[{"language":[{"iso":"eng"}],"corr_author":"1","date_created":"2018-12-11T11:48:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaNo"}],"year":"2017","intvolume":"         9","day":"19","doi":"10.1126/scitranslmed.aao0972","publisher":"American Association for the Advancement of Science","scopus_import":"1","publist_id":"6993","author":[{"orcid":"0000-0002-7673-7178","last_name":"Novarino","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"date_published":"2017-07-19T00:00:00Z","title":"The riddle of CHD8 haploinsufficiency in autism spectrum disorder","quality_controlled":"1","publication":"Science Translational Medicine","publication_status":"published","page":"eaao0972","status":"public","_id":"702","publication_identifier":{"issn":["1946-6234"]},"type":"journal_article","citation":{"ieee":"G. Novarino, “The riddle of CHD8 haploinsufficiency in autism spectrum disorder,” <i>Science Translational Medicine</i>, vol. 9, no. 399. American Association for the Advancement of Science, p. eaao0972, 2017.","chicago":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">https://doi.org/10.1126/scitranslmed.aao0972</a>.","mla":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” <i>Science Translational Medicine</i>, vol. 9, no. 399, American Association for the Advancement of Science, 2017, p. eaao0972, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">10.1126/scitranslmed.aao0972</a>.","short":"G. Novarino, Science Translational Medicine 9 (2017) eaao0972.","ista":"Novarino G. 2017. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 9(399), eaao0972.","apa":"Novarino, G. (2017). The riddle of CHD8 haploinsufficiency in autism spectrum disorder. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">https://doi.org/10.1126/scitranslmed.aao0972</a>","ama":"Novarino G. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. <i>Science Translational Medicine</i>. 2017;9(399):eaao0972. doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">10.1126/scitranslmed.aao0972</a>"},"article_processing_charge":"No","oa_version":"None","issue":"399","date_updated":"2025-07-10T11:54:10Z","abstract":[{"text":"Leading autism-associated mutation in mouse partially mimics human disorder.\r\n\r\n","lang":"eng"}],"volume":9,"month":"07"},{"day":"14","publisher":"eLife Sciences Publications","doi":"10.7554/eLife.25125","scopus_import":"1","ddc":["576"],"publist_id":"6971","corr_author":"1","external_id":{"isi":["000407617200001"]},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:50Z","oa":1,"license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2018-12-11T11:48:05Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"call_identifier":"FWF","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"GaNo"},{"_id":"SiHi"}],"year":"2017","intvolume":"         6","status":"public","_id":"713","citation":{"apa":"Andergassen, D., Dotter, C., Wenzel, D., Sigl, V., Bammer, P., Muckenhuber, M., … Hudson, Q. (2017). Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.25125\">https://doi.org/10.7554/eLife.25125</a>","ama":"Andergassen D, Dotter C, Wenzel D, et al. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.25125\">10.7554/eLife.25125</a>","chicago":"Andergassen, Daniel, Christoph Dotter, Dyniel Wenzel, Verena Sigl, Philipp Bammer, Markus Muckenhuber, Daniela Mayer, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.25125\">https://doi.org/10.7554/eLife.25125</a>.","ieee":"D. Andergassen <i>et al.</i>, “Mapping the mouse Allelome reveals tissue specific regulation of allelic expression,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","mla":"Andergassen, Daniel, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” <i>ELife</i>, vol. 6, e25125, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.25125\">10.7554/eLife.25125</a>.","short":"D. Andergassen, C. Dotter, D. Wenzel, V. Sigl, P. Bammer, M. Muckenhuber, D. Mayer, T. Kulinski, H. Theussl, J. Penninger, C. Bock, D. Barlow, F. Pauler, Q. Hudson, ELife 6 (2017).","ista":"Andergassen D, Dotter C, Wenzel D, Sigl V, Bammer P, Muckenhuber M, Mayer D, Kulinski T, Theussl H, Penninger J, Bock C, Barlow D, Pauler F, Hudson Q. 2017. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. eLife. 6, e25125."},"article_processing_charge":"No","publication_identifier":{"issn":["2050-084X"]},"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"oa_version":"Published Version","has_accepted_license":"1","pubrep_id":"885","date_updated":"2025-09-10T11:02:33Z","month":"08","volume":6,"abstract":[{"text":"To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta.","lang":"eng"}],"author":[{"full_name":"Andergassen, Daniel","last_name":"Andergassen","first_name":"Daniel"},{"full_name":"Dotter, Christoph","last_name":"Dotter","orcid":"0000-0002-9033-9096","first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dyniel","full_name":"Wenzel, Dyniel","last_name":"Wenzel"},{"first_name":"Verena","full_name":"Sigl, Verena","last_name":"Sigl"},{"last_name":"Bammer","full_name":"Bammer, Philipp","first_name":"Philipp"},{"first_name":"Markus","full_name":"Muckenhuber, Markus","last_name":"Muckenhuber"},{"first_name":"Daniela","full_name":"Mayer, Daniela","last_name":"Mayer"},{"full_name":"Kulinski, Tomasz","last_name":"Kulinski","first_name":"Tomasz"},{"first_name":"Hans","full_name":"Theussl, Hans","last_name":"Theussl"},{"first_name":"Josef","last_name":"Penninger","full_name":"Penninger, Josef"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"last_name":"Barlow","full_name":"Barlow, Denise","first_name":"Denise"},{"full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Quanah","full_name":"Hudson, Quanah","last_name":"Hudson"}],"article_number":"e25125","date_published":"2017-08-14T00:00:00Z","title":"Mapping the mouse Allelome reveals tissue specific regulation of allelic expression","publication":"eLife","file":[{"date_updated":"2020-07-14T12:47:50Z","relation":"main_file","creator":"system","checksum":"1ace3462e64a971b9ead896091829549","access_level":"open_access","file_name":"IST-2017-885-v1+1_elife-25125-figures-v2.pdf","content_type":"application/pdf","file_id":"5020","date_created":"2018-12-12T10:13:36Z","file_size":6399510},{"date_updated":"2020-07-14T12:47:50Z","creator":"system","checksum":"6241dc31eeb87b03facadec3a53a6827","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"5021","file_name":"IST-2017-885-v1+2_elife-25125-v2.pdf","file_size":4264398,"date_created":"2018-12-12T10:13:36Z"}],"quality_controlled":"1","publication_status":"published"},{"pmid":1,"quality_controlled":"1","publication":"Drug and Alcohol Dependence","page":"7 - 14","publication_status":"published","author":[{"first_name":"Gabriela","last_name":"Brailoiu","full_name":"Brailoiu, Gabriela"},{"first_name":"Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","full_name":"Deliu, Elena","last_name":"Deliu","orcid":"0000-0002-7370-5293"},{"last_name":"Barr","full_name":"Barr, Jeffrey","first_name":"Jeffrey"},{"first_name":"Linda","last_name":"Console Bram","full_name":"Console Bram, Linda"},{"first_name":"Alexandra","full_name":"Ciuciu, Alexandra","last_name":"Ciuciu"},{"last_name":"Abood","full_name":"Abood, Mary","first_name":"Mary"},{"full_name":"Unterwald, Ellen","last_name":"Unterwald","first_name":"Ellen"},{"first_name":"Eugen","full_name":"Brǎiloiu, Eugen","last_name":"Brǎiloiu"}],"date_published":"2017-09-01T00:00:00Z","title":"HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens","isi":1,"oa_version":"Submitted Version","article_type":"original","date_updated":"2026-04-16T10:01:59Z","month":"09","volume":178,"abstract":[{"text":"Background HIV-1 infection and drug abuse are frequently co-morbid and their association greatly increases the severity of HIV-1-induced neuropathology. While nucleus accumbens (NAcc) function is severely perturbed by drugs of abuse, little is known about how HIV-1 infection affects NAcc. Methods We used calcium and voltage imaging to investigate the effect of HIV-1 trans-activator of transcription (Tat) on rat NAcc. Based on previous neuronal studies, we hypothesized that Tat modulates intracellular Ca2+ homeostasis of NAcc neurons. Results We provide evidence that Tat triggers a Ca2+ signaling cascade in NAcc medium spiny neurons (MSN) expressing D1-like dopamine receptors leading to neuronal depolarization. Firstly, Tat induced inositol 1,4,5-trisphsophate (IP3) receptor-mediated Ca2+ release from endoplasmic reticulum, followed by Ca2+ and Na+ influx via transient receptor potential canonical channels. The influx of cations depolarizes the membrane promoting additional Ca2+ entry through voltage-gated P/Q-type Ca2+ channels and opening of tetrodotoxin-sensitive Na+ channels. By activating this mechanism, Tat elicits a feed-forward depolarization increasing the excitability of D1-phosphatidylinositol-linked NAcc MSN. We previously found that cocaine targets NAcc neurons directly (independent of the inhibition of dopamine transporter) only when IP3-generating mechanisms are concomitantly initiated. When tested here, cocaine produced a dose-dependent potentiation of the effect of Tat on cytosolic Ca2+. Conclusion We describe for the first time a HIV-1 Tat-triggered Ca2+ signaling in MSN of NAcc involving TRPC and depolarization and a potentiation of the effect of Tat by cocaine, which may be relevant for the reward axis in cocaine-abusing HIV-1-positive patients.","lang":"eng"}],"_id":"714","status":"public","publication_identifier":{"issn":["0376-8716"]},"type":"journal_article","citation":{"mla":"Brailoiu, Gabriela, et al. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” <i>Drug and Alcohol Dependence</i>, vol. 178, Elsevier, 2017, pp. 7–14, doi:<a href=\"https://doi.org/10.1016/j.drugalcdep.2017.04.015\">10.1016/j.drugalcdep.2017.04.015</a>.","chicago":"Brailoiu, Gabriela, Elena Deliu, Jeffrey Barr, Linda Console Bram, Alexandra Ciuciu, Mary Abood, Ellen Unterwald, and Eugen Brǎiloiu. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” <i>Drug and Alcohol Dependence</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.drugalcdep.2017.04.015\">https://doi.org/10.1016/j.drugalcdep.2017.04.015</a>.","ieee":"G. Brailoiu <i>et al.</i>, “HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens,” <i>Drug and Alcohol Dependence</i>, vol. 178. Elsevier, pp. 7–14, 2017.","ista":"Brailoiu G, Deliu E, Barr J, Console Bram L, Ciuciu A, Abood M, Unterwald E, Brǎiloiu E. 2017. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 178, 7–14.","short":"G. Brailoiu, E. Deliu, J. Barr, L. Console Bram, A. Ciuciu, M. Abood, E. Unterwald, E. Brǎiloiu, Drug and Alcohol Dependence 178 (2017) 7–14.","apa":"Brailoiu, G., Deliu, E., Barr, J., Console Bram, L., Ciuciu, A., Abood, M., … Brǎiloiu, E. (2017). HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. <i>Drug and Alcohol Dependence</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.drugalcdep.2017.04.015\">https://doi.org/10.1016/j.drugalcdep.2017.04.015</a>","ama":"Brailoiu G, Deliu E, Barr J, et al. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. <i>Drug and Alcohol Dependence</i>. 2017;178:7-14. doi:<a href=\"https://doi.org/10.1016/j.drugalcdep.2017.04.015\">10.1016/j.drugalcdep.2017.04.015</a>"},"article_processing_charge":"No","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797705","open_access":"1"}],"department":[{"_id":"GaNo"}],"intvolume":"       178","year":"2017","external_id":{"isi":["000409152300002"],"pmid":["28623807"]},"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:48:05Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"acknowledgement":"This work was supported by the National Institutes of Health grants DA035926 (to MEA), and P30DA013429 (to EMU).","scopus_import":"1","publist_id":"6967","day":"01","doi":"10.1016/j.drugalcdep.2017.04.015","publisher":"Elsevier"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:48:06Z","language":[{"iso":"eng"}],"corr_author":"1","year":"2017","department":[{"_id":"GaNo"}],"intvolume":"         9","doi":"10.1126/scitranslmed.aao4218","publisher":"American Association for the Advancement of Science","day":"30","publist_id":"6968","scopus_import":"1","title":"More excitation for Rett syndrome","date_published":"2017-08-30T00:00:00Z","article_number":"aao4218","author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"publication_status":"published","quality_controlled":"1","publication":"Science Translational Medicine","type":"journal_article","publication_identifier":{"issn":["1946-6234"]},"article_processing_charge":"No","citation":{"apa":"Novarino, G. (2017). More excitation for Rett syndrome. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aao4218\">https://doi.org/10.1126/scitranslmed.aao4218</a>","ama":"Novarino G. More excitation for Rett syndrome. <i>Science Translational Medicine</i>. 2017;9(405). doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao4218\">10.1126/scitranslmed.aao4218</a>","ieee":"G. Novarino, “More excitation for Rett syndrome,” <i>Science Translational Medicine</i>, vol. 9, no. 405. American Association for the Advancement of Science, 2017.","chicago":"Novarino, Gaia. “More Excitation for Rett Syndrome.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aao4218\">https://doi.org/10.1126/scitranslmed.aao4218</a>.","mla":"Novarino, Gaia. “More Excitation for Rett Syndrome.” <i>Science Translational Medicine</i>, vol. 9, no. 405, aao4218, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao4218\">10.1126/scitranslmed.aao4218</a>.","short":"G. Novarino, Science Translational Medicine 9 (2017).","ista":"Novarino G. 2017. More excitation for Rett syndrome. Science Translational Medicine. 9(405), aao4218."},"_id":"715","status":"public","month":"08","volume":9,"abstract":[{"text":"D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome.","lang":"eng"}],"issue":"405","date_updated":"2025-07-10T11:54:16Z","oa_version":"None"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:48:12Z","language":[{"iso":"eng"}],"corr_author":"1","year":"2017","department":[{"_id":"GaNo"}],"intvolume":"         9","doi":"10.1126/scitranslmed.aap8168","publisher":"American Association for the Advancement of Science","day":"11","publist_id":"6938","scopus_import":"1","title":"The science of love in ASD and ADHD","author":[{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"article_number":"eaap8168","date_published":"2017-10-11T00:00:00Z","publication_status":"published","quality_controlled":"1","publication":"Science Translational Medicine","publication_identifier":{"issn":["1946-6234"]},"type":"journal_article","citation":{"mla":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” <i>Science Translational Medicine</i>, vol. 9, no. 411, eaap8168, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aap8168\">10.1126/scitranslmed.aap8168</a>.","chicago":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aap8168\">https://doi.org/10.1126/scitranslmed.aap8168</a>.","ieee":"G. Novarino, “The science of love in ASD and ADHD,” <i>Science Translational Medicine</i>, vol. 9, no. 411. American Association for the Advancement of Science, 2017.","ista":"Novarino G. 2017. The science of love in ASD and ADHD. Science Translational Medicine. 9(411), eaap8168.","short":"G. Novarino, Science Translational Medicine 9 (2017).","apa":"Novarino, G. (2017). The science of love in ASD and ADHD. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aap8168\">https://doi.org/10.1126/scitranslmed.aap8168</a>","ama":"Novarino G. The science of love in ASD and ADHD. <i>Science Translational Medicine</i>. 2017;9(411). doi:<a href=\"https://doi.org/10.1126/scitranslmed.aap8168\">10.1126/scitranslmed.aap8168</a>"},"article_processing_charge":"No","_id":"731","status":"public","issue":"411","date_updated":"2025-07-10T11:54:29Z","abstract":[{"lang":"eng","text":"Genetic variations in the oxytocin receptor gene affect patients with ASD and ADHD differently."}],"month":"10","volume":9,"oa_version":"None"},{"publication_status":"published","page":"23 - 32","quality_controlled":"1","pmid":1,"publication":"Neuroscience","title":"Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus","date_published":"2017-12-04T00:00:00Z","author":[{"last_name":"Brǎiloiu","full_name":"Brǎiloiu, Eugen","first_name":"Eugen"},{"first_name":"Matthew","last_name":"Mcguire","full_name":"Mcguire, Matthew"},{"first_name":"Shadaria","last_name":"Shuler","full_name":"Shuler, Shadaria"},{"last_name":"Deliu","orcid":"0000-0002-7370-5293","full_name":"Deliu, Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"last_name":"Barr","full_name":"Barr, Jeffrey","first_name":"Jeffrey"},{"full_name":"Abood, Mary","last_name":"Abood","first_name":"Mary"},{"first_name":"Gabriela","last_name":"Brailoiu","full_name":"Brailoiu, Gabriela"}],"article_type":"original","volume":365,"month":"12","abstract":[{"lang":"eng","text":"Bradykinin (BK), a component of the kallikrein-kininogen-kinin system exerts multiple effects via B1 and B2 receptor activation. In the cardiovascular system, bradykinin has cardioprotective and vasodilator properties. We investigated the effect of BK on cardiac-projecting neurons of nucleus ambiguus, a key site for the parasympathetic cardiac regulation. BK produced a dose-dependent increase in cytosolic Ca2+ concentration. Pretreatment with HOE140, a B2 receptor antagonist, but not with R715, a B1 receptor antagonist, abolished the response to BK. A selective B2 receptor agonist, but not a B1 receptor agonist, elicited an increase in cytosolic Ca2+ similarly to BK. Inhibition of N-type voltage-gated Ca2+ channels with ω-conotoxin GVIA had no effect on the Ca2+ signal produced by BK, while pretreatment with ω-conotoxin MVIIC, a blocker of P/Q-type of Ca2+ channels, significantly diminished the effect of BK. Pretreatment with xestospongin C and 2-aminoethoxydiphenyl borate, antagonists of inositol 1,4,5-trisphosphate receptors, abolished the response to BK. Inhibition of ryanodine receptors reduced the BK-induced Ca2+ increase, while disruption of lysosomal Ca2+ stores with bafilomycin A1 did not affect the response. BK produced a dose-dependent depolarization of nucleus ambiguus neurons, which was prevented by the B2 receptor antagonist. In vivo studies indicate that microinjection of BK into nucleus ambiguus elicited bradycardia in conscious rats via B2 receptors. In summary, in cardiac vagal neurons of nucleus ambiguus, BK activates B2 receptors promoting Ca2+ influx and Ca2+ release from endoplasmic reticulum, and membrane depolarization; these effects are translated in vivo by bradycardia."}],"date_updated":"2026-04-16T10:04:53Z","isi":1,"oa_version":"Submitted Version","type":"journal_article","publication_identifier":{"issn":["0306-4522"]},"article_processing_charge":"No","citation":{"ama":"Brǎiloiu E, Mcguire M, Shuler S, et al. Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. <i>Neuroscience</i>. 2017;365:23-32. doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2017.09.034\">10.1016/j.neuroscience.2017.09.034</a>","apa":"Brǎiloiu, E., Mcguire, M., Shuler, S., Deliu, E., Barr, J., Abood, M., &#38; Brailoiu, G. (2017). Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. <i>Neuroscience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuroscience.2017.09.034\">https://doi.org/10.1016/j.neuroscience.2017.09.034</a>","short":"E. Brǎiloiu, M. Mcguire, S. Shuler, E. Deliu, J. Barr, M. Abood, G. Brailoiu, Neuroscience 365 (2017) 23–32.","ista":"Brǎiloiu E, Mcguire M, Shuler S, Deliu E, Barr J, Abood M, Brailoiu G. 2017. Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus. Neuroscience. 365, 23–32.","chicago":"Brǎiloiu, Eugen, Matthew Mcguire, Shadaria Shuler, Elena Deliu, Jeffrey Barr, Mary Abood, and Gabriela Brailoiu. “Modulation of Cardiac Vagal Tone by Bradykinin Acting on Nucleus Ambiguus.” <i>Neuroscience</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.neuroscience.2017.09.034\">https://doi.org/10.1016/j.neuroscience.2017.09.034</a>.","ieee":"E. Brǎiloiu <i>et al.</i>, “Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus,” <i>Neuroscience</i>, vol. 365. Elsevier, pp. 23–32, 2017.","mla":"Brǎiloiu, Eugen, et al. “Modulation of Cardiac Vagal Tone by Bradykinin Acting on Nucleus Ambiguus.” <i>Neuroscience</i>, vol. 365, Elsevier, 2017, pp. 23–32, doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2017.09.034\">10.1016/j.neuroscience.2017.09.034</a>."},"status":"public","_id":"747","year":"2017","intvolume":"       365","department":[{"_id":"GaNo"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798458","open_access":"1"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2018-12-11T11:48:17Z","oa":1,"language":[{"iso":"eng"}],"external_id":{"pmid":["28951324"],"isi":["000415966200003"]},"publist_id":"6911","scopus_import":"1","doi":"10.1016/j.neuroscience.2017.09.034","publisher":"Elsevier","day":"04"},{"scopus_import":"1","ddc":["576"],"acknowledgement":"This study was partly funded by the Austrian Science Fund (FWF F43-B09, FWF W1207-B09). PMG is a recipient of a DOC Fellowship of the Austrian Academy of Sciences.\r\nWe thank Ruth Klement, Tomasz Kulinski, Elisangela Valente, Elisabeth Salzer,\r\nand Roland Jäger for technical/bioinformatic assistance and advice, the CeMM\r\nIT department and José Manuel Molero for help and advice on software usage,\r\nthe Biomedical Sequencing Facility (http://biomedical-sequencing.at/) for\r\nsequencing and advice, Jacques Colinge, Daniel Andergassen, and Tomasz\r\nKulinski for discussions, Quanah Hudson and Jörg Menche for reading and\r\ncommenting on the manuscript.","publist_id":"6093","day":"29","publisher":"BioMed Central","doi":"10.1186/s13059-016-0873-8","intvolume":"        17","year":"2016","department":[{"_id":"GaNo"}],"external_id":{"isi":["000368904100001"]},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:41Z","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:53Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","isi":1,"has_accepted_license":"1","pubrep_id":"709","date_updated":"2025-09-22T09:17:40Z","issue":"1","volume":17,"month":"01","abstract":[{"text":"Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs. An unexplored factor potentially confounding lncRNA identification is inter-individual expression variability. Here, we characterize lncRNA natural expression variability in human primary granulocytes. Results: We annotate granulocyte lncRNAs and mRNAs in RNA-seq data from 10 healthy individuals, identifying multiple lncRNAs absent from reference annotations, and use this to investigate three known features (higher tissue-specificity, lower expression, and reduced splicing efficiency) of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals sampled three times at 1- or more than 1-month intervals. We show that lncRNAs display significantly more inter-individual expression variability compared to mRNAs. We confirm this finding in two independent human datasets by analyzing multiple tissues from the GTEx project and lymphoblastoid cell lines from the GEUVADIS project. Using the latter dataset we also show that including more human donors into the transcriptome annotation pipeline allows identification of an increasing number of lncRNAs, but minimally affects mRNA gene number. Conclusions: A comprehensive annotation of lncRNAs is known to require an approach that is sensitive to low and tight tissue-specific expression. Here we show that increased inter-individual expression variability is an additional general lncRNA feature to consider when creating a comprehensive annotation of human lncRNAs or proposing their use as prognostic or disease markers.","lang":"eng"}],"_id":"1240","status":"public","citation":{"short":"A. Kornienko, C. Dotter, P. Guenzl, H. Gisslinger, B. Gisslinger, C. Cleary, R. Kralovics, F. Pauler, D. Barlow, Genome Biology 17 (2016).","ista":"Kornienko A, Dotter C, Guenzl P, Gisslinger H, Gisslinger B, Cleary C, Kralovics R, Pauler F, Barlow D. 2016. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biology. 17(1), 14.","ieee":"A. Kornienko <i>et al.</i>, “Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans,” <i>Genome Biology</i>, vol. 17, no. 1. BioMed Central, 2016.","chicago":"Kornienko, Aleksandra, Christoph Dotter, Philipp Guenzl, Heinz Gisslinger, Bettina Gisslinger, Ciara Cleary, Robert Kralovics, Florian Pauler, and Denise Barlow. “Long Non-Coding RNAs Display Higher Natural Expression Variation than Protein-Coding Genes in Healthy Humans.” <i>Genome Biology</i>. BioMed Central, 2016. <a href=\"https://doi.org/10.1186/s13059-016-0873-8\">https://doi.org/10.1186/s13059-016-0873-8</a>.","mla":"Kornienko, Aleksandra, et al. “Long Non-Coding RNAs Display Higher Natural Expression Variation than Protein-Coding Genes in Healthy Humans.” <i>Genome Biology</i>, vol. 17, no. 1, 14, BioMed Central, 2016, doi:<a href=\"https://doi.org/10.1186/s13059-016-0873-8\">10.1186/s13059-016-0873-8</a>.","ama":"Kornienko A, Dotter C, Guenzl P, et al. Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. <i>Genome Biology</i>. 2016;17(1). doi:<a href=\"https://doi.org/10.1186/s13059-016-0873-8\">10.1186/s13059-016-0873-8</a>","apa":"Kornienko, A., Dotter, C., Guenzl, P., Gisslinger, H., Gisslinger, B., Cleary, C., … Barlow, D. (2016). Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-016-0873-8\">https://doi.org/10.1186/s13059-016-0873-8</a>"},"article_processing_charge":"No","type":"journal_article","publication":"Genome Biology","file":[{"creator":"system","checksum":"a268beee1a690801c83ec6729f9ebc5b","relation":"main_file","date_updated":"2020-07-14T12:44:41Z","date_created":"2018-12-12T10:10:05Z","file_size":2914601,"file_name":"IST-2016-709-v1+1_s13059-016-0873-8.pdf","access_level":"open_access","file_id":"4789","content_type":"application/pdf"}],"quality_controlled":"1","publication_status":"published","author":[{"full_name":"Kornienko, Aleksandra","last_name":"Kornienko","first_name":"Aleksandra"},{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter","full_name":"Dotter, Christoph"},{"first_name":"Philipp","full_name":"Guenzl, Philipp","last_name":"Guenzl"},{"last_name":"Gisslinger","full_name":"Gisslinger, Heinz","first_name":"Heinz"},{"full_name":"Gisslinger, Bettina","last_name":"Gisslinger","first_name":"Bettina"},{"full_name":"Cleary, Ciara","last_name":"Cleary","first_name":"Ciara"},{"full_name":"Kralovics, Robert","last_name":"Kralovics","first_name":"Robert"},{"full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Denise","last_name":"Barlow","full_name":"Barlow, Denise"}],"date_published":"2016-01-29T00:00:00Z","article_number":"14","title":"Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans"},{"department":[{"_id":"GaNo"}],"year":"2016","intvolume":"       167","project":[{"name":"Transmembrane Transporters in Health and Disease","_id":"25473368-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"F03523"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000389470500012"]},"date_created":"2018-12-11T11:50:35Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"file_date_updated":"2020-07-14T12:44:37Z","ddc":["576","616"],"acknowledgement":"This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\nWe thank A.C. Manzano, Mike Liu, and F. Marr for technical assistance, and R. Shigemoto and the IST Austria Electron Microscopy (EM) Facility for assistance. We acknowledge support from CIDR for genome-wide SNP analysis (X01HG008823) and Broad Institute Center for Mendelian Disorders (UM1HG008900 to D. MacArthur), the Yale Center for Mendelian Disorders (U54HG006504 to M.G.), the Gregory M. Kiez and Mehmet Kutman Foundation (M.G.), Italian Ministry of Instruction University and Research (PON01_00937 to C.I.), and NIH (R01-GM108911 to A.S.). This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\n\r\n#EMFacility","scopus_import":"1","publist_id":"6170","day":"01","doi":"10.1016/j.cell.2016.11.013","publisher":"Cell Press","quality_controlled":"1","file":[{"file_name":"IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf","access_level":"open_access","file_id":"5030","content_type":"application/pdf","date_created":"2018-12-12T10:13:44Z","file_size":73907957,"date_updated":"2020-07-14T12:44:37Z","relation":"main_file","checksum":"7fe01ab12a6610d3db421e0136db2f77","creator":"system"}],"publication":"Cell","page":"1481 - 1494","publication_status":"published","date_published":"2016-12-01T00:00:00Z","author":[{"last_name":"Tarlungeanu","full_name":"Tarlungeanu, Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","first_name":"Dora-Clara"},{"orcid":"0000-0002-7370-5293","last_name":"Deliu","full_name":"Deliu, Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Dotter","orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph"},{"first_name":"Majdi","full_name":"Kara, Majdi","last_name":"Kara"},{"first_name":"Philipp","full_name":"Janiesch, Philipp","last_name":"Janiesch"},{"full_name":"Scalise, Mariafrancesca","last_name":"Scalise","first_name":"Mariafrancesca"},{"last_name":"Galluccio","full_name":"Galluccio, Michele","first_name":"Michele"},{"first_name":"Mateja","full_name":"Tesulov, Mateja","last_name":"Tesulov"},{"full_name":"Morelli, Emanuela","last_name":"Morelli","first_name":"Emanuela","id":"3F4D1282-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fatma","last_name":"Sönmez","full_name":"Sönmez, Fatma"},{"full_name":"Bilgüvar, Kaya","last_name":"Bilgüvar","first_name":"Kaya"},{"first_name":"Ryuichi","last_name":"Ohgaki","full_name":"Ohgaki, Ryuichi"},{"first_name":"Yoshikatsu","full_name":"Kanai, Yoshikatsu","last_name":"Kanai"},{"first_name":"Anide","full_name":"Johansen, Anide","last_name":"Johansen"},{"first_name":"Seham","full_name":"Esharif, Seham","last_name":"Esharif"},{"first_name":"Tawfeg","full_name":"Ben Omran, Tawfeg","last_name":"Ben Omran"},{"first_name":"Meral","full_name":"Topcu, Meral","last_name":"Topcu"},{"first_name":"Avner","last_name":"Schlessinger","full_name":"Schlessinger, Avner"},{"first_name":"Cesare","full_name":"Indiveri, Cesare","last_name":"Indiveri"},{"last_name":"Duncan","full_name":"Duncan, Kent","first_name":"Kent"},{"first_name":"Ahmet","full_name":"Caglayan, Ahmet","last_name":"Caglayan"},{"full_name":"Günel, Murat","last_name":"Günel","first_name":"Murat"},{"first_name":"Joseph","last_name":"Gleeson","full_name":"Gleeson, Joseph"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"title":"Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder","has_accepted_license":"1","isi":1,"oa_version":"Submitted Version","article_type":"original","related_material":{"record":[{"status":"public","id":"395","relation":"dissertation_contains"}]},"abstract":[{"text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function.","lang":"eng"}],"volume":167,"month":"12","pubrep_id":"771","issue":"6","date_updated":"2026-08-31T22:30:51Z","_id":"1183","status":"public","type":"journal_article","article_processing_charge":"No","citation":{"short":"D.-C. Tarlungeanu, E. Deliu, C. Dotter, M. Kara, P. Janiesch, M. Scalise, M. Galluccio, M. Tesulov, E. Morelli, F. Sönmez, K. Bilgüvar, R. Ohgaki, Y. Kanai, A. Johansen, S. Esharif, T. Ben Omran, M. Topcu, A. Schlessinger, C. Indiveri, K. Duncan, A. Caglayan, M. Günel, J. Gleeson, G. Novarino, Cell 167 (2016) 1481–1494.","ista":"Tarlungeanu D-C, Deliu E, Dotter C, Kara M, Janiesch P, Scalise M, Galluccio M, Tesulov M, Morelli E, Sönmez F, Bilgüvar K, Ohgaki R, Kanai Y, Johansen A, Esharif S, Ben Omran T, Topcu M, Schlessinger A, Indiveri C, Duncan K, Caglayan A, Günel M, Gleeson J, Novarino G. 2016. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 167(6), 1481–1494.","chicago":"Tarlungeanu, Dora-Clara, Elena Deliu, Christoph Dotter, Majdi Kara, Philipp Janiesch, Mariafrancesca Scalise, Michele Galluccio, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” <i>Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">https://doi.org/10.1016/j.cell.2016.11.013</a>.","ieee":"D.-C. Tarlungeanu <i>et al.</i>, “Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder,” <i>Cell</i>, vol. 167, no. 6. Cell Press, pp. 1481–1494, 2016.","mla":"Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” <i>Cell</i>, vol. 167, no. 6, Cell Press, 2016, pp. 1481–94, doi:<a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">10.1016/j.cell.2016.11.013</a>.","ama":"Tarlungeanu D-C, Deliu E, Dotter C, et al. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. <i>Cell</i>. 2016;167(6):1481-1494. doi:<a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">10.1016/j.cell.2016.11.013</a>","apa":"Tarlungeanu, D.-C., Deliu, E., Dotter, C., Kara, M., Janiesch, P., Scalise, M., … Novarino, G. (2016). Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">https://doi.org/10.1016/j.cell.2016.11.013</a>"}},{"isi":1,"oa_version":"Published Version","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"issue":"21","date_updated":"2025-09-23T07:45:31Z","volume":43,"month":"07","abstract":[{"lang":"eng","text":"Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide."}],"status":"public","_id":"1497","type":"journal_article","citation":{"apa":"Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow, D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkv727\">https://doi.org/10.1093/nar/gkv727</a>","ama":"Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. <i>Nucleic Acids Research</i>. 2015;43(21). doi:<a href=\"https://doi.org/10.1093/nar/gkv727\">10.1093/nar/gkv727</a>","mla":"Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” <i>Nucleic Acids Research</i>, vol. 43, no. 21, e146, Oxford University Press, 2015, doi:<a href=\"https://doi.org/10.1093/nar/gkv727\">10.1093/nar/gkv727</a>.","chicago":"Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl, Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” <i>Nucleic Acids Research</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/nar/gkv727\">https://doi.org/10.1093/nar/gkv727</a>.","ieee":"D. Andergassen <i>et al.</i>, “Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data,” <i>Nucleic Acids Research</i>, vol. 43, no. 21. Oxford University Press, 2015.","ista":"Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 43(21), e146.","short":"D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow, F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015)."},"article_processing_charge":"No","quality_controlled":"1","publication":"Nucleic Acids Research","file":[{"date_updated":"2020-07-14T12:44:58Z","creator":"dernst","checksum":"385b83854fd0eb2e4f386867da2823e2","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5768","file_name":"2015_NucleicAcidsRes_Andergassen.pdf","file_size":6863297,"date_created":"2018-12-20T14:18:57Z"}],"publication_status":"published","author":[{"first_name":"Daniel","full_name":"Andergassen, Daniel","last_name":"Andergassen"},{"first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter"},{"first_name":"Tomasz","full_name":"Kulinski, Tomasz","last_name":"Kulinski"},{"first_name":"Philipp","last_name":"Guenzl","full_name":"Guenzl, Philipp"},{"first_name":"Philipp","last_name":"Bammer","full_name":"Bammer, Philipp"},{"last_name":"Barlow","full_name":"Barlow, Denise","first_name":"Denise"},{"last_name":"Pauler","full_name":"Pauler, Florian","first_name":"Florian"},{"first_name":"Quanah","last_name":"Hudson","full_name":"Hudson, Quanah"}],"article_number":"e146","date_published":"2015-07-21T00:00:00Z","title":"Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data","ddc":["570"],"acknowledgement":"Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09]. Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser for advice during the early stages of this project. High-throughput sequencing was conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna.","scopus_import":"1","publist_id":"5682","day":"21","doi":"10.1093/nar/gkv727","publisher":"Oxford University Press","year":"2015","intvolume":"        43","department":[{"_id":"GaNo"}],"external_id":{"isi":["000366410900009"]},"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:52:22Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2020-07-14T12:44:58Z","oa":1},{"volume":23,"month":"06","abstract":[{"text":"Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID.","lang":"eng"}],"issue":"6","date_updated":"2025-09-23T09:30:27Z","isi":1,"oa_version":"Submitted Version","article_processing_charge":"No","citation":{"ieee":"A. Kuechler <i>et al.</i>, “Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome,” <i>European Journal of Human Genetics</i>, vol. 23, no. 6. Nature Publishing Group, pp. 753–760, 2015.","chicago":"Kuechler, Alma, Alexander Zink, Thomas Wieland, Hermann Lüdecke, Kirsten Cremer, Leonardo Salviati, Pamela Magini, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” <i>European Journal of Human Genetics</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ejhg.2014.165\">https://doi.org/10.1038/ejhg.2014.165</a>.","mla":"Kuechler, Alma, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” <i>European Journal of Human Genetics</i>, vol. 23, no. 6, Nature Publishing Group, 2015, pp. 753–60, doi:<a href=\"https://doi.org/10.1038/ejhg.2014.165\">10.1038/ejhg.2014.165</a>.","short":"A. Kuechler, A. Zink, T. Wieland, H. Lüdecke, K. Cremer, L. Salviati, P. Magini, K. Najafi, C. Zweier, J. Czeschik, S. Aretz, S. Endele, F. Tamburrino, C. Pinato, M. Clementi, J. Gundlach, C. Maylahn, L. Mazzanti, E. Wohlleber, T. Schwarzmayr, R. Kariminejad, A. Schlessinger, D. Wieczorek, T. Strom, G. Novarino, H. Engels, European Journal of Human Genetics 23 (2015) 753–760.","ista":"Kuechler A, Zink A, Wieland T, Lüdecke H, Cremer K, Salviati L, Magini P, Najafi K, Zweier C, Czeschik J, Aretz S, Endele S, Tamburrino F, Pinato C, Clementi M, Gundlach J, Maylahn C, Mazzanti L, Wohlleber E, Schwarzmayr T, Kariminejad R, Schlessinger A, Wieczorek D, Strom T, Novarino G, Engels H. 2015. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 23(6), 753–760.","apa":"Kuechler, A., Zink, A., Wieland, T., Lüdecke, H., Cremer, K., Salviati, L., … Engels, H. (2015). Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. <i>European Journal of Human Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ejhg.2014.165\">https://doi.org/10.1038/ejhg.2014.165</a>","ama":"Kuechler A, Zink A, Wieland T, et al. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. <i>European Journal of Human Genetics</i>. 2015;23(6):753-760. doi:<a href=\"https://doi.org/10.1038/ejhg.2014.165\">10.1038/ejhg.2014.165</a>"},"type":"journal_article","_id":"1789","status":"public","page":"753 - 760","publication_status":"published","publication":"European Journal of Human Genetics","quality_controlled":"1","pmid":1,"title":"Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome","date_published":"2015-06-15T00:00:00Z","author":[{"last_name":"Kuechler","full_name":"Kuechler, Alma","first_name":"Alma"},{"first_name":"Alexander","last_name":"Zink","full_name":"Zink, Alexander"},{"first_name":"Thomas","last_name":"Wieland","full_name":"Wieland, Thomas"},{"last_name":"Lüdecke","full_name":"Lüdecke, Hermann","first_name":"Hermann"},{"first_name":"Kirsten","last_name":"Cremer","full_name":"Cremer, Kirsten"},{"first_name":"Leonardo","full_name":"Salviati, Leonardo","last_name":"Salviati"},{"last_name":"Magini","full_name":"Magini, Pamela","first_name":"Pamela"},{"first_name":"Kimia","last_name":"Najafi","full_name":"Najafi, Kimia"},{"full_name":"Zweier, Christiane","last_name":"Zweier","first_name":"Christiane"},{"last_name":"Czeschik","full_name":"Czeschik, Johanna","first_name":"Johanna"},{"first_name":"Stefan","last_name":"Aretz","full_name":"Aretz, Stefan"},{"full_name":"Endele, Sabine","last_name":"Endele","first_name":"Sabine"},{"first_name":"Federica","last_name":"Tamburrino","full_name":"Tamburrino, Federica"},{"last_name":"Pinato","full_name":"Pinato, Claudia","first_name":"Claudia"},{"last_name":"Clementi","full_name":"Clementi, Maurizio","first_name":"Maurizio"},{"full_name":"Gundlach, Jasmin","last_name":"Gundlach","first_name":"Jasmin"},{"first_name":"Carina","last_name":"Maylahn","full_name":"Maylahn, Carina"},{"first_name":"Laura","last_name":"Mazzanti","full_name":"Mazzanti, Laura"},{"last_name":"Wohlleber","full_name":"Wohlleber, Eva","first_name":"Eva"},{"first_name":"Thomas","last_name":"Schwarzmayr","full_name":"Schwarzmayr, Thomas"},{"last_name":"Kariminejad","full_name":"Kariminejad, Roxana","first_name":"Roxana"},{"first_name":"Avner","last_name":"Schlessinger","full_name":"Schlessinger, Avner"},{"first_name":"Dagmar","last_name":"Wieczorek","full_name":"Wieczorek, Dagmar"},{"first_name":"Tim","full_name":"Strom, Tim","last_name":"Strom"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","full_name":"Novarino, Gaia"},{"first_name":"Hartmut","full_name":"Engels, Hartmut","last_name":"Engels"}],"publist_id":"5324","publisher":"Nature Publishing Group","doi":"10.1038/ejhg.2014.165","day":"15","department":[{"_id":"GaNo"}],"year":"2015","intvolume":"        23","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795044/"}],"oa":1,"date_created":"2018-12-11T11:54:01Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"external_id":{"pmid":["25138099"],"isi":["000354474600013"]}},{"external_id":{"pmid":["24482476"],"isi":["000330343700038"]},"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:54:42Z","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157572/"}],"intvolume":"       343","department":[{"_id":"GaNo"}],"year":"2014","day":"31","doi":"10.1126/science.1247363","publisher":"American Association for the Advancement of Science","acknowledgement":"Supported by the Deutsche Forschungsgemeinschaft (G.N.)","scopus_import":"1","publist_id":"5178","author":[{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178"},{"first_name":"Ali","full_name":"Fenstermaker, Ali","last_name":"Fenstermaker"},{"first_name":"Maha","full_name":"Zaki, Maha","last_name":"Zaki"},{"full_name":"Hofree, Matan","last_name":"Hofree","first_name":"Matan"},{"first_name":"Jennifer","last_name":"Silhavy","full_name":"Silhavy, Jennifer"},{"full_name":"Heiberg, Andrew","last_name":"Heiberg","first_name":"Andrew"},{"last_name":"Abdellateef","full_name":"Abdellateef, Mostafa","first_name":"Mostafa"},{"first_name":"Başak","full_name":"Rosti, Başak","last_name":"Rosti"},{"first_name":"Eric","full_name":"Scott, Eric","last_name":"Scott"},{"full_name":"Mansour, Lobna","last_name":"Mansour","first_name":"Lobna"},{"last_name":"Masri","full_name":"Masri, Amira","first_name":"Amira"},{"first_name":"Hülya","last_name":"Kayserili","full_name":"Kayserili, Hülya"},{"first_name":"Jumana","full_name":"Al Aama, Jumana","last_name":"Al Aama"},{"first_name":"Ghada","last_name":"Abdel Salam","full_name":"Abdel Salam, Ghada"},{"first_name":"Ariana","last_name":"Karminejad","full_name":"Karminejad, Ariana"},{"first_name":"Majdi","last_name":"Kara","full_name":"Kara, Majdi"},{"first_name":"Bülent","last_name":"Kara","full_name":"Kara, Bülent"},{"first_name":"Bita","last_name":"Bozorgmehri","full_name":"Bozorgmehri, Bita"},{"first_name":"Tawfeg","full_name":"Ben Omran, Tawfeg","last_name":"Ben Omran"},{"first_name":"Faezeh","last_name":"Mojahedi","full_name":"Mojahedi, Faezeh"},{"first_name":"Iman","full_name":"Mahmoud, Iman","last_name":"Mahmoud"},{"full_name":"Bouslam, Naïma","last_name":"Bouslam","first_name":"Naïma"},{"last_name":"Bouhouche","full_name":"Bouhouche, Ahmed","first_name":"Ahmed"},{"first_name":"Ali","last_name":"Benomar","full_name":"Benomar, Ali"},{"first_name":"Sylvain","last_name":"Hanein","full_name":"Hanein, Sylvain"},{"full_name":"Raymond, Laure","last_name":"Raymond","first_name":"Laure"},{"last_name":"Forlani","full_name":"Forlani, Sylvie","first_name":"Sylvie"},{"full_name":"Mascaro, Massimo","last_name":"Mascaro","first_name":"Massimo"},{"first_name":"Laila","full_name":"Selim, Laila","last_name":"Selim"},{"last_name":"Shehata","full_name":"Shehata, Nabil","first_name":"Nabil"},{"full_name":"Al Allawi, Nasir","last_name":"Al Allawi","first_name":"Nasir"},{"last_name":"Bindu","full_name":"Bindu, Parayil","first_name":"Parayil"},{"first_name":"Matloob","last_name":"Azam","full_name":"Azam, Matloob"},{"full_name":"Günel, Murat","last_name":"Günel","first_name":"Murat"},{"first_name":"Ahmet","full_name":"Caglayan, Ahmet","last_name":"Caglayan"},{"last_name":"Bilgüvar","full_name":"Bilgüvar, Kaya","first_name":"Kaya"},{"first_name":"Aslihan","last_name":"Tolun","full_name":"Tolun, Aslihan"},{"first_name":"Mahmoud","full_name":"Issa, Mahmoud","last_name":"Issa"},{"first_name":"Jana","last_name":"Schroth","full_name":"Schroth, Jana"},{"first_name":"Emily","full_name":"Spencer, Emily","last_name":"Spencer"},{"last_name":"Rosti","full_name":"Rosti, Rasim","first_name":"Rasim"},{"first_name":"Naiara","last_name":"Akizu","full_name":"Akizu, Naiara"},{"full_name":"Vaux, Keith","last_name":"Vaux","first_name":"Keith"},{"first_name":"Anide","full_name":"Johansen, Anide","last_name":"Johansen"},{"first_name":"Alice","full_name":"Koh, Alice","last_name":"Koh"},{"first_name":"Hisham","last_name":"Megahed","full_name":"Megahed, Hisham"},{"first_name":"Alexandra","last_name":"Dürr","full_name":"Dürr, Alexandra"},{"last_name":"Brice","full_name":"Brice, Alexis","first_name":"Alexis"},{"first_name":"Giovanni","full_name":"Stévanin, Giovanni","last_name":"Stévanin"},{"first_name":"Stacy","last_name":"Gabriel","full_name":"Gabriel, Stacy"},{"first_name":"Trey","last_name":"Ideker","full_name":"Ideker, Trey"},{"first_name":"Joseph","last_name":"Gleeson","full_name":"Gleeson, Joseph"}],"date_published":"2014-01-31T00:00:00Z","title":"Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders","pmid":1,"quality_controlled":"1","publication":"Science","page":"506 - 511","publication_status":"published","_id":"1916","status":"public","type":"journal_article","citation":{"short":"G. Novarino, A. Fenstermaker, M. Zaki, M. Hofree, J. Silhavy, A. Heiberg, M. Abdellateef, B. Rosti, E. Scott, L. Mansour, A. Masri, H. Kayserili, J. Al Aama, G. Abdel Salam, A. Karminejad, M. Kara, B. Kara, B. Bozorgmehri, T. Ben Omran, F. Mojahedi, I. Mahmoud, N. Bouslam, A. Bouhouche, A. Benomar, S. Hanein, L. Raymond, S. Forlani, M. Mascaro, L. Selim, N. Shehata, N. Al Allawi, P. Bindu, M. Azam, M. Günel, A. Caglayan, K. Bilgüvar, A. Tolun, M. Issa, J. Schroth, E. Spencer, R. Rosti, N. Akizu, K. Vaux, A. Johansen, A. Koh, H. Megahed, A. Dürr, A. Brice, G. Stévanin, S. Gabriel, T. Ideker, J. Gleeson, Science 343 (2014) 506–511.","ista":"Novarino G, Fenstermaker A, Zaki M, Hofree M, Silhavy J, Heiberg A, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al Aama J, Abdel Salam G, Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben Omran T, Mojahedi F, Mahmoud I, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al Allawi N, Bindu P, Azam M, Günel M, Caglayan A, Bilgüvar K, Tolun A, Issa M, Schroth J, Spencer E, Rosti R, Akizu N, Vaux K, Johansen A, Koh A, Megahed H, Dürr A, Brice A, Stévanin G, Gabriel S, Ideker T, Gleeson J. 2014. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 343(6170), 506–511.","chicago":"Novarino, Gaia, Ali Fenstermaker, Maha Zaki, Matan Hofree, Jennifer Silhavy, Andrew Heiberg, Mostafa Abdellateef, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1247363\">https://doi.org/10.1126/science.1247363</a>.","ieee":"G. Novarino <i>et al.</i>, “Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders,” <i>Science</i>, vol. 343, no. 6170. American Association for the Advancement of Science, pp. 506–511, 2014.","mla":"Novarino, Gaia, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” <i>Science</i>, vol. 343, no. 6170, American Association for the Advancement of Science, 2014, pp. 506–11, doi:<a href=\"https://doi.org/10.1126/science.1247363\">10.1126/science.1247363</a>.","ama":"Novarino G, Fenstermaker A, Zaki M, et al. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. <i>Science</i>. 2014;343(6170):506-511. doi:<a href=\"https://doi.org/10.1126/science.1247363\">10.1126/science.1247363</a>","apa":"Novarino, G., Fenstermaker, A., Zaki, M., Hofree, M., Silhavy, J., Heiberg, A., … Gleeson, J. (2014). Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1247363\">https://doi.org/10.1126/science.1247363</a>"},"article_processing_charge":"No","isi":1,"oa_version":"Submitted Version","article_type":"original","issue":"6170","date_updated":"2025-09-29T12:22:05Z","volume":343,"abstract":[{"lang":"eng","text":"Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in combination with network analysis, we identified 18 previously unknown putative HSP genes and validated nearly all of these genes functionally or genetically. The pathways highlighted by these mutations link HSP to cellular transport, nucleotide metabolism, and synapse and axon development. Network analysis revealed a host of further candidate genes, of which three were mutated in our cohort. Our analysis links HSP to other neurodegenerative disorders and can facilitate gene discovery and mechanistic understanding of disease."}],"month":"01"}]