CURRICULUM VITAE
LOHITH REDDY MADIREDDY
415-939-0936
lohith.madireddy@ucsf.edu
226 Font Blvd, San Francisco, CA-94132
Education
Jan 2008 – Aug 2009
Aug 2006 – Dec 2008
Sep 2002 – June 2006
Arizona State University
Graduate Certificate in Statistics
Arizona State University (ASU)
Professional Science Master’s in Computational Biosciences
Jawaharlal Nehru Technological University
Bachelor of Technology in Biotechnology (Engineering)
Tempe, AZ, USA
GPA 3.87/4.00
Tempe, AZ, USA
GPA 3.89/4.00
Hyderabad, India
GPA 81/100
Work Experience
Bioinformatician, Multiple Sclerosis Genetics Group, Department of Neurology, UCSF, USA
08/09- present
 Currently analyzing next-generation genome sequence data from 3 families with RRMS and 49 PPMS cases to
investigate causal variants, genes and pathways. Designed and implemented a MySQL database to store and query
various variant data. Performed analysis using R, Python and shell scripting. Linkage analysis, Identical By Descent
(IBD), susceptibility of each genome to various traits, presence of exogenous DNA, small variations, copy number
and structural variations, pathway analysis are being explored.
 Performed SNP imputation using Beagle genetics software on 930 trios using DCEG reference (>2M SNPs) with
very high accuracy even for SNPs with minor allele frequency less than 5% in the reference population.
 Scrutinized differences between a cell line genome transformed with EBV and the same person’s normal genome to
see whether cell lines transformed with EBV are good sources for maintaining a genome without significant
alternations.
 Analyzed qPCR and ELISA expression data and built classifiers using various machine learning algorithms in
Interferon Beta time course study for genetic signatures classifying responders and non-responders. Investigated
association of targeted blood biomarkers with interferon β-1a treatment administration, magnetic resonance imaging
activity and treatment response. Designed algorithms and programmed in R for analysis and extensive data
visualization.
 Designed and currently implementing a dynamic web based data portal for analyzing microarray datasets.
 Discovered aberrations in FREM1gene as the cause for a rare disease, MOTA (Manitoba-Oculo-Tricho-Anal)
syndrome.
 Identified potential markers for astrocytes and astrocyte precursors in spinal cord and brain by identifying genes that
are turned on or off during development.
 Conducted a microarray analysis in R looking for differences in gene expression among astrocyte subdomains in
postnatal cord by comparing astrocytes from each subdomain to all astrocyte controls.
 Performed several other microarray analyses using R and BioConductor mostly on data from Affymetrix platforms.
Bioinformatics Specialist/Programmer, Proteomics Lab, Center for Metabolic Biology, ASU, USA
02/09-08/09
 Developed software in Python language that identifies phosphorylated residues on peptide sequences by comparing
computationally generated theoretical ion mass data with that of sample’s Tandem Mass spectra.
 Extracted proteins from thawed muscle biopsies, estimated concentrations, performed Immunoprecipitation, gel
electrophoresis. Extracted proteins from the gels and digested the gel pieces with Trypsin. Phosphopeptide enriched
samples were then run through HPLC-ESI-MS/MS and the raw data was analyzed.
 306 unique in vivo phosphorylation sites were identified in 127 proteins with ~18:4:1 ratio of phosphoserines,
phosphothreonines, and phosphotyrosines.
Research Assistant, Cancer Eradication Group, School of Life Sciences, Biodesign Institute, ASU, USA
09/07-12/08
 Bootstrap Searched LC-MS/MS spectra for fusion peptides derived from t(11;22) reciprocal translocation in brain
cancer (Master’s Applied Project and oral defense).
 Developed Read-through peptide libraries in Perl using BioPerl for human 3’UTR and Encode sequences (NCBI).
Research Assistant, Center for Biological Physics, Arizona State University, Tempe, USA
01/07-08/07
 Protein Structure Refinement using the physical principles of folding mechanism, the ZAM algorithm.
 Developed Python scripts to find shared native contacts, hydrophobic interactions and secondary structure residues
among seeds of proteins which are further used as restraints in ZAM (Zipping and Assembly Method) simulations.
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Performed ZAM simulations on supercomputing cluster for several CASP targets and achieved 1-2 A0 refinements.
Developed Python HTML data parser to fetch PDB models for any target from CASP8 website (Voluntary work).
Teaching Assistant, Department of Mathematics and Statistics, Arizona State University, Tempe, USA
08/06-05/07
 Served as TA for the following courses at ASU: Spring 2007 – MAT 343 (Applied Linear Algebra), MAT362
(Advanced Mathematics for Engineers and Scientists), Fall 2006 – MAT 254 (Elementary differential equations).
Skill Set
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Computing Skills
 Language Proficiencies: Python, Perl, Matlab, Java, C and Shell scripting
 Statistical Computing: R and BioConductor, Minitab, Design Expert, JMP
 Web technologies: HTML, XML, CSS, JavaScript, Ajax, PHP, Dreamweaver, MODx CMS/CMF, Photoshop
 Databases: Entity-Relationship modeling, MySQL, MS-Access,WinRDBI, MySQL Workbench, phpMyAdmin.
 Microarray and pathway analysis: Nexus Copy Number, Affymetrix GTC, Cytoscape, GSEA, MeV, etc
 Operating Systems: Linux (system administrator), grid computing, Mac OSX and Windows
 Bioinformatics Tools: Beagle, Merlin, PLINK, IGV, Mascot, Scaffold, MEGA, BLAST, PHYLIP, Genome
Browser, PyMol, VMD, etc.
Wet Lab Skills
 Micro-Array, DNA sequencing, RT-PCR (q-PCR), Mass-Spectrometry(HPLC-ESI-MS/MS), Molecular
Biology, Immunological, Biochemical, Microbiological, Instrumental Methods of analysis, Tissue Culture,
Bioprocess Engineering, Genetic Engineering, Down Stream Processing Techniques, etc.,
Graduate Course Projects and Presentations
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Developed E-commerce web application for shopping books and CDs using MySQL, PHP (DBMS course, Fall 08).
Designed an experiment for optimum growth factor levels for a microbe using factorial design (Fall08).
Implemented a decision tree classifier in Matlab on tic-tac-toe data set from UCI (Data Mining, Spring 08).
Coded Apriori algorithm in Matlab for Association rule mining on congressional data (Data Mining, Spring 08).
Coded local (Smith-Waterman) and global alignment (Needleman-Wunsch) algorithms in Matlab (Spring 07).
Estimated if a given protein is extracellular or intracellular using training and testing sets of proteins (Spring 07).
Programmed in Matlab to decide whether or not a DNA sequence is a CpG island (Spring 07).
Performed parameter estimation for Hidden Markov Models (HMMs) by Baulm-Welch and Viterbi training, applied
to identification of CpG islands (Coded Viterbi algorithm for HMMs in Matlab) (Spring 07).
Journal Publications
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Madireddy L, Baranzini SE, “A fast relational database schema and automatic upload tool for Complete Genomics
Incorporation whole genome sequence variant data” (in preparation)
Baranzini SE, Madireddy L, Cree BAC, “Association of targeted blood biomarkers with interferon β-1a treatment
administration, magnetic resonance imaging activity and treatment response” (in preparation)
Khankhanian P, Baranzini SE, Johnson B, Madireddy L, Nickles D, Lennox D, Yvonne W, “Deep sequencing of
IL6 in a case-control study in Cerebral Palsy” (submitted to American Journal of Medical Genetics)
Nickles D, Chen HP, Li MM, Khankhanian P, Madireddy L, Stacy CJ, Santaniello A, Cree BAC, Pelletier D,
Hauser SL, Oksenberg JR, Baranzini SE, "RNA profiling in multiple sclerosis reveals novel transcripts potentially
involved in disease pathogenesis" (submitted to American Human Molecular Genetics)
Nickles D, Madireddy L, Yang S, Khankhanian P, Lincoln S, Hauser SL, Oksenberg JR, Baranzini SE, “In depth
comparison of an individual’s DNA and its lymphoblastoid cell line using whole genome sequencing”, BMC
Genomics. 2012 Sep 14;13:477
Slavotinek AM, Baranzini SE, Schanze D, Labelle-Dumais C, Short KM, Chao R, Yahyavi M, Bijlsma EK, Chu C,
Musone S, Wheatley A, Kwok PY, Marles S, Fryns JP, Maga AM, Hassan MG, Gould DB, Madireddy L, Li C,
Cox TC, Smyth I, Chudley AE, Zenker M, “Manitoba-Oculo-Tricho-Anal (MOTA) is caused by mutations in
FREM1”, J Med Genet. 2011 Jun; 48(6):375-82.
Højlund K, Bowen BP, Hwang H, Flynn CR, Madireddy L, Geetha T, Langlais P, Meyer C, Mandarino LJ, Yi Z,
“In vivo Phosphoproteome of Human Skeletal Muscle Revealed by Phosphopeptide Enrichment and HPLC-ESIMS/MS”, Journal of Proteome Research, 2009 8 (11), 4954-4965.
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