Philipp Khaitovich

Summary

Affiliation: Max Planck Institute for Evolutionary Anthropology
Country: Germany

Publications

  1. ncbi Human brain evolution
    Hilliary Creely
    Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz, D-04103 Leipzig, Germany
    Prog Brain Res 158:295-309. 2006
  2. ncbi 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
  3. ncbi Toward a neutral evolutionary model of gene expression
    Philipp Khaitovich
    Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
    Genetics 170:929-39. 2005
  4. ncbi 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
  5. ncbi 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. ncbi 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. ncbi 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
  8. ncbi 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
  9. ncbi Functionality of intergenic transcription: an evolutionary comparison
    Philipp Khaitovich
    Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
    PLoS Genet 2:e171. 2006
  10. ncbi 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

Publications38

  1. ncbi Human brain evolution
    Hilliary Creely
    Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz, D-04103 Leipzig, Germany
    Prog Brain Res 158:295-309. 2006
  2. ncbi 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...
  3. ncbi 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...
  4. ncbi 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%)...
  5. ncbi 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. ncbi 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
    ..CONCLUSION: We conclude that postmortem human brain samples are suitable for investigating gene expression patterns in humans, but that caution is warranted in interpreting results for individual genes...
  7. ncbi 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...
  8. ncbi 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...
  9. ncbi 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...
  10. ncbi 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. ncbi 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
    ....
  12. ncbi 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
    ....
  13. ncbi 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...
  14. ncbi 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...
  15. ncbi 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...
  16. ncbi 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...
  17. ncbi 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...
  18. ncbi 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...
  19. ncbi 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...
  20. ncbi 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...
  21. ncbi 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...
  22. ncbi 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. CONTACT: lachmann@eva.mpg.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online...
  23. ncbi 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
    ....
  24. ncbi 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...
  25. ncbi 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...
  26. ncbi 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...
  27. ncbi 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
    ....
  28. ncbi 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
    ....
  29. ncbi 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...
  30. ncbi 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
  31. ncbi 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...
  32. ncbi 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
    ....
  33. ncbi 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/...
  34. ncbi 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...
  35. ncbi 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
    ....
  36. ncbi 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...
  37. ncbi Positive selection on gene expression in the human brain
    Philipp Khaitovich
    Curr Biol 16:R356-8. 2006
  38. ncbi Gene expression becomes heterogeneous with age
    Mehmet Somel
    Curr Biol 16:R359-60. 2006