, 2006 .

Transcriptome analysis of the circadian clock gene BMAL1 deletion with opposite carcinogenic effects

I. Kavakli, Nuri Ozturk, Seref Gul, 2020, Functional & Integrative Genomics.

MEMS biosensor for parallel and highly sensitive and specific detection of hepatitis

B. E. Alaca, E. Timurdogan, I. Kavakli, 2011, 2011 IEEE 24th International Conference on Micro Electro Mechanical Systems.

Bidirectional optical neuromodulation using capacitive charge-transfer.

S. B. Srivastava, I. Kavakli, S. Nizamoglu, 2020, Biomedical optics express.

Transcriptional expression characteristics and subcellular localization of ADP-glucose pyrophosphorylase in the oil plant Perilla frutescens.

I. Kavakli, T. Okita, K. Kim, 2001, Plant & cell physiology.

In Silico Identification of Widely Used and Well Tolerated Drugs That May Inhibit SARSCov- 2 3C-like Protease and Viral RNA-Dependent RNA Polymerase Activities, and May Have Potential to Be Directly Used in Clinical Trials

I. Kavakli, Seref Gul, I. Baris, 2020 .

In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials

I. Kavakli, Seref Gul, I. Baris, 2020, Journal of biomolecular structure & dynamics.

Purification and characterization of a type III photolyase from Caulobacter crescentus.

I. Kavakli, A. Sancar, Ya-Ting Kao, 2008, Biochemistry.

Structure Based Discovery of Small Molecules to Regulate the Activity of Human Insulin Degrading Enzyme

I. Kavakli, Onur Dagliyan, S. Kizilel, 2012, PloS one.

CRY1‐CBS binding regulates circadian clock function and metabolism

J. Hogenesch, R. Anafi, I. Kavakli, 2020, The FEBS journal.

CRY1-CBS binding regulates circadian clock function and metabolism

J. Hogenesch, R. Anafi, I. Kavakli, 2020, bioRxiv.

DNA repair by photolyases.

I. Kavakli, Nuri Ozturk, Seref Gul, 2019, Advances in protein chemistry and structural biology.

The secondary pocket of cryptochrome 2 is important for the regulation of its stability and localization

I. Kavakli, Seref Gul, I. Baris, 2022, The Journal of biological chemistry.

The Arg-293 of Cryptochrome1 is responsible for the allosteric regulation of CLOCK-CRY1 binding in circadian rhythm.

I. Kavakli, Cihan Aydın, Seref Gul, 2020, The Journal of biological chemistry.

Optimization Based Tumor Classification from Microarray Gene Expression Data

I. Halil Kavakli, Metin Turkay, Onur Dagliyan, 2011, PloS one.

Understanding lipid metabolism in high-lipid-producing Chlorella vulgaris mutants at the genome-wide level

I. Kavakli, Mehmet Tardu, C. Erkey, 2017 .

Upgrading blends of microalgae feedstocks and heavy oils in supercritical water

I. Kavakli, C. Erkey, R. O. Caniaz, 2017 .

Cryptochrome deletion in p53 mutant mice enhances apoptotic and anti-tumorigenic responses to UV damage at the transcriptome level

Ayse Derya Cavga, O. Keskin, A. Gursoy, 2019, Functional & Integrative Genomics.

Erratum: Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism (Cell Metabolism (2017) 25(4) (961–974.e4) (S1550413117301717) (10.1016/j.cmet.2017.03.019))

Anthony O. Olarerin-George, C. Dang, J. Hogenesch, 2017 .

Identification of two Amino Acids in the C-terminal Domain of Mouse CRY2 Essential for PER2 Interaction

I. Kavakli, E. B. Unal, Gulnaz Tatlici, 2010, BMC Molecular Biology.

3D printed poly(lactic acid) scaffolds modified with chitosan and hydroxyapatite for bone repair applications

I. Kavakli, I. Yilgor, E. Yilgor, 2020 .

New biocompatible antibacterial wound dressing candidates; agar-locust bean gum and agar-salep films.

I. Kavakli, H. Turkmen, N. Yeşilçubuk, 2020, International journal of biological macromolecules.

RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae

I. Kavakli, Mehmet Tardu, I. Baris, 2016, Functional & Integrative Genomics.

Proteome analysis of the circadian clock protein PERIOD2

I. Kavakli, Nurhan Ozlu, Nuri Ozturk, 2022, Proteins.

Diurnal Changes in Capecitabine Clock-Controlled Metabolism Enzymes Are Responsible for Its Pharmacokinetics in Male Mice

I. Kavakli, F. Lévi, Seref Gul, 2023, Journal of biological rhythms.

Discovery of a small molecule that selectively destabilizes Cryptochrome 1 and enhances life span in p53 knockout mice

M. Turkay, I. Kavakli, M. Guzel, 2021, bioRxiv.

The Arg-293 of Cryptochrome1 is responsible for the allosteric regulation of CLOCK-CRY1 binding in circadian rhythm

I. Kavakli, Cihan Aydın, Seref Gul, 2020, The Journal of Biological Chemistry.

Purification and Characterization of Three Members of the Photolyase/Cryptochrome Family Blue-light Photoreceptors from Vibrio cholerae*

I. Kavakli, A. Sancar, E. Worthington, 2003, Journal of Biological Chemistry.

Biocompatible Quantum Funnels for Neural Photostimulation

I. Kavakli, I. B. Dogru, S. Nizamoglu, 2019, Nano letters.

Purification and characterization of five members of photolyase/cryptochrome family from Cyanidioschyzon merolae.

I. Kavakli, H. Asimgil, 2012, Plant science : an international journal of experimental plant biology.

The Photolyase/Cryptochrome Family of Proteins as DNA Repair Enzymes and Transcriptional Repressors

I. Kavakli, Mehmet Tardu, S. Bulut, 2017, Photochemistry and photobiology.

Ultrafast dynamics of resonance energy transfer in cryptochrome.

I. Kavakli, A. Sancar, D. Zhong, 2005, Journal of the American Chemical Society.

Transcriptomic and fatty acid analyses of Neochloris aquatica grown under different nitrogen concentration

I. Kavakli, Ehsan Sarayloo, G. Cevahir, 2022, Functional & Integrative Genomics.

Comparative RNA-seq analysis of the drought-sensitive lentil (Lens culinaris) root and leaf under short- and long-term water deficits

I. Kavakli, Mehmet Tardu, G. Cevahir, 2019, Functional & Integrative Genomics.

Human CRY1 variants associate with attention deficit/hyperactivity disorder.

J. Casanova, I. Kavakli, K. Bilguvar, 2020, The Journal of clinical investigation.

Engineering starch for increased quantity and quality.

I. Kavakli, T. Okita, I H Kavakli, 2000, Trends in plant science.

Day-Time Isoflurane Administration Suppresses Circadian Gene Expressions in Both the Brain and a Peripheral Organ, Liver.

I. Kavakli, N. Gökmen, O. Yılmaz, 2017, Turkish journal of anaesthesiology and reanimation.

Identification of novel small molecules targeting core clock proteins to regulate circadian rhythm

M. Turkay, I. Kavakli, Seref Gul, 2022, Current Opinion in Chemical Engineering.

Circadian photoreception in humans and mice.

I. Kavakli, A. Sancar, 2002, Molecular interventions.

Centriolar satellites are required for efficient ciliogenesis and ciliary content regulation

I. Kavakli, Ezgi Odabasi, E. N. Firat-Karalar, 2019, EMBO reports.

Microcantilever based disposable viscosity sensor for serum and blood plasma measurements.

Hakan Urey, Caglar Elbuken, Ibrahim Halil Kavakli, 2013, Methods.

Milp-hyperbox classification for structure-based drug design in the discovery of small molecule inhibitors of SIRTUIN6

I. Halil Kavakli, Metin Türkay, Fatih Rahim, 2016, RAIRO Oper. Res..

Analysis of the role of intraprotein electron transfer in photoreactivation by DNA photolyase in vivo.

I. Kavakli, A. Sancar, 2004, Biochemistry.

The crystal structure of Vibrio cholerae (6-4) photolyase reveals interactions with cofactors and a DNA-binding region

I. Kavakli, H. Demirci, Barış Çakilkaya, 2022, bioRxiv.

Crystal structure of Vibrio cholerae (6-4) photolyase with DNA binding region

I. Kavakli, H. Demirci, Barış Çakilkaya, 2022 .

Identification and characterization of a new class of (6-4) photolyase from Vibrio cholerae.

I. Kavakli, Mehmet Tardu, Nuri Ozturk, 2019, Biochemistry.

Protein interaction networks of the mammalian core clock proteins.

I. Kavakli, Nuri Ozturk, I. Baris, 2022, Advances in protein chemistry and structural biology.

MEMS biosensor for detection of Hepatitis A and C viruses in serum.

Hakan Urey, Erman Timurdogan, B. E. Alaca, 2011, Biosensors & bioelectronics.

Effective Neural Photostimulation Using Indium-Based Type-II Quantum Dots

I. Kavakli, S. Nizamoglu, M. Sahin, 2018, ACS nano.

Plasmon-Coupled Photocapacitor Neuromodulators

S. B. Srivastava, I. Kavakli, B. Ulgut, 2020, bioRxiv.

A novel BHLHE41 variant is associated with short sleep and resistance to sleep deprivation in humans.

H. Hakonarson, A. Pack, D. Dinges, 2014, Sleep.

NOVEL BHLHE41 VARIANT ASSOCIATED WITH SHORT SLEEP AND RESISTANCE TO SLEEP LOSS

H. Hakonarson, A. Pack, D. Dinges, 2014 .

Classification of drug molecules considering their IC50 values using mixed-integer linear programming based hyper-boxes method

I. Halil Kavakli, Fadime Üney Yüksektepe, Metin Türkay, 2008, BMC Bioinformatics.

A CLOCK-binding small molecule disrupts the interaction between CLOCK and BMAL1 and enhances circadian rhythm amplitude

I. Kavakli, Nuri Ozturk, Seref Gul, 2020, The Journal of Biological Chemistry.

Directed molecular evolution of ADP-glucose pyrophosphorylase

I. Kavakli, T. Okita, Casey J. Slattery, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Investigation of the Interaction between the Large and Small Subunits of Potato ADP-Glucose Pyrophosphorylase

Aytug Tuncel, I. Halil Kavakli, Ozlem Keskin, 2009, PLoS Comput. Biol..

Nanoengineering InP Quantum Dot-Based Photoactive Biointerfaces for Optical Control of Neurons

S. B. Srivastava, I. Kavakli, M. M. Aria, 2021, Frontiers in Neuroscience.

Subcellular compartmentation and allosteric regulation of the rice endosperm ADPglucose pyrophosphorylase

I. Kavakli, T. Okita, Chotipa Sakulsingharoj, 2001 .

Tetra-functional Multilayer Coatings for Cardiovascular Stent Materials

I. Kavakli, A. Motallebzadeh, O. Yalcin, 2023, Colloids and Surfaces A: Physicochemical and Engineering Aspects.

Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism.

Anthony O. Olarerin-George, C. Dang, J. Hogenesch, 2017, Cell metabolism.

Molecular Approaches to Genetic Diversity

I. Kavakli, M. Caliskan, Guul Cevahir Oz, 2015 .

Oncogenic K-Ras4B dimerization enhances downstream MAPK signaling.

R. Nussinov, Chung-Jung Tsai, O. Keskin, 2020, Journal of molecular biology.

Structure-based design and classifications of small molecules regulating the circadian rhythm period

M. Turkay, I. Kavakli, Nuri Ozturk, 2021, Scientific Reports.

Insights into subunit interactions in the heterotetrameric structure of potato ADP-glucose pyrophosphorylase.

Ozlem Keskin, Ibrahim Halil Kavakli, O. Keskin, 2008, Biophysical journal.

Classification of Cytochrome P450 Inhibitors with Respect to Binding Free Energy and pIC50 Using Common Molecular Descriptors

I. Halil Kavakli, Metin Türkay, Onur Dagliyan, 2009, J. Chem. Inf. Model..

Structure-based design and analysis of cytochrome P 450 inhibitors for the treatment of prostate cancer

M. Turkay, I. Kavakli, M. Ozdemir, 2006 .

Structure-Based Design and Analysis of Cytochrome P450 Inhibitors for the Treatment of Prostate Cancer

I. Halil Kavakli, Metin Türkay, Muhittin Emre Özdemir, 2006, BIOCOMP.

In vitro antibacterial and cytotoxicity assessment of magnetron sputtered Ti1.5ZrTa0.5Nb0.5W0.5 refractory high-entropy alloy doped with Ag nanoparticles

I. Kavakli, H. Acar, M. Hashemkhani, 2022, Vacuum.

Organic Photovoltaic Pseudocapacitors for Neurostimulation

S. B. Srivastava, I. Kavakli, S. Nizamoglu, 2020, ACS applied materials & interfaces.

Bulk-heterojunction photocapacitors with high open-circuit voltage for low light intensity photostimulation of neurons

S. B. Srivastava, I. Kavakli, S. Nizamoglu, 2021, Journal of Materials Chemistry C.

Comparative RNA-seq analysis of the drought-sensitive lentil (Lens culinaris) root and leaf under short- and long-term water deficits

I. Kavakli, Mehmet Tardu, G. Cevahir, 2019, Functional & Integrative Genomics.

Identification of two Amino Acids in the C-terminal Domain of Mouse CRY2 Essential for PER2 Interaction

I. Kavakli, Natali Ozber, Ibrahim Baris, 2010, BMC Molecular Biology.

Functional characterization of the CRY2 circadian clock component variant p.Ser420Phe revealed a new degradation pathway for CRY2

I. Kavakli, Seref Gul, I. Baris, 2023, The Journal of biological chemistry.

Dynamic regulation of the serine loop by distant mutations reveals allostery in cryptochrome1.

I. Kavakli, Seref Gul, Onur Ozcan, 2023, Journal of biomolecular structure & dynamics.

Computational and experimental investigation of DNA repair protein photolyase interactions with low molecular weight drugs

R. Kizilel, B. Erman, I. Kavakli, 2013, Journal of molecular recognition : JMR.

Allosteric Regulation of CRYs in Mammalian Circadian Clock

I. Kavakli, Seref Gul, Onur Ozcan, 2021, 31st European Symposium on Computer Aided Process Engineering.

A novel smart disinfection system using 3D-printed and electrically conductive composite hydrogel

S. A. Khan, I. Kavakli, Seref Gul, 2024, Emergent Materials.

In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials

I. Kavakli, Seref Gul, I. Baris, 2020, Journal of biomolecular structure & dynamics.

The role of the circadian timing system on drug metabolism and detoxification: an update

I. Kavakli, A. Okyar, S. Surme, 2024, Expert opinion on drug metabolism & toxicology.