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Philipp Khaitovich

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Mehmet Somel; Xiling Liu; Philipp Khaitovich
Human brain evolution: transcripts, metabolites and their regulators.
Pavel Mazin; Zhibin Ning; Yi-Ping Phoebe Chen; Mehmet Somel; Jieyi Xiong; Zheng Yan; Hongyi Yang; Yuan Yuan; Rong Zeng; Xiaoyu Zhang; Wei Chen; Ning Fu; Mikhail Gelfand; Liu He; Yuhui Hu; Mingshuang Li; Na Li; Xiling Liu; Philipp Khaitovich
Widespread splicing changes in human brain development and aging.
Julien Meunier; Magali Soumillon; Manuela Weier; Katerina Guschanski; Haiyang Hu; Philipp Khaitovich; Frédéric Lemoine; Angélica Liechti; Henrik Kaessmann
Birth and expression evolution of mammalian microRNA genes.

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All Publications

2013: Mehmet Somel; Xiling Liu; Philipp Khaitovich
Human brain evolution: transcripts, metabolites and their regulators.
Nature reviews. Neuroscience 2013;14(2):112-27.
2013: Pavel Mazin; Zhibin Ning; Yi-Ping Phoebe Chen; Mehmet Somel; Jieyi Xiong; Zheng Yan; Hongyi Yang; Yuan Yuan; Rong Zeng; Xiaoyu Zhang; Wei Chen; Ning Fu; Mikhail Gelfand; Liu He; Yuhui Hu; Mingshuang Li; Na Li; Xiling Liu; Philipp Khaitovich
Widespread splicing changes in human brain development and aging.
Molecular systems biology 2013;9():633.
2013: Julien Meunier; Magali Soumillon; Manuela Weier; Katerina Guschanski; Haiyang Hu; Philipp Khaitovich; Frédéric Lemoine; Angélica Liechti; Henrik Kaessmann
Birth and expression evolution of mammalian microRNA genes.
Genome research 2013;23(1):34-45.
2012: Yixing Han; Philipp Khaitovich; Zheng Yan; Jerome D Boyd-Kirkup; Christopher D Green; Dali Han; Jing-Dong J Han
Stress-associated H3K4 methylation accumulates during postnatal development and aging of rhesus macaque brain.
Aging cell 2012;11(6):1055-64.
2012: Yuan Yuan; Jerome Boyd-Kirkup; Yi-Ping Phoebe Chen; Philipp Khaitovich; Mehmet Somel
Accelerated aging-related transcriptome changes in the female prefrontal cortex.
Aging cell 2012;11(5):894-901.
2012: Xiling Liu; Anna Oleksiak; Svante Pääbo; Zilong Qiu; Mehmet Somel; Lin Tang; Zheng Yan; Yuan Yuan; Yan Zhang; Wei Chen; Song Guo; Liu He; Yuhui Hu; Xi Jiang; Na Li; Philipp Khaitovich
Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques.
Genome research 2012;22(4):611-22.
2012: Hai Yang Hu; Kseniya Fominykh; Song Guo; Liu He; Jie Li; Jianmei Liu; Lin Tang; Martin S Taylor; Wen Wang; Zheng Yan; Haijing Yu; Xiaoyu Zhang; Philipp Khaitovich
Evolution of the human-specific microRNA miR-941.
Nature communications 2012;3():1145.
2012: Kai Weng; Augix Guohua Xu; Haiyang Hu; Philipp Khaitovich; Mehmet Somel
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.
2012: Philipp Khaitovich
Layer cake: the first bite at gene expression diversity in the human brain.
Genome biology 2012;13(5):157.
2012: Ekaterina E Khrameeva; Andrey A Mironov; Gennady G Fedonin; Philipp Khaitovich; Mikhail S Gelfand
Spatial proximity and similarity of the epigenetic state of genome domains.
PloS one 2012;7(4):e33947.
2011: David Brawand; Gábor Csárdi; Frank Grützner; Patrick Harrigan; Philippe Julien; Frank W Albert; Ayinuer Aximu-Petri; Sven Bergmann; Philipp Khaitovich; Martin Kircher; Angélica Liechti; Anamaria Necsulea; Rasmus Nielsen; Svante Pääbo; Magali Soumillon; Manuela Weier; Ulrich Zeller; Henrik Kaessmann
The evolution of gene expression levels in mammalian organs.
Nature 2011;478(7369):343-8.
2011: Hai Yang Hu; Wei Chen; Ning Fu; Song Guo; Hongyu Liang; Corinna Menzel; Svante Pääbo; Jiang Xi; Zheng Yan; Hongyi Yang; Rong Zeng; Xiaoyu Zhang; Min Zhao; Philipp Khaitovich
MicroRNA expression and regulation in human, chimpanzee, and macaque brains.
PLoS genetics 2011;7(10):e1002327.
2011: Chunyu Jin; Philipp Khaitovich; Jing Li; Jiancheng Liu; Nicholas Shukeir; Xia Tang; Dan Wang; Bo Xian; Zheng Yan; Xiaoming Yu; Hong Zhang; Xiongwen Cao; Charlie D Chen; Christopher D Green; Dali Han; Lei Hou; Xinxin Huang; Thomas Jenuwein; Jing-Dong J Han
Histone demethylase UTX-1 regulates C. elegans life span by targeting the insulin/IGF-1 signaling pathway.
Cell metabolism 2011;14(2):161-72.
2011: Zheng Yan; Na Li; Vera Maierhofer; Elena Neb; Wei Chen; Liu He; Hao Hu; Hai Yang Hu; Yuhui Hu; Xi Jiang; Philipp Khaitovich
Widespread expression of piRNA-like molecules in somatic tissues.
Nucleic acids research 2011;39(15):6596-607.
2011: Xing Fu; Patrick Giavalisco; Xiling Liu; Gareth Catchpole; Ning Fu; Zhi-Bin Ning; Song Guo; Zheng Yan; Mehmet Somel; Svante Pääbo; Rong Zeng; Lothar Willmitzer; Philipp Khaitovich
Rapid metabolic evolution in human prefrontal cortex.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(15):6181-6.
2011: Yi Liu; Dali Han; Yixing Han; Zheng Yan; Bin Xie; Jing Li; Nan Qiao; Haiyang Hu; Philipp Khaitovich; Yuan Gao; Jing-Dong J Han
Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq.
Nucleic acids research 2011;39(4):1408-18.
2011: Yuan Yuan; Yi-Ping Phoebe Chen; Shengyu Ni; Mehmet Somel; Lin Tang; Martin Vingron; Augix Guohua Xu; Philipp Khaitovich
Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series.
BMC bioinformatics 2011;12():347.
2010: Mehmet Somel; Song Guo; Ning Fu; Zheng Yan; Hai Yang Hu; Ying Xu; Yuan Yuan; Zhibin Ning; Yuhui Hu; Corinna Menzel; Hao Hu; Michael Lachmann; Rong Zeng; Wei Chen; Philipp Khaitovich
MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain.
Genome research 2010;20(9):1207-18.
2010: Yuting Liu; Wenchao Hu; Haifang Wang; Minghua Lu; Chunxuan Shao; Corinna Menzel; Zheng Yan; Ying Li; Sen Zhao; Philipp Khaitovich; Mofang Liu; Wei Chen; Brian Barnes; Jun Yan
Genomic analysis of miRNAs in an extreme mammalian hibernator, the Arctic ground squirrel.
Physiological genomics 2010;42A(1):39-51.
2010: Thomas Giger; Philipp Khaitovich; Mehmet Somel; Anna Lorenc; Esther Lizano; Laura W Harris; Margaret M Ryan; Martin Lan; Matthew T Wayland; Sabine Bahn; Svante Pääbo
Evolution of neuronal and endothelial transcriptomes in primates.
Genome biology and evolution 2010;2():284-92.
2010: Philipp Khaitovich
Annotating conserved and novel features of primate transcriptomes using sequencing.
Genome biology 2010;11(7):125.
2010: Augix Guohua Xu; Liu He; Zhongshan Li; Ying Xu; Mingfeng Li; Xing Fu; Zheng Yan; Yuan Yuan; Corinna Menzel; Na Li; Mehmet Somel; Hao Hu; Wei Chen; Svante Pääbo; Philipp Khaitovich
Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq.
PLoS computational biology 2010;6():e1000843.
2010: Ning-Yi Shao; Hai Yang Hu; Zheng Yan; Ying Xu; Hao Hu; Corinna Menzel; Na Li; Wei Chen; Philipp Khaitovich
Comprehensive survey of human brain microRNA by deep sequencing.
BMC genomics 2010;11():409.
2009: Michael Dannemann; Anna Lorenc; Ines Hellmann; Philipp Khaitovich; Michael Lachmann
The effects of probe binding affinity differences on gene expression measurements and how to deal with them.
Bioinformatics (Oxford, England) 2009;25(21):2772-9.
2009: Mehmet Somel; Henriette Franz; Zheng Yan; Anna Lorenc; Song Guo; Thomas Giger; Janet Kelso; Birgit Nickel; Michael Dannemann; Sabine Bahn; Maree Webster; Cynthia S Weickert; Michael Lachmann; Svante Pääbo; Philipp Khaitovich
Transcriptional neoteny in the human brain.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(14):5743-8.
2009: Hai Yang Hu; Zheng Yan; Ying Xu; Hao Hu; Corinna Menzel; Yan Hong Zhou; Wei Chen; Philipp Khaitovich
Sequence features associated with microRNA strand selection in humans and flies.
BMC genomics 2009;10():413.
2009: Xing Fu; Ning Fu; Song Guo; Zheng Yan; Ying Xu; Hao Hu; Corinna Menzel; Wei Chen; Yixue Li; Rong Zeng; Philipp Khaitovich
Estimating accuracy of RNA-Seq and microarrays with proteomics.
BMC genomics 2009;10():161.
2008: Lilla M Farkas; Christiane Haffner; Thomas Giger; Philipp Khaitovich; Katja Nowick; Carmen Birchmeier; Svante Pääbo; Wieland B Huttner
Insulinoma-associated 1 has a panneurogenic role and promotes the generation and expansion of basal progenitors in the developing mouse neocortex.
Neuron 2008;60(1):40-55.
2008: Jérôme Bonnefont; Sergey I Nikolaev; Anselme L Perrier; Song Guo; Laetitia Cartier; Silvia Sorce; Térèse Laforge; Laetitia Aubry; Philipp Khaitovich; Marc Peschanski; Stylianos E Antonarakis; Karl-Heinz Krause
Evolutionary forces shape the human RFPL1,2,3 genes toward a role in neocortex development.
American journal of human genetics 2008;83(2):208-18.
2008: Philipp Khaitovich; Helen E Lockstone; Matthew Wayland; Tsz M Tsang; Samantha D Jayatilaka; Arfu J Guo; Jie Zhou; Mehmet Somel; Laura W Harris; Elaine Holmes; Svante Pääbo; Sabine Bahn
Metabolic changes in schizophrenia and human brain evolution.
Genome biology 2008;9(8):R124.
2008: Mehmet Somel; Hilliary Creely; Henriette Franz; Uwe Mueller; Michael Lachmann; Philipp Khaitovich; Svante Pääbo
Human and chimpanzee gene expression differences replicated in mice fed different diets.
PloS one 2008;3(1):e1504.
2007: Philipp Khaitovich
Brain expression--is it all in our SNPs?
Molecular systems biology 2007;3():155.
2007: Ning Fu; Ines Drinnenberg; Janet Kelso; Jia-Rui Wu; Svante Pääbo; Rong Zeng; Philipp Khaitovich
Comparison of protein and mRNA expression evolution in humans and chimpanzees.
PloS one 2007;2(2):e216.
2007: Kay Prüfer; Bjoern Muetzel; Hong-Hai Do; Gunter Weiss; Philipp Khaitovich; Erhard Rahm; Svante Pääbo; Michael Lachmann; Wolfgang Enard
FUNC: a package for detecting significant associations between gene sets and ontological annotations.
BMC bioinformatics 2007;8():41.
2006: Philipp Khaitovich; Janet Kelso; Henriette Franz; Johann Visagie; Thomas Giger; Sabrina Joerchel; Ekkehard Petzold; Richard E Green; Michael Lachmann; Svante Pääbo
Functionality of intergenic transcription: an evolutionary comparison.
PLoS genetics 2006;2(10):e171.
2006: Philipp Khaitovich; Wolfgang Enard; Michael Lachmann; Svante Pääbo
Evolution of primate gene expression.
Nature reviews. Genetics 2006;7(9):693-702.
2006: Mehmet Somel; Philipp Khaitovich; Sabine Bahn; Svante Pääbo; Michael Lachmann
Gene expression becomes heterogeneous with age.
Current biology : CB 2006;16(10):R359-60.
2006: Philipp Khaitovich; Kun Tang; Henriette Franz; Janet Kelso; Ines Hellmann; Wolfgang Enard; Michael Lachmann; Svante Pääbo
Positive selection on gene expression in the human brain.
Current biology : CB 2006;16(10):R356-8.
2006: Hilliary Creely; Philipp Khaitovich
Human brain evolution.
Progress in brain research 2006;158():295-309.
2005: Philipp Khaitovich; Ines Hellmann; Wolfgang Enard; Katja Nowick; Marcus Leinweber; Henriette Franz; Gunter Weiss; Michael Lachmann; Svante Pääbo
Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees.
Science (New York, N.Y.) 2005;309(5742):1850-4.
2005: Ze Cheng; ventura Mario; Xinwei She; Philipp Khaitovich; Tina Graves; Kazutoyo Osoegawa; Deanna Church; Pieter DeJong; Richard K Wilson; Svante Pääbo; Mariano Rocchi; Evan E Eichler
A genome-wide comparison of recent chimpanzee and human segmental duplications.
Nature 2005;437(7055):88-93.
2005: Hunter B Fraser; Philipp Khaitovich; Joshua B Plotkin; Svante Pääbo; Michael B Eisen
Aging and gene expression in the primate brain.
PLoS biology 2005;3(9):e274.
2005: Philipp Khaitovich; Svante Pääbo; Gunter Weiss
Toward a neutral evolutionary model of gene expression.
Genetics 2005;170(2):929-39.
2005: Chris T Yohn; Zhaoshi Jiang; Sean D McGrath; Karen E Hayden; Philipp Khaitovich; Matthew E Johnson; Marla Y Eichler; John D McPherson; Shaying Zhao; Svante Pääbo; Evan E Eichler
Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans.
PLoS biology 2005;3(4):e110.
2005: Henriette Franz; Claudia Ullmann; Albert Becker; Margaret Ryan; Sabine Bahn; Thomas Arendt; Matthias Simon; Svante Pääbo; Philipp Khaitovich
Systematic analysis of gene expression in human brains before and after death.
Genome biology 2005;6(13):R112.
2005: Florian Heissig; Johannes Krause; Jaroslaw Bryk; Philipp Khaitovich; Wolfgang Enard; Svante Pääbo
Functional analysis of human and chimpanzee promoters.
Genome biology 2005;6(7):R57.
2004: Philipp Khaitovich; Bjoern Muetzel; Xinwei She; Michael Lachmann; Ines Hellmann; Janko Dietzsch; Stephan Steigele; Hong-Hai Do; Gunter Weiss; Wolfgang Enard; Florian Heissig; Thomas Arendt; Kay Nieselt-Struwe; Evan E Eichler; Svante Pääbo
Regional patterns of gene expression in human and chimpanzee brains.
Genome research 2004;14(8):1462-73.
2004: Philipp Khaitovich; Gunter Weiss; Michael Lachmann; Ines Hellmann; Wolfgang Enard; Bjoern Muetzel; Ute Wirkner; Wilhelm Ansorge; Svante Pääbo
A neutral model of transcriptome evolution.
PLoS biology 2004;2(5):E132.
2002: Wolfgang Enard; Philipp Khaitovich; Joachim Klose; Sebastian K Zoellner ; Florian Heissig; Patrick Giavalisco; Kay Nieselt-Struwe; Elaine Muchmore; Ajit Varki; Rivka Ravid; Gaby M Doxiadis; Ronald E Bontrop; Svante Pääbo
Intra- and interspecific variation in primate gene expression patterns.
Science (New York, N.Y.) 2002;296(5566):340-3.