JLAB

Publications

JLAB.Publications History

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(:cell width=50%:) %newwin%[[https://www.researchgate.net/profile/Malik_Yousef/|Yousef M]]%%, %newwin%[[https://www.researchgate.net/researcher/2048557909_Hung_V_Trinh|Trin HV]]%%, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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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%newwin%[[http://www.eurekaselect.com/122243/article|abstract/pdf]]%%
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(:cell width=50%:) %newwin%[[https://www.researchgate.net/profile/Hamid_Hamzeiy/|Hamzeiy H]]%%, %newwin%[[https://www.researchgate.net/profile/Malik_Yousef/|Yousef M]]%%, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
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%newwin%[[http://dx.doi.org/10.1007/978-1-62703-748-8_12|abstract/pdf]]%%
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(:cell width=50%:) %newwin%[[https://www.researchgate.net/profile/Duygu_Sacar/|Saçar MD]]%% and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
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%newwin%[[http://link.springer.com/protocol/10.1007%2F978-1-62703-748-8_10|abstract/pdf]]%%
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(:cell width=50%:) %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
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%newwin%[[http://link.springer.com/protocol/10.1007/978-1-62703-748-8_9|abstract/pdf]]%%
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(:cell width=50%:)%newwin%[[https://www.researchgate.net/profile/Ibrahim_celik2|Çelik I]]%%, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, %newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|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.
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(:cell width=50%:)%newwin%[[https://www.researchgate.net/profile/Ibrahim_celik2|Çelik I]]%%, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, %newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|Doğanlar S]]%%, %newwin%[[https://www.researchgate.net/profile/Anne_Frary|Frary A]]%% (2014) Development of genomic simple sequence repeat markers in opium poppy by next generation sequencing, doi:10.1007/s11032-014-0036-0.
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(:cell width=50%:)Şelale H, Çelik İ, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, %newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|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.
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(:cell width=50%:)Şelale H, Çelik İ, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, %newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|Doğanlar S]]%%, and %newwin%[[https://www.researchgate.net/profile/Anne_Frary|Frary A]]%% (2013) Development of EST-SSR markers for diversity and breeding studies in opium poppy, Plant Breeding, doi:10.1111/pbr.12059.
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(:cell width=85%:)%newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|Doğanlar S]]%%, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, and Frary A (2012) Development of Genomic Tools for Eggplant, International Symposium on Biotechnology and other Omics in Vegetable Science, Antalya, Turkey.
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(:cell width=85%:)%newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|Doğanlar S]]%%, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, and %newwin%[[https://www.researchgate.net/profile/Anne_Frary|Frary A]]%% (2012) Development of Genomic Tools for Eggplant, International Symposium on Biotechnology and other Omics in Vegetable Science, Antalya, Turkey.
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(:cell width=85%:)Tekin P, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, Frary A and %newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|Doğanlar S]]%% (2011) Genomic SSR Marker Development from Genomic Sequence of Sesame (Sesamum indicum L.), International Congress on Bioinformatics and Biomics, Kusadasi, Aydin, Turkey. %newwin%[[(Attach:)ICBB2011PTekin.pdf | poster]]%%
to:
(:cell width=85%:)Tekin P, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, %newwin%[[https://www.researchgate.net/profile/Anne_Frary|Frary A]]%% and %newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|Doğanlar S]]%% (2011) Genomic SSR Marker Development from Genomic Sequence of Sesame (Sesamum indicum L.), International Congress on Bioinformatics and Biomics, Kusadasi, Aydin, Turkey. %newwin%[[(Attach:)ICBB2011PTekin.pdf | poster]]%%
Changed line 133 from:
-<Tekin P, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, Frary A and %newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|Doğanlar S]]%% (2011) Genomic SSR Marker Development from Genomic Sequence of Poppy (Papaver somniferum), International Congress on Bioinformatics and Biomics, Kusadasi, Aydin, Turkey. %newwin%[[(Attach:)SesamumAbstract.pdf | abstract]]%%
to:
-<Tekin P, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, %newwin%[[https://www.researchgate.net/profile/Anne_Frary|Frary A]]%% and %newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|Doğanlar S]]%% (2011) Genomic SSR Marker Development from Genomic Sequence of Poppy (Papaver somniferum), International Congress on Bioinformatics and Biomics, Kusadasi, Aydin, Turkey. %newwin%[[(Attach:)SesamumAbstract.pdf | abstract]]%%
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(:cell width=50%:)%newwin%[[https://www.researchgate.net/profile/Ibrahim_celik2|Çelik I]]%, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
to:
(:cell width=50%:)%newwin%[[https://www.researchgate.net/profile/Ibrahim_celik2|Çelik I]]%%, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, %newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|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.
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(:cell width=50%:)Şelale H, Çelik İ, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
to:
(:cell width=50%:)Şelale H, Çelik İ, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, %newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|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.
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(:cell width=85%:)Doğanlar S, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, and Frary A (2012) Development of Genomic Tools for Eggplant, International Symposium on Biotechnology and other Omics in Vegetable Science, Antalya, Turkey.
to:
(:cell width=85%:)%newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|Doğanlar S]]%%, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, and Frary A (2012) Development of Genomic Tools for Eggplant, International Symposium on Biotechnology and other Omics in Vegetable Science, Antalya, Turkey.
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(:cell width=85%:)Tekin P, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[(Attach:)ICBB2011PTekin.pdf | poster]]%%
to:
(:cell width=85%:)Tekin P, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, Frary A and %newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|Doğanlar S]]%% (2011) Genomic SSR Marker Development from Genomic Sequence of Sesame (Sesamum indicum L.), International Congress on Bioinformatics and Biomics, Kusadasi, Aydin, Turkey. %newwin%[[(Attach:)ICBB2011PTekin.pdf | poster]]%%
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-<Tekin P, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[(Attach:)SesamumAbstract.pdf | abstract]]%%
to:
-<Tekin P, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, Frary A and %newwin%[[https://www.researchgate.net/profile/Sami_Doganlar|Doğanlar S]]%% (2011) Genomic SSR Marker Development from Genomic Sequence of Poppy (Papaver somniferum), International Congress on Bioinformatics and Biomics, Kusadasi, Aydin, Turkey. %newwin%[[(Attach:)SesamumAbstract.pdf | abstract]]%%
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(:cell width=50%:)Çelik I, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
to:
(:cell width=50%:)%newwin%[[https://www.researchgate.net/profile/Ibrahim_celik2|Çelik I]]%, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
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(:cell width=50%:)Editors: Yusuf M and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2013) miRNomics: MicroRNA Biology and Computational Analysis, Methods in Molecular Biology, ISBN: 978-1627037471.
to:
(:cell width=50%:)Editors: %newwin%[[https://www.researchgate.net/profile/Malik_Yousef/|Yousef M]]%% and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2013) miRNomics: MicroRNA Biology and Computational Analysis, Methods in Molecular Biology, ISBN: 978-1627037471.
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-<%newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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, %newwin%[[http://www.frontiersin.org/bioinformatics_and_computational_biology/10.3389/fgene.2012.00209/abstract|abstract]]%%.
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-<%newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% and %newwin%[[https://www.researchgate.net/profile/Malik_Yousef/|Yousef M]]%% (2012) Computational methods for ab initio detection of microRNAs, Frontiers in Bioinformatics and Computational Biology, doi:10.3389/fgene.2012.00209, %newwin%[[http://www.frontiersin.org/bioinformatics_and_computational_biology/10.3389/fgene.2012.00209/abstract|abstract]]%%.
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(:cell width=30%:)Attach:impact.jpg
(:cell width=50%:)%newwin%[[https://www.researchgate.net/profile/Duygu_Sacar/|Saçar MD]]%% and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
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%newwin%[[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6661685|abstract/pdf]]%%
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Has, C and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2013) Genomics and Proteomics: Towards Better Gene Models, International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany
to:
%newwin%[[https://www.researchgate.net/profile/Canan_Has/|Has C]]%% and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2013) Genomics and Proteomics: Towards Better Gene Models, International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany
Changed line 14 from:
(:cell width=50%:)Has C, Kundakci CU, %newwin%[[https://www.researchgate.net/profile/Aybuge_Altay/|Altay A]]%%, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
to:
(:cell width=50%:)%newwin%[[https://www.researchgate.net/profile/Canan_Has/|Has C]]%%, Kundakci CU, %newwin%[[https://www.researchgate.net/profile/Aybuge_Altay/|Altay A]]%%, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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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Has C, Toprak M, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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
to:
%newwin%[[https://www.researchgate.net/profile/Canan_Has/|Has C]]%%, Toprak M, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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
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(:cell width=50%:)Editors: Has C, Yılmaz Ş, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) Biyoinformatikte Dizi Kıyaslaması (Sequence Alignment in Bioinformatics), Nobel Publishing, Ankara, Turkey, ISBN: 978-605-133-297-0.
to:
(:cell width=50%:)Editors: %newwin%[[https://www.researchgate.net/profile/Canan_Has/|Has C]]%%, Yılmaz Ş, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) Biyoinformatikte Dizi Kıyaslaması (Sequence Alignment in Bioinformatics), Nobel Publishing, Ankara, Turkey, ISBN: 978-605-133-297-0.
Changed lines 88-97 from:
-<Has C, Boz S, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[http://www.eccb12.org/poster/accepted/|abstract]]%%

-<Has C, Toprak M, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins, ECCB’12, 11th European Conference on Computational Biology, Basel, Switzerland. %newwin%[[http://www.eccb12.org/poster/accepted/|abstract]]%%

-<Has C, Yılmaz Ş, Aytun B, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[http://bioinformatics.cemm.oeaw.ac.at/images/files/cpw-eccb12-detailed-program.pdf|abstract]]%%

-<Akçimen F, Sayın S, Bakırbaş A, Firatligil B, Has C, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) Genome Annotation of Sesamum Indicum, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. %newwin%[[(Attach:)HIBITAkcimen.pdf | poster]]%%

-<Boz S, Has C, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) Using Proteomics Data for the Validation of Gene Models, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. %newwin%[[(Attach:)HIBITBoz.pdf | poster]]%%
to:
-<%newwin%[[https://www.researchgate.net/profile/Canan_Has/|Has C]]%%, Boz S, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[http://www.eccb12.org/poster/accepted/|abstract]]%%

-<%newwin%[[https://www.researchgate.net/profile/Canan_Has/|Has C]]%%, Toprak M, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins, ECCB’12, 11th European Conference on Computational Biology, Basel, Switzerland. %newwin%[[http://www.eccb12.org/poster/accepted/|abstract]]%%

-<%newwin%[[https://www.researchgate.net/profile/Canan_Has/|Has C]]%%, Yılmaz Ş, Aytun B, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[http://bioinformatics.cemm.oeaw.ac.at/images/files/cpw-eccb12-detailed-program.pdf|abstract]]%%

-<Akçimen F, Sayın S, Bakırbaş A, Firatligil B, %newwin%[[https://www.researchgate.net/profile/Canan_Has/|Has C]]%%, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) Genome Annotation of Sesamum Indicum, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. %newwin%[[(Attach:)HIBITAkcimen.pdf | poster]]%%

-<Boz S, %newwin%[[https://www.researchgate.net/profile/Canan_Has/|Has C]]%%, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) Using Proteomics Data for the Validation of Gene Models, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. %newwin%[[(Attach:)HIBITBoz.pdf | poster]]%%
Changed line 100 from:
-<Toprak M, Has C, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) Prometheus Secondary Structural Elements’ Profiles of Proteins, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. %newwin%[[(Attach:)HIBITToprak.pdf | poster]]%%
to:
-<Toprak M, %newwin%[[https://www.researchgate.net/profile/Canan_Has/|Has C]]%%, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) Prometheus Secondary Structural Elements’ Profiles of Proteins, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. %newwin%[[(Attach:)HIBITToprak.pdf | poster]]%%
Added lines 12-18:
(:table border=0 cellpadding=5 cellspacing=0 width=100%:)
(:cell width=30%:)Attach:ranking.jpg
(:cell width=50%:)Has C, Kundakci CU, %newwin%[[https://www.researchgate.net/profile/Aybuge_Altay/|Altay A]]%%, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
(:cell width=20%:)
%newwin%[[http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6661686|abstract/pdf]]%%
(:tableend:)
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(:cell width=50%:)Saçar MD, Hamzeiy H, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
to:
(:cell width=50%:)%newwin%[[https://www.researchgate.net/profile/Duygu_Sacar/|Saçar MD]]%%, %newwin%[[https://www.researchgate.net/profile/Hamid_Hamzeiy/|Hamzeiy H]]%%, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
Changed line 37 from:
(:cell width=50%:)Saçar MD and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2013) Comparison of four ''Ab Initio'' MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona, Spain, %newwin%[[http://dx.doi.org/10.5220/0004248201900195|doi:10.5220/0004248201900195]]%%
to:
(:cell width=50%:)%newwin%[[https://www.researchgate.net/profile/Duygu_Sacar/|Saçar MD]]%% and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2013) Comparison of four ''Ab Initio'' MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona, Spain, %newwin%[[http://dx.doi.org/10.5220/0004248201900195|doi:10.5220/0004248201900195]]%%
Changed lines 53-55 from:
Hamzeiy H, Karaçalı B, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2013) The Human Transcriptomic Fold Space, International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany
to:
%newwin%[[https://www.researchgate.net/profile/Hamid_Hamzeiy/|Hamzeiy H]]%%, Karaçalı B, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2013) The Human Transcriptomic Fold Space, International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany
Changed lines 91-92 from:
-<Hamzeiy H, Sacar MD, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[(Attach:)HIBITSacar.pdf | poster]]%%
to:
-<%newwin%[[https://www.researchgate.net/profile/Hamid_Hamzeiy/|Hamzeiy H]]%%, %newwin%[[https://www.researchgate.net/profile/Duygu_Sacar/|Saçar MD]]%%, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[(Attach:)HIBITSacar.pdf | poster]]%%
Changed lines 95-96 from:
-<Hamzeiy H, Saçar MD, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) The Predictive Power of Specific Features Used for miRNA Discovery, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. %newwin%[[(Attach:)HIBITHamzeiy.pdf| poster]]%%
to:
-<%newwin%[[https://www.researchgate.net/profile/Hamid_Hamzeiy/|Hamzeiy H]]%%, %newwin%[[https://www.researchgate.net/profile/Duygu_Sacar/|Saçar MD]]%%, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) The Predictive Power of Specific Features Used for miRNA Discovery, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. %newwin%[[(Attach:)HIBITHamzeiy.pdf| poster]]%%
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-<Sacar MD, Hamzeiy H, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
to:
-<%newwin%[[https://www.researchgate.net/profile/Duygu_Sacar/|Saçar MD]]%%, %newwin%[[https://www.researchgate.net/profile/Hamid_Hamzeiy/|Hamzeiy H]]%%, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
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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
to:
Has, C and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2013) Genomics and Proteomics: Towards Better Gene Models, International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany
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(:cell width=50%:)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.
to:
(:cell width=50%:)Çelik I, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
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(:cell width=50%:)Allmer J (2013) Determining the C-Terminal Amino Acid of a Peptide from MS/MS Data, doi:10.5584/jiomics.v2013i2013.137.
to:
(:cell width=50%:)%newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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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(:cell width=50%:)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.
to:
(:cell width=50%:)Şelale H, Çelik İ, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
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(:cell width=50%:)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.
to:
(:cell width=50%:)Saçar MD, Hamzeiy H, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
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(:cell width=50%:)Saçar MD and Allmer J (2013) Comparison of four ''Ab Initio'' MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona, Spain, %newwin%[[http://dx.doi.org/10.5220/0004248201900195|doi:10.5220/0004248201900195]]%%
to:
(:cell width=50%:)Saçar MD and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2013) Comparison of four ''Ab Initio'' MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona, Spain, %newwin%[[http://dx.doi.org/10.5220/0004248201900195|doi:10.5220/0004248201900195]]%%
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(:cell width=50%:)Editors: Yusuf M and Allmer J (2013) miRNomics: MicroRNA Biology and Computational Analysis, Methods in Molecular Biology, ISBN: 978-1627037471.
to:
(:cell width=50%:)Editors: Yusuf M and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2013) miRNomics: MicroRNA Biology and Computational Analysis, Methods in Molecular Biology, ISBN: 978-1627037471.
Changed lines 53-57 from:
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
to:
Has C, Toprak M, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2013) The Human Transcriptomic Fold Space, International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany
Changed line 61 from:
-<Allmer J (2012) A Call for Benchmark Data in Mass Spectrometry-Based Proteomics, Journal of Integrative OMICS, doi: 10.5584/jiomics.v2012i2012.113.
to:
-<%newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) A Call for Benchmark Data in Mass Spectrometry-Based Proteomics, Journal of Integrative OMICS, doi: 10.5584/jiomics.v2012i2012.113.
Changed lines 65-69 from:
-<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. %newwin%[[http://dx.doi.org/10.1109/HIBIT.2012.6209038|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. &nbsp;&nbsp;&nbsp; %newwin% [[http://dx.doi.org/10.1109/HIBIT.2012.6209053|abstract/pdf]]%%
to:
-<Takan S and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[http://dx.doi.org/10.1109/HIBIT.2012.6209038|abstract/pdf]]%%

-<Bagci C and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. &nbsp;&nbsp;&nbsp; %newwin% [[http://dx.doi.org/10.1109/HIBIT.2012.6209053|abstract/pdf]]%%
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(:cell width=50%:)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.
to:
(:cell width=50%:)Editors: Has C, Yılmaz Ş, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) Biyoinformatikte Dizi Kıyaslaması (Sequence Alignment in Bioinformatics), Nobel Publishing, Ankara, Turkey, ISBN: 978-605-133-297-0.
Changed lines 78-81 from:
-<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, %newwin%[[http://www.frontiersin.org/bioinformatics_and_computational_biology/10.3389/fgene.2012.00209/abstract|abstract]]%%.
to:
-<%newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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, %newwin%[[http://www.frontiersin.org/bioinformatics_and_computational_biology/10.3389/fgene.2012.00209/abstract|abstract]]%%.
Changed lines 83-101 from:
-<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. %newwin%[[http://www.eccb12.org/poster/accepted/|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. %newwin%[[http://www.eccb12.org/poster/accepted/|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. %newwin%[[http://bioinformatics.cemm.oeaw.ac.at/images/files/cpw-eccb12-detailed-program.pdf|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. %newwin%[[(Attach:)HIBITAkcimen.pdf | 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. %newwin%[[(Attach:)HIBITBoz.pdf | poster]]%%

-<Hamzeiy H, Sacar 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. %newwin%[[(Attach:)HIBITSacar.pdf | 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. %newwin%[[(Attach:)HIBITToprak.pdf | 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. %newwin%[[(Attach:)HIBITHamzeiy.pdf| 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. %newwin%[[(Attach:)HIBITYilmaz.pdf | poster]]%%
to:
-<Has C, Boz S, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[http://www.eccb12.org/poster/accepted/|abstract]]%%

-<Has C, Toprak M, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins, ECCB’12, 11th European Conference on Computational Biology, Basel, Switzerland. %newwin%[[http://www.eccb12.org/poster/accepted/|abstract]]%%

-<Has C, Yılmaz Ş, Aytun B, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[http://bioinformatics.cemm.oeaw.ac.at/images/files/cpw-eccb12-detailed-program.pdf|abstract]]%%

-<Akçimen F, Sayın S, Bakırbaş A, Firatligil B, Has C, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) Genome Annotation of Sesamum Indicum, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. %newwin%[[(Attach:)HIBITAkcimen.pdf | poster]]%%

-<Boz S, Has C, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) Using Proteomics Data for the Validation of Gene Models, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. %newwin%[[(Attach:)HIBITBoz.pdf | poster]]%%

-<Hamzeiy H, Sacar MD, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[(Attach:)HIBITSacar.pdf | poster]]%%

-<Toprak M, Has C, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) Prometheus Secondary Structural Elements’ Profiles of Proteins, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. %newwin%[[(Attach:)HIBITToprak.pdf | poster]]%%

-<Hamzeiy H, Saçar MD, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) The Predictive Power of Specific Features Used for miRNA Discovery, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. %newwin%[[(Attach:)HIBITHamzeiy.pdf| poster]]%%

-<Yilmaz S and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%% (2012) RAy: Increasing the Scope of Mass Spectrometry-Homology Based Database Search, 7th International Symposium on Health Informatics and Bioinformatics, Capadocia, Turkey. %newwin%[[(Attach:)HIBITYilmaz.pdf | poster]]%%
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-<Sacar 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.
to:
-<Sacar MD, Hamzeiy H, and %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.

-<%newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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.
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(:cell width=85%:)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.
to:
(:cell width=85%:)Doğanlar S, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|Allmer J]]%%, and Frary A (2012) Development of Genomic Tools for Eggplant, International Symposium on Biotechnology and other Omics in Vegetable Science, Antalya, Turkey.
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(:cell width=85%:)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. %newwin%[[(Attach:)ICBB2011PTekin.pdf | poster]]%%
to:
(:cell width=85%:)Tekin P, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[(Attach:)ICBB2011PTekin.pdf | poster]]%%
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-<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. %newwin%[[(Attach:)SesamumAbstract.pdf | abstract]]%%

-<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. %newwin%[[(Attach:)PoppyAbstract.pdf | abstract]]%%
to:
-<Tekin P, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[(Attach:)SesamumAbstract.pdf | abstract]]%%

-<Çelik İ, Gültekin V, %newwin%[[https://www.researchgate.net/profile/Jens_Allmer/|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. %newwin%[[(Attach:)PoppyAbstract.pdf | abstract]]%%
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(
:cell width=50%:)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.
to:
(:cell width=30%:)Attach:celal.jpg
(:
cell width=50%:)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.
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%newwin%[[|]]%%
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%newwin%[[http://link.springer.com/article/10.1007/s11032-014-0036-0|abstract/pdf]]%%
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!!2014
!!! Full Papers
(:table border=0 cellpadding=5 cellspacing=0 width=100%:)
(:cell width=30%:)
(:cell width=50%:)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.
%newwin%[[|]]%%
(:tableend:)
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(:cell width=20%:)%newwin%[[http://www.bioinformatics.biostec.org/|Conference Link]]%%
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(:cell width=20%:)%newwin%[[http://www.amazon.com/miRNomics-MicroRNA-Computational-Analysis-Molecular/dp/1627037470/ref=sr_1_1?ie=UTF8&qid=1385238144&sr=8-1&keywords=mirnomics|Amazon]]%%
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!!! Books and Book Chapters
(:table border=0 cellpadding=5 cellspacing=0 width=100%:)
(:cell width=30%:)%newwin% [[http://www.amazon.com/miRNomics-MicroRNA-Computational-Analysis-Molecular/dp/1627037470/ref=sr_1_1?ie=UTF8&qid=1385238144&sr=8-1&keywords=mirnomics|http://ecx.images-amazon.com/images/I/41V6UivLYcL._AA160_.jpg]]%%
(:cell width=50%:)Editors: Yusuf M and Allmer J (2013) miRNomics: MicroRNA Biology and Computational Analysis, Methods in Molecular Biology, ISBN: 978-1627037471.
(:cell width=20%:)%newwin%[[http://www.nobelyayin.com/detay.asp?u=3611|web]]%%
(:tableend:)
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(:cell width=30%:)Attach:jiom1.jpg
(:cell width=50%:)Allmer J (2013) Determining the C-Terminal Amino Acid of a Peptide from MS/MS Data, doi:10.5584/jiomics.v2013i2013.137.
(:cell width=20%:)
%newwin%[[http://www.jiomics.com/index.php/jio/article/view/137|abstract/pdf]]%%
(:tableend:)
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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
to:
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
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Hamzeiy H, Karaçalı B, Allmer J (2013) International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany
to:
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
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!!! Invited Talks
to:
!!! Abstracts, Talks, and Invited Talks
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!!! 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) International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation, Bielefeld, Germany
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(:cell width=50%:)Saçar MD and Allmer J (2013) Comparison of four ''Ab Initio'' MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona, Spain.
to:
(:cell width=50%:)Saçar MD and Allmer J (2013) Comparison of four ''Ab Initio'' MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona, Spain, %newwin%[[http://dx.doi.org/10.5220/0004248201900195|doi:10.5220/0004248201900195]]%%
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(:cell width=50%:)Sacar 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.
to:
(:cell width=50%:)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.
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(:cell width=50%:)Sacar MD and Allmer J (2013) Comparison of four ''Ab Initio'' MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona, Spain.
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(:cell width=50%:)Saçar MD and Allmer J (2013) Comparison of four ''Ab Initio'' MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona, Spain.
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http://onlinelibrary.wiley.com/doi/10.1111/pbr.12059/abstract
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(:cell width=50%:)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.
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http://onlinelibrary.wiley.com/doi/10.1111/pbr.12059/abstract
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(:cell width=50%:)Sacar 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, Germany.
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(:cell width=50%:)Sacar 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.
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(:cell width=50%:)Sacar MD, Hamzeiy H, and Allmer J (accepted) Can MiRBase Provide Positive Data for Machine Learning for the Detection of MiRNA Hairpins? 9th International Symposium on Integrative Bioinformatics 2013, Gatersleben, Germany.
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!!! Invited Talks
-<Sacar 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.
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(:cell width=85%:)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. %newwin%[[(Attach:)ICBB2011PTekin.pdf | poster]]%%
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(:cell width=85%:)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.
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!!2011
!!! Abstracts and Posters

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(:cell width=85%:)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. %newwin%[[(Attach:)ICBB2011PTekin.pdf | poster]]%%
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!!! Invited Talks
-<Sacar 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.

(:table border=0 cellpadding=5 cellspacing=0 width=100%:)
(:cell width=15%:)%newwin% [[Attach:certificate.jpg|Attach:goldMedal.gif]]%%
(:cell width=85%:)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.
(:tableend:)
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-<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. %newwin%[[(Attach:)HIBITYilmaz.pdf | poster]]%%
to:
-<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. %newwin%[[(Attach:)SesamumAbstract.pdf | abstract]]%%

-<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. %newwin%[[(Attach:)PoppyAbstract.pdf | abstract]]%%
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-<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. %newwin%[[(Attach:)HIBITYilmaz.pdf | poster]]%%
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-<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. %newwin%[[(Attach:)HIBITYilmaz.pdf | poster]]%%
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-<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. %newwin%[[(Attach:)SesamumAbstract.pdf | abstract]]%%

-<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. %newwin%[[(Attach:)HIBITYilmaz.pdf | poster]]%%
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!!! Invited Talks
-<Sacar 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.
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!!! Invited Talks
-<Sacar 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.
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-<Has C, Toprak M, Allmer J (2012) PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins, ECCB’12, 11th European Conference on Computational Biology, Basel, Switzerland.
->%newwin%[[http://www.eccb12.org/poster/accepted/|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.
->%newwin%[[http://bioinformatics.cemm.oeaw.ac.at/images/files/cpw-eccb12-detailed-program.pdf|abstract]]%%
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Sacar MD and Allmer J (accepted) Comparison of four ''Ab Initio'' MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona, Spain.
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-<Sacar MD and Allmer J (accepted) Comparison of four ''Ab Initio'' MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona, Spain.
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Sacar MD and Allmer J (accepted) Comparison of four ''Ab Initio'' MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona Spain.
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Sacar MD and Allmer J (accepted) Comparison of four ''Ab Initio'' MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona, Spain.
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Sacar MD and Allmer J (accepted) Comparison of four Ab Initio MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona Spain.
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Sacar MD and Allmer J (accepted) Comparison of four ''Ab Initio'' MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona Spain.
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!!2013
!!! Full Papers
Sacar MD and Allmer J (accepted) Comparison of four Ab Initio MicroRNA Prediction Tools, Bioinformatics 2013, Barcelona Spain.
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%newwin%[[http://www.jiomics.com/index.php/jio/article/view/113|abstract]]%% %newwin%[[http://www.jiomics.com/index.php/jio/article/view/113/92|pdf]]%%
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-<Allmer J (2012) A Call for Benchmark Data in Mass Spectrometry-Based Proteomics, Journal of Integrative OMICS, doi: 10.5584/jiomics.v2012i2012.113. %newwin%[[http://www.jiomics.com/index.php/jio/article/view/113|abstract]]%%
to:
-<Allmer J (2012) A Call for Benchmark Data in Mass Spectrometry-Based Proteomics, Journal of Integrative OMICS, doi: 10.5584/jiomics.v2012i2012.113. %newwin%[[http://www.jiomics.com/index.php/jio/article/view/113|abstract]]%% %newwin%[[http://www.jiomics.com/index.php/jio/article/view/113/92|pdf]]%%
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Allmer J (2012) A Call for Benchmark Data in Mass Spectrometry-Based Proteomics, Journal of Integrative OMICS, doi: 10.5584/jiomics.v2012i2012.113. %newwin%[[http://www.jiomics.com/index.php/jio/article/view/113|abstract]]%%
to:
-<Allmer J (2012) A Call for Benchmark Data in Mass Spectrometry-Based Proteomics, Journal of Integrative OMICS, doi: 10.5584/jiomics.v2012i2012.113. %newwin%[[http://www.jiomics.com/index.php/jio/article/view/113|abstract]]%%
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Allmer J (2012) A Call for Benchmark Data in Mass Spectrometry-Based Proteomics, Journal of Integrative OMICS, doi: 10.5584/jiomics.v2012i2012.113. %newwin%[[http://www.jiomics.com/index.php/jio/article/view/113|abstract]]%%
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-<Allmer J and Yousef M (2012) Computational methods for ab initio detection of microRNAs, Frontiers in Bioinformatics and Computational Biology, %newwin%[[http://www.frontiersin.org/bioinformatics_and_computational_biology/10.3389/fgene.2012.00209/abstract|abstract]]%% doi:10.3389/fgene.2012.00209.
to:
-<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, %newwin%[[http://www.frontiersin.org/bioinformatics_and_computational_biology/10.3389/fgene.2012.00209/abstract|abstract]]%%.
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-<Allmer J and Yousef M (2012) Computational methods for ab initio detection of microRNAs, Frontiers in Bioinformatics and Computational Biology, [[http://www.frontiersin.org/bioinformatics_and_computational_biology/10.3389/fgene.2012.00209/abstract|abstract]]doi:10.3389/fgene.2012.00209.
to:
-<Allmer J and Yousef M (2012) Computational methods for ab initio detection of microRNAs, Frontiers in Bioinformatics and Computational Biology, %newwin%[[http://www.frontiersin.org/bioinformatics_and_computational_biology/10.3389/fgene.2012.00209/abstract|abstract]]%% doi:10.3389/fgene.2012.00209.
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-<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, (accepted).
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-<Allmer J and Yousef M (2012) Computational methods for ab initio detection of microRNAs, Frontiers in Bioinformatics and Computational Biology, [[http://www.frontiersin.org/bioinformatics_and_computational_biology/10.3389/fgene.2012.00209/abstract|abstract]]doi:10.3389/fgene.2012.00209.
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-<Allmer J and Yousef M (2012) Computational methods for ab initio detection of microRNAs, Frontiers in Bioinformatics and Computational Biology, (accepted).
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-<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, (accepted).
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-<Allmer J and Yousef M (2012) Computational methods for ab initio detection of microRNAs, Frontiers in Bioinformatics and Computational Biology, (accepted).
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-<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. %newwin%[[(Attach:)HIBITBoz.pdf | Using Proteomics Data for the Validation of Gene Models ]]%%
to:
-<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. %newwin%[[(Attach:)HIBITBoz.pdf | poster]]%%
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-<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.
-<Hamzeiy H, Sacar 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.

-<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.

-<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.

-<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.
to:
-<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. %newwin%[[(Attach:)HIBITBoz.pdf | Using Proteomics Data for the Validation of Gene Models ]]%%

-<Hamzeiy H, Sacar MD, and Allmer J (2012) A Closer Look at Features Used in In Silico miRNA Hairpin Fingerprinting and Predicting
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-<Toprak M, Has C,
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-<Hamzeiy H, Saçar MD,
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-<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,
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[[(Attach:)HIBITBoz.pdf | Using Proteomics Data for the Validation of Gene Models ]]\\
[[(Attach:)HIBITHamzeiy.pdf| The Predictive Power of Specific Features Used for miRNA Discovery]]\\
[[(Attach:)HIBITToprak.pdf | PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins]]\\
[[(Attach:)HIBITSacar.pdf | A Closer Look at Features Used for In silico miRNA Hairpin Fingerprinting and Prediction]]\\
[[(Attach:)HIBITYilmaz.pdf | RAy: Increasing the scope of Mass Spectrometry – Homology based Database Search]]
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-<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.
to:
-<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. %newwin%[[(Attach:)HIBITAkcimen.pdf | poster]]%%
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[[(Attach:)HIBITAkcimen.pdf | Genome annotation of Sesame indicum]]\\
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-<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.
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-<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.
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to:
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>>>>>>>
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-<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.
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to:
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to:
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to:
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[[http://dx.doi.org/10.1109/HIBIT.2012.6209053|abstract/pdf]]
to:
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-<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.[[http://dx.doi.org/10.1109/HIBIT.2012.6209053|abstract/pdf]]
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-<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. [[http://dx.doi.org/10.1109/HIBIT.2012.6209038|abstract/pdf]]
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-<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.[[http://dx.doi.org/10.1109/HIBIT.2012.6209038|abstract/pdf]]
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[[http://dx.doi.org/10.1109/HIBIT.2012.6209053|abstract/pdf]]
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[[http://dx.doi.org/10.1109/HIBIT.2012.6209038]|-<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.]
to:
-<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. [[http://dx.doi.org/10.1109/HIBIT.2012.6209038|abstract/pdf]]
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-<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.
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[[http://dx.doi.org/10.1109/HIBIT.2012.6209038]|-<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.]
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-<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.
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-<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.
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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.
to:
-<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.
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-<Allmer J, editor (2012) Biyoinformatikte Dizi Kıyaslaması (Sequence Alignment in Bioinformatics), Nobel Publishing, ISBN: 978-605-133-297-0.
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!!! Invited Talks
to:
!!! Invited Talks
-<Sacar 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.
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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.

Has C, Toprak M, Allmer J (2012) PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins, ECCB’12, 11th European Conference on Computational Biology, Basel, Switzerland.

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.

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.

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.

Hamzeiy H, Sacar 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.

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.

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.

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.
to:

-<
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.

-<Has C, Toprak M, Allmer J (2012) PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins, ECCB’12, 11th European Conference on Computational Biology, Basel, Switzerland.

-<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.

-<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.

-<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.

-<Hamzeiy H, Sacar 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.

-<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.

-<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.

-<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.
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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.

Has C, Toprak M, Allmer J (2012) PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins, ECCB’12, 11th European Conference on Computational Biology, Basel, Switzerland.

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.

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.

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.

Hamzeiy H, Sacar 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.

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.

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.

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.

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.
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-<-<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.
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-<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.
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-<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.
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-<-<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.
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!!! HIBIT'12
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!!! Full Papers
-<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.

-<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.

!!! Books and Book Chapters

!!! Abstracts and Posters
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[[(Attach:)HIBITYilmaz.pdf | RAy: Increasing the scope of Mass Spectrometry – Homology based Database Search]]
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[[(Attach:)HIBITYilmaz.pdf | RAy: Increasing the scope of Mass Spectrometry – Homology based Database Search]]

!!! Invited Talks
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[[(Attach:)HIBITHamzeiy.pdf| The Predictive Power of Specific Features Used for miRNA Discovery]]\\
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[[(Attach:)HIBITSacar.pdf | A Closer Look at Features Used for In silico miRNA Hairpin Fingerprinting and Prediction]]\\
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[[(Attach:)HIBITAkcimen.pdf | Gene annotation]]
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[[(Attach:)HIBITAkcimen.pdf | Genome annotation of Sesame indicum]]\\
[[(
Attach:)HIBITBoz.pdf | Using Proteomics Data for the Validation of Gene Models ]]\\
[[(
Attach:)HIBITToprak.pdf | PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins]]\\
[[(Attach:)
HIBITYilmaz.pdf | RAy: Increasing the scope of Mass Spectrometry – Homology based Database Search]]
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[[Gene annotation|(Attach:)HIBITAkcimen.pdf]]
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[[(Attach:)HIBITAkcimen.pdf | Gene annotation]]
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[[Gene annotation|(Attach:)HIBITAkcimen.pdf]]
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[[(Attach:)HIBITAkcimen.pdf]]
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Gene Annotation of Sesame indicum\\ [[Attach:)HIBITAkcimen.pdf]]
Using Proteomics Data for the Validation of Gene Models\\
The Predictive Power of Specific Features Used for miRNA Discovery\\
PROMAttach
:file.ext
RAy
: Increasing the scope of Mass Spectrometry – Homology based Database Search
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[[Attach:)HIBITAkcimen.pdf]]
Attach:HIBITBoz.pdf
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:HIBITToprak.pdf
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Gene Annotation of Sesame indicum
Using Proteomics Data for the Validation of Gene Models
The Predictive Power of Specific Features Used for miRNA Discovery
PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins
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Gene Annotation of Sesame indicum\\ [[Attach:)HIBITAkcimen.pdf]]
Using
Proteomics Data for the Validation of Gene Models\\
The Predictive Power of Specific Features Used for miRNA Discovery\\
PROMAttach
:file.ext
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[[JLAB.AkcimenHIBIT | Gene Annotation of Sesame indicum]]\\
[[JLAB.BozHasAllmerHIBIT | Using Proteomics Data for the Validation
of Gene Models]]\\
[[JLAB.HamzeiySacarAllmerHIBIT | The Predictive Power of Specific Features Used for miRNA Discovery ]]\\
[[JLAB.ToprakHasAllmerHIBIT | PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins]]\\
[[JLAB.YilmazAllmerHIBIT | RAy: Increasing the scope of Mass Spectrometry – Homology based Database Search]]
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Gene Annotation of Sesame indicum
Using Proteomics Data for the Validation of Gene Models
The Predictive Power
of Specific Features Used for miRNA Discovery
PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins
RAy: Increasing the scope of Mass Spectrometry – Homology based Database Search
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!!| HIBIT'12
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!!! HIBIT'12
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!! HIBIT'12
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!!| HIBIT'12
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!!2010
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!!2012

!! HIBIT'12
[[JLAB.AkcimenHIBIT | Gene Annotation of Sesame indicum]]\\
[[JLAB.BozHasAllmerHIBIT | Using Proteomics Data for the Validation of Gene Models]]\\
[[JLAB.HamzeiySacarAllmerHIBIT | The Predictive Power of Specific Features Used for miRNA Discovery ]]\\
[[JLAB.ToprakHasAllmerHIBIT | PROMETHEUS: Secondary Structural Elements’ Profiles of Proteins]]\\
[[JLAB.YilmazAllmerHIBIT | RAy: Increasing the scope of Mass Spectrometry – Homology based Database Search]]
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!!2010