Fred Long
Bioinformatics Specialist (part-time), Department of Microbiology & Molecular Genetics, UC Irvine
Biography
Fred Long is a Senior Software Engineer at AT&T/DirecTV, where he works on porting Android to DIRECTV STREAM set-top boxes and fixing Android platform bugs. He also serves as a part-time Bioinformatics Specialist in the Department of Microbiology & Molecular Genetics at UC Irvine and as a Bioinformatics Consultant for VRISD and PRISM. Long holds a B.A. in Computer Science from UC San Diego and completed two years in the Computer Science Ph.D. program at UC Santa Cruz, where he also worked as a teaching assistant.
Long has over 30 years of professional experience spanning software engineering, bioinformatics, and system administration. His work encompasses Android platform development, genomic and proteomic software, and Linux cluster management. At SDG Systems from 2012 to 2020, he ported Android AOSP to Trimble's Juno T41 smartphone, fixing hundreds of issues across the Linux kernel, bootloaders, and Android framework. He designed multiple frameworks for barcode scanning and RFID tag reading used in various commercial Android applications. His bioinformatics work includes developing software for sequence alignment and assembly, comparative genomics, and mass spectrometry data analysis.
Long is a co-inventor on a U.S. patent for generating local addresses and communication sets for data-parallel programs. He has co-authored numerous peer-reviewed publications in computational biology, genomics, and proteomics journals, including work on DNA methylation profiling, antimicrobial resistance gene detection, and mass spectrometry-based proteomics. His earlier career included developing simulation software for Navy personnel, web development for Ziff Davis Media, and enterprise software for financial services. Long holds certifications as a Sun Certified Programmer for Java 2 Platform, Microsoft Certified Professional in Visual Basic 6.0, and Oracle8 Certified Database Administrator.
Return to topAreas of Expertise
- Bioinformatics Software Development
- Genomic Sequence Alignment
- Proteomic Pipeline Optimization
- PCR Primer Design Algorithms
- Android Platform Porting
- RFID Scanner Framework Integration
- Parallel Computing Job Control
Recent Publications
- Porwollik S, Santiviago CA, Cheng P, Long F, Desai P, “Defined Single-Gene and Multi-Gene Deletion Mutant Collections in Salmonella enterica sv Typhimurium” (opens in new tab), PLoS ONE, vol. 9, no. 7, pp. e99820, 2014.
- Desai PT, Porwollik S, Long F, Cheng P, Wollam A, Bhonagiri-Palsikar V, Hallsworth-Pepin K, Clifton SW, Weinstock GM, McClelland M, “Evolutionary Genomics of Salmonella enterica Subspecies” (opens in new tab), mBio, vol. 4, no. 2, pp. e00579-12, 2013.
- Koziol J.A., Griffin N.M., Long F., Li Y., Latterich M., Schnitzer J.E., “On protein abundance distributions in complex mixtures” (opens in new tab), Proteome Science, vol. 11, 2013.
- Noelle M Griffin, Jingyi Yu, Fred Long, Phil Oh, Sabrina Shore, Yan Li, Jim A Koziol, Jan E Schnitzer, “Label-free, normalized quantification of complex mass spectrometry data for proteomics analysis” (opens in new tab), Nature Biotechnology, vol. 28, no. 1, pp. 83–89, 2010.
- Lee EJ, Mcclelland M, Wang Y, Long F, Choi SH, Lee JH, “Distinct DNA methylation profiles between adenocarcinoma and squamous cell carcinoma of human uterine cervix” (opens in new tab), Oncology Research, vol. 18, no. 9, pp. 401-8, 2010.
- Frye JG, Lindsey RL, Rondeau G, Porwollik S, Long F, McClelland M, Jackson CR, Englen MD, Meinersmann RJ, Berrang ME, Davis JA, Barrett JB, Turpin JB, Thitaram SN, Fedorka-Cray PJ, “Development of a DNA Microarray to Detect Antimicrobial Resistance Genes Identified in the National Center for Biotechnology Information Database” (opens in new tab), Microbial Drug Resistance, vol. 16, no. 1, pp. 9–19, 2010.
- Kucerova E, Clifton SW, Xia X-Q, Long F, Porwollik S, “Genome Sequence of Cronobacter sakazakii BAA-894 and Comparative Genomic Hybridization Analysis with Other Cronobacter Species” (opens in new tab), PLoS ONE, vol. 5, no. 3, pp. e9556, 2010.
- Xiao-Qin Xia, Zhenyu Jia, Steffen Porwollik, Fred Long, Claudia Hoemme, Kai Ye, Carsten Müller-Tidow, Michael McClelland, Yipeng Wang, “Evaluating oligonucleotide properties for DNA microarray probe design” (opens in new tab), Nucleic Acids Research, vol. 38, pp. 1–10, 2010.
- Yan Li, Jingyi Yu, Yipeng Wang, Noelle M. Griffin, Fred Long, Sabrina Shore, Phil Oh, Jan E. Schnitzer, “Enhancing identifications of lipid-embedded proteins by mass spectrometry for improved mapping of endothelial plasma membranes in vivo” (opens in new tab), Molecular and Cellular Proteomics, vol. 8, pp. 1219-1235, 2009.
- Carlos A. Santiviago, M. Megan Reynolds, Steffen Porwollik, Sang-Ho Choi, Fred Long, Helene L. Andrews-Polymenis, Michael McClelland, “Analysis of Pools of Targeted Salmonella Deletion Mutants Identifies Novel Genes Affecting Fitness during Competitive Infection in Mice” (opens in new tab), PLoS Pathogens, vol. 5, no. 7, pp. e1000477, 2009.
- Arrach N., Porwollik S., Cheng P., Cho A., Long F., Choi S-H., McClelland M., “Salmonella serovar identification using PCR-based detection of gene presence and absence” (opens in new tab), Journal of Clinical Microbiology, vol. 46, pp. 2581-2589, 2008.
- Yipeng Wang, Fred Long, Cecilia Urbina, Xiaoqin Xia, Michael McClelland, “High throughput high resolution DNA methylation profiling in prostate cancer cell lines”, Proc Amer Assoc Cancer Res, vol. 47, 2006.
- Frye JG, Jesse T, Long F, Rondeau G, Porwollik S, McClelland M, Jackson CR, Englen M, Fedorka-Cray PJ, “DNA microarray detection of antimicrobial resistance genes in diverse bacteria” (opens in new tab), International Journal of Antimicrobial Agents, vol. 27, pp. 138-51, 2006.
- Wang Y, Hayakawa J, Long F, Yu Q, Cho AH, Rondeau G, Welsh J, Mittal S, DE Belle I, Adamson E, McClelland M, Mercola D, “Promoter array studies identify cohorts of genes directly regulated by methylation, copy number change, or transcription factor binding in human cancer cells” (opens in new tab), Annals of the New York Academy of Sciences, vol. 1058, pp. 162–185, 2005.
- S. Chatterjee, J. R. Gilbert, F. J. E. Long, R. Schreiber, S.-H. Teng, “Generating Local Addresses and Communication Sets for Data-parallel Programs” (opens in new tab), Journal of Parallel and Distributed Computing, vol. 26, no. 1, pp. 72-84, 1995.
- S. Chatterjee, J. Gilbert, F. Long, R. Schreiber, S. Teng, “Generating Local Addresses and Communication Sets for Data Parallel Programs” (opens in new tab), ACM SIGPLAN Notices, vol. 28, no. 7, pp. 149-158, 1993.
- Pat-Anthony Federico, Randy R. Ullrich, Brian L. Van de Wetering, Christel I. Tomlinson, Dean R. E. Long, Fred J. E. Long, Thomas E. Bridges, “Human-Computer Interfaces for Tactical Decision Making, Analysis, and Assessment Using Intelligent Platforms: Volume I, Software Design and Database Descriptions for BATMAN & ROBIN”, NPRDC-TN-91-20, 1991.
- Kasi Anantha, Fred Long, “Code Compaction for Parallel Architectures” (opens in new tab), Software—Practice & Experience, vol. 20, no. 6, pp. 537-554, 1990.
Contact Information
Email: flong1@uci.edu
Phone: (949) 824-2583
Address: Med Surge I, Room 132, Irvine, CA 92697-4025
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Last updated on 3/12/2026.