K
Katja Schwartz
Researcher at Stanford University
Publications - 22
Citations - 2217
Katja Schwartz is an academic researcher from Stanford University. The author has contributed to research in topics: Gene & Saccharomyces cerevisiae. The author has an hindex of 14, co-authored 21 publications receiving 1832 citations.
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Journal ArticleDOI
GC-content normalization for RNA-Seq data.
TL;DR: The authors' within-lane normalization procedures, followed by between-lanenormalization, reduce GC-content bias and lead to more accurate estimates of expression fold-changes and tests of differential expression.
Journal ArticleDOI
Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions
Alicia N. Schep,Jason D. Buenrostro,Sarah K. Denny,Katja Schwartz,Gavin Sherlock,William J. Greenleaf +5 more
TL;DR: This work observes a highly structured pattern of DNA fragment lengths and positions around nucleosomes in Saccharomyces cerevisiae, and uses this distinctive two-dimensional nucleosomal "fingerprint" as the basis for a new nucleosome-positioning algorithm called NucleoATAC, which can identify the rotational and translational positions ofucleosomes with up to base-pair resolution.
Journal ArticleDOI
BIM1 encodes a microtubule-binding protein in yeast.
TL;DR: The sequence of BIM1 shows substantial similarity to sequences from organisms across the evolutionary spectrum and a systematic study of 51 tub1 alleles suggests a correlation between specific failure to interact with Bim1p in the two-hybrid assay and synthetic lethality with the bim1Delta allele.
Journal ArticleDOI
Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae.
TL;DR: It is demonstrated that natural S. cerevisiae yeasts are capable of utilizing xylose as the sole carbon source, the genetic basis for this trait as well as the endogenous xylOSE utilization pathway are characterized, and the feasibility of BSA is demonstrated using high-throughput sequencing.
Journal ArticleDOI
Gene flow contributes to diversification of the major fungal pathogen Candida albicans.
Jeanne Ropars,Jeanne Ropars,Corinne Maufrais,Dorothée Diogo,Marina Marcet-Houben,Marina Marcet-Houben,Aurélie Perin,Natacha Sertour,Kevin Mosca,Emmanuelle Permal,Guillaume Laval,Christiane Bouchier,Laurence Ma,Katja Schwartz,Kerstin Voelz,Robin C. May,Julie Poulain,Julie Poulain,Christophe Battail,Patrick Wincker,Patrick Wincker,Andrew M. Borman,Anuradha Chowdhary,Shangrong Fan,Soo Hyun Kim,Patrice Le Pape,Orazio Romeo,Jong Hee Shin,Toni Gabaldón,Gavin Sherlock,Marie-Elisabeth Bougnoux,Marie-Elisabeth Bougnoux,Marie-Elisabeth Bougnoux,Christophe d'Enfert +33 more
TL;DR: Evidence of gene flow between previously known and newly identified genetic clusters is found, supporting the occurrence of parasexuality in nature and thus C. albicans takes advantage of both clonality and gene flow to diversify.