JLAB

Publications

2014

Full Papers

Attach:inter.jpg Δ Yousef M, Trin HV, and Allmer J (2014) Intersection of MicroRNA and Gene Regulatory Networks and their Implication in Cancer, Current Pharmaceutical Biotechnology, 15(5), doi: 10.2174/1389201015666140519120855.

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Attach:tp.jpg Δ Hamzeiy H, Yousef M, and Allmer J (2014) Computational Methods for miRNA Target Prediction, Methods in Molecular Biology, 1107:207-221, doi: 10.1007/978-1-62703-748-8_12.

abstract/pdf

Attach:mlmp.jpg Δ Saçar MD and Allmer J (2014) Machine Learning methods for miRNA Gene prediction, Methods in Molecular Biology, 1107:177-187, doi: 10.1007/978-1-62703-748-8_10.

abstract/pdf

Attach:mgp.jpg Δ Allmer J (2014) Computational and Bioinformatics Methods for miRNA Gene Prediction, Methods in Molecular Biology, 1107:157-175, doi: 10.1007/978-1-62703-748-8_9.

abstract/pdf

Çelik I, Gültekin V, Allmer J, Doğanlar S, Frary A (2014) Development of genomic simple sequence repeat markers in opium poppy by next generation sequencing, doi:10.1007/s11032-014-0036-0.

abstract/pdf

2013

Full Papers

Saçar MD and Allmer J (2013) Data mining for microrna gene prediction: On the impact of class imbalance and feature number for microrna gene prediction,IEEE Xplorer, doi: 10.1109/HIBIT.2013.6661685.

abstract/pdf

Has C, Kundakci CU, Altay A, and Allmer J (2013) Ranking tandem mass spectra: And the impact of database size and scoring function on peptide spectrum matches,IEEE Xplorer, doi: 10.1109/HIBIT.2013.6661686.

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Allmer J (2013) Determining the C-Terminal Amino Acid of a Peptide from MS/MS Data, doi:10.5584/jiomics.v2013i2013.137.

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Şelale H, Çelik İ, Gültekin V, Allmer J, Doğanlar S, and Frary A (2013) Development of EST-SSR markers for diversity and breeding studies in opium poppy, Plant Breeding, doi:10.1111/pbr.12059.

abstract/pdf

Saçar MD, Hamzeiy H, and Allmer J (2013) Can MiRBase Provide Positive Data for Machine Learning for the Detection of MiRNA Hairpins? Journal of Integrative Bioinformatics, doi:10.2390/biecoll-jib-2013-215.

abstract/pdf

IB2013

Saçar MD and Allmer J (2013) Comparison of four Ab Initio MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona, Spain, doi:10.5220/0004248201900195 Amazon

Books and Book Chapters

Editors: Yousef M and Allmer J (2013) miRNomics: MicroRNA Biology and Computational Analysis, Methods in Molecular Biology, ISBN: 978-1627037471. web

Abstracts, Talks, and Invited Talks

Has C and Allmer J (2013) Genomics and Proteomics: Towards Better Gene Models, International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany

Has C, Toprak M, and Allmer J (2013) AthenaDB, Data Integration for Protein Secondary Structure Analyses, International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany

Hamzeiy H, Karaçalı B, Allmer J (2013) The Human Transcriptomic Fold Space, International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany

2012

Full Papers

Allmer J (2012) A Call for Benchmark Data in Mass Spectrometry-Based Proteomics, Journal of Integrative OMICS, doi: 10.5584/jiomics.v2012i2012.113.
Takan S and Allmer J (2012) De Novo Markup Language, a Standard to Represent De Novo Sequencing Results from MS/MS Data, 7th International Symposium on Health Informatics and Bioinformatics pp31-36, Capadocia, Turkey. abstract/pdf
Bagci C and Allmer J (2012) Removing Contaminations from Genomic Sequences Based on Vector Reference Libraries, 7th International Symposium on Health Informatics and Bioinformatics pp118-122, Capadocia, Turkey.     abstract/pdf

Books and Book Chapters

Editors: Has C, Yılmaz Ş, and Allmer J (2012) Biyoinformatikte Dizi Kıyaslaması (Sequence Alignment in Bioinformatics), Nobel Publishing, Ankara, Turkey, ISBN: 978-605-133-297-0. web
Allmer J and Yousef M (2012) Computational methods for ab initio detection of microRNAs, Frontiers in Bioinformatics and Computational Biology, doi:10.3389/fgene.2012.00209, abstract.

Abstracts and Posters

Has C, Boz S, Allmer J (2012) Using Human Blood Plasma Proteomics Data for the Validation of Gene Models, ECCB’12, 11th European Conference on Computational Biology, Basel, Switzerland. abstract
Has C, Toprak M, Allmer J (2012) PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins, ECCB’12, 11th European Conference on Computational Biology, Basel, Switzerland. abstract
Has C, Yılmaz Ş, Aytun B, Allmer J (2012) COMAS: Ant Colony Optimization a De Novo Sequencing Algorithm, ECCB’12, 11th European Conference on Computational Biology, Workshop: From Mass Spectrometry to Protein Complexes, Basel, Switzerland. abstract
Akçimen F, Sayın S, Bakırbaş A, Firatligil B, Has C, and Allmer J (2012) Genome Annotation of Sesamum Indicum, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. poster
Boz S, Has C, and Allmer J (2012) Using Proteomics Data for the Validation of Gene Models, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. poster
Hamzeiy H, Saçar MD, and Allmer J (2012) A Closer Look at Features Used in In Silico miRNA Hairpin Fingerprinting and Predicting, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. poster
Toprak M, Has C, and Allmer J (2012) Prometheus Secondary Structural Elements’ Profiles of Proteins, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. poster
Hamzeiy H, Saçar MD, and Allmer J (2012) The Predictive Power of Specific Features Used for miRNA Discovery, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. poster
Yilmaz S and Allmer J (2012) RAy: Increasing the Scope of Mass Spectrometry-Homology Based Database Search, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. poster

Invited Talks

Saçar MD, Hamzeiy H, and Allmer J (2012) Have Features for miRNA Hairpin Detection been Saturated?, International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany.
Allmer J (2012) A Bioinformatics View on Sequence Similarity and Homology, International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany.
Doğanlar S, Gültekin V, Allmer J, and Frary A (2012) Development of Genomic Tools for Eggplant, International Symposium on Biotechnology and other Omics in Vegetable Science, Antalya, Turkey.

2011

Abstracts and Posters

Tekin P, Gültekin V, Allmer J, Frary A and Doğanlar S (2011) Genomic SSR Marker Development from Genomic Sequence of Sesame (Sesamum indicum L.), International Congress on Bioinformatics and Biomics, Kusadasi, Aydin, Turkey. poster
Tekin P, Gültekin V, Allmer J, Frary A and Doğanlar S (2011) Genomic SSR Marker Development from Genomic Sequence of Poppy (Papaver somniferum), International Congress on Bioinformatics and Biomics, Kusadasi, Aydin, Turkey. abstract Δ
Çelik İ, Gültekin V, Allmer J and Anne F (2011) Genomic SSR Marker Development from Genomic Sequence of Sesame (Sesamum indicum L.), International Congress on Bioinformatics and Biomics, Kusadasi, Aydin, Turkey. abstract Δ
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