Deliverables
NEOGENE Data Management Plan: The project involves production of human and sheep ancient DNA data (generated by whole genome shotgun sequencing and genotyping) and radiocarbon data. It also includes compiling genetic data and archaeological material culture data from literature surveys and correspondence with research teams. We will ensure that the data remains findable, accessible, interoperable and re-usable in the following ways: - All mapped genome sequencing data (in .bam format) will be made available through the European Nucleotide Archive (https://www.ebi.ac.uk/ena), following the current standard procedure in the archaeogenomics field; - All processed genome datasets (in PLINK flat files format, .map and .ped) and radiocarbon dating results of the biological samples will be available through our local web server at METU; - All raw material culture datasets (in spreadsheet format) will be available through our local web server at METU; - All computer code used in the analyses will be shared through GitHub (github.com), and also through our local web server at METU; - All raw sequencing data (in .fastq format) will be available upon request, following the current standard procedure in the aDNA field (raw aDNA shotgun sequencing reads are usually not submitted to databases as the majority of reads represent microbial contamination, thus hindering data reuse); - All raw sequencing data and radiocarbon dating results will be stored in two physically separate servers at METU for ensuring data safety; - All analysis results will be published in open access journals or choosing the open access option. We will further encourage all archaeology and anthropology teams working with us to openly share their data through “Open Context” (www.opencontext.org; a subproject of Alexandria Archive Institute) and through Digital Archaeology Record (www.tdar.org).
Publications
Author(s):
Mehmet Somel, N. Ezgi Altınışık, Yılmaz Selim Erdal, Çiğdem Atakuman, Füsun Özer
Published in:
"Kinship, sex, and biological relatedness: the contribution of archaeogenetics to the understanding of social and biological relations"", ed: Meller, Krause, Haak, Risch.", 2023, Page(s) 137-147, ISBN 978-3-96929-259-4
Publisher:
Landesmuseum für Vorgeschichte
DOI:
10.11588/propylaeum.1280
Author(s):
Yaka R., Doğu A., Kaptan D., Dağtaş N. D. , Chyleński M., Vural K. B. , Altınışık N. E. , Mapelli I., Koptekin D., Karamurat C., Gemici H. C. , Yorulmaz S., Lagerholm V. K. , Fer E., Işıldak U., Ghalichi A., Kılınç G. M. , Mazzucato C., Juras A., Marciniak A., Larsen C. S. , Pilloud M., Haddow S. D. , Knüsel C. J. , Togan İ., Götherström A., Erdal Y. S. , Sürer E. , Özer F., Ata
Published in:
Peopling the Landscape of Çatalhöyük, 2021, Page(s) 395-405
Publisher:
The British Institute of Archaeology at Ankara
Author(s):
Erinç Yurtman, Onur Özer, Eren Yüncü, Nihan Dilşad Dağtaş, Dilek Koptekin, Yasin Gökhan Çakan, Mustafa Özkan, Ali Akbaba, Damla Kaptan, Gözde Atağ, Kıvılcım Başak Vural, Can Yümni Gündem, Louise Martin, Gülşah Merve Kılınç, Ayshin Ghalichi, Sinan Can Açan, Reyhan Yaka, Ekin Sağlıcan, Vendela Kempe Lagerholm, Maja Krzewińska, Torsten Günther, Pedro Morell Miranda, Evange
Published in:
Communications Biology volume, Issue 4, Article number: 1279 (2021), 2021, ISSN 2399-3642
Publisher:
NATURE
DOI:
10.1038/s42003-021-02794-8
Author(s):
Camilla Mazzucato, Michele Coscia, Ayça Küçükakdağ Doğu, Scott Haddow, Muhammed Sıddık Kılıç, Eren Yüncü, Mehmet Somel
Published in:
Journal of Archaeological Method and Theory., 2024, ISSN 2331-8422
Publisher:
Cornell University [1991]-
DOI:
10.48550/arxiv.2406.19149
Author(s):
Arda Söylev, Sevim Seda Çokoglu, Dilek Koptekin, Can Alkan, Mehmet Somel
Published in:
Plos Computational Biology, 2022, ISSN 1553-7358
Publisher:
Plos Computational Biology
DOI:
10.1371/journal.pcbi.1010788
Author(s):
Reyhan Yaka, Igor Mapelli, Damla Kaptan, Ayça Doğu, Maciej Chyleński, Ömür Dilek Erdal, Dilek Koptekin, Kıvılcım Başak Vural, Alex Bayliss, Camilla Mazzucato, Evrim Fer, Sevim Seda Çokoğlu, Vendela Kempe Lagerholm, Maja Krzewińska, Cansu Karamurat, Hasan Can Gemici, Arda Sevkar, Nihan Dilşad Dağtaş, Gülşah Merve Kılınç, Donovan Adams, Mehmet Somel
Published in:
Current Biology, 2021, ISSN 0960-9822
Publisher:
Cell Press
DOI:
10.1016/j.cub.2021.03.050
Author(s):
Murat Karakoç; Hasan Can Gemici; Murat Dirican; Okşan Başoğlu; Çiğdem Atakuman
Published in:
Documenta Praehistorica, Vol 50 (2023), Issue 4, 2023, ISSN 1854-2492
Publisher:
Ljubljana: Založba Univerze v Ljubljani
DOI:
10.4312/dp.50.5
Author(s):
Dilek Koptekin, Eren Yüncü, Ricardo Rodríguez-Varela, N. Ezgi Altınışık, Nikolaos Psonis,Natalia Kashuba, Sevgi Yorulmaz, Robert George, Duygu Deniz Kazancı, Damla Kaptan, Kanat Gürün, Kıvılcım Başak Vural, Hasan Can Gemici, Despoina Vassou, Evangelia Daskalaki, Cansu Karamurat, Vendela K. Lagerholm, Ömür Dilek Erdal, Emrah Kırdök, Aurelio Marangoni, Andreas Schachner, Handan Üs
Published in:
Current Biology, Issue Volume 33, Issue 1, 9 January 2023,, 2022, Page(s) Pages 41-57.e15, ISSN 1879-0445
Publisher:
Science Direct
DOI:
10.1016/j.cub.2022.11.034
Author(s):
N. Ezgi Altınışık; Duygu Deniz Kazancı; Ayça Aydoğan; Hasan Can Gemici; Ömür Dilek Erdal; Savaş Sarıaltun; Kıvılcım Başak Vural; Dilek Koptekin; Kanat Gürün; Ekin Sağlıcan; Daniel Fernandes; Gökhan Çakan; Meliha Melis Koruyucu; Vendela Kempe Lagerholm; Cansu Karamurat; Mustafa Özkan; Gülşah Merve Kılınç; Arda Sevkar; Elif Sürer; Anders Götherström; Çiğdem Atakuman;
Published in:
Science Advances, Issue 7, 2022, ISSN 2375-2548
Publisher:
Science Advances
DOI:
10.1126/sciadv.abo3609
Author(s):
Ceballos, Francisco C.; Gürün, Kanat; Altınışık, N. Ezgi; Gemici, Hasan Can; Karamurat, Cansu; Koptekin, Dilek; Vural, Kıvılcım Başak; Mapelli, Igor; Sağlıcan, Ekin; Sürer, Elif; Erdal, Yılmaz Selim; Götherström, Anders; Özer, Füsun; Atakuman, Çiğdem; Somel, Mehmet
Published in:
CURRENT BIOLOGY, Issue 2, 2021, Page(s) P3925-3934.e8, ISSN 1097-4172
Publisher:
CELL PRESS
DOI:
10.1016/j.cub.2021.06.027
Author(s):
Mustafa Özkan; Kanat Gürün; Eren Yüncü; Kıvılcım Başak Vural; Gözde Atağ; Ali Akbaba; Fatma Rabia Fidan; Ekin Sağlıcan; N. Ezgi Altınışık; Dilek Koptekin; Kamilla Pawłowska; Ian Hodder; Sarah E. Adcock; Benjamin S. Arbuckle; Sharon R. Steadman; Gregory McMahon; Yılmaz Selim Erdal; C. Can Bilgin; Eva-Maria Geigl; Anders Götherstrom; Thierry Grange; İnci Togan; Füsun Özer; Meh
Published in:
Molecular Ecology- Biorvix, Issue 7, 2023, ISSN 0962-1083
Publisher:
Blackwell Publishing Inc.
DOI:
10.1101/2023.06.05.543765
Author(s):
Şevval Aktürk, Igor Mapelli, Merve N. Güler, Kanat Gürün, Büşra Katırcıoğlu, Kıvılcım Başak Vural, Ekin Sağlıcan, Mehmet Çetin, Reyhan Yaka, Elif Sürer, Gözde Atağ, Sevim Seda Çokoğlu, Arda Sevkar, N. Ezgi Altınışık, Dilek Koptekin, Mehmet Somel
Published in:
Molecular Ecology Resources, 2024, ISSN 1755-098X
Publisher:
Blackwell Publishing Inc.
DOI:
10.1111/1755-0998.13960
Author(s):
Gözde Atağ; Kıvılcım Başak Vural; Damla Kaptan; Mustafa Özkan; Dilek Koptekin; Ekin Sağlıcan; Sevcan Doğramacı; Mevlüt Köz; Ardan Yılmaz; Arda Söylev; İnci Togan; Mehmet Somel; Füsun Özer
Published in:
Open Research Europe, Issue 5, 2022, ISSN 2732-5121
Publisher:
Open research Europe
DOI:
10.1101/2022.06.06.491147
Author(s):
Sevim Seda Çokoğlu; Dilek Koptekin; Fatma Rabia Fidan; Mehmet Somel
Published in:
Evolutionary Applications, 2023, ISSN 0071-3260
Publisher:
Kluwer Academic/Plenum Publishers
DOI:
10.1101/2023.11.04.565610
Author(s):
Gözde Atağ, Damla Kaptan, Eren Yüncü, Kıvılcım Başak Vural, Paolo Mereu, Monica Pirastru, Mario Barbato, Giovanni Giuseppe Leoni, Merve Nur Güler, Tuğçe Er, Elifnaz Eker, Tunca Deniz Yazıcı, Muhammed Sıddık Kılıç, Nefize Ezgi Altınışık, Ecem Ayşe Çelik, Pedro Morell Miranda, Marianne Dehasque, Viviana Floridia, Anders Götherström, Cemal Can Bilgin, İnci Togan, Tors
Published in:
Genome Biology and Evolution, Issue Volume 16, Issue 5, 2024, ISSN 1759-6653
Publisher:
Oxford University Press
DOI:
10.1093/gbe/evae090
Author(s):
Reyhan Yaka; Maja Krzewińska; Vendela Kempe Lagerholm; Anna Linderholm; Füsun Özer; Mehmet Somel & Anders Götherström
Published in:
Biotechniques, Issue Volume 76, 2024 - Issue 5: BioTechniques, 2023, ISSN 1940-9818
Publisher:
Future Science Ltd
DOI:
10.2144/btn-2023-0107
Author(s):
Reyhan Yaka
Published in:
2020
Publisher:
METU
Author(s):
Eren Yüncü, Ayça Küçükakdağ Doğu, Damla Kaptan, MuhammedSıddık Kılıç, Camilla Mazzucato, MerveN. Güler, Elifnaz Eker, Büşra Katırcıoğlu, Maciej Chyleński, Kıvılcım Başak Vural, Arda Sevkar, Gözde Atağ, N. Ezgi Altınışık, Fatma Küçük Baloğlu, Defne Bozkurt, Jessica Pearson, Marco Milella, Cansu Karamurat, Şevval Aktürk, Ekin Sağlıcan, Nisan Yıldız
Published in:
BioRxiv (awaiting editorial decision from Science), 2024, ISSN 0000-0000
Publisher:
Cold Spring Harbor Labaratory
DOI:
10.1101/2024.06.23.600259
Author(s):
Erkin Alaçamlı, Thijessen Naidoo, Şevval Aktürk, Merve N. Güler, Igor Mapelli, Kıvılcım Başak Vural, Mehmet Somel, Helena Malmström, Torsten Günther
Published in:
bioRxiv, Genome Biology (under second round of revision), 2024, ISSN 1474-760X
Publisher:
London: BioMed Central Ltd, 2001
DOI:
10.1101/2024.01.23.576660
Author(s):
Dilek Koptekin, Ayca Aydogan, Cansu Karamurat, N. Ezgi Altinisik, Kivilcim Basak Vural, D. Deniz Kazanci, Ayca Kucukakdag Dogu, Damla Kaptan, Hasan Can Gemici, Eren Yuncu, Gulsun Umurtak, Refik Duru, Erkan Fidan, Ozlem Cevik, Burcin Erdogu, Taner Korkut, Christopher J. Knusel, Scott Haddow, Clark Spencer Larsen, Rana Ozbal, Fokke Gerritsen, Eylem Ozdogan, Uygar Ozan Usanmaz, Yasin Cemre Derici, Mi
Published in:
"bioRxiv- awaiting editorial decision from ""Science""", 2024, ISSN 2692-8205
Publisher:
bioRxiv
DOI:
10.1101/2024.06.23.599747
Author(s):
Gözde Atağ, Kıvılcım Başak Vural, Damla Kaptan, Mustafa Özkan, Dilek Koptekin, Ekin Sağlıcan, Sevcan Doğramacı, Mevlüt Köz, Ardan Yılmaz, Arda Söylev, İnci Togan, Mehmet Somel, Füsun Özer
Published in:
Open Research Europe, 2022, ISSN 1539-3704
Publisher:
PUBMED, National Institute of Health
DOI:
10.12688/openreseurope.14936.3
Author(s):
Gözde Atağ; Mehmet Somel
Published in:
bioRxiv, Genetics (under second revision), 2024, ISSN 1943-2631
Publisher:
Genetics
DOI:
10.1101/2024.02.17.580509
Author(s):
Dilek Koptekin, Etka Yapar, Kıvılcım Başak Vural, Ekin Sağlıcan, N. Ezgi Altınışık, Anna-Sapfo Malaspinas, Can Alkan, Mehmet Somel
Published in:
bioRxiv, Genome Biology (under second round of revision), 2023, ISSN 1474-760X
Publisher:
London BioMed Central Ltd 2001-
DOI:
10.1101/2023.11.11.566695
Author(s):
Schotsmans, E M J; Busacca, G; Lin, S C; Vasi��, M; Lingle, A M; Veropoulidou, R; Mazzucato, C; Tibbetts, B; Haddow, S D; Somel, M; Toksoy-K��ksal, F; Kn��sel, C J; Milella, M
Published in:
NATURE-Scientific Reports, Issue 7, 2022, ISSN 2045-2322
Publisher:
Nature Publishing Group
DOI:
10.1038/s41598-022-07284-3
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