OLIVER SERANG

CITIZENSHIP /USA

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POSITIONS HELD
WHERE ARE YOU GOING, WHERE HAVE YOU BEEN?

OCTOBER 2023 -- FEBRUARY 2024
CHICAGO, IL

SENIOR SOFTWARE ENGINEER @WOLVERINE TRADING
Wrote low-latency C++ for use in options trading. Benchmarked techniques at nanosecond level and developed strategies for improving latency of core trading systems. Found and made >10% speedup to overall trade latency, which is applicable to all company trading engines. Scored 92.6% on options trading final exam.

NOVEMBER 2021 -- AUGUST 2023
SEATTLE, WA

SENIOR MACHINE LEARNING SCIENTIST @A-ALPHA BIO
Solved problems and created machine learning tools and models at scale. Programming in C++, Python, basic GPU/multi-GPU computing, using Amazon EC2. Pioneered successful ML strategy for custom Ab design: As first ML hire, designed core ML stack and models (sole author as of Aug 2022); the current version of this ML platform is now branded as "AlphaBind®". Built other critical infrastructure and maths capabilities at a Series A startup company. Designed and implemented the company's generative AI infrastructure for antibodies. Scaled inference to >1B Ab sequences. Designed and implemented new algorithms for solving combinatoric problems that arise in Ab engineering, DNA synthesis, expression, discovery, and statistical analysis. Contributed to a successful fundraising cycle. Discovered simple generalization of Wasserstein distance using higher moments. In passing, invented novel, simple linear algorithm for selection on a list. Designed company t-shirt for 2021.

AUGUST 2017 -- OCTOBER 2021
MISSOULA, MONTANA

ASSISTANT PROFESSOR @UNIVERSITY OF MONTANA
DEPT. OF COMPUTER SCIENCE, COLLEGE OF HUMANITIES AND SCIENCES

Wrote object oriented software in C, C++, and python. Developed new algorithms for combinatoric problems, including a novel, optimal algorithm for selection on Cartesian products. My implementation (written with students) of this algorithm powers the current fastest exact isotope calculator. Instructor of record for algorithms, optimization of C++ code, and cybersecurity. Created basic C++ vector class for primitive data that is ~7x faster than std::vector. With student, wrote template-recursive, AVX512 Strassen-Winograd implementation outperforming BLAS. Mentored graduate and undergradaute students. Taught six unique course preps. Wrote >700 pages of publicly available course notes, including on algorithms and on C++. Created The Junior Guide to Combinatorial Chemistry, a client-side interactive webpage that teaches basic programming from up to dynamic programming and teaches basic chemistry and physics up to relativistic mass defect. Awarded over 1.8M USD in total grant funding (direct + indirect).

AUGUST 2018 -- OCTOBER 2021
MISSOULA, MONTANA

FACULTY AFFILIATE @UNIVERSITY OF MONTANA
DEPT. OF BIOCHEMISTRY

MAY 2015 -- JULY 2017
BERLIN, GERMANY

JUNIORPROFESSOR (W1, PROF. DR.) / CHAIR OF METAGENOMICS @FREIE UNIVERSITÄT BERLIN
DEPT. OF BIOINFORMATIK / INFORMATIK / MATHEMATIK
Taught three unique course preps. Mentored graduate students. Wrote object oriented software in C++. Created C++ cache-oblivious bit-reversal method for template-recursive FFT. Created new moment-based approximation algorithm for building fast semiring algorithms like max-convolution. Created C++ engine for inference on probabilistic cardinal graphical models. Wrote template-recursive C++ library for efficient operations on tensors.

MAY 2015 -- JULY 2017
KÖPENICK, GERMANY

JANUARY 2014 -- APRIL 2014

AUGUST 2013 -- DECEMBER 2014
BREMEN, GERMANY

SOFTWARE RESEARCH SCIENTIST @THERMO FISHER SCIENTIFIC
Wrote software in C# and C++. Built dynamic programming algorithms for cardinal graphical models, shipped in Thermo Fisher's Proteome Discoverer™. Optimized existing code. Prepared a patent, and helped protect against infringement of existing IP.

JANUARY 2014 -- JUNE 2014
BREMEN, GERMANY

LECTURER @UNIVERSITÄT BREMEN
Developed a course in scientific computing.

JULY 2011 -- JUNE 2013
BOSTON, MASSACHUSETTS

RESEARCH FELLOW @HARVARD MEDICAL SCHOOL & BOSTON CHILDREN'S HOSPITAL
DEPT. OF NEUROBIOLOGY AND DEPT. OF PATHOLOGY
ADVISORS: PROF. JUDITH STEEN & PROF. HANNO STEEN
Wrote object oriented software in C++ and python. Created de novo mass spectrometry algorithms. Wrote and implemented a Dirichlet-based goodness of fit measure for determining the location of diminishing returns in false discovery rate curves.

MAY 2013 -- JULY 2013
PIRACICABA, BRAZIL

VISITING SCIENTIST @UNIVERSITY OF SÃO PAULO ESALQ
DEPT. OF AGRONOMY
LAB OF PROF. ANTONIO AUGUSTO FRANCO GARCIA

SEPTEMBER 2006 -- APRIL 2011
SEATTLE, WASHINGTON

JUNE 2003 -- JULY 2006
RALEIGH, NORTH CAROLINA

TECHNICIAN @NORTH CAROLINA STATE UNIVERSITY
LABS OF PROF. JEFF THORNE, PROF. BRUCE WEIR

AUGUST 2002 -- MAY 2006
RALEIGH, NORTH CAROLINA

B.S. COMPUTER ENGINEERING @NORTH CAROLINA STATE UNIVERSITY
SENIOR DESIGN PROJECT: EPISTATIC ASSOCIATION MAPPING WITH UNDERDETERMINED SAMPLE SIZES USING NEURAL NETWORKS [ADVISED BY PROF. HIROHISA KISHINO @UNIVERSITY OF TOKYO]


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PUBLICATIONS (KEY PUBLICATIONS BOLDED)
THE NACHMAN STORIES

2021
JOURNAL OF MACHINE LEARNING RESEARCH

"ON SOLVING PROBABILISTIC LINEAR DIOPHANTINE EQUATIONS"
P. KREITZBERG, O. SERANG

2021
PEERJ COMPUTER SCIENCE

"SELECTION ON X_1+ X_2+⋯+ X_M VIA CARTESIAN PRODUCT TREES"
P. KREITZBERG, K. LUCKE, J. PENNINGTON, O. SERANG

2021
PEERJ COMPUTER SCIENCE

"OPTIMALLY SELECTING THE TOP K VALUES FROM X+Y WITH LAYER-ORDERED HEAPS"
O. SERANG

2021
JOURNAL OF PROTEOME RESEARCH

"PERFORMING SELECTION ON A MONOTONIC FUNCTION IN LIEU OF SORTING USING LAYER-ORDERED HEAPS"
K. LUCKE, J. PENNINGTON, P. KREITZBERG, L. KÄLL, O. SERANG

2020
ANALYTICAL CHEMISTRY

"FAST EXACT COMPUTATION OF THE K MOST ABUNDANT ISOTOPE PEAKS WITH LAYER-ORDERED HEAPS"
P. KREITZBERG, J. PENNINGTON, K. LUCKE, O. SERANG

2020
JOURNAL OF PROTEOME RESEARCH

"EPIFANY: A METHOD FOR EFFICIENT HIGH-CONFIDENCE PROTEIN INFERENCE"
J. PFEUFFER, T. SACHSENBERG, T. DIJKSTRA, O. SERANG, K. REINERT, O. KOHLBACHER

2019
JOURNAL OF PROTEOME RESEARCH

"ALPHABET PROJECTION OF SPECTRA"
P. KREITZBERG, M. BERN, Q. SHU, F. YANG, O. SERANG

2017
PROGRAMMING

"TRIOT: FASTER TENSOR MANIPULATION IN C++11"
F. HEYL & O. SERANG

2016
BBA - PROTEINS AND PROTEOMICS

"YEAST MEMBRANE PROTEOMICS USING LEUCINE METABOLIC LABELLING: BIOINFORMATIC DATA PROCESSING AND EXEMPLARY APPLICATION TO THE ER-INTRAMEMBRANE PROTEASE YPF1"
L. NILSE, D. AVCI, P. HEISTERKAMP, O. SERANG, M. LEMBERG, O. SCHILLING

2016
JOURNAL OF MACHINE LEARNING RESEARCH

"A BOUNDED P-NORM APPROXIMATION OF MAX-CONVOLUTION FOR SUB-QUADRATIC BAYESIAN INFERENCE ON ADDITIVE FACTORS"
J. PFEUFFER & O. SERANG

2015
JOURNAL OF PROTEOME RESEARCH

"THE SOLUTION TO STATISTICAL CHALLENGES IN PROTEOMICS IS MORE STATISTICS, NOT LESS"
O. SERANG & L. KÄLL

2015
JOURNAL OF COMPUTATIONAL BIOLOGY

"A FAST NUMERICAL METHOD FOR MAX-CONVOLUTION AND THE APPLICATION TO EFFICIENT MAX-PRODUCT INFERENCE IN BAYESIAN NETWORKS"
O. SERANG

2014
PLOS ONE

"THE PROBABILISTIC CONVOLUTION TREE: EFFICIENT EXACT BAYESIAN INFERENCE FOR FASTER LC-MS/MS PROTEIN INFERENCE"
O. SERANG

2013
NATURE SCIENTIFIC REPORTS

"SNP GENOTYPING ALLOWS AN IN-DEPTH CHARACTERIZATION OF THE GENOME OF SUGARCANE AND OTHER COMPLEX AUTOPOLYPLOIDS"
A.A.F. GARCIA, M. MOLLINARI, T. MARCONI, O. SERANG, R. SILVA, R. VICENTINI, E. COSTA, M. MANCINI, M. GARCIA, M. PASTINA, R. GAZAFFI, P. BUNDOCK, R. HENRY, M. SLUYS, M. LANDELL, M. CARNEIRO, M. VINCENTZ, L. PINTO, R. VENCOVSKY, A.P. SOUZA

2013
JOURNAL OF PROTEOME RESEARCH

"NONPARAMETRIC BAYESIAN EVALUATION OF DIFFERENTIAL PROTEIN QUANTIFICATION"
O. SERANG, A.E. CANSIZOGLU, L. KÄLL, H. STEEN, J.A. STEEN

2013
SPRINGER METHODS IN MOLECULAR BIOLOGY [INVITED BOOK CHAPTER]

"QUANTITATIVE SNP GENOTYPING OF POLYPLOIDS WITH MASSARRAY AND OTHER PLATFORMS"
O. SERANG, M. MOLLINARI

2013
MOLECULAR & CELLULAR PROTEOMICS

"SWEETSEQER: SIMPLE DE NOVO FILTERING AND ANNOTATION OF GLYCOCONJUGATE MASS SPECTRA"
O. SERANG*, J. FROEHLICH*, J. MUNTEL, G. MCDOWELL, H. STEEN, R. LEE, J.A. STEEN
*CONTRIBUTED EQUALLY

2013
MOLECULAR & CELLULAR PROTEOMICS

"A CLASSIFIER BASED ON ACCURATE MASS MEASUREMENTS TO AID LARGE-SCALE, UNBIASED GLYCOPROTEOMICS"
J. FROEHLICH, E. DODDS, M. WILHELM, O. SERANG, J.A. STEEN, R. LEE

2013
MOLECULAR & CELLULAR PROTEOMICS

"A NON-PARAMETRIC CUTOUT INDEX FOR ROBUST EVALUATION OF IDENTIFIED PROTEINS"
O. SERANG, J. PAULO, H. STEEN, J.A. STEEN

2013
BIOINFORMATICS

"CONCERNING THE ACCURACY OF FIDO AND PARAMETER CHOICE"
O. SERANG

2012
PLOS ONE

"CONIC SAMPLING: AN EFFICIENT METHOD FOR SOLVING LINEAR AND QUADRATIC PROGRAMMING BY RANDOMLY LINKING CONSTRAINTS WITHIN THE INTERIOR"
O. SERANG

2012
JOURNAL OF PROTEOME RESEARCH

"RECOGNIZING UNCERTAINTY INCREASES ROBUSTNESS AND REPRODUCIBILITY OF MASS SPECTROMETRY-BASED PROTEIN INFERENCES"
O. SERANG, L. MORUZ, M. HOOPMANN, L. KÄLL

2012
IEEE TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

"FASTER MASS SPECTROMETRY-BASED PROTEIN INFERENCE: JUNCTION TREES ARE MORE EFFICIENT THAN SAMPLING AND MARGINALIZATION BY ENUMERATION"
O. SERANG & W.S. NOBLE

2012
PLOS ONE

"EFFICIENT EXACT MAXIMUM A POSTERIORI COMPUTATION FOR BAYESIAN SNP GENOTYPING IN POLYPLOIDS"
O. SERANG, M. MOLLINARI, A.A.F. GARCIA

2012
STATISTICS AND ITS INTERFACE

"A REVIEW OF STATISTICAL METHODS FOR PROTEIN IDENTIFICATION USING TANDEM MASS SPECTROMETRY"
O. SERANG & W.S. NOBLE

2010
JOURNAL OF PROTEOME RESEARCH

"EFFICIENT MARGINALIZATION TO COMPUTE PROTEIN POSTERIOR PROBABILITIES FROM SHOTGUN MASS SPECTROMETRY DATA"
O. SERANG, M. MACCOSS, W.S. NOBLE

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NON-REFEREED PAPERS
NOTES FROM THE UNDERGROUND

2022

"MEDIAN OF HEAPS: LINEAR-TIME SELECTION BY RECURSIVELY CONSTRUCTING BINARY HEAPS"
O. SERANG

2022

"ADVERSARIAL NETWORK TRAINING USING HIGHER-ORDER MOMENTS IN A MODIFIED WASSERSTEIN DISTANCE"
O. SERANG

2017

"PRACTICALLY EFFICIENT METHODS FOR PERFORMING BIT-REVERSED PERMUTATION IN C++11 ON THE x86-64 ARCHITECTURE"
C. KNAUTH, B. ADAS, D. WHITFIELD, X. WANG, L. ICKLER, T. CONRAD, O. SERANG


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TEXTBOOKS, COURSE NOTES, AND COURSE MATERIALS
MY SIDE OF THE MOUNTAIN

2020

2019

"ALGORITHMS IN PYTHON" [TEXT]
O. SERANG

2019

2018

"CODE OPTIMIZATION IN C++11" [TEXT]
O. SERANG


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INVITED SEMINARS
THE VISITOR

2021
A-ALPHA BIO
SEATTLE, WA

"MACHINE LEARNING FOR MASS SPECTROMETRY AND FOR Ab DISCOVERY"

2021
COMPUTER SCIENCE, IDAHO STATE UNIVERSITY
IDAHO FALLS, IDAHO

"AN OPTIMAL ALGORITHM FOR SELECTION ON X+Y: LAYER-ORDERED HEAPS AND THE CURRENT FASTEST ISOTOPE CALCULATOR FOR CHEMICAL COMPOUNDS"

2020
COMPUTER SCIENCE, MONTANA STATE UNIVERSITY
BOZEMAN, MONTANA

"AN OPTIMAL ALGORITHM FOR GENERATING THE SMALLEST K VALUES IN A CARTESIAN SUM"

2019
BIOCHEMISTRY, UNIVERSITY OF CALGARY
CALGARY, CANADA

"BIG DATA HUNTING CLUB"

2017
PROGRAMMING 2017 [CONFERENCE]
BRUSSELS, BELGIUM

"TRIOT: FASTER TENSOR MANIPULATION IN C++11"

2017
UNIWERSYTET WARSZAWSKI
WARSAW, POLAND

"APPROXIMATING ALGORITHMS ON SEMIRINGS BY EXTRAPOLATING MOMENTS VIA FAST ALGORITHMS ON Lp SPACES"

2017
COMPUTER SCIENCE, UNIVERSITY OF MONTANA
MISSOULA, MONTANA

"ALGORITHMS FOR PROCESSING HIGH-DIMENSIONAL DISTRIBUTIONS"

2016
LEIDEN UNIVERSITY MEDICAL CENTER
LEIDEN, NETHERLANDS

"ANALYSIS OF *OMICS DATA: NEW DYNAMIC PROGRAMMING ALGORITHMS FOR PUTTING THE LEGOS BACK TOGETHER"

2016
SYSTEMS BIOLOGY, ETH ZÜRICH
LEISSIGEN, SWITZERLAND

[FACULTY PANELIST IN CAREER ROUNDTABLE DISCUSSION]

2016
SYSTEMS BIOLOGY, ETH ZÜRICH
LEISSIGEN, SWITZERLAND

"LOW-LEVEL OPTIMIZATIONS IN COMPUTATIONAL BIOLOGY: REACHING FOR THE HIGHER-HANGING FRUIT"

2016
SCHLOß DAGSTUHL
WADERN, GERMANY

"EVERGREEN: INSIDE AN ENGINE FOR FAST BAYESIAN INFERENCE"

2016
SCHLOß DAGSTUHL
WADERN, GERMANY

"EXPLOITING SYMMETRIES TO PERFORM FAST P-NORM INFERENCE FOR PROTEOMICS"

2016
SCILIFELAB, KTH ROYAL INSTITUTE OF TECHNOLOGY
STOCKHOLM, SWEDEN

"AN ENGINE FOR FASTER BAYESIAN ANALYSIS"

2015
STATISTICS, NORTH CAROLINA STATE UNIVERSITY
RALEIGH, NORTH CAROLINA

"DYNAMIC PROGRAMMING FOR BAYESIAN METAGENOMICS: CONVOLUTION TREES, FAST MAX-CONVOLUTION, A NOVEL APPROACH TO SORTING X+Y, AND FASTER ALL-PAIRS SHORTEST PATHS SOLUTION"

2015
FREIBURG UNIVERSITY
FREIBURG, GERMANY

"THE NECESSARILY COMPUTATIONAL AND STATISTICAL FUTURE OF PROTEOMICS"

2015
UNIVERSITÄT TÜBINGEN
TÜBINGEN, GERMANY

"A FAST AND GENERIC INFERENCE ENGINE FOR PROTOTYPING AND HARNESSING GRAPHICAL MODELS"

2015
OPENMS USER MEETING [CONFERENCE]
BOCHUM, GERMANY

"FAST COMBINATORICS AND THE ANALYSIS OF BIG DATA IN MS/MS"

2015
SCILIFELAB, KTH ROYAL INSTITUTE OF TECHNOLOGY
STOCKHOLM, SWEDEN

"FAST NUMERICAL MAX-CONVOLUTION: A FAST NEW NUMERICAL METHOD FOR THE GRAPHICAL BAYESIAN ANALYSIS OF META*OMICS MIXTURES"

2014
THE BERLIN CENTER FOR GENOMICS IN BIODIVERSITY RESEARCH
BERLIN, GERMANY

"PUTTING THE LEGOS BACK TOGETHER AGAIN: A FORMAL FRAMEWORK FOR CHARACTERIZING METAGENOMIC MIXTURES"

2014
ROBERT KOCH INSTITUTE
BERLIN, GERMANY

"THE CONVOLUTION TREE: A NEW SUBQUADRATIC DYNAMIC PROGRAMMING ALGORITHM"

2014
FREIE UNIVERSITÄT BERLIN / LEIBNIZ INSTITUTE OF FRESHWATER ECOLOGY AND INLAND FISHERIES
BERLIN, GERMANY

"THE COMBINATORIC CHALLENGES OF SHARED DATA IN *OMICS AND META*OMICS"

2014
INFORMATIK, UNIVERSITÄT BREMEN
BREMEN, GERMANY

"THE CONVOLUTION TREE: A SUBQUADRATIC DYNAMIC PROGRAMMING ALGORITHM FOR EXACT PROBABILISTIC INFERENCE"

2013
AUSTRIAN PROTEOMICS ASSOCIATION (AUPA)
SALZBURG, AUSTRIA

"THE REVOLUTION WILL NOT BE PARAMETERIZED: NONPARAMETRICS AND THE NEXT GENERATION OF VALIDATION FOR HIGH-THROUGHPUT PROTEOMICS"

2013
MATHWORKS
NATICK, MASSACHUSETTS

"THE REVOLUTION WILL NOT BE PARAMETERIZED: ROBUST GRAPHICAL INFERENCE ON HIGH-THROUGHPUT DATA AND A NONPARAMETRIC BAYESIAN ALTERNATIVE TO KULLBACK-LEIBLER DIVERGENCE AND THE KOLMOGOROV-SMIRNOV TEST"

2013
AMERICAN SOCIETY FOR MASS SPECTROMETRY (ASMS) [CONFERENCE]
MINNEAPOLIS, MINNESOTA

"AVOIDING ARBITRARY PARAMETERS IN QUANTITATIVE PROTEOMICS: IS `DIFFERENTIAL' A 1.1-FOLD OR 1.2-FOLD CHANGE?"

2012
SCILIFELAB, KTH ROYAL INSTITUTE OF TECHNOLOGY
STOCKHOLM, SWEDEN

"A GENERIC GRAPHICAL METHOD FOR USING EMPIRICAL NULL DISTRIBUTIONS IN THE ROBUST EVALUATION OF DISCOVERIES"

2012
AMERICAN SOCIETY FOR MASS SPECTROMETRY (ASMS) [CONFERENCE]
VANCOUVER, CANADA

"UNBIASED NONPARAMETRIC EVALUATION OF PROTEIN IDENTIFICATIONS IN SHOTGUN PROTEOMICS: 1 PEPTIDE IN 2 REPLICATES OR 2 PEPTIDES IN 1 REPLICATE?"

2014
MATHEMATICS, ROYAL INSTITUTE OF TECHNOLOGY (KTH)
STOCKHOLM, SWEDEN

"A GRAPHICAL, NONPARAMETRIC BAYESIAN APPROACH FOR THE ROBUST DECOMPOSITION OF MIXTURES"

2012
THERMO FISHER SCIENTIFIC
BREMEN, GERMANY

"A GRAPHICAL BAYESIAN APPROACH TO MASS SPECTROMETRY-BASED PROTEIN IDENTIFICATION"

2011
SCILIFELAB, KTH ROYAL INSTITUTE OF TECHNOLOGY
STOCKHOLM, SWEDEN

"ROBUST NONPARAMETRIC EVALUATION OF PROTEIN IDENTIFICATIONS IN SHOTGUN PROTEOMICS"

2011
UNIVERSITY OF SÃO PAULO ESALQ
PIRACICABA, BRAZIL

"EFFICIENT EXACT MAXIMUM A POSTERIORI COMPUTATION FOR BAYESIAN SNP GENOTYPING IN POLYPLOIDS"

2011
UNIVERSITY OF SÃO PAULO ESALQ
PIRACICABA, BRAZIL

"GRAPHICAL MODELS"

2011
HARVARD MEDICAL SCHOOL AND BOSTON CHILDREN'S HOSPITAL
BOSTON, MASSACHUSETTS

"A PRACTICALLY EFFICIENT GRAPH-THEORETIC APPROACH TO PROTEIN IDENTIFICATION IN MASS SPECTROMETRY"

2011
UNIVERSITY OF TORONTO
TORONTO, CANADA

"A PRACTICALLY EFFICIENT GRAPH-THEORETIC APPROACH TO PROTEIN IDENTIFICATION IN MASS SPECTROMETRY"

2011
PALO ALTO RESEARCH CENTER (PARC)
PALO ALTO, CALIFORNIA

"A PRACTICALLY EFFICIENT GRAPH-THEORETIC APPROACH TO PROTEIN IDENTIFICATION IN MASS SPECTROMETRY"

2009
AMERICAN SOCIETY OF MASS SPECTROMETRY (ASMS) [CONFERENCE]
PHILADELPHIA, PENNSYLVANIA

"A PROBABILISTIC ALGORITHM FOR PROTEIN IDENTIFICATION USING A SIMPLE, REALISTIC MODEL THAT RECOGNIZES DEGENERACY"

2008
INSTITUTE CURIE / ECOLE NATIONALE SUPERIEURE DES MINES
PARIS, FRANCE

"PROTEIN IDENTIFICATION WITH LINEAR OPTIMIZATION"


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FUNDING
DRACULA

GRANTS

@THE UNIVERSITY OF MONTANA:

  • PI, NSF CAREER: STATISTICAL METHODS AND ALGORITHMS FOR THE ANALYSIS OF COMBINATORIAL MASS SPECTROMETRY DATA (NSF, VALUE $751,309 DIRECT, $1,052,460 TOTAL)
  • CO-PI*, OVERCOMING COMBINATORIC COMPLEXITY PROBLEMS IN COMPUTATIONAL MASS SPECTROMETRY (NSF, VALUE $751,309 TOTAL)
    *CHANGE OF PI AFTER AWARDED SIMULTANEOUS WITH NSF CAREER GRANT
  • PI, COBRE GRANT, GRAPHICAL MODELS FOR COMPUTATIONAL BIOLOGY (NIH, VALUE $40716 DIRECT, $56916 TOTAL)
  • PI, UM PILOT PROJECT GRANT, DEVELOPMENT OF EVERGREENFOREST GRAPHICAL MODELS LIBRARY (VALUE $4928)

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TEACHING, MENTORING, AND OUTREACH
THE DHARMA BUMS

TEACHING

@THE UNIVERSITY OF MONTANA:

  • ALGORITHMS: SPRING 2021
  • COMPUTATIONAL LINGUISTICS: SPRING 2021
  • COMPUTATIONAL BIOLOGY: AUTUMN 2020
  • INTRODUCTION TO CYBERSECURITY: AUTUMN 2020
  • ALGORITHMS: SPRING 2020
  • NATURAL LANGUAGE PROCESSING: SPRING 2020
  • SOFTWARE OPTIMIZATION: AUTUMN 2019
  • INTRODUCTION TO CYBERSECURITY: AUTUMN 2019
  • ALGORITHMS: SPRING 2019
  • COMPUTATIONAL BIOLOGY / BIOINFORMATICS: SPRING 2019
  • INDEPENDENT STUDY (COMPILER DESIGN): AUTUMN 2018
  • INTRODUCTION TO COMPUTING IN THE SCIENCES: AUTUMN 2018
  • COMPUTATIONAL BIOLOGY / BIOINFORMATICS: AUTUMN 2018
  • INDEPENDENT STUDY (COMPILER DESIGN): SPRING 2018
  • ALGORITHMS: SPRING 2018
  • SOFTWARE OPTIMIZATION: AUTUMN 2017

@FREIE UNIVERSITÄT BERLIN:

  • SCIENTIFIC COMPUTING: WINTER 2016
  • SCIENTIFIC COMPUTING: SUMMER 2016
  • SCIENTIFIC COMPUTING: WINTER 2015
  • ALGORITHMS (WITH PROF. ALEXANDER BOCKMAYR): WINTER 2016
  • ALGORITHMS (WITH PROF. ALEXANDER BOCKMAYR): WINTER 2015
  • OPTIMIZATION (WITH PROF. ALEXANDER BOCKMAYR): WINTER 2015
  • INTRODUCTION TO ADVANCED BIOLOGY (GUEST LECTURER): WINTER 2015

@UNIVERSITÄT BREMEN AND @BREMEN UNIVERSITY OF APPLIED SCIENCES:

  • SCIENTIFIC COMPUTING: SPRING 2014

@UNIVERSITY OF WASHINGTON:

  • CSI: SEATTLE (TEACHING ASSISTANT TO PROF. CELESTE BERG AND PROF. BONNY BREWER): SUMMER 2009
  • INTRODUCTION TO GENETICS (TEACHING ASSISTANT TO PROF. MARY KUHNER): SPRING 2008

STUDENT SUPERVISION

@UNIVERSITY OF MONTANA

  • MASTERS THESIS COMMITTEE, ANDRÉ GILAN (COMPUTER SCIENCE): DEFENSE 2021
  • MASTERS THESIS COMMITTEE, MICHAEL MORRIS (MATHEMATICS): DEFENSE 2021
  • MASTERS ADVISOR, KYLE LUCKE (COMPUTER SCIENCE): DEFENSE 2021
  • MASTERS ADVISOR, JAKE PENNINGTON (MATHEMATICS): DEFENSE 2021
  • PH.D. ADVISOR, PATRICK KREITZBERG (COMPUTER SCIENCE): 2019 -- 2021 (ADVISING CONTINUED BY PROF. CORY PALMER IN MATHEMATICS)
  • MASTERS ADVISOR, PATRICK KREITZBERG (COMPUTER SCIENCE): DEFENSE 2019
  • PH.D. THESIS COMMITTEE, NHAN NGUYEN (MATHEMATICS): DEFENSE 2018
  • MASTERS THESIS COMMITTEE, ALEXANDER NORD (COMPUTER SCIENCE): DEFENSE 2018

@FREIE UNIVERSITÄT BERLIN

  • SUPERVISOR, XIAO LIANG (VISITING PH.D. STUDENT, FREIE UNIVERSITÄT BERLIN): 2015 - 2016
  • SUPERVISOR, JULIANUS PFEUFFER (VISITING PH.D. STUDENT, UNIVERSITÄT TÜBINGEN): 2015 - 2016
  • PH.D. THESIS COMMITTEE, KONSTANTIN OKONECHNIKOV (PH.D. DER BIOINFORMATIK): DEFENDED 2015
  • PH.D. THESIS COMMITTEE, FRANZISKA ZICKMANN (PH.D. DER BIOINFORMATIK): DEFENDED 2015

@OTHER INSTITUTIONS

  • MASTERS THESIS COMMITTEE, TRAVIS BINGEMAN (MOLECULAR MICROBIOLOGY, UNIVERSITY OF CALGARY): DEFENSE 2019

OUTREACH

  • VOLUNTEER, POTOMAC SCHOOL, 2021
    POTOMAC, MONTANA
  • INSTRUCTOR, SpectrUM SUMMER CAMP, 2021
    MISSOULA, MONTANA
  • VOLUNTEER, POTOMAC SCHOOL, 2019
    POTOMAC, MONTANA
  • VOLUNTEER, LEWIS AND CLARK ELEMENTARY SCHOOL, 2019
    MISSOULA, MONTANA
  • MENTOR, SENIOR HIGH SCHOOL SCIENCE FAIR PROJECT (NES LEGEND OF ZELDA REMAKE), ALEKSI ANDERSON, 2018-2019 SCHOOL YEAR
    MISSOULA, MONTANA
  • INSTRUCTOR, UNIVERSITY OF MONTANA COMPUTER SCIENCE SUMMER SCHOOL FOR HIGH SCHOOL STUDENTS, 2018
    MISSOULA, MONTANA
  • VOLUNTEER, UNIVERSITY OF MONTANA HIGH SCHOOL ALL-STAR CHOIR, 2018
    MISSOULA, MONTANA
  • VOLUNTEER, LEWIS AND CLARK ELEMENTARY SCHOOL, 2018
    MISSOULA, MONTANA
  • ``EXPLORING SCIENTIFIC WILDERNESS'' PODCAST MINISERIES, 2017-2018
  • VOLUNTEER, MATH DAY (HIGH K-12 OUTREACH), 2017
    MISSOULA, MONTANA
  • PRE-KINDERGARTEN SCIENCE TUTORIALS BOSTON CHILDREN'S HOSPITAL, 2012
    BOSTON, MASSACHUSETTS
  • HIGH SCHOOL MENTOR ("AUTOMATED CELL IDENTIFICATION IN MICROSCOPE IMAGES") NORTHWEST ASSOCIATION FOR BIOMEDICAL RESEARCHERS (NWABR), AUTUMN 2010 -- SPRING 2011
    SEATTLE, WASHINGTON
  • VOLUNTEER, PACIFIC SCIENCE CENTER, 2010
    SEATTLE, WASHINGTON
  • VOLUNTEER, PACIFIC SCIENCE CENTER, 2007
    SEATTLE, WASHINGTON

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SERVICE, AWARDS, AND OTHER ACTIVITIES
IN SEARCH OF LOST TIME

REVIEWER (JOURNALS)

Advances in Bioinformatics
Analytical Chemistry
Annals of Applied Statistics
Australian & New Zealand Journal of Statistics
Bayesian Analysis
Bioinformatics
BMC Bioinformatics
CELL Systems
Conference on Systems Bioinformatics (CSB)
Genetics
German Conference for Bioinformatics (GCB)
IEEE Transactions on Signal Processing
International Conference on Machine Learning (ICML)
International Joint Conference on Artificial Intelligence (IJCAI)
International Society for Computational Biology (ISMB)
Journal of Proteome Research
Molecular Biology of the Cell
Nature Methods
Neural Information Processing Systems (NIPS)
Nucleic Acids Research
PLOS Computational Biology
PLOS ONE
PROTEOMICS
Proteome Science
RECOMB
Statistics in Medicine
Theoretical and Applied Genetics

EDITOR (JOURNALS)

NATURE SCIENTIFIC DATA [EDITORIAL BOARD MEMBER, 2018- ]
PLOS COMPUTATIONAL BIOLOGY [GUEST EDITOR, 2017]

REVIEWER (FUNDING AGENCIES)

FRENCH NATIONAL RESEARCH AGENCY (ANR) [FRENCH EQUIVALENT TO AMERICAN NIH]

OTHER ACTIVITIES

  • UNIVERSITY WRITING COMMITTEE MEMBER
    UNIVERSITY OF MONTANA, 2020-2021
    MISSOULA, MONTANA
  • UNIT STANDARDS COMMITTEE MEMBER
    UNIVERSITY OF MONTANA, 2018
    MISSOULA, MONTANA
  • STUDENT EVALUATION COMMITTEE FACULTY ADVISOR
    DEPARTMENT OF COMPUTER SCIENCE
    UNIVERSITY OF MONTANA, 2017-2021
    MISSOULA, MONTANA
  • CONFERENCE SESSION CHAIR (SESSION "INFORMATICS: ALGORITHMIC AND STATISTICAL ADVANCES")
    AMERICAN SOCIETY FOR MASS SPECTROMETRY (ASMS), 2015
    ST. LOUIS, MISSOURI
  • CONSULTANT ON GRAPH ANALYSIS AND CLUSTERING ALGORITHMS FOR ANALYZING GLOBAL ECONOMIC ACTIVITY
    INTERNATIONAL MONETARY FUND (IMF), 2013
    WASHINGTON, D.C.

AWARDS

  • CONTRIBUTION BONUS
    WOLVERINE TRADING
    2024 (POST RESIGNATION)
  • INVENTION BONUS
    A-ALPHA BIO
    2023 (POST RESIGNATION)
  • RESEARCH BONUS
    THERMO FISHER SCIENTIFIC
    2016 (POST RESIGNATION)
  • PUSHCART PRIZE NOMINEE, "SECONDHAND SMOKER"
    NOMINATED BY THE CHICAGO CENTER FOR LITERATURE AND PHOTOGRAPHY
    2016
  • IEEE SOFTWARE ENGINEERING TEAM CONTEST, FOURTH PLACE
    2004
  • UNDERGRADUATE RESEARCH AWARD
    NORTH CAROLINA STATE UNIVERSITY
    2004
  • HOWARD HUGHES SUMMER RESEARCH AWARD
    2002
  • FRESHMAN ENGINEERING DESIGN COMPETITION (COMPILER CATEGORY), FIRST PRIZE
    DEPARTMENT OF ENGINEERING, NORTH CAROLINA STATE UNIVERSITY
    2002
  • NATIONAL MERIT SCHOLAR
    2002 -- 2006
  • MATHEMATICS SCHOLARSHIP AWARD
    2002
  • BEST UNDERGRADUATE PAPER, "AN INVESTIGATION OF FINITE METHODS IN INFINITE PROBLEM SOLVING THROUGH ADAPTATION"
    AMERICAN ASSOCIATION OF PHYSICS TEACHERS
    2002
  • WAKE FOREST UNIVERSITY MATH CLUB CONTEST WINNER
    WAKE FOREST UNIVERSITY
    2001

FICTION

  • AT OCEAN [NOVEL], 2016
  • SECONDHAND SMOKER [SHORT STORY], 2015
  • STAY CLOSE, LITTLE GHOST [NOVEL], 2013