Mark D Schroeder
Rockefeller University
6 Papers
Mark D Schroeder is an academic researcher from Rockefeller University. The author has contributed to research in topics: Genome & Regulation of gene expression. The author has an hindex of 6, co-authored 6 publications. Previous affiliations of Mark D Schroeder include Ludwig Maximilian University of Munich.
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Papers
Decay Rates of Human mRNAs: Correlation With Functional Characteristics and Sequence Attributes
Edward Yang,Erik van Nimwegen,Mihaela Zavolan,Nikolaus Rajewsky,Mark D Schroeder,Marcelo O. Magnasco,James E. Darnell +6 more
TL;DR: This work measures mRNA decay rates in two human cell lines with high-density oligonucleotide arrays and investigates the dependence of decay rates on sequence composition, that is, the presence or absence of short mRNA motifs in various regions of the mRNA transcript.
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Predicting expression patterns from regulatory sequence in Drosophila segmentation
TL;DR: A novel thermodynamic model is described that computes expression patterns as a function of cis-regulatory sequence and of the binding-site preferences and expression of participating transcription factors and is applied to the segmentation gene network of Drosophila melanogaster.
How to make stripes: deciphering the transition from non-periodic to periodic patterns in Drosophila segmentation
TL;DR: A comprehensive systems-level examination of the regulatory architecture underlying pair-rule stripe formation in Drosophila embryo finds that runt, fushi tarazu (ftz) and odd skipped (odd) establish most of their pattern through stripe-specific elements, arguing for a reclassification of ftz and odd as primary pair- rule genes.
Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome
Shuba Gopal,Mark D Schroeder,Ursula Pieper,Alexander Sczyrba,Gulriz Aytekin-Kurban,Stefan Bekiranov,J. Eduardo Fajardo,Narayanan Eswar,Roberto Sanchez,Andrej Sali,Terry Gaasterland +10 more
TL;DR: A two-stage approach that combines the merits of stringent genome annotation with the benefits of over-prediction of putative genes is developed and validated 1,042 novel candidate genes after filtering 19,410 plausible genes.
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Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila
TL;DR: It is demonstrated that the use of a second genome (D. pseudoobscura) for cross-species comparison significantly improves the prediction accuracy of Stubb, and is a more sensitive approach than intersecting the results of separate runs over the two genomes.