Philipp Khaitovich

Summary

Affiliation: Max Planck Institute for Evolutionary Anthropology
Country: Germany

Publications

  1. ncbi request reprint Intra- and interspecific variation in primate gene expression patterns
    Wolfgang Enard
    Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D 04103 Leipzig, Germany
    Science 296:340-3. 2002
  2. pmc Toward a neutral evolutionary model of gene expression
    Philipp Khaitovich
    Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
    Genetics 170:929-39. 2005
  3. ncbi request reprint A genome-wide comparison of recent chimpanzee and human segmental duplications
    Ze Cheng
    Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington 98195, USA
    Nature 437:88-93. 2005
  4. ncbi request reprint Human brain evolution
    Hilliary Creely
    Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, D 04103 Leipzig, Germany
    Prog Brain Res 158:295-309. 2006
  5. pmc Human and chimpanzee gene expression differences replicated in mice fed different diets
    Mehmet Somel
    Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 3:e1504. 2008
  6. pmc Systematic analysis of gene expression in human brains before and after death
    Henriette Franz
    Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, D 04103 Leipzig, Germany
    Genome Biol 6:R112. 2005
  7. pmc Layer cake: the first bite at gene expression diversity in the human brain
    Philipp Khaitovich
    CAS MPG Partner Institute for Computational Biology, Yue Yang Road 320, Shanghai, 200031, China
    Genome Biol 13:157. 2012
  8. pmc Gene expression in the prefrontal cortex during adolescence: implications for the onset of schizophrenia
    Laura W Harris
    Institute of Biotechnology, University of Cambridge, Cambridge, UK
    BMC Med Genomics 2:28. 2009
  9. pmc Metabolic changes in schizophrenia and human brain evolution
    Philipp Khaitovich
    Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Yue Yang Road, Shanghai, 200031, PR China
    Genome Biol 9:R124. 2008
  10. pmc Annotating conserved and novel features of primate transcriptomes using sequencing
    Philipp Khaitovich
    Partner Institute for Computational Biology, Chinese Academy of Sciences, 320 Yue Yang Road, 200031 Shanghai, China
    Genome Biol 11:125. 2010

Collaborators

Detail Information

Publications50

  1. ncbi request reprint Intra- and interspecific variation in primate gene expression patterns
    Wolfgang Enard
    Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D 04103 Leipzig, Germany
    Science 296:340-3. 2002
    ..We identified species-specific gene expression patterns indicating that changes in protein and gene expression have been particularly pronounced in the human brain...
  2. pmc Toward a neutral evolutionary model of gene expression
    Philipp Khaitovich
    Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
    Genetics 170:929-39. 2005
    ..We discuss the latter result with respect to a neutral model of transcriptome evolution and show that a small number of genes expressed in brain can account for the observed data...
  3. ncbi request reprint A genome-wide comparison of recent chimpanzee and human segmental duplications
    Ze Cheng
    Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington 98195, USA
    Nature 437:88-93. 2005
    ..Nevertheless, base per base, large segmental duplication events have had a greater impact (2.7%) in altering the genomic landscape of these two species than single-base-pair substitution (1.2%)...
  4. ncbi request reprint Human brain evolution
    Hilliary Creely
    Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, D 04103 Leipzig, Germany
    Prog Brain Res 158:295-309. 2006
  5. pmc Human and chimpanzee gene expression differences replicated in mice fed different diets
    Mehmet Somel
    Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 3:e1504. 2008
    ..Our results suggest that the mouse can be used to study at least some aspects of human-specific traits...
  6. pmc Systematic analysis of gene expression in human brains before and after death
    Henriette Franz
    Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, D 04103 Leipzig, Germany
    Genome Biol 6:R112. 2005
    ..The vast majority of human samples available for research are obtained from deceased individuals. This raises questions about how well gene expression patterns in such samples reflect those of living individuals...
  7. pmc Layer cake: the first bite at gene expression diversity in the human brain
    Philipp Khaitovich
    CAS MPG Partner Institute for Computational Biology, Yue Yang Road 320, Shanghai, 200031, China
    Genome Biol 13:157. 2012
    ..A recent publication has provided a comprehensive atlas of gene expression profiles of 995 genes linked to neuronal functions in two regions of the human brain neocortex...
  8. pmc Gene expression in the prefrontal cortex during adolescence: implications for the onset of schizophrenia
    Laura W Harris
    Institute of Biotechnology, University of Cambridge, Cambridge, UK
    BMC Med Genomics 2:28. 2009
    ..CONCLUSION: The observed changes imply that molecular mechanisms critical for adolescent brain development are disturbed in schizophrenia patients...
  9. pmc Metabolic changes in schizophrenia and human brain evolution
    Philipp Khaitovich
    Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Yue Yang Road, Shanghai, 200031, PR China
    Genome Biol 9:R124. 2008
    ....
  10. pmc Annotating conserved and novel features of primate transcriptomes using sequencing
    Philipp Khaitovich
    Partner Institute for Computational Biology, Chinese Academy of Sciences, 320 Yue Yang Road, 200031 Shanghai, China
    Genome Biol 11:125. 2010
    ..Recent high-throughput sequencing of chimpanzee brain and liver transcriptomes published in Genome Biology reveals multiple transcripts lost in the human genome and highlights the incompleteness of primate genome annotations...
  11. pmc Regional patterns of gene expression in human and chimpanzee brains
    Philipp Khaitovich
    Max Planck Institute for Evolutionary Anthropology, D 04103 Leipzig, Germany
    Genome Res 14:1462-73. 2004
    ..Furthermore, genes that show an elevated expression level in humans are statistically significantly enriched in regions that are recently duplicated in humans...
  12. pmc Functionality of intergenic transcription: an evolutionary comparison
    Philipp Khaitovich
    Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
    PLoS Genet 2:e171. 2006
    ..Further, we find that about half of the expression differences between humans and chimpanzees are due to intergenic transcripts...
  13. ncbi request reprint Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees
    Philipp Khaitovich
    Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D 04103 Leipzig, Germany
    Science 309:1850-4. 2005
    ....
  14. pmc MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates
    Mehmet Somel
    Key laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
    PLoS Biol 9:e1001214. 2011
    ....
  15. pmc MicroRNA expression and regulation in human, chimpanzee, and macaque brains
    Hai yang Hu
    Key laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
    PLoS Genet 7:e1002327. 2011
    ..Taken together these results indicate that changes in miRNA expression might have contributed to evolution of human cognitive functions...
  16. pmc Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq
    Augix Guohua Xu
    Partner Institute for Computational Biology, Shanghai, China
    PLoS Comput Biol 6:e1000843. 2010
    ..Some of these transcripts may play roles in transcriptional regulation and contribute to evolution of human-specific phenotypic traits...
  17. pmc Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques
    Xiling Liu
    Key laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, 200031 Shanghai, China
    Genome Res 22:611-22. 2012
    ..Evolutionarily, this change may have taken place after the split of the human and the Neanderthal lineages...
  18. pmc A neutral model of transcriptome evolution
    Philipp Khaitovich
    Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
    PLoS Biol 2:E132. 2004
    ..Furthermore, it may be possible to apply a molecular clock based on expression differences to infer the evolutionary history of tissues...
  19. pmc Widespread splicing changes in human brain development and aging
    Pavel Mazin
    Key laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
    Mol Syst Biol 9:633. 2013
    ..More than 60% of all splicing changes represented a single splicing pattern reflecting preferential inclusion of gene segments potentially targeting transcripts for nonsense-mediated decay in infants and elderly...
  20. pmc Transcriptional neoteny in the human brain
    Mehmet Somel
    Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
    Proc Natl Acad Sci U S A 106:5743-8. 2009
    ..This delay is not uniform across the human transcriptome but affects a specific subset of genes that play a potential role in neural development...
  21. pmc Comprehensive survey of human brain microRNA by deep sequencing
    Ning Yi Shao
    Partner Institute for Computational Biology, 320 Yueyang Road, 200031 Shanghai, China
    BMC Genomics 11:409. 2010
    ..Here, we use deep sequencing to characterize a population of small RNA expressed in human and rhesus macaques brain cortex...
  22. pmc Comparison of protein and mRNA expression evolution in humans and chimpanzees
    Ning Fu
    Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 2:e216. 2007
    ..Our study opens the door to a new level of understanding of regulatory evolution and poses many new questions that remain to be answered...
  23. pmc FUNC: a package for detecting significant associations between gene sets and ontological annotations
    Kay Prüfer
    Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D 04103 Leipzig, Germany
    BMC Bioinformatics 8:41. 2007
    ..However, it is often difficult to assess the statistical significance of such analyses since many inter-dependent categories are tested simultaneously...
  24. pmc Sequence features associated with microRNA strand selection in humans and flies
    Hai yang Hu
    Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, PR China
    BMC Genomics 10:413. 2009
    ..While thermodynamic asymmetry of the duplex ends appears to play a decisive role in the strand selection process, the details of the selection mechanism are not yet understood...
  25. ncbi request reprint Evolution of primate gene expression
    Philipp Khaitovich
    Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D 04103 Leipzig, Germany
    Nat Rev Genet 7:693-702. 2006
    ....
  26. pmc Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series
    Yuan Yuan
    Key Laboratory for Computational Biology, CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
    BMC Bioinformatics 12:347. 2011
    ..While many powerful computation tools for time series alignment have been developed, they do not provide significance estimates for time shift measurements...
  27. pmc MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain
    Mehmet Somel
    Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Genome Res 20:1207-18. 2010
    ..These results suggest a direct link between developmental regulation and expression changes taking place in aging...
  28. doi request reprint The effects of probe binding affinity differences on gene expression measurements and how to deal with them
    Michael Dannemann
    Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
    Bioinformatics 25:2772-9. 2009
    ..We argue that the method should be used even when sequence data are available...
  29. pmc Evolution of the human-specific microRNA miR-941
    Hai yang Hu
    CAS Key Laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai 200031, China
    Nat Commun 3:1145. 2012
    ..Taken together, these results implicate miR-941 in human evolution, and provide an example of rapid regulatory evolution in the human linage...
  30. pmc Widespread expression of piRNA-like molecules in somatic tissues
    Zheng Yan
    Key laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
    Nucleic Acids Res 39:6596-607. 2011
    ..Further, using western blot, we have shown the expression of Miwi protein in mouse pancreas. These findings indicate that piRNA-like molecules might play important roles outside of the germline...
  31. pmc Rapid metabolic evolution in human prefrontal cortex
    Xing Fu
    Key laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, 200031 Shanghai, China
    Proc Natl Acad Sci U S A 108:6181-6. 2011
    ..These human-specific metabolic changes are paralleled by changes in expression patterns of the corresponding enzymes, and affect pathways involved in synaptic transmission, memory, and learning...
  32. pmc Mechanisms of dietary response in mice and primates: a role for EGR1 in regulating the reaction to human-specific nutritional content
    Kai Weng
    Key laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 7:e43915. 2012
    ..Here, we addressed this question by investigating whether the gene expression response observed in mice fed human and chimpanzee diets involves the same regulatory mechanisms as expression differences between humans and chimpanzees...
  33. pmc Accelerated aging-related transcriptome changes in the female prefrontal cortex
    Yuan Yuan
    Key Laboratory for Computational Biology, CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
    Aging Cell 11:894-901. 2012
    ..Accelerated aging-related changes in the female SFG transcriptome may provide a link between a higher stress exposure or sensitivity in women and the higher prevalence of AD...
  34. doi request reprint Stress-associated H3K4 methylation accumulates during postnatal development and aging of rhesus macaque brain
    Yixing Han
    Chinese Academy of Sciences Key Laboratory for Computational Biology, Chinese Academy of Sciences Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
    Aging Cell 11:1055-64. 2012
    ..In support of this, we also observed increased expression of two H3K4 methyltransferases, SETD7 and DPY30, in aged macaque brain...
  35. doi request reprint Human brain evolution: transcripts, metabolites and their regulators
    Mehmet Somel
    CAS Key Laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
    Nat Rev Neurosci 14:112-27. 2013
    ..In this Review we show how this strategy has yielded some of the first hints about the mechanisms of human cognition...
  36. pmc Functional analysis of human and chimpanzee promoters
    Florian Heissig
    Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D 04103 Leipzig, Germany
    Genome Biol 6:R57. 2005
    ....
  37. doi request reprint Genomic analysis of miRNAs in an extreme mammalian hibernator, the Arctic ground squirrel
    Yuting Liu
    CAS MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, Shanghai, China
    Physiol Genomics 42:39-51. 2010
    ..High-throughput sequencing data and microarray data have been submitted to GEO database with accession: GSE19808...
  38. pmc Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness
    Katarzyna Bozek
    CAS Key Laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Shanghai, China Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
    PLoS Biol 12:e1001871. 2014
    ..The results suggest that, while humans are characterized by superior cognition, their muscular performance might be markedly inferior to that of chimpanzees and macaque monkeys. ..
  39. pmc Brain expression--is it all in our SNPs?
    Philipp Khaitovich
    Department of Comparative Biology, Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Mol Syst Biol 3:155. 2007
  40. ncbi request reprint Deep sequencing reveals a novel class of bidirectional promoters associated with neuronal genes
    Hai yang Hu
    CAS Key Laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, 320 Yue Yang Road, 200031 Shanghai, China
    BMC Genomics 15:457. 2014
    ..Comprehensive annotation of transcripts expressed in a given tissue is a critical step towards the understanding of regulatory and functional pathways that shape the transcriptome...
  41. pmc Evolution of human longevity uncoupled from caloric restriction mechanisms
    Guodong Zhao
    CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China Graduate School of Chinese Academy of Sciences, Beijing, China
    PLoS ONE 9:e84117. 2014
    ..Consequently, application of CR or CR-mimicking agents may yet offer a promising direction for the extension of healthy human lifespan. ..
  42. pmc Estimating accuracy of RNA-Seq and microarrays with proteomics
    Xing Fu
    Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, China Academy of Sciences, Shanghai, 200031, PR China
    BMC Genomics 10:161. 2009
    ..At present, high throughput sequencing is emerging as an alternative methodology for transcriptome studies. Although free of many limitations imposed by microarray design, its potential to estimate absolute transcript levels is unknown...
  43. doi request reprint Evidence for human microRNA-offset RNAs in small RNA sequencing data
    David Langenberger
    Department of Computer Science, University of Leipzig, Leipzig, Germany
    Bioinformatics 25:2298-301. 2009
    ....
  44. pmc Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation
    Zhisong He
    CAS Key Laboratory of Computational Biology, CAS MPG Partner Institute for Computational Biology, Shanghai 200031, China Graduate School of Chinese Academy of Sciences, 100039 Beijing, China
    RNA 20:1103-11. 2014
    ..These results support the potential functionality of lincRNA in primate PFC development. ..
  45. pmc Fast mapping of short sequences with mismatches, insertions and deletions using index structures
    Steve Hoffmann
    Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
    PLoS Comput Biol 5:e1000502. 2009
    ..Our approach is implemented in the software segemehl available at http://www.bioinf.uni-leipzig.de/Software/segemehl/...
  46. pmc Aging and gene expression in the primate brain
    Hunter B Fraser
    Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
    PLoS Biol 3:e274. 2005
    ....
  47. pmc Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans
    Chris T Yohn
    Department of Genetics, Case Western Reserve University, Cleveland, Ohio, USA
    PLoS Biol 3:e110. 2005
    ..We speculate on the potential impact of such recent events on the evolution of humans and great apes...
  48. pmc Evolutionary forces shape the human RFPL1,2,3 genes toward a role in neocortex development
    Jérôme Bonnefont
    Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Rue Michel Servet 1, 1211 Geneva, Switzerland
    Am J Hum Genet 83:208-18. 2008
    ..Thus, we propose that the recent emergence and multiplication of the RFPL1,2,3 genes contribute to changes in primate neocortex size and/or organization...
  49. ncbi request reprint Gene expression becomes heterogeneous with age
    Mehmet Somel
    Curr Biol 16:R359-60. 2006
  50. ncbi request reprint Positive selection on gene expression in the human brain
    Philipp Khaitovich
    Curr Biol 16:R356-8. 2006