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Items: 1 to 50 of 86

1.

Lipidome evolution in mammalian tissues.

Khrameeva E, Kurochkin I, Bozek K, Giavalisco P, Khaitovich P.

Mol Biol Evol. 2018 May 11. doi: 10.1093/molbev/msy097. [Epub ahead of print]

PMID:
29762743
2.

Recently Evolved Tumor Suppressor Transcript TP73-AS1 Functions as Sponge of Human-Specific miR-941.

Hu H, Liu JM, Hu Z, Jiang X, Yang X, Li J, Zhang Y, Yu H, Khaitovich P.

Mol Biol Evol. 2018 May 1;35(5):1063-1077. doi: 10.1093/molbev/msy022.

3.

Predominant patterns of splicing evolution on human, chimpanzee and macaque evolutionary lineages.

Xiong J, Jiang X, Ditsiou A, Gao Y, Sun J, Lowenstein ED, Huang S, Khaitovich P.

Hum Mol Genet. 2018 Apr 15;27(8):1474-1485. doi: 10.1093/hmg/ddy058.

PMID:
29452398
4.

Conservation, evolution, and regulation of splicing during prefrontal cortex development in humans, chimpanzees, and macaques.

Mazin PV, Jiang X, Fu N, Han D, Guo M, Gelfand MS, Khaitovich P.

RNA. 2018 Apr;24(4):585-596. doi: 10.1261/rna.064931.117. Epub 2018 Jan 23.

PMID:
29363555
5.

Constrained vertebrate evolution by pleiotropic genes.

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.

Nat Ecol Evol. 2017 Nov;1(11):1722-1730. doi: 10.1038/s41559-017-0318-0. Epub 2017 Sep 25.

PMID:
28963548
6.

Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity.

Dönertaş HM, İzgi H, Kamacıoğlu A, He Z, Khaitovich P, Somel M.

Sci Rep. 2017 Jul 19;7(1):5894. doi: 10.1038/s41598-017-05927-4.

7.

Comprehensive transcriptome analysis of neocortical layers in humans, chimpanzees and macaques.

He Z, Han D, Efimova O, Guijarro P, Yu Q, Oleksiak A, Jiang S, Anokhin K, Velichkovsky B, Grünewald S, Khaitovich P.

Nat Neurosci. 2017 Jun;20(6):886-895. doi: 10.1038/nn.4548. Epub 2017 Apr 17.

PMID:
28414332
8.

Changes in Lipidome Composition during Brain Development in Humans, Chimpanzees, and Macaque Monkeys.

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.

Mol Biol Evol. 2017 May 1;34(5):1155-1166. doi: 10.1093/molbev/msx065.

9.

Lipidome determinants of maximal lifespan in mammals.

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.

Sci Rep. 2017 Jan 31;7(1):5. doi: 10.1038/s41598-017-00037-7.

10.

Disruption of an Evolutionarily Novel Synaptic Expression Pattern in Autism.

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.

PLoS Biol. 2016 Sep 29;14(9):e1002558. doi: 10.1371/journal.pbio.1002558. eCollection 2016 Sep.

11.

Fluoxetine Treatment Rescues Energy Metabolism Pathway Alterations in a Posttraumatic Stress Disorder Mouse Model.

Kao CY, He Z, Henes K, Asara JM, Webhofer C, Filiou MD, Khaitovich P, Wotjak CT, Turck CW.

Mol Neuropsychiatry. 2016 May;2(1):46-59. doi: 10.1159/000445377. Epub 2016 Apr 30.

12.

Mice carrying a human GLUD2 gene recapitulate aspects of human transcriptome and metabolome development.

Li Q, Guo S, Jiang X, Bryk J, Naumann R, Enard W, Tomita M, Sugimoto M, Khaitovich P, Pääbo S.

Proc Natl Acad Sci U S A. 2016 May 10;113(19):5358-63. doi: 10.1073/pnas.1519261113. Epub 2016 Apr 26.

13.

Changes in snoRNA and snRNA Abundance in the Human, Chimpanzee, Macaque, and Mouse Brain.

Zhang B, Han D, Korostelev Y, Yan Z, Shao N, Khrameeva E, Velichkovsky BM, Chen YP, Gelfand MS, Khaitovich P.

Genome Biol Evol. 2016 Mar 23;8(3):840-50. doi: 10.1093/gbe/evw038.

14.

Fluoxetine treatment prevents the inflammatory response in a mouse model of posttraumatic stress disorder.

Kao CY, He Z, Zannas AS, Hahn O, Kühne C, Reichel JM, Binder EB, Wotjak CT, Khaitovich P, Turck CW.

J Psychiatr Res. 2016 May;76:74-83. doi: 10.1016/j.jpsychires.2016.02.003. Epub 2016 Feb 8.

PMID:
26897419
15.

Evaluating intra- and inter-individual variation in the human placental transcriptome.

Hughes DA, Kircher M, He Z, Guo S, Fairbrother GL, Moreno CS, Khaitovich P, Stoneking M.

Genome Biol. 2015 Mar 19;16:54. doi: 10.1186/s13059-015-0627-z.

16.

Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging.

Wei YN, Hu HY, Xie GC, Fu N, Ning ZB, Zeng R, Khaitovich P.

Genome Biol. 2015 Feb 22;16:41. doi: 10.1186/s13059-015-0608-2.

17.

Organization and evolution of brain lipidome revealed by large-scale analysis of human, chimpanzee, macaque, and mouse tissues.

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.

Neuron. 2015 Feb 18;85(4):695-702. doi: 10.1016/j.neuron.2015.01.003. Epub 2015 Feb 5.

18.

De novo identification and quantification of single amino-acid variants in human brain.

Su ZD, Sheng QH, Li QR, Chi H, Jiang X, Yan Z, Fu N, He SM, Khaitovich P, Wu JR, Zeng R.

J Mol Cell Biol. 2014 Oct;6(5):421-33. doi: 10.1093/jmcb/mju031. Epub 2014 Jul 9.

PMID:
25007923
19.

Deep sequencing reveals a novel class of bidirectional promoters associated with neuronal genes.

Hu HY, He L, Khaitovich P.

BMC Genomics. 2014 Jun 10;15:457. doi: 10.1186/1471-2164-15-457.

20.

Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness.

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.

PLoS Biol. 2014 May 27;12(5):e1001871. doi: 10.1371/journal.pbio.1001871. eCollection 2014 May.

21.

Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation.

He Z, Bammann H, Han D, Xie G, Khaitovich P.

RNA. 2014 Jul;20(7):1103-11. doi: 10.1261/rna.043075.113. Epub 2014 May 20.

22.

Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans.

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.

Nat Commun. 2014 Apr 1;5:3584. doi: 10.1038/ncomms4584.

23.

Evolution of human longevity uncoupled from caloric restriction mechanisms.

Zhao G, Guo S, Somel M, Khaitovich P.

PLoS One. 2014 Jan 6;9(1):e84117. doi: 10.1371/journal.pone.0084117. eCollection 2014.

24.

Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee, and macaque brains.

Li Z, Bammann H, Li M, Liang H, Yan Z, Phoebe Chen YP, Zhao M, Khaitovich P.

RNA. 2013 Dec;19(12):1693-702. doi: 10.1261/rna.039206.113. Epub 2013 Oct 23.

25.

Widespread splicing changes in human brain development and aging.

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.

Mol Syst Biol. 2013;9:633. doi: 10.1038/msb.2012.67.

26.

Human brain evolution: transcripts, metabolites and their regulators.

Somel M, Liu X, Khaitovich P.

Nat Rev Neurosci. 2013 Feb;14(2):112-27. doi: 10.1038/nrn3372. Epub 2013 Jan 17. Review.

PMID:
23324662
27.

Evolution of the human-specific microRNA miR-941.

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.

Nat Commun. 2012;3:1145. doi: 10.1038/ncomms2146.

28.

Birth and expression evolution of mammalian microRNA genes.

Meunier J, Lemoine F, Soumillon M, Liechti A, Weier M, Guschanski K, Hu H, Khaitovich P, Kaessmann H.

Genome Res. 2013 Jan;23(1):34-45. doi: 10.1101/gr.140269.112. Epub 2012 Oct 3.

29.

Stress-associated H3K4 methylation accumulates during postnatal development and aging of rhesus macaque brain.

Han Y, Han D, Yan Z, Boyd-Kirkup JD, Green CD, Khaitovich P, Han JD.

Aging Cell. 2012 Dec;11(6):1055-64. doi: 10.1111/acel.12007. Epub 2012 Oct 18.

30.

Mechanisms of dietary response in mice and primates: a role for EGR1 in regulating the reaction to human-specific nutritional content.

Weng K, Hu H, Xu AG, Khaitovich P, Somel M.

PLoS One. 2012;7(8):e43915. doi: 10.1371/journal.pone.0043915. Epub 2012 Aug 24.

31.

Accelerated aging-related transcriptome changes in the female prefrontal cortex.

Yuan Y, Chen YP, Boyd-Kirkup J, Khaitovich P, Somel M.

Aging Cell. 2012 Oct;11(5):894-901. doi: 10.1111/j.1474-9726.2012.00859.x. Epub 2012 Aug 2.

32.

Layer cake: the first bite at gene expression diversity in the human brain.

Khaitovich P.

Genome Biol. 2012 May 22;13(5):157. doi: 10.1186/gb-2012-13-5-157.

33.

Spatial proximity and similarity of the epigenetic state of genome domains.

Khrameeva EE, Mironov AA, Fedonin GG, Khaitovich P, Gelfand MS.

PLoS One. 2012;7(4):e33947. doi: 10.1371/journal.pone.0033947. Epub 2012 Apr 4.

34.

Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques.

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.

Genome Res. 2012 Apr;22(4):611-22. doi: 10.1101/gr.127324.111. Epub 2012 Feb 2.

35.

MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates.

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.

PLoS Biol. 2011 Dec;9(12):e1001214. doi: 10.1371/journal.pbio.1001214. Epub 2011 Dec 6.

36.

MicroRNA expression and regulation in human, chimpanzee, and macaque brains.

Hu HY, Guo S, Xi J, Yan Z, Fu N, Zhang X, Menzel C, Liang H, Yang H, Zhao M, Zeng R, Chen W, Pääbo S, Khaitovich P.

PLoS Genet. 2011 Oct;7(10):e1002327. doi: 10.1371/journal.pgen.1002327. Epub 2011 Oct 13.

37.

The evolution of gene expression levels in mammalian organs.

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, Grützner F, Bergmann S, Nielsen R, Pääbo S, Kaessmann H.

Nature. 2011 Oct 19;478(7369):343-8. doi: 10.1038/nature10532.

PMID:
22012392
38.

Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series.

Yuan Y, Chen YP, Ni S, Xu AG, Tang L, Vingron M, Somel M, Khaitovich P.

BMC Bioinformatics. 2011 Aug 18;12:347. doi: 10.1186/1471-2105-12-347.

39.

Histone demethylase UTX-1 regulates C. elegans life span by targeting the insulin/IGF-1 signaling pathway.

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 CD, Zhang H, Jenuwein T, Han JD.

Cell Metab. 2011 Aug 3;14(2):161-72. doi: 10.1016/j.cmet.2011.07.001.

40.

Widespread expression of piRNA-like molecules in somatic tissues.

Yan Z, Hu HY, Jiang X, Maierhofer V, Neb E, He L, Hu Y, Hu H, Li N, Chen W, Khaitovich P.

Nucleic Acids Res. 2011 Aug;39(15):6596-607. doi: 10.1093/nar/gkr298. Epub 2011 May 5.

41.

Rapid metabolic evolution in human prefrontal cortex.

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.

Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6181-6. doi: 10.1073/pnas.1019164108. Epub 2011 Mar 28.

42.

Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq.

Liu Y, Han D, Han Y, Yan Z, Xie B, Li J, Qiao N, Hu H, Khaitovich P, Gao Y, Han JD.

Nucleic Acids Res. 2011 Mar;39(4):1408-18. doi: 10.1093/nar/gkq956. Epub 2010 Oct 14.

43.

MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain.

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.

Genome Res. 2010 Sep;20(9):1207-18. doi: 10.1101/gr.106849.110. Epub 2010 Jul 20.

44.

Evolution of neuronal and endothelial transcriptomes in primates.

Giger T, Khaitovich P, Somel M, Lorenc A, Lizano E, Harris LW, Ryan MM, Lan M, Wayland MT, Bahn S, Pääbo S.

Genome Biol Evol. 2010 Jul 12;2:284-92. doi: 10.1093/gbe/evq018.

45.

Annotating conserved and novel features of primate transcriptomes using sequencing.

Khaitovich P.

Genome Biol. 2010;11(7):125. doi: 10.1186/gb-2010-11-7-125. Epub 2010 Jul 23.

46.

Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq.

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.

PLoS Comput Biol. 2010 Jul 1;6:e1000843. doi: 10.1371/journal.pcbi.1000843.

47.

Comprehensive survey of human brain microRNA by deep sequencing.

Shao NY, Hu HY, Yan Z, Xu Y, Hu H, Menzel C, Li N, Chen W, Khaitovich P.

BMC Genomics. 2010 Jun 30;11:409. doi: 10.1186/1471-2164-11-409.

48.

Genomic analysis of miRNAs in an extreme mammalian hibernator, the Arctic ground squirrel.

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.

Physiol Genomics. 2010 Sep;42A(1):39-51. doi: 10.1152/physiolgenomics.00054.2010. Epub 2010 May 4.

PMID:
20442247
49.

Fast mapping of short sequences with mismatches, insertions and deletions using index structures.

Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J.

PLoS Comput Biol. 2009 Sep;5(9):e1000502. doi: 10.1371/journal.pcbi.1000502. Epub 2009 Sep 11.

50.

Sequence features associated with microRNA strand selection in humans and flies.

Hu HY, Yan Z, Xu Y, Hu H, Menzel C, Zhou YH, Chen W, Khaitovich P.

BMC Genomics. 2009 Sep 4;10:413. doi: 10.1186/1471-2164-10-413.

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