This document provides a summary of Oleg Alferov's research interests and professional experience. He has over 20 years of experience developing algorithms and software for statistical analysis, pattern recognition, genomics sequencing, and modeling complex systems. Some of his past roles include senior computational research scientist at Complete Genomics where he developed algorithms for sequencing data analysis, and assistant mathematician at Argonne National Laboratory where he created software for processing DNA databases and analyzing microarray data. He holds a Ph.D. in Physics and Mathematics from the Russian Academy of Sciences and has authored over 10 publications and presentations in the fields of genomics and bioinformatics.

1. OLEG ALFEROV, PH.D.
1111 W. El Camino Real, Ste 109-289
Sunnyvale, CA 94087
Phone: (630) 460-0267
Email: oalferov1@gmail.com
work@secoh.net
RESEARCH INTERESTS
• Development of high-speed algorithms for statistical analysis of experimental
data, pattern recognition, signals detection.
• Algorithms for genomics sequence search, mapping, indexing.
• Development of custom research software.
• Computer modeling of complex systems.
• Development of software-hardware systems for scientific or experimental
devices, custom software controls.
PROFESSIONAL EXPERIENCE
COMPLETE GENOMICS, INC, Mountain View, California, USA
Sr. Computational Research Scientist May 2008–Nov 2016
• Developed statistical model of readout signals from sequencing instrument in
various operating modes. Created high-speed algorithm based on this model for
data detection and recovery. Performance better than “naive” methods was
demonstrated.
• Developed high-speed multithreaded indexing modules for applications in
genome mapping and deNovo assembly. Indexed fragment sizes varied from as
short as 5-base to theoretically unlimited length. Emphasis was made to compact
data representation and low overheads, as well as moderate creation time.
• Created software pipeline to support LFR (Long Read Fragments) technology.
Suggested simple method to detect candidates to long Structural Variation of
test subject’s genome by processing LFR sequencing.
• Developed simple but efficient mapper for genomics reads comprising of short
chunks separated by variable distance.
• Developed software to simulate experimental data.
• Developed custom high-speed compressor for genomics sequences and
alignments. Developed fast program to find unique (or repeating) substring in
very large genomics sequence.
• Created multiple in-house C/C++ and script programs to process data from
experimental lab.

2. AURORA PHOTONICS, INC, Lake Barrington, Illinois, USA
Software Consultant 2005–2008
• Adaptation of software licensed by the company to the production devices;
development and optimization of data processing schemes; testing of newly
acquired or developed hardware;
• Developed microprocessor-controlled portable high-speed precision thermal
table with wide range of temperature stabilization. Available for live
demonstration.
ARGONNE NATIONAL LABORATORY, Argonne, Illinois, USA
Biochip Technology Center, Energy Systems Division
Assistant Mathematician 1999–2007
• Developed high-speed tools for processing of large-scale DNA sequence
database, used for selection of hybridization probes for individual
microorganisms and their phylogenetic groups.
• Developed automated statistical algorithms for high-speed pathogen recognition
with high reliability of interpretation and low probability of false-positive calls
using hybridization image acquired by CCD camera.
• Developed fully automated laboratory fluorescent scanning microscope with
uniform illumination, multicolor capability, wide-range temperature
stabilization, fast temperature response, and humidity control. This device is
used in the Biochip Center at Argonne as a tool for biological experiments with
hybridization microarrays, including thermal dissociation experiments.
• Developed control software for the microscopic equipment in the Biochip
Center at Argonne, to conduct experiments, acquire and analyze images, and
retrieve numerical data. The project included creation of custom drivers for
various CCD cameras and other hardware controllers. Demo version of the
software is available for demonstration.
• Developed tool for analysis of thermal dissociation curves that calculates the
transition temperature and the speed of transition, which is immune to
experimental noise.
• Participated in development of the portable version of the thermally controlled
laser-powered multicolor microscope.
• Participated in development of drivers and control software for custom
microarray manufacturing robots.
• Participated in development of databases for biochip manufacture and quality
control.
• Administrated local file server (Linux) for group of 15 researchers for data
access and file sharing in heterogeneous computing environment (1 Linux, 2
Macs, 4 Winows 95, all other were Windows 2000/XP).

3. RUSSIAN ACADEMY OF SCIENCES, Moscow, Russia
Institute for Problems in Mechanics
Research Associate 1995–1999
• Developed differential numerical scheme for calculation of turbulent flow with
presence of Coriolis force and small obstacles on the surface.
• Created a tool for web-based data upload and retrieval with configurable
permissions.
• Developed microcontroller-portable Morse code reader and transmitter with
automatic recognition, adjustment of reception, and logging capability via serial
port.
MOSCOW STATE UNIVERSITY, Moscow, Russia
Student 1990–1995
• Studied turbulent flow of liquid over a rotating rough surface and numerical and
analytical methods for solving differential equations.
PROFESSIONAL SKILLS
• Applied mathematics: statistical models, numerical methods, combinatorics,
Fourier transform, curve fitting, custom process models, pattern recognition.
• Bioinformatics: alignments, phylogenetic trees, probe selection, indexing, LFR.
• Parallel computing.
• Programming and scripting languages: C/C++, MATLAB, MCR, awk, bash,
LabVIEW, PHP, TeX; also worked with Python, SQL, Basic/Visual Basic,
Pascal/Delphi, FORTRAN, FoxPro, JavaScript.
• Fluorescent microscopy, geometry optics.
• Basic electronics design, microcontroller-based systems.
• Computer platforms: Windows, Linux, DOS, MSX-1/2, PDP/RSX.
• Microcontroller platforms: Zilog eZ80, Basic Stamp; also: Rabbit2000.
• Familiar with database tools: MS Access, MySQL, ODBC interface.
EDUCATION
RUSSIAN ACADEMY OF SCIENCES, Moscow, Russia.
Institute for Problems in Mechanics
Ph.D., Physics and Mathematics 1999
Supervisor: Dr. Alexander G. Petrov
MOSCOW STATE UNIVERSITY, Moscow, Russia.
Faculty of Mechanics and Mathematics
M.S., Mechanics, Applied Mathematics 1995

4. PATENTS
 U.S. Patent #9,514,272
Kermani; Bahram Ghaffarzadeh, Drmanac; Radoje, Alferov; Oleg
Identification of DNA fragments and structural variations
December 6, 2016
 U.S. Patent #6,620,623
Gennady Yershov, Oleg Alferov, Alexander Kukhtin
Biochip Reader with Enhanced Illumination and Bioarray Positioning Apparatus
September 16, 2003
 U.S. Patent Application #20070201734
Oleg Alferov
Automated multicolor fluorescent microscope with scanning and thermostatic
ability
Filed: August 30, 2007
SOFTWARE COPYRIGHTS
• MicroChip Imager, Argonne National Laboratory, 2002.
• MicroChip Reader, Argonne National Laboratory, 2002.
• Universal Positioner, Argonne National Laboratory, 2004.
HONORS AND AWARDS
Argonne National Laboratory Pacesetter Award, 2001.
CITIZENSHIP
US Citizen.
Retained Russian citizenship.

5. PUBLICATIONS AND PRESENTATIONS
1. Peters B., Kermani B., Sparks A., Alferov O., Hong P., Alexeev A., Jiang Y.,
Dahl F., Tang Y. T., Haas J., Robasky K., Zaranek A. W., Lee J., Ball M. P.,
Peterson J. E., Perazich H., Yeung G., Liu J., Chen L., Kennemer M. I.,
Pothuraju K., Konvicka K., Tsoupko-Sitnikov M., Pant K. P., Ebert J. C., Nilsen
G. B., Baccash J., Halpern A. L., Church G. M., Drmanac R. Accurate whole-
genome sequencing and haplotyping from 10 to 20 human cells. NATURE, 12
JULY 2012, Vol.487, pp.190-195.
2. Peters B. A., Kermani B. G., Alferov O., Agarwal M. R., McElwain M. A.,
Gulbahce N., Hayden D. M., Tang Y. T., Zhang R. Y., Tearle R., Crain B.,
Prates R., Berkeley A., Munne S., Drmanac R. Detection and phasing of single
base de novo mutations in biopsies from human in vitro fertilized embryos by
advanced whole-genome sequencing. Genome Res. February 11, 2015, 25: 426-
434, doi:10.1101/gr.181255.114.
3. Bavykin S., Mikhailovich V., Zakharyev V., Lysov Y., Kelly J., Alferov O.,
Gavin I., Kukhtin A., Jackman J., Stahl D., Chandler D., Mirzabekov A.
Discrimination of Bacillus anthracis and closely related microorganisms by
analysis of 16S and 23S rRNA with oligonucleotide microarray. Chemico-
Biological Interaction, 2007, doi:10.1016/j.cbi.2007.09.002.
4. Bavykin S., Yershov G., KellyJ., Kukhtin A., Alferov O., Chernov B, Golova J.,
Perov A., Chandler D. Portable System For Microbial Sample Preparation And
Bacillus Cereus Group Pathogen Analysis With Oligonucleotide Microarray.
Chemico-Biological Interactions, 161(3) 177, 2006.
5. Bavykin S., Yershov G., Kelly J., Kukhtin A., Alferov O., Chernov B., Golova
J., Perov A. Chandler D. Portable System for Microbial Sample Preparation and
Bacillus cereus Group Pathogen Analysis with Oligonucleotide Microarray.
Argonne National Laboratory, Argonne, USA, 2006.
6. Chandler D. P., Alferov O., Chernov B., Daly D. S., Golova J., Perov A., Protic
M., Robison R., Schipma M., White A., Willse A. Diagnostic Oligonucleotide
Microarray Fingerprinting of Bacillus Isolates. J. of Clinical Microbiology, Jan.
2006, pp. 244–250
7. Bavykin S., Lysov Y., Zakhariev V., Kelly J., Alferov O., Kukhtin A., Ershov
G., Chernov B., Golova J., Jackman J., Stahl D., Cherni A., Chandler D. rRNA
and gyrB Genes as a New Tool for Identification of Bacillus cereus Group
Microorganisms. 4th
SISPAT Singapore International Symposium on Protection
Against Toxic Substances, Singapore, 2004.
8. Yershov G., Kukhtin A., Chernov B., Golova J., Alferov O., Nelson M.,
Chandler D. Characterization and Standardization of "Biochip-Sample-Reader"
System. IBC’s 11th
Annual International Microarray and Microtechnology
Conference (Chips to Hits), Boston, USA, 2004.
9. Yershov G., Alferov O., Kukhtin A., Pates D., Perov A., Nelson M., Chernov
B., Golova J., Pedrac C. Development of Multicolor Reader With
Thermocontrolled Biochip Holder And Flow Cell Option. Argonne National
Laboratory, Argonne, USA, 2004.

6. 10. Yershov G., Alferov O., Kukhtin A. Instrument and Software for Bacteria
Identification on 3D Biochip Platform. Biological Agent Identification
Technologies (BAIT 2002, DARPA), LasVegas, USA, 2002.
11. Kukhtin A., Alferov O., Yershov G., Bavykin S., Hamman K., Regunathan A.,
Bronuskas J. Detection Limits for Bacteria Identification and Reusability for
ANL 3D Biochip Platform. Biological Agent Identification Technologies (BAIT
2002, DARPA), LasVegas, USA, 2002.
12. Jackman J., Bavykin S., Sullivan P., Kukhtin A., Yershov G., Alferov O.,
Kelly J., Stahl D. Rapid species-specific identification of bacteria without PCR
using microarray technology. Sensors, and Command, Control,
Communications, and Intelligence (C3I) Technologies for Homeland Defense
and Law Enforcement. Proc. of SPIE, Vol. 4708. AeroSense, 2002.
13. Jackman J., Bavykin S., Sullivan P., Barsky V., Kukhtin A., Yershov G.,
Alferov O., Kelly J., Stahl D., Mirzabekov A. Rapid Species-Specific
Identification Of Bacteria Without PCR. Seventh Int. Symposium on Protection
Against Chemical and Biological Warfare Agents, Stockholm, Sweeden, 2001.
14. Alferov O.S., Nekrasov I.V., Petrov A.G. Turbulent Flow over a Gently
Sloping Two-Dimensional Hill. Izvestia, Atmospheric and Oceanic Physics,
Vol. 36, No. 1, 2000, pp. 48-56.
15. Alferov O.S., Petrov A.G. Two-Layer Turbulent Flow Over a Rough Rotating
Surface. Fluid Dynamics, Vol. 30, No. 4, 1995, pp. 537-543.
16. Alferov O.S., Petrov A.G. Turbulent Flow Over Rotating Rough Surface. Proc.
of the Second Int. Conf. AiM’96, Saint Petersburg, Russia, 1997, pp.1-8.
PERSONAL INTERESTS
Amateur Radio Operator (WD6SK);
Civil Air Patrol volunteer;
Private Pilot;
Other: photography, biking, sailing, science fiction, mountain hiking.
REFERENCES
Available upon request.