Classification of Terahertz Images via Caustic Lens and Transfer Learning

Authors: Arik, Dogan Tunca, Sahin, Asaf Behzat, Ersoy, Ozgun

Source: 2024 8th International Artificial Intelligence and Data Processing Symposium (IDAP) Artificial Intelligence and Data Processing Symposium (IDAP), 2024 8th International. :1-4 Sep, 2024

Relation: 2024 8th International Artificial Intelligence and Data Processing Symposium (IDAP)

Multi-modal Representation Learning Enables Accurate Protein Function Prediction in Low-Data Setting

Authors: Ünsal, Serbülent, Özdemir, Sinem, Kasap, Bünyamin, Kalaycı, M. Erşan, Turhan, Kemal, Doğan, Tunca, Acar, Aybar C.

Subject Terms: Quantitative Biology - Biomolecules, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2412.08649

Compressive Sensing Imaging Using Caustic Lens Mask Generated by Periodic Perturbation in a Ripple Tank

Authors: Arık, Doğan Tunca, Şahin, Asaf Behzat, Ersoy, Özgün

Subject Terms: Electrical Engineering and Systems Science - Signal Processing

Access URL: http://arxiv.org/abs/2405.00407

SELFormer: Molecular Representation Learning via SELFIES Language Models

Authors: Yüksel, Atakan, Ulusoy, Erva, Ünlü, Atabey, Doğan, Tunca

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Machine Learning, 68T07, I.2.1, I.2.6, I.5.4

Access URL: http://arxiv.org/abs/2304.04662

Target Specific De Novo Design of Drug Candidate Molecules with Graph Transformer-based Generative Adversarial Networks

Authors: Ünlü, Atabey, Çevrim, Elif, Sarıgün, Ahmet, Yiğit, Melih Gökay, Çelikbilek, Hayriye, Bayram, Osman, Güvenilir, Heval Ataş, Koyaş, Altay, Kahraman, Deniz Cansen, Olğaç, Abdurrahman, Rifaioğlu, Ahmet, Banoğlu, Erden, Doğan, Tunca

Subject Terms: Computer Science - Machine Learning, Quantitative Biology - Biomolecules, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2302.07868

Democratising Knowledge Representation with BioCypher

Authors: Lobentanzer, Sebastian, Aloy, Patrick, Baumbach, Jan, Bohar, Balazs, Charoentong, Pornpimol, Danhauser, Katharina, Doğan, Tunca, Dreo, Johann, Dunham, Ian, Fernandez-Torras, Adrià, Gyori, Benjamin M., Hartung, Michael, Hoyt, Charles Tapley, Klein, Christoph, Korcsmaros, Tamas, Maier, Andreas, Mann, Matthias, Ochoa, David, Pareja-Lorente, Elena, Popp, Ferdinand, Preusse, Martin, Probul, Niklas, Schwikowski, Benno, Sen, Bünyamin, Strauss, Maximilian T., Turei, Denes, Ulusoy, Erva, Wodke, Judith Andrea Heidrun, Saez-Rodriguez, Julio

Subject Terms: Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/2212.13543

Protein language models for predicting drug–target interactions: Novel approaches, emerging methods, and future directions

Authors: Ünlü, Atabey ^{a, b, 1}, Ulusoy, Erva ^{a, b, 1}, Yiğit, Melih Gökay ^{a, c, 1}, Darcan, Melih ^{a, 1}, Doğan, Tunca ^{a, b, d, ⁎}

Source: In Current Opinion in Structural Biology April 2025 91

Target Classification with FMCW Radar Using Features Extracted from Fourier Transform of Radar Cross Section

Authors: Arik, Dogan Tunca, Sahin, Asaf Behzat

Source: 2019 27th Signal Processing and Communications Applications Conference (SIU) Signal Processing and Communications Applications Conference (SIU), 2019 27th. :1-4 Apr, 2019

Relation: 2019 27th Signal Processing and Communications Applications Conference (SIU)

An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data

Authors: Shojaei, Mona, Mohammadvand, Navid, Doğan, Tunca, Alkan, Can, Çetin Atalay, Rengül, Acar, Aybar C.

Source: In Computers in Biology and Medicine February 2024 169

Multi-task Deep Neural Networks in Automated Protein Function Prediction

Authors: Rifaioglu, Ahmet Sureyya, Doğan, Tunca, Martin, Maria Jesus, Cetin-Atalay, Rengul, Atalay, Mehmet Volkan

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1705.04802

Evolutionary relationships between gene sequences via nonlinear embedding

Authors: Dogan, Tunca, Karacah, Bilge

Source: 2010 15th National Biomedical Engineering Meeting Biomedical Engineering Meeting (BIYOMUT), 2010 15th National. :1-4 Apr, 2010

Relation: 2010 15th National Biomedical Engineering Meeting (BIYOMUT 2010)

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Authors: Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T, Bankapur, Asma R, D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S, Kahanda, Indika, Verspoor, Karin M, Ben-Hur, Asa, Koo, Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed ME, Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T, Chapman, Samuel, C., Dukka B K., Khan, Ishita K, Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E, Hieta, Reija, Legge, Duncan, Lovering, Ruth C, Magrane, Michele, Melidoni, Anna N, Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L, Lee, David, Lees, Jonathan G, Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E, Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E, Pavlidis, Paul, Feng, Shou, Cejuela, Juan M, Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel, Piovesan, Damiano, Tosatto, Silvio, del Pozo, Angela, Fernández, José M, Maietta, Paolo, Valencia, Alfonso, Tress, Michael L, Benso, Alfredo, Di Carlo, Stefano, Politano, Gianfranco, Savino, Alessandro, Rehman, Hafeez Ur, Re, Matteo, Mesiti, Marco, Valentini, Giorgio, Bargsten, Joachim W, van Dijk, Aalt DJ, Gemovic, Branislava, Glisic, Sanja, Perovic, Vladmir, Veljkovic, Veljko, Veljkovic, Nevena, Almeida-e-Silva, Danillo C, Vencio, Ricardo ZN, Sharan, Malvika, Vogel, Jörg, Kansakar, Lakesh, Zhang, Shanshan, Vucetic, Slobodan, Wang, Zheng, Sternberg, Michael JE, Wass, Mark N, Huntley, Rachael P, Martin, Maria J, O'Donovan, Claire, Robinson, Peter N, Moreau, Yves, Tramontano, Anna, Babbitt, Patricia C, Brenner, Steven E, Linial, Michal, Orengo, Christine A, Rost, Burkhard, Greene, Casey S, Mooney, Sean D, Friedberg, Iddo, Radivojac, Predrag

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1601.00891

Design, synthesis, and evaluation of novel Indole‐Based small molecules as sirtuin inhibitors with anticancer activities.

Authors: Binarci, Busra, Kilic, Ensar Korkut, Dogan, Tunca, Cetin Atalay, Rengul, Kahraman, Deniz Cansen, Nacak Baytas, Sultan

Source: Drug Development Research; Nov2024, Vol. 85 Issue 7, p1-15, 15p

Subject Terms: SMALL molecules, CHRONIC active hepatitis, HEPATOCELLULAR carcinoma, MOLECULAR docking, CELL lines

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Authors: Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy, Lee, Alexandra, Kacsoh, Balint, Crocker, Alex, Lewis, Kimberley, Georghiou, George, Nguyen, Huy, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca, Freddolino, Peter, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José, Gemovic, Branislava, Perovic, Vladimir, Davidović, Radoslav, Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad, Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex, Antczak, Magdalena, Fabris, Fabio, Wass, Mark, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel, Reeb, Jonas, Ritchie, David, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Falda, Marco, Berselli, Michele, Tosatto, Silvio, Carraro, Marco, Piovesan, Damiano, Ur Rehman, Hafeez, Mao, Qizhong, Zhang, Shanshan, Vucetic, Slobodan, Black, Gage, Jo, Dane, Suh, Erica, Dayton, Jonathan, Larsen, Dallas, Omdahl, Ashton, McGuffin, Liam, Brackenridge, Danielle, Babbitt, Patricia, Yunes, Jeffrey, Fontana, Paolo, Zhang, Feng, Zhu, Shanfeng, You, Ronghui, Zhang, Zihan, Dai, Suyang, Yao, Shuwei, Tian, Weidong, Cao, Renzhi, Chandler, Caleb, Amezola, Miguel, Johnson, Devon, Chang, Jia-Ming, Liao, Wen-Hung, Liu, Yi-Wei, Pascarelli, Stefano, Frank, Yotam, Hoehndorf, Robert, Kulmanov, Maxat, Boudellioua, Imane, Politano, Gianfranco, Di Carlo, Stefano, Benso, Alfredo, Hakala, Kai, Ginter, Filip, Mehryary, Farrokh, Kaewphan, Suwisa, Björne, Jari, Moen, Hans, Tolvanen, Martti, Salakoski, Tapio, Kihara, Daisuke, Jain, Aashish, Šmuc, Tomislav, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Brenner, Steven, Orengo, Christine, Jeffery, Constance, Bosco, Giovanni, Hogan, Deborah, Martin, Maria, O'Donovan, Claire, Mooney, Sean, Greene, Casey, Radivojac, Predrag, Friedberg, Iddo

Source: Genome biology. 20(1):1-23

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190701351.0x000001&indx=1&recIds=ETOCvdc_100190701351.0x000001

A Structural Perspective on the Modulation of Protein-Protein Interactions with Small Molecules

Authors: Demirel, Habibe Cansu, Dogan, Tunca, Tuncbag, Nurcan

Source: Current topics in medicinal chemistry. 18(8):700-713

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100078031796.0x000001&indx=1&recIds=ETOCvdc_100078031796.0x000001

ASCARIS: Positional feature annotation and protein structure-based representation of single amino acid variations

Authors: Cankara, Fatma, Doğan, Tunca

Source: In Computational and Structural Biotechnology Journal 2023 21:4743-4758

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