{"id":{"repo_id":"utswmed","oai_identifier":"oai:utswmed-ir.tdl.org:2152.5/10239"},"canonical_url":"https://search.dev.ndltd.org/etd/utswmed/oai:utswmed-ir.tdl.org:2152.5/10239","repository":{"repo_id":"utswmed","name":"University of Texas Southwestern Medical Center","base_url":"https://utswmed-ir.tdl.org/server/oai/request"},"display":{"title":"Molecular Underpinnings of Human Brain Evolution and Cognition at Cellular Resolution","abstract":"The second part of Chapter 1 is modified from a commissioned book chapter (accepted for publication) titled "Differences in brain gene expression between humans and primates", which has been accepted for publication as a chapter in the book titled "The evolutionary roots of human brain diseases". This chapter is an edited version of the author's own original writing with additional edits by the author's thesis supervisor and from feedback from the editors of the book. The citation to the book is included below.","abstract_html":"The second part of Chapter 1 is modified from a commissioned book chapter (accepted for publication) titled "Differences in brain gene expression between humans and primates", which has been accepted for publication as a chapter in the book titled "The evolutionary roots of human brain diseases". This chapter is an edited version of the author's own original writing with additional edits by the author's thesis supervisor and from feedback from the editors of the book. The citation to the book is included below.","abstract_has_math":false,"creators":["Caglayan, Emre"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":["Chahrour, Maria","Hon, Gary C.","Madabhushi, Ram","Sun, Lu O.","Konopka, Genevieve"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2024,"date_issued":"2024-01-11T20:20:32Z","date_published":"2024-01-11T20:20:32Z","updated_at":"2026-07-24T05:52:36Z","subjects":["Autism Spectrum Disorder","Cell Nucleus","Evolution, Molecular","Gyrus Cinguli","Memory, Episodic","RNA","Temporal Lobe","Transcriptome"],"languages":["en"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["Konopka, G., & Caglayan, E. (2024). Differences in brain gene expression between humans and primates. In N. J. Diederich, M. Brüne, K. Amunts, & C. G. Goetz (Eds.), The evolutionary roots of human brain diseases. Oxford University Press.","Caglayan, E., Ayhan, F., Liu, Y., Vollmer, R. M., Oh, E., Sherwood, C. C., Preuss, T. M., Yi, S. V., & Konopka, G. (2023). Molecular features driving cellular complexity of human brain evolution. Nature, 620(7972), 145-153. https://doi.org/10.1038/s41586-023-06338-4","Caglayan, E., Liu, Y., & Konopka, G. (2022). Neuronal ambient RNA contamination causes misinterpreted and masked cell types in brain single-nuclei datasets. Neuron, 110(24), 4043-4056 e4045. https://doi.org/10.1016/j.neuron.2022.09.010","Berto, S., Treacher, A. H., Caglayan, E., Luo, D., Haney, J. R., Gandal, M. J., Geschwind, D. H., Montillo, A. A., & Konopka, G. (2022). Association between resting-state functional brain connectivity and gene expression is altered in autism spectrum disorder. Nat Commun, 13(1), 3328. https://doi.org/10.1038/s41467-022-31053-5","Berto, S., Fontenot, M. R., Seger, S., Ayhan, F., Caglayan, E., Kulkarni, A., Douglas, C., Tamminga, C. A., Lega, B. C., & Konopka, G. (2021). Gene-expression correlates of the oscillatory signatures supporting human episodic memory encoding. Nat Neurosci, 24(4), 554-564. https://doi.org/10.1038/s41593-021-00803-x","1417098721"],"render_values":[{"text":"Konopka, G., & Caglayan, E. (2024). Differences in brain gene expression between humans and primates. In N. J. Diederich, M. Brüne, K. Amunts, & C. G. Goetz (Eds.), The evolutionary roots of human brain diseases. Oxford University Press.","href":null,"code":true},{"text":"Caglayan, E., Ayhan, F., Liu, Y., Vollmer, R. M., Oh, E., Sherwood, C. C., Preuss, T. M., Yi, S. V., & Konopka, G. (2023). Molecular features driving cellular complexity of human brain evolution. Nature, 620(7972), 145-153. https://doi.org/10.1038/s41586-023-06338-4","href":"https://doi.org/10.1038/s41586-023-06338-4","code":true},{"text":"Caglayan, E., Liu, Y., & Konopka, G. (2022). Neuronal ambient RNA contamination causes misinterpreted and masked cell types in brain single-nuclei datasets. Neuron, 110(24), 4043-4056 e4045. https://doi.org/10.1016/j.neuron.2022.09.010","href":"https://doi.org/10.1016/j.neuron.2022.09.010","code":true},{"text":"Berto, S., Treacher, A. H., Caglayan, E., Luo, D., Haney, J. R., Gandal, M. J., Geschwind, D. H., Montillo, A. A., & Konopka, G. (2022). Association between resting-state functional brain connectivity and gene expression is altered in autism spectrum disorder. Nat Commun, 13(1), 3328. https://doi.org/10.1038/s41467-022-31053-5","href":"https://doi.org/10.1038/s41467-022-31053-5","code":true},{"text":"Berto, S., Fontenot, M. R., Seger, S., Ayhan, F., Caglayan, E., Kulkarni, A., Douglas, C., Tamminga, C. A., Lega, B. C., & Konopka, G. (2021). Gene-expression correlates of the oscillatory signatures supporting human episodic memory encoding. Nat Neurosci, 24(4), 554-564. https://doi.org/10.1038/s41593-021-00803-x","href":"https://doi.org/10.1038/s41593-021-00803-x","code":true},{"text":"1417098721","href":null,"code":true}]}]},"links":{"outbound_url":"https://hdl.handle.net/2152.5/10239","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Chahrour, Maria","Hon, Gary C.","Madabhushi, Ram","Sun, Lu O.","Konopka, Genevieve"]},{"key":"dc:creator","label":"Author","values":["Caglayan, Emre"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2024-01-11T20:20:32Z","2023-12","December 2023"]},{"key":"dc:relation","label":"Dc Relation","values":["https://doi.org/10.1038/s41586-023-06338-4","https://doi.org/10.1016/j.neuron.2022.09.010","https://doi.org/10.1038/s41467-022-31053-5","https://doi.org/10.1038/s41593-021-00803-x"]},{"key":"dc:type","label":"Dc Type","values":["Thesis","text"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Autism Spectrum Disorder","Cell Nucleus","Evolution, Molecular","Gyrus Cinguli","Memory, Episodic","RNA","Temporal Lobe","Transcriptome"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["Konopka, G., & Caglayan, E. (2024). Differences in brain gene expression between humans and primates. In N. J. Diederich, M. Brüne, K. Amunts, & C. G. Goetz (Eds.), The evolutionary roots of human brain diseases. Oxford University Press.","Caglayan, E., Ayhan, F., Liu, Y., Vollmer, R. M., Oh, E., Sherwood, C. C., Preuss, T. M., Yi, S. V., & Konopka, G. (2023). Molecular features driving cellular complexity of human brain evolution. Nature, 620(7972), 145-153. https://doi.org/10.1038/s41586-023-06338-4","Caglayan, E., Liu, Y., & Konopka, G. (2022). Neuronal ambient RNA contamination causes misinterpreted and masked cell types in brain single-nuclei datasets. Neuron, 110(24), 4043-4056 e4045. https://doi.org/10.1016/j.neuron.2022.09.010","Berto, S., Treacher, A. H., Caglayan, E., Luo, D., Haney, J. R., Gandal, M. J., Geschwind, D. H., Montillo, A. A., & Konopka, G. (2022). Association between resting-state functional brain connectivity and gene expression is altered in autism spectrum disorder. Nat Commun, 13(1), 3328. https://doi.org/10.1038/s41467-022-31053-5","Berto, S., Fontenot, M. R., Seger, S., Ayhan, F., Caglayan, E., Kulkarni, A., Douglas, C., Tamminga, C. A., Lega, B. C., & Konopka, G. (2021). Gene-expression correlates of the oscillatory signatures supporting human episodic memory encoding. Nat Neurosci, 24(4), 554-564. https://doi.org/10.1038/s41593-021-00803-x","https://hdl.handle.net/2152.5/10239","1417098721"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["The second part of Chapter 1 is modified from a commissioned book chapter (accepted for publication) titled "Differences in brain gene expression between humans and primates", which has been accepted for publication as a chapter in the book titled "The evolutionary roots of human brain diseases". This chapter is an edited version of the author's own original writing with additional edits by the author's thesis supervisor and from feedback from the editors of the book. The citation to the book is included below.","Chapters 2-5 were published as individual journal articles, and the citations are listed below. Links to the journals are also included as related URIs.","Molecular and functional characterization of the human brain is challenging due to its experimental inaccessibility. Most of our understanding about human brain function relies on the assumption that biological processes uncovered in model organisms are conserved in humans. Comparisons of the humanii brain with non-human primate brains offer to both uncover the novelties in human brain evolution and better evaluate the insights obtained from model organisms about human brain function. To achieve this, highthroughput sequencing methods on post-mortem brain tissues provide a rewarding readout to understand human brain evolution at the molecular level. In addition to their use in comparative studies, these technologies were also utilized with a hope to understand molecular underpinnings of measurable human brain activity metrics. During my dissertation, I read relevant literature extensively (Chapter 1) and sought to understand human-specific epigenomic and transcriptomic changes at cellular resolution in the cortical brain (Chapter 2). Additionally, after in-depth analysis of many human brain single-nuclei RNA-seq datasets, I found a pervasive ambient RNA contamination problem, and devised in silico solutions to tackle this problem. My efforts improved the analytical approach in the field as well as in my research (Chapter 3). I have also been involved in efforts to identify transcriptomic correlates of brain activity in human subjects (Chapters 4-5). After detailing these efforts, I discuss the implications of these findings, weigh their impact on our understanding of human brain function and offer ideas for further research (Chapter 6)."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Molecular Underpinnings of Human Brain Evolution and Cognition at Cellular Resolution"]}]}],"canonical_facts":{"dc:contributor":["Chahrour, Maria","Hon, Gary C.","Madabhushi, Ram","Sun, Lu O.","Konopka, Genevieve"],"dc:creator":["Caglayan, Emre"],"dc:date":["2024-01-11T20:20:32Z","2023-12","December 2023"],"dc:description":["The second part of Chapter 1 is modified from a commissioned book chapter (accepted for publication) titled "Differences in brain gene expression between humans and primates", which has been accepted for publication as a chapter in the book titled "The evolutionary roots of human brain diseases". This chapter is an edited version of the author's own original writing with additional edits by the author's thesis supervisor and from feedback from the editors of the book. The citation to the book is included below.","Chapters 2-5 were published as individual journal articles, and the citations are listed below. Links to the journals are also included as related URIs.","Molecular and functional characterization of the human brain is challenging due to its experimental inaccessibility. Most of our understanding about human brain function relies on the assumption that biological processes uncovered in model organisms are conserved in humans. Comparisons of the humanii brain with non-human primate brains offer to both uncover the novelties in human brain evolution and better evaluate the insights obtained from model organisms about human brain function. To achieve this, highthroughput sequencing methods on post-mortem brain tissues provide a rewarding readout to understand human brain evolution at the molecular level. In addition to their use in comparative studies, these technologies were also utilized with a hope to understand molecular underpinnings of measurable human brain activity metrics. During my dissertation, I read relevant literature extensively (Chapter 1) and sought to understand human-specific epigenomic and transcriptomic changes at cellular resolution in the cortical brain (Chapter 2). Additionally, after in-depth analysis of many human brain single-nuclei RNA-seq datasets, I found a pervasive ambient RNA contamination problem, and devised in silico solutions to tackle this problem. My efforts improved the analytical approach in the field as well as in my research (Chapter 3). I have also been involved in efforts to identify transcriptomic correlates of brain activity in human subjects (Chapters 4-5). After detailing these efforts, I discuss the implications of these findings, weigh their impact on our understanding of human brain function and offer ideas for further research (Chapter 6)."],"dc:format":["application/pdf"],"dc:identifier":["Konopka, G., & Caglayan, E. (2024). Differences in brain gene expression between humans and primates. In N. J. Diederich, M. Brüne, K. Amunts, & C. G. Goetz (Eds.), The evolutionary roots of human brain diseases. Oxford University Press.","Caglayan, E., Ayhan, F., Liu, Y., Vollmer, R. M., Oh, E., Sherwood, C. C., Preuss, T. M., Yi, S. V., & Konopka, G. (2023). Molecular features driving cellular complexity of human brain evolution. Nature, 620(7972), 145-153. https://doi.org/10.1038/s41586-023-06338-4","Caglayan, E., Liu, Y., & Konopka, G. (2022). Neuronal ambient RNA contamination causes misinterpreted and masked cell types in brain single-nuclei datasets. Neuron, 110(24), 4043-4056 e4045. https://doi.org/10.1016/j.neuron.2022.09.010","Berto, S., Treacher, A. H., Caglayan, E., Luo, D., Haney, J. R., Gandal, M. J., Geschwind, D. H., Montillo, A. A., & Konopka, G. (2022). Association between resting-state functional brain connectivity and gene expression is altered in autism spectrum disorder. Nat Commun, 13(1), 3328. https://doi.org/10.1038/s41467-022-31053-5","Berto, S., Fontenot, M. R., Seger, S., Ayhan, F., Caglayan, E., Kulkarni, A., Douglas, C., Tamminga, C. A., Lega, B. C., & Konopka, G. (2021). Gene-expression correlates of the oscillatory signatures supporting human episodic memory encoding. Nat Neurosci, 24(4), 554-564. https://doi.org/10.1038/s41593-021-00803-x","https://hdl.handle.net/2152.5/10239","1417098721"],"dc:language":["en"],"dc:relation":["https://doi.org/10.1038/s41586-023-06338-4","https://doi.org/10.1016/j.neuron.2022.09.010","https://doi.org/10.1038/s41467-022-31053-5","https://doi.org/10.1038/s41593-021-00803-x"],"dc:subject":["Autism Spectrum Disorder","Cell Nucleus","Evolution, Molecular","Gyrus Cinguli","Memory, Episodic","RNA","Temporal Lobe","Transcriptome"],"dc:title":["Molecular Underpinnings of Human Brain Evolution and Cognition at Cellular Resolution"],"dc:type":["Thesis","text"]},"updated_at":"2026-07-24T05:52:36Z"}