Ken Livak - Academia.edu (original) (raw)

Papers by Ken Livak

Research paper thumbnail of Detection and quantitation of human papillomavirus type 16, 18 and 52 DNA in the peripheral blood of cervical cancer patients

Gynecologic Oncology, 2005

Research paper thumbnail of Efficient Automated Synthesis of Molecular Beacons

Nucleosides, Nucleotides & Nucleic Acids, Jun 1, 1999

Research paper thumbnail of Global distribution of allele frequencies at the human dopamine D4 receptor locus

American Journal of Human Genetics, Sep 1, 1994

ABSTRACT The dopamine D4 receptor (DRD4) is a candidate gene for schizophrenia because the dopami... more ABSTRACT The dopamine D4 receptor (DRD4) is a candidate gene for schizophrenia because the dopaminergic system has been implicated in this neuropsychiatric disorder. Several research groups have reported an association between allelic variants at DRD4 and schizophrenia, while others have been unable to replicate that finding. Knowledge of the appropriate gene frequencies in the underlying populations may resolve these inconsistencies. We have determined the frequencies of 8 different alleles of the 48 bp imperfect tandem repeat of exon 3 at the DRD4 locus in samples from 33 populations around the world. The frequencies vary considerably in the different populations with the most common allele ranging from 16% to 95%. Frequencies and Fst values will be presented for the 3 most common alleles (4-, 7-, and 2- repeat) by continental groupings, but the individual populations vary significantly around the averages. The populations averaged 4.3 alleles (range 2 to 7).

Research paper thumbnail of Increased Nuclease-Susceptibility of Active Chromatin at Heat-Shock Loci in Drosophila

Research paper thumbnail of Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of reprogramming outcome

Research paper thumbnail of 115 Spatial dissection of T cell clonotype identity, transcriptional profiles, and cell-cell interactions in the tumor microenvironment and tertiary lymphoid structures

Regular and Young Investigator Award Abstracts, Nov 1, 2022

Research paper thumbnail of Quantitative peR Technology

Research paper thumbnail of 115 Spatial dissection of T cell clonotype identity, transcriptional profiles, and cell-cell interactions in the tumor microenvironment and tertiary lymphoid structures

Regular and Young Investigator Award Abstracts

Research paper thumbnail of Quantitative peR Technology

Research paper thumbnail of Seven-Color, Homogeneous Detection of Six PCR

We describe an extension of the fluoro genic PCR 5 ′ -nuclease assay, or “Taq Man ™ ” assay. Sequ... more We describe an extension of the fluoro genic PCR 5 ′ -nuclease assay, or “Taq Man ™ ” assay. Sequence-specific probe s consisted of a novel nonfluorescent quench er, nitrothiazole blue (NTB), at the 3 ′ term i nus and six different reporter dyes at the 5 ′ terminus. The six reporters were 6-FAM , dR110, dR6G, dTMR, dROX and JAZ dyes . The seventh color was from aluminum ph thalocyanine tetrasulfonate and was utilized as a “passive reference” to calibrate concen tration variations. Our test system was a se t of three single-nucleotide polymorphism s (SNPs). Each SNP system consisted of two primers and two sequence-specific probes , each labeled with a different reporter dy e and NTB. Following PCR, the reactions wer e diluted with water and measured in a m i crocuvette on a luminescence spectromete r in synchronous scanning mode. In thi s method, both the excitation and emission wavelengths were scanned, with a fixed wavelength difference (Δ λ ) between excita tion and emission wavel...

Research paper thumbnail of Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of reprogramming outcome

Cellular reprogramming through manipulation of defined factors holds great promise for large-scal... more Cellular reprogramming through manipulation of defined factors holds great promise for large-scale production of cell types needed for use in therapy, as well as for expanding our understanding of the general principles of gene regulation. MYOD-mediated myogenic reprogramming, which converts many cell types into contractile myotubes, remains one of the best characterized model system for direct conversion by defined factors. However, why MYOD can efficiently convert some cell types into myotubes but not others remains poorly understood. Here, we analyze MYOD-mediated reprogramming of human fibroblasts at pseudotemporal resolution using single-cell RNA-Seq. Successfully reprogrammed cells navigate a trajectory with two branches that correspond to two barriers to reprogramming, with cells that select incorrect branches terminating at aberrant or incomplete reprogramming outcomes. Differential analysis of the major branch points alongside alignment of the successful reprogramming path ...

Research paper thumbnail of Efficient Automated Synthesis of Molecular Beacons

Nucleosides and Nucleotides, 1999

Research paper thumbnail of Efficient synthesis of double dye-labeled oligodeoxyribonucleotide probes and their application in a real time PCR assay

Nucleic Acids Research, 1998

Research paper thumbnail of Increased Nuclease-Susceptibility of Active Chromatin at Heat-Shock Loci in Drosophila

Differentiation and Development, 1978

Research paper thumbnail of Alleles at the dopamine D4 receptor locus do not contribute to the genetic susceptibility to schizophrenia in a large Swedish kindred

American Journal of Medical Genetics, 1993

The discovery of a functional polymrphism within the dopamine D4 receptor gene (DRD4) has not onl... more The discovery of a functional polymrphism within the dopamine D4 receptor gene (DRD4) has not only strengthened the hypotheses implicating DRD4 in the etiology of neuropyschiatic disorders, but also provided a genetic marker for testing these hypotheses. The possibility of the dopamine D4 receptor as a candidate gene for schizophrenia was investigated in a large Swedish kindred segregating for schizophrenia. Linkage to schizophrenia was tested by linkage analyses of 6 polymorphic markers (at 4 loci) in chromosome 11p15.5 including the dopamine D4 receptor (DRD4) and the tyrosine hydroxylase (TH) loci. Schizophrenia was excluded from close linkage to the DRD4 locus using two of the polymorphisms located within the dopamine D4 receptor gene. The first DRD4 polymorphism consists of variation in the number of a 48 bp imperfect direct repeat in the third exon; the second consists of a variable number of repeated G nucleotides in the first intron. In addition, some of the individuals homo...

Research paper thumbnail of SNPing Away at Complex Diseases: Analysis of Single-Nucleotide Polymorphisms around APOE in Alzheimer Disease

The American Journal of Human Genetics, 2000

Research paper thumbnail of Quantitative PCR Technology

Gene Quantification, 1996

Page 113. Quantitative PCR Technology Lincoln McBride, Ken Livak, Mike Lucero. ... Jeff Lucas, Ke... more Page 113. Quantitative PCR Technology Lincoln McBride, Ken Livak, Mike Lucero. ... Jeff Lucas, Kevin Bodner, Robert Grossman, Bashar Mullah. Charles Connell, LindaLee, and Mark Oldham Introduction Higuchi et al.(1992. ...

Research paper thumbnail of Detection and quantitation of human papillomavirus type 16, 18 and 52 DNA in the peripheral blood of cervical cancer patients

Gynecologic Oncology, 2005

Research paper thumbnail of Efficient Automated Synthesis of Molecular Beacons

Nucleosides, Nucleotides & Nucleic Acids, Jun 1, 1999

Research paper thumbnail of Global distribution of allele frequencies at the human dopamine D4 receptor locus

American Journal of Human Genetics, Sep 1, 1994

ABSTRACT The dopamine D4 receptor (DRD4) is a candidate gene for schizophrenia because the dopami... more ABSTRACT The dopamine D4 receptor (DRD4) is a candidate gene for schizophrenia because the dopaminergic system has been implicated in this neuropsychiatric disorder. Several research groups have reported an association between allelic variants at DRD4 and schizophrenia, while others have been unable to replicate that finding. Knowledge of the appropriate gene frequencies in the underlying populations may resolve these inconsistencies. We have determined the frequencies of 8 different alleles of the 48 bp imperfect tandem repeat of exon 3 at the DRD4 locus in samples from 33 populations around the world. The frequencies vary considerably in the different populations with the most common allele ranging from 16% to 95%. Frequencies and Fst values will be presented for the 3 most common alleles (4-, 7-, and 2- repeat) by continental groupings, but the individual populations vary significantly around the averages. The populations averaged 4.3 alleles (range 2 to 7).

Research paper thumbnail of Increased Nuclease-Susceptibility of Active Chromatin at Heat-Shock Loci in Drosophila

Research paper thumbnail of Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of reprogramming outcome

Research paper thumbnail of 115 Spatial dissection of T cell clonotype identity, transcriptional profiles, and cell-cell interactions in the tumor microenvironment and tertiary lymphoid structures

Regular and Young Investigator Award Abstracts, Nov 1, 2022

Research paper thumbnail of Quantitative peR Technology

Research paper thumbnail of 115 Spatial dissection of T cell clonotype identity, transcriptional profiles, and cell-cell interactions in the tumor microenvironment and tertiary lymphoid structures

Regular and Young Investigator Award Abstracts

Research paper thumbnail of Quantitative peR Technology

Research paper thumbnail of Seven-Color, Homogeneous Detection of Six PCR

We describe an extension of the fluoro genic PCR 5 ′ -nuclease assay, or “Taq Man ™ ” assay. Sequ... more We describe an extension of the fluoro genic PCR 5 ′ -nuclease assay, or “Taq Man ™ ” assay. Sequence-specific probe s consisted of a novel nonfluorescent quench er, nitrothiazole blue (NTB), at the 3 ′ term i nus and six different reporter dyes at the 5 ′ terminus. The six reporters were 6-FAM , dR110, dR6G, dTMR, dROX and JAZ dyes . The seventh color was from aluminum ph thalocyanine tetrasulfonate and was utilized as a “passive reference” to calibrate concen tration variations. Our test system was a se t of three single-nucleotide polymorphism s (SNPs). Each SNP system consisted of two primers and two sequence-specific probes , each labeled with a different reporter dy e and NTB. Following PCR, the reactions wer e diluted with water and measured in a m i crocuvette on a luminescence spectromete r in synchronous scanning mode. In thi s method, both the excitation and emission wavelengths were scanned, with a fixed wavelength difference (Δ λ ) between excita tion and emission wavel...

Research paper thumbnail of Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of reprogramming outcome

Cellular reprogramming through manipulation of defined factors holds great promise for large-scal... more Cellular reprogramming through manipulation of defined factors holds great promise for large-scale production of cell types needed for use in therapy, as well as for expanding our understanding of the general principles of gene regulation. MYOD-mediated myogenic reprogramming, which converts many cell types into contractile myotubes, remains one of the best characterized model system for direct conversion by defined factors. However, why MYOD can efficiently convert some cell types into myotubes but not others remains poorly understood. Here, we analyze MYOD-mediated reprogramming of human fibroblasts at pseudotemporal resolution using single-cell RNA-Seq. Successfully reprogrammed cells navigate a trajectory with two branches that correspond to two barriers to reprogramming, with cells that select incorrect branches terminating at aberrant or incomplete reprogramming outcomes. Differential analysis of the major branch points alongside alignment of the successful reprogramming path ...

Research paper thumbnail of Efficient Automated Synthesis of Molecular Beacons

Nucleosides and Nucleotides, 1999

Research paper thumbnail of Efficient synthesis of double dye-labeled oligodeoxyribonucleotide probes and their application in a real time PCR assay

Nucleic Acids Research, 1998

Research paper thumbnail of Increased Nuclease-Susceptibility of Active Chromatin at Heat-Shock Loci in Drosophila

Differentiation and Development, 1978

Research paper thumbnail of Alleles at the dopamine D4 receptor locus do not contribute to the genetic susceptibility to schizophrenia in a large Swedish kindred

American Journal of Medical Genetics, 1993

The discovery of a functional polymrphism within the dopamine D4 receptor gene (DRD4) has not onl... more The discovery of a functional polymrphism within the dopamine D4 receptor gene (DRD4) has not only strengthened the hypotheses implicating DRD4 in the etiology of neuropyschiatic disorders, but also provided a genetic marker for testing these hypotheses. The possibility of the dopamine D4 receptor as a candidate gene for schizophrenia was investigated in a large Swedish kindred segregating for schizophrenia. Linkage to schizophrenia was tested by linkage analyses of 6 polymorphic markers (at 4 loci) in chromosome 11p15.5 including the dopamine D4 receptor (DRD4) and the tyrosine hydroxylase (TH) loci. Schizophrenia was excluded from close linkage to the DRD4 locus using two of the polymorphisms located within the dopamine D4 receptor gene. The first DRD4 polymorphism consists of variation in the number of a 48 bp imperfect direct repeat in the third exon; the second consists of a variable number of repeated G nucleotides in the first intron. In addition, some of the individuals homo...

Research paper thumbnail of SNPing Away at Complex Diseases: Analysis of Single-Nucleotide Polymorphisms around APOE in Alzheimer Disease

The American Journal of Human Genetics, 2000

Research paper thumbnail of Quantitative PCR Technology

Gene Quantification, 1996

Page 113. Quantitative PCR Technology Lincoln McBride, Ken Livak, Mike Lucero. ... Jeff Lucas, Ke... more Page 113. Quantitative PCR Technology Lincoln McBride, Ken Livak, Mike Lucero. ... Jeff Lucas, Kevin Bodner, Robert Grossman, Bashar Mullah. Charles Connell, LindaLee, and Mark Oldham Introduction Higuchi et al.(1992. ...