OzU Machine Learning in Finance and Bioinformatics Lab

DeepPTM: Protein Post-translational Modification Prediction from Protein Sequences by Combining Deep Protein Language Model with Vision Transformers

Published in: Current Bioinformatics, 2023

Authors: NN Soylu, E Sefer

Year: 2023

BERT2OME: Prediction of 2'-O-methylation Modifications from RNA Sequence by Transformer Architecture Based on BERT

Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2023

Authors: NN Soylu, E Sefer

Year: 2023

NFT Primary Sale Price and Secondary Sale Prediction via Deep Learning

Published in: 4th ACM International Conference on AI in Finance, 116-123, 2023

Authors: B Seyhan, E Sefer

Year: 2023

A comparison of topologically associating domain callers over mammals at high resolution

Published in: BMC bioinformatics 23 (1), 127, 2022

Authors: E Sefer

Year: 2022

ProbC: joint modeling of epigenome and transcriptome effects in 3D genome

Published in: BMC genomics 23 (1), 287, 2022

Authors: E Sefer

Year: 2022

Asset price and direction prediction via deep 2D transformer and convolutional neural networks

Published in: Proceedings of the Third ACM International Conference on AI in Finance, 79-86, 2022

Authors: T Tuncer, U Kaya, E Sefer, O Alacam, T Hoser

Year: 2022

A Novel GBT-Based Approach for Cross-Channel Fraud Detection on Real-World Banking Transactions

Published in: IFIP International Conference on Artificial Intelligence Applications and …, 2022

Authors: U Dolu, E Sefer

Year: 2022

BioCode: A Data-Driven Procedure to Learn the Growth of Biological Networks

Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics 19 (6 …, 2022

Authors: E Sefer

Year: 2022

MOCMIN: convex inferring of modular low-rank contact networks over COVID diffusion data

Published in: Turkish Journal of Electrical Engineering and Computer Sciences 30 (7), 2568 …, 2022

Authors: E Sefer

Year: 2022

Hi–C interaction graph analysis reveals the impact of histone modifications in chromatin shape

Published in: Applied Network Science 6 (1), 54, 2021

Authors: E Sefer

Year: 2021

Metric labeling and semimetric embedding for protein annotation prediction

Published in: Journal of Computational Biology 28 (5), 514-525, 2021

Authors: E Sefer, C Kingsford

Year: 2021

Joint modeling of histone modifications in 3D genome shape through Hi-C interaction graph

Published in: Complex Networks & Their Applications IX: Volume 2, Proceedings of the Ninth …, 2021

Authors: E Sefer

Year: 2021

Semi-nonparametric modeling of topological domain formation from epigenetic data

Published in: Algorithms for Molecular Biology 14, 1-11, 2019

Authors: E Sefer, C Kingsford

Year: 2019

Selecting the most appropriate time points to profile in high-throughput studies

Published in: Elife 6, e18541, 2017

Authors: M Kleyman, E Sefer, T Nicola, C Espinoza, D Chhabra, JS Hagood, ...

Year: 2017

Tradeoffs between dense and replicate sampling strategies for high-throughput time series experiments

Published in: Cell systems 3 (1), 35-42, 2016

Authors: E Sefer, M Kleyman, Z Bar-Joseph

Year: 2016

Diffusion archeology for diffusion progression history reconstruction

Published in: Knowledge and information systems 49, 403-427, 2016

Authors: E Sefer, C Kingsford

Year: 2016

Deconvolution of ensemble chromatin interaction data reveals the latent mixing structures in cell subpopulations

Published in: Journal of Computational Biology 23 (6), 425-438, 2016

Authors: E Sefer, G Duggal, C Kingsford

Year: 2016

Dynamic Changes Of Dna Methylation During Different Stages Of Normal Mouse Lung Development

Published in: A71. EPIGENETICS, A2344-A2344, 2016

Authors: CR Espinoza, D Chhabra, T Nicola, N Ambalavanan, N Kaminski, E Sefer, ...

Year: 2016

Identification Of Optimal Time Points And Proteomic Profiling During Murine Lung Alveolar Septation

Published in: D25. NEONATAL AND CONGENITAL LUNG DISEASES, A6561-A6561, 2016

Authors: T Nicola, E Sefer, CR Espinoza, F Ahangari, D Chhabra, JS Hagood, ...

Year: 2016

Shall We Dense? Comparing Design Strategies for Time Series Expression Experiments.

Published in: RECOMB, 244-245, 2016

Authors: E Sefer, Z Bar-Joseph

Year: 2016

D25 NEONATAL AND CONGENITAL LUNG DISEASES: Identification Of Optimal Time Points And Proteomic Profiling During Murine Lung Alveolar Septation

Published in: American Journal of Respiratory and Critical Care Medicine 193, 1, 2016

Authors: T Nicola, E Sefer, CR Espinoza, F Ahangari, D Chhabra, JS Hagood, ...

Year: 2016

Convex risk minimization to infer networks from probabilistic diffusion data at multiple scales

Published in: 2015 IEEE 31st International Conference on Data Engineering, 663-674, 2015

Authors: E Sefer, C Kingsford

Year: 2015

Resolving spatial inconsistencies in chromosome conformation measurements

Published in: Algorithms for Molecular Biology 8, 1-10, 2013

Authors: G Duggal, R Patro, E Sefer, H Wang, D Filippova, S Khuller, C Kingsford

Year: 2013

Parsimonious reconstruction of network evolution

Published in: Algorithms for Molecular Biology 7, 1-11, 2012

Authors: R Patro, E Sefer, J Malin, G Marçais, S Navlakha, C Kingsford

Year: 2012

The missing models: A data-driven approach for learning how networks grow

Published in: Proceedings of the 18th ACM SIGKDD international conference on Knowledge …, 2012

Authors: R Patro, G Duggal, E Sefer, H Wang, D Filippova, C Kingsford

Year: 2012

Resolving spatial inconsistencies in chromosome conformation data

Published in: Algorithms in Bioinformatics: 12th International Workshop, WABI 2012 …, 2012

Authors: G Duggal, R Patro, E Sefer, H Wang, D Filippova, S Khuller, C Kingsford

Year: 2012

NetVisia: Heat map & matrix visualization of dynamic social network statistics & content

Published in: 2011 IEEE third international conference on privacy, security, risk and …, 2011

Authors: R Gove, N Gramsky, R Kirby, E Sefer, A Sopan, C Dunne, B Shneiderman, ...

Year: 2011

Metric labeling and semi-metric embedding for protein annotation prediction

Published in: International Conference on Research in Computational Molecular Biology, 392-407, 2011

Authors: E Sefer, C Kingsford

Year: 2011

Parsimonious reconstruction of network evolution

Published in: Algorithms in Bioinformatics: 11th International Workshop, WABI 2011 …, 2011

Authors: R Patro, E Sefer, J Malin, G Marçais, S Navlakha, C Kingsford

Year: 2011

Real-time a* search with depth-k lookahead

Published in: Proceedings of the International Symposium on Combinatorial Search, 2009

Authors: E Sefer, U Kuter, D Nau

Year: 2009

Thinking ahead in real-time search

Published in: Proceedings of the International Conference on Automated Planning and …, 2009

Authors: D Nau, U Kuter, E Sefer

Year: 2009