Yu Q, He Z, Zubkov D, Huang S, Kurochkin I, Yang X, Halene T, Willmitzer L, Giavalisco P, Akbarian S, Khaitovich P. Lipidome alterations in human prefrontal cortex during development, aging, and cognitive disorders. Mol Psychiatry. 2018 Aug 8.
Xu C, Li Q, Efimova O, He L, Tatsumoto S, Stepanova V, Oishi T, Udono T, Yamaguchi K, Shigenobu S, Kakita A, Nawa H, Khaitovich P, Go Y. Human-specific features of spatial gene expression and regulation in eight brain regions. Genome Res. 2018 Aug;28(8):1097-1110.
Khrameeva E, Kurochkin I, Bozek K, Giavalisco P, Khaitovich P. Lipidome Evolution in Mammalian Tissues. Mol Biol Evol. 2018 Aug 1;35(8):1947-1957.
Hu H, Liu JM, Hu Z, Jiang X, Yang X, Li J, Zhang Y, Yu H, Khaitovich P. Recently Evolved Tumor Suppressor Transcript TP73-AS1 Functions as Sponge of Human-Specific miR-941. Mol Biol Evol. 2018 May 1;35(5):1063-1077.
Xiong J, Jiang X, Ditsiou A, Gao Y, Sun J, Lowenstein ED, Huang S, Khaitovich P. Predominant patterns of splicing evolution on human, chimpanzee and macaque evolutionary lineages. Hum Mol Genet. 2018 Apr 15;27(8):1474-1485.
Mazin PV, Jiang X, Fu N, Han D, Guo M, Gelfand MS, Khaitovich P. Conservation, evolution, and regulation of splicing during prefrontal cortex development in humans, chimpanzees, and macaques. RNA. 2018 Apr;24(4):585-596.
He Z, Yu Q. Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation. BMC Genomics. 2018, 19:262.
Voigt M, Wich SA, Ancrenaz M, Meijaard E, Abram N, Banes GL, et al. Global Demand for Natural Resources Eliminated More Than 100,000 Bornean Orangutans. Current Biology. 2018, 28:1-9.
Banes GL, Chua W, Elder ML and Kao J. Orang-utans Pongo spp in Asian zoos: current status, challenges and progress towards long-term population sustainability. International Zoo Yearbook. 2018, 52:1-14
2017:
Hu H, Uesaka M, Guo S, Shimai K, Lu TM, Li F, Fujimoto S, Ishikawa M, Liu S, Sasagawa Y, Zhang G, Kuratani S, Yu JK, Kusakabe TG, Khaitovich P, Irie N; EXPANDE Consortium. Constrained vertebrate evolution by pleiotropic genes. Nat Ecol Evol. 2017 Nov;1(11):1722-1730.
Santika T, Ancrenaz M, Wilson KA, Spehar S, Abram N, Banes GL, Campbell-Smith G, Curran L, d'Arcy L, Delgado RA, Erman A, Goossens B, Hartanto H, Houghton M, Husson SJ, Kühl HS, Lackman I, Leiman A, Llano Sanchez K, Makinuddin N, Marshall AJ, Meididit A, Mengersen K, Musnanda, Nardiyono, Nurcahyo A, Odom K, Panda A, Prasetyo D, Purnomo, Rafiastanto A, Raharjo S, Ratnasari D, Russon AE, Santana AH, Santoso E, Sapari I, Sihite J, Suyoko A, Tjiu A, Utami-Atmoko SS, van Schaik CP, Voigt M, Wells J, Wich SA, Willems EP, Meijaard E. First integrative trend analysis for a great ape species in Borneo. Sci Rep. 2017 Jul 7;7(1):4839.
Dönertaş HM, İzgi H, Kamacıoğlu A, He Z, Khaitovich P, Somel M. Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity. Sci Rep. 2017 Jul 19;7(1):5894.
Yu Q, He Z. Comprehensive investigation of temporal and autism-associated cell type composition-dependent and independent gene expression changes in human brains. Sci Rep. 2017;7:4121.
He Z, Han D, Efimova O, Guijarro P, Yu Q, Oleksiak A, Jiang S, Anokhin K, Velichkovsky B, Grünewald S, Khaitovich P. Comprehensive transcriptome analysis of neocortical layers in humans, chimpanzees and macaques. Nat Neurosci. 2017 doi:10.1038/nn.4548
Li Q, Bozek K, Xu C, Guo Y, Sun J, Pääbo S, Sherwood CC, Hof PR, Ely JJ, Li Y, Willmitzer L, Giavalisco P, Khaitovich P. Changes in lipidome composition during brain development in humans, chimpanzees, and macaque monkeys. Mol Biol Evol. 2017 Jan 31
Bozek K, Khrameeva EE, Reznick J, Omerbašić D, Bennett NC, Lewin GR, Azpurua J, Gorbunova V, Seluanov A, Regnard P, Wanert F, Marchal J, Pifferi F, Aujard F, Liu Z, Shi P, Pääbo S, Schroeder F, Willmitzer L, Giavalisco P, Khaitovich P. Lipidome determinants of maximal lifespan in mammals. Sci Rep. 2017 Dec;7(1):5
2016:
Banes GL, Galdikas BMF. Effective Characterisation of the Complete Orang-Utan Mitochondrial DNA Control Region, in the Face of Persistent Focus in Many Taxa on Shorter Hypervariable Regions. PLoS ONE 2016 11(12): e0168715.
Liu X, Han D, Somel M, Jiang X, Hu H, Guijarro P, Zhang N, Mitchell A, Halene T, Ely JJ, Sherwood CC, Hof PR, Qiu Z, Pääbo S, Akbarian S, Khaitovich P. Disruption of an evolutionarily novel synaptic expression pattern in autism. PLoS Biol. 2016 Sep 29;14(9):e1002558.
Kao CY, He Z, Henes K, Asara JM, Webhofer C, Filiou MD, Khaitovich P, Wotjak CT, Turck CW. Fluoxetine Treatment Rescues Energy Metabolism Pathway Alterations in a Posttraumatic Stress Disorder Mouse Model. Mol Neuropsychiatry. 2016 May;2(1):46-59.
Li Q, Guo S, Jiang X, Bryk J, Naumann R, Enard W, Tomita M, Sugimoto M, Khaitovich P, Pääbo S. Mice carrying a human GLUD2 gene recapitulate aspects of human transcriptome and metabolome development. Proc Natl Acad Sci U S A. 2016 May 10;113(19):5358-63.
Zhang B, Han D, Korostelev Y, Yan Z, Shao N, Khrameeva E, Velichkovsky BM, Chen YP, Gelfand MS, Khaitovich P. Changes in snoRNA and snRNA Abundance in the Human, Chimpanzee, Macaque, and Mouse Brain. Genome Biol Evol. 2016 Mar 23;8(3):840-50.
Kao CY, He Z, Zannas AS, Hahn O, Kühne C, Reichel JM, Binder EB, Wotjak CT, Khaitovich P, Turck CW. Fluoxetine treatment prevents the inflammatory response in a mouse model of posttraumatic stress disorder. J Psychiatr Res. 2016 May;76:74-83.
Banes GL, Galdikas BM, Vigilant L. Reintroduction of confiscated and displaced mammals risks outbreeding and introgression in natural populations, as evidenced by orang-utans of divergent subspecies. Sci Rep. 2016 Feb 25;6:22026.
2015:
Hughes DA, Kircher M, He Z, Guo S, Fairbrother GL, Moreno CS, Khaitovich P, Stoneking M. Evaluating intra- and inter-individual variation in the human placental transcriptome. Genome Biol. 2015 Mar 19;16:54. doi: 10.1186/s13059-015-0627-z.
Wei YN, Hu HY, Xie GC, Fu N, Ning ZB, Zeng R, Khaitovich P. Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging. Genome Biol. 2015 Feb 22;16:41. doi: 10.1186/s13059-015-0608-2.
Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto M, Tomita M, Pääbo S, Sherwood CC, Hof PR, Ely JJ, Li Y, Steinhauser D, Willmitzer L, Giavalisco P, Khaitovich P. Organization and evolution of brain lipidome revealed by large-scale analysis of human, chimpanzee, macaque, and mouse tissues. Neuron. 2015 Feb 18;85(4):695-702. doi: 10.1016/j.neuron.2015.01.003. Epub 2015 Feb 5.
2014:
Su ZD, Sheng QH, Li QR, Chi H, Jiang X, Yan Z, Fu N, He SM, Khaitovich P, Wu JR, Zeng R. De novo identification and quantification of single amino-acid variants in human brain. J Mol Cell Biol. 2014 Oct;6(5):421-33.
Hu HY, He L, Khaitovich P. Deep sequencing reveals a novel class of bidirectional promoters associated with neuronal genes. BMC Genomics. 2014 Jun 10;15:457.
Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto M, Tomita M, Pääbo S, Pieszek R, Sherwood CC, Hof PR, Ely JJ, Steinhauser D, Willmitzer L, Bangsbo J, Hansson O, Call J, Giavalisco P, Khaitovich P. Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. PLoS Biol. 2014 May 27;12(5):e1001871.
He Z, Bammann H, Han D, Xie G, Khaitovich P. Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation. RNA. 2014 May 20
Khrameeva EE, Bozek K, He L, Yan Z, Jiang X, Wei Y, Tang K, Gelfand MS, Prufer K, Kelso J, Paabo S, Giavalisco P, Lachmann M, Khaitovich P. Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. Nat Commun. 2014 Apr 1;5:3584. doi: 10.1038/ncomms4584.
Zhao G, Guo S, Somel M, Khaitovich P. (2014) Evolution of human longevity uncoupled from caloric restriction mechanisms. PLoS One. 2014;9(1):e84117.
2013:
Li Z, Bammann H, Li M, Liang H, Yan Z, Phoebe Chen YP, Zhao M, Khaitovich P. (2013) Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee, and macaque brains. RNA. 2013 Oct 23.
Mazin P, Xiong J, Liu X, Yan Z, Zhang X, Li M, He L, Somel M, Yuan Y, Phoebe Chen YP, Li N, Hu Y, Fu N, Ning Z, Zeng R, Yang H, Chen W, Gelfand M, Khaitovich P. (2013) Widespread splicing changes in human brain development and aging. Mol Syst Biol. 2013 Jan 22;9:633. doi: 10.1038/msb.2012.67.
Somel M, Liu X, Khaitovich P. (2013) Human brain evolution: transcripts, metabolites and their regulators. Nat Rev Neurosci. 2013 Feb;14(2):112-27. doi: 10.1038/nrn3372.
Meunier J, Lemoine F, Soumillon M, Liechti A, Weier M, Guschanski K, Hu H, Khaitovich P, Kaessmann H. (2013) Birth and expression evolution of mammalian microRNA genes. Genome Res. 2013 Jan;23(1):34-45. doi: 10.1101/gr.140269.112.
2012:
Hu HY, He L, Fominykh K, Yan Z, Guo S, Zhang X, Taylor MS, Tang L, Li J, Liu J, Wang W, Yu H, Khaitovich P. (2012) Evolution of the human-specific microRNA miR-941. Nat Commun. 2012 Oct 23;3:1145. doi: 10.1038/ncomms2146.
Han Y, Han D, Yan Z, Boyd-Kirkup JD, Green CD, Khaitovich P, Han JD. (2012) Stress-associated H3K4 methylation accumulates during postnatal development and aging of Rhesus macaque brain. Aging Cell. 2012 Sep 15. doi: 10.1111/acel.12007.
Weng K, Hu H, Xu AG, Khaitovich P, Somel M. (2012) Mechanisms of Dietary Response in Mice and Primates: A Role for EGR1 in Regulating the Reaction to Human-Specific Nutritional Content. PLoS One. 2012;7(8):e43915. Epub 2012 Aug 24.
Yuan Y, Chen YP, Boyd-Kirkup J, Khaitovich P, Somel M. (2012) Accelerated aging-related transcriptome changes in the female prefrontal cortex. Aging Cell. 2012 Jul 11. doi: 10.1111/j.1474-9726.2012.00859.x.
Khaitovich P. (2012) Layer cake: the first bite at gene expression diversity in the human brain. Genome Biol. 13(5):157
Khrameeva EE, Mironov AA, Fedonin GG, Khaitovich P, Gelfand MS. (2012) Spatial proximity and similarity of the epigenetic state of genome domains. PLoS One. 2012;7(4):e33947. Epub 2012 Apr 4
Liu X, Somel M, Tang L, Yan Z, Jiang X, Guo S, Yuan Y, He L, Oleksiak A, Zhang Y, Li N, Hu Y, Chen W, Qiu Z, Pääbo S, Khaitovich P. (2012) Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques. Genome Res, (2012-02-02)
2011:
Somel M, Liu X, Tang L, Yan Z, Hu H, Guo S, Jiang X, Zhang X, Xu G, Xie G, Li N, Hu Y, Chen W, Pääbo S, Khaitovich P. (2011) MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates. PLoS Biol. 9(12): e1001214.
Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert FW, Zeller U, Khaitovich P, Grutzner F, Bergmann S, Nielsen R, Pääbo S, Kaessmann H. (2011) The evolution of gene expression levels in mammalian organs. Nature Oct 19;478(7369):343-8.
Hu HY, Guo S, Jiang X, Yan Z, Fu N, Zhang X, Menzel C, Liang H, Yang H, Zhao M, Zeng R, Chen W, Pääbo S, Khaitovich P. (2011) MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains. PLoS Genetics. 7(10): e1002327.
Yuan Y, Chen YP, Ni S, Xu AG, Tang L, Vingron M, Somel M, Khaitovich P. (2011) Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expresion time series. BMC Bioinformatics. 12(1):347
Jin C, Li J, Green CD, Yu X, Tang X, Han D, Xian B, Wang D, Huang X, Cao X, Yan Z, Hou L, Liu J, Shukeir N, Khaitovich P, Chen C D, Zhang H, Jenuwein T, Han JD. (2011) Histone Demethylase UTX-1 Regulates C. elegans Life Span by Targeting the Insulin/IGF-1 Signaling Pathway. Cell Metabolism. 14(2):161-172.
Yan Z, Hu H, Jiang X, Maierhofer V, Neb E, He L, Hu Y, Hu H, Li N, Chen W and Khaitovich P. (2011) Widespread expression of piRNA-like molecules in somatic tissues. Nucleic Acids Research. May 5.
Fu X, Giavalisco P, Liu X, Catchpole G, Fu N, Ning ZB, Guo S, Yan Z, Somel M, Pääbo S, Zeng R, Willmitzer L, Khaitovich P. (2011) Rapid metabolic evolution in human prefrontal cortex. Proc Natl Acad Sci U S A. Mar 28.
Liu Y, Han D, Han Y, Yan Z, Xie B, Li J, Qiao N, Hu H, Khaitovich P, Gao Y, Han JD. (2011) Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. Nucleic Acids Res 39(4):1408-1418.
2010:
Somel M, Guo S, Fu N, Yan Z, Hu HY, Xu Y, Yuan Y, Ning Z, Hu Y, Menzel C, Hu H, Lachmann M, Zeng R, Chen W, Khaitovich P. (2010) MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. Genome Res 20(9):1207-18.
Liu Y, Hu W, Wang H, Lu M, Shao C, Menzel C, Yan Z, Li Y, Zhao S, Khaitovich P, Liu M, Chen W, Barnes BM, Yan J. Genomic analysis of miRNAs in an extreme mammalian hibernator, the Arctic ground squirrel. Physiol Genomics 42A(1):39-51.
Giger T, Khaitovich P, Somel M, Lorenc A, Lizano E, Harris LW, Ryan MM, Lan M, Wayland MT, Bahn S, Pääbo S. (2010) Evolution of neuronal and endothelial transcriptomes in primates. Genome Biol Evol 12;2:284-92.
Xu AG, He L, Li Z, Xu Y, Li M, Fu X, Yan Z, Yuan Y, Menzel C, Li N, Somel M, Hu H, Chen W, Pääbo S, Khaitovich P. (2010) Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PLoS Comput Biol 1;6:e1000843.
Shao NY, Hu HY, Yan Z, Xu Y, Hu H, Menzel C, Li N, Chen W, Khaitovich P. (2010) Comprehensive survey of human brain microRNA by deep sequencing. BMC Genomics 11:409.
Khaitovich P. (2010) Annotating conserved and novel features of primate transcriptomes using sequencing. Genome Biol 11(7):125.
2009:
Dannemann M, Lorenc A, Hellmann I, Khaitovich P, Lachmann M. (2009) The effects of probe binding affinity differences on gene expression measurements and how to deal with them. Bioinformatics 25(21):2772-9.
Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovich P, Stadler PF. (2009) Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics 25(18):2298-301.
Hu HY, Yan Z, Xu Y, Hu H, Menzel C, Zhou YH, Chen W, Khaitovich P. (2009) Sequence features associated with microRNA strand selection in humans and flies. BMC Genomics 10:413.
Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J. (2009) Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol 5(9):e1000502.
Harris LW, Lockstone HE, Khaitovich P, Weickert CS, Webster MJ, Bahn S. (2009) Gene expression in the prefrontal cortex during adolescence: implications for the onset of schizophrenia. BMC Med Genomics 20;2:28.
Weickert CS, Elashoff M, Richards AB, Sinclair D, Bahn S, Pääbo S, Khaitovich P, Webster MJ. (2009) Transcriptome analysis of male-female differences in prefrontal cortical development. Mol Psychiatry 14(6):558-61.
Fu X, Fu N, Guo S, Yan Z, Xu Y, Hu H, Menzel C, Chen W, Li Y, Zeng R, Khaitovich P. (2009) Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics 10(1):161
Somel M, Franz H, Yan Z, Lorenc A, Guo S, Giger T, Kelso J, Nickel B, Dannemann M, Bahn S, Webster MJ, Weickert CS, Lachmann M, Pääbo S, Khaitovich P. (2009) Transcriptional neoteny in the human brain. Proc Natl Acad Sci U S A 106(14):5743-8.
2008:
Farkas LM, Haffner C, Giger T, Khaitovich P, Nowick K, Birchmeier C, Pääbo S, Huttner WB. (2008) Insulinoma-associated 1 has a panneurogenic role and promotes the generation and expansion of basal progenitors in the developing mouse neocortex. Neuron 9;60(1):40-55
Chaix R, Somel M, Kreil DP, Khaitovich P, Lunter GA. (2008) Evolution of primate gene expression: drift and corrective sweeps? Genetics 180(3):1379-89
Khaitovich P, Lockstone HE, Wayland MT, Tsang TM, Jayatilaka SD, Guo AJ, Zhou J, Somel M, Harris LW, Holmes E, Pääbo S, Bahn S. (2008) Metabolic changes in schizophrenia and human brain evolution. Genome Biol. 9(8):R124.
Bonnefont J, Nikolaev SI, Perrier AL, Guo S, Cartier L, Sorce S, Laforge T, Aubry L, Khaitovich P, Peschanski M, Antonarakis SE, Krause KH. (2008) Evolutionary forces shape the human RFPL1,2,3 genes toward a role in neocortex development. Am J Hum Genet. 83(2):208-18.
Somel M, Creely H, Franz H, Mueller U, Lachmann M, Khaitovich P, Pääbo S. (2008) Human and chimpanzee gene expression differences replicated in mice fed different diets. PLoS ONE 3(1):e1504.
2007:
Khaitovich P. (2007) Brain expression--is it all in our SNPs? Mol Syst Biol. 3:155
Fu, N., Drinnenberg, I., Kelso, J., Wu, J.R., Paabo, S., Zeng, R., and Khaitovich, P. (2007). Comparison of protein and mRNA expression evolution in humans and chimpanzees. PLoS ONE2, e216. [PDF]
Prufer, K., Muetzel, B., Do, H.H., Weiss, G., Khaitovich, P., Rahm, E., Paabo, S., Lachmann, M., and Enard, W. (2007). FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics8, 41. [PDF]
2006:
Somel, M., Khaitovich, P., Bahn, S., Paabo, S., and Lachmann, M. (2006). Gene expression becomes heterogeneous with age. Curr Biol16, R359-360. [PDF]
Khaitovich, P., Tang, K., Franz, H., Kelso, J., Hellmann, I., Enard, W., Lachmann, M., and Paabo, S. (2006). Positive selection on gene expression in the human brain. Curr Biol16, R356-358. [PDF]
Khaitovich, P., Kelso, J., Franz, H., Visagie, J., Giger, T., Joerchel, S., Petzold, E., Green, R.E., Lachmann, M., and Paabo, S. (2006). Functionality of intergenic transcription: an evolutionary comparison. PLoS Genet2, e171. [PDF]
Khaitovich, P., Enard, W., Lachmann, M., and Paabo, S. (2006). Evolution of primate gene expression. Nat Rev Genet7, 693-702. [PDF]
Creely, H., and Khaitovich, P. (2006). Human brain evolution. Prog Brain Res158, 295-309. [PDF]
2005:
Yohn, C.T., Jiang, Z., McGrath, S.D., Hayden, K.E., Khaitovich, P., Johnson, M.E., Eichler, M.Y., McPherson, J.D., Zhao, S., Paabo, S., et al. (2005). Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans. PLoS Biol3, 1-11. [PDF]
Khaitovich, P., Paabo, S., and Weiss, G. (2005). Toward a neutral evolutionary model of gene expression. Genetics170, 929-939. [PDF]
Khaitovich, P., Hellmann, I., Enard, W., Nowick, K., Leinweber, M., Franz, H., Weiss, G., Lachmann, M., and Paabo, S. (2005). Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science309, 1850-1854. [PDF]
Heissig, F., Krause, J., Bryk, J., Khaitovich, P., Enard, W., and Paabo, S. (2005). Functional analysis of human and chimpanzee promoters. Genome Biol6, R57. [PDF]
Fraser, H.B., Khaitovich, P., Plotkin, J.B., Paabo, S., and Eisen, M.B. (2005). Aging and Gene Expression in the Primate Brain. PLoS Biol3, e274. [PDF]
Franz, H., Ullmann, C., Becker, A., Ryan, M., Bahn, S., Arendt, T., Simon, M., Paabo, S., and Khaitovich, P. (2005). Systematic analysis of gene expression in human brains before and after death. Genome Biol6, R112. [PDF]
Cheng, Z., Ventura, M., She, X., Khaitovich, P., Graves, T., Osoegawa, K., Church, D., DeJong, P., Wilson, R.K., Paabo, S., et al. (2005). A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature437, 88-93. [PDF]
