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Sidney Ochs (1924-2014).
J Neurol
July 2024
Department of Psychology, Division of Brain, Behavior and Cognition, Faculty of Philosophy, Aristotelian University, Thessaloníki, Greece.
Enter the Matrix: Factorization Uncovers Knowledge from Omics.
Trends Genet
October 2018
Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA. Electronic address:
Omics data contain signals from the molecular, physical, and kinetic inter- and intracellular interactions that control biological systems. Matrix factorization (MF) techniques can reveal low-dimensional structure from high-dimensional data that reflect these interactions. These techniques can uncover new biological knowledge from diverse high-throughput omics data in applications ranging from pathway discovery to timecourse analysis.
View Article and Find Full Text PDFSplice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.
Bioinformatics
June 2018
Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center.
Motivation: Current bioinformatics methods to detect changes in gene isoform usage in distinct phenotypes compare the relative expected isoform usage in phenotypes. These statistics model differences in isoform usage in normal tissues, which have stable regulation of gene splicing. Pathological conditions, such as cancer, can have broken regulation of splicing that increases the heterogeneity of the expression of splice variants.
View Article and Find Full Text PDFCoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network.
Oncotarget
November 2016
Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
Patients with oncogene driven tumors are treated with targeted therapeutics including EGFR inhibitors. Genomic data from The Cancer Genome Atlas (TCGA) demonstrates molecular alterations to EGFR, MAPK, and PI3K pathways in previously untreated tumors. Therefore, this study uses bioinformatics algorithms to delineate interactions resulting from EGFR inhibitor use in cancer cells with these genetic alterations.
View Article and Find Full Text PDFSuccessful hematopoietic cell transplantation in a patient with X-linked agammaglobulinemia and acute myeloid leukemia.
Pediatr Blood Cancer
September 2015
Pediatric Blood and Marrow Transplant, Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, Maryland.
X-linked agammaglobulinemia (XLA) is a primary immunodeficiency characterized by marked reduction in all classes of serum immunoglobulins and the near absence of mature CD19(+) B-cells. Although malignancy has been observed in patients with XLA, we present the first reported case of acute myeloid leukemia (AML) in a patient with XLA. We also demonstrate the complete correction of the XLA phenotype following allogeneic hematopoietic cell transplantation for treatment of the patient's leukemia.
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