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<title>JCollinsMSc_Bioinformatics-DataScience_Resume_2022</title>
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<p class="Basic-Paragraph" style="left: -45px;"><span class="Character-Style-19 CharOverride-65" style=
"font-size: 5rem; transform: translate(22px,5px); display: inline-flex;">𝒥</span><span class=
"Character-Style-19">ohn Collins</span></p><br />
</div>
<div>
<p><span class="CharOverride-66">Bioinformatics Python Software Engineering</span></p>
<p class="Basic-Paragraph ParaOverride-9"><span class="CharOverride-73">Personalized Genomics &
Biomolecular Diagnostics</span></p>
<p class="Basic-Paragraph ParaOverride-9"><span class="CharOverride-70">NGS Pipelines | Data Science |
Immuno-Oncology | Custom Full-Stack Web Apps</span></p><span class="CharOverride-73" style=
"font-size: 0.6rem;">Written: November 2017</span><br />
<span class="CharOverride-73" style="font-size: 0.6rem;">Last Updated: October 2022</span><br />
<br />
<div>
<p class="ParaOverride-26"><span class="Character-Style-7 CharOverride-127">CONTACT</span></p>
<p class="Basic-Paragraph ParaOverride-10"><span class="CharOverride-128">805.647.5033</span></p>
<p class="Basic-Paragraph ParaOverride-10">email me: <a href=
"mailto:jcollins.bioinformatics%40gmail.com?subject="><span class=
"Hyperlink CharOverride-129">[email protected]</span></a></p>
<!-- <p class="Basic-Paragraph ParaOverride-10"><span class=
"CharOverride-137">LinkedIn</span><span class="CharOverride-138">:</span> <a href=
"https://linkedin.com/in/johncollins-bioinformatics"><span class=
"Hyperlink CharOverride-140">/in/johncollins-bioinformatics</span></a></p> -->
<p class="Basic-Paragraph ParaOverride-10"><span class="CharOverride-141">Ventura, California
🌅</span></p>
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<h1 style="font-size: 1rem; line-height: unset; display: unset;">Links</h1><br />
<a id="pers-links" target="_blank" rel="noopener noreferrer" href=
"https://stackoverflow.com/users/6714627/john-collins"><img src=
"https://stackoverflow.design/assets/img/logos/so/logo-stackoverflow.png" style=
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<br />
<div class="underline">
<h1 style="font-size: 1rem; line-height: unset; display: unset;">Contents</h1><br />
<div class="contents">
<a class="contents-item" href="#bioinformatics">Bioinformatics</a> <a class="contents-item" href=
"#experience">Experience</a> <a class="contents-item" href="#publications">Publications</a> <a class=
"contents-item" href="#education">Education</a>
</div>
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<div class="underline">
<p class="jc-anim-active" id="bioinformatics">BIOINFORMATICS</p><br />
<p id="underline" class="Paragraph-Style-1 ParaOverride-1"><span class="CharOverride-67-sub">First-hand
data analysis on hundreds of next-generation high-throughput sequencing runs</span></p>
<p class="Paragraph-Style-10 ParaOverride-14"><span class="CharOverride-81">Diverse Illumina® expertise
(HiSeq™, MiSeq™, NextSeq™, NovaSeq™)—spanning secondary through tertiary pipeline analysis for
computational interpretation of NGS raw sequence data; including, ultra-deep targeted panels, variant
calling and genotyping, single-cell, unique molecular barcoding, and transcriptomics.</span></p>
</div><br />
<br />
<div class="underline">
<p class="Paragraph-Style-1 ParaOverride-1"><span class="CharOverride-67-sub">Advanced software development
proficiency creating complex custom omics-based analytics using the Python data science stack</span></p>
<p class="Paragraph-Style-10 ParaOverride-14"><span class="CharOverride-81">Daily use of SciPy, NumPy,
Pandas, Jupyter, Conda (pkg./virtualenv mgmt.), scikit-learn, matplotlib, in a Linux/UNIX environment; with
strong shell scripting, parallel programming, statistics, and machine learning (theano, caffe, keras)
skills. Moderate fluency in R and HTML5/CSS3, and working knowledge of C/C++, Java, and
JavaScript.</span></p><br />
</div><br />
<div class="underline">
<p class="Paragraph-Style-1 ParaOverride-1"><span class="CharOverride-67-sub">Extensive academic and
professional history of analysis incorporating myriad open source bioinformatics tools and
databases</span></p>
<p class="Paragraph-Style-10 ParaOverride-14"><span class="CharOverride-81">Mapping: BWA(-MEM), Samtools,
Bedtools, Bowtie2, STAR; Annotation: UCSC Genome Browser, GENCODE, Ensembl; NCBI: BLAST, RefSeq, SRA, GEO,
db-[GaP/SNP/Var], ClinVar/OMIM; Cancer Genomics: TCGA, COSMIC; QC/Other: The Broad
Institute—IGV/GATK/Picard/BD2K/LINCS, NIST’s GiaB (NA12878), Platinum genomes; R-Bioconductor; Google
Genomics API on GCP; 1000Genomes Project, etc.</span></p>
</div><br />
<div class="underline">
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</div><br />
<p class="Paragraph-Style-10 ParaOverride-14"><span class="CharOverride-68">Rapidly improving
command</span> <span class="CharOverride-81">of</span> <span class="CharOverride-87">state-of-the-art best
practices for designing and deploying fast, scalable, high-performance pipelines.</span> <span class=
"CharOverride-81">Namely, distributed task management for larger-than-memory size datasets (e.g.,
multi-genomic) using efficient data structures and MapReduce-based cluster computing.<br /></span></p>
<ul>
<li><b>Cloud computing</b> — cross-platform expertise (Amazon's AWS, MS Azure,
GoogleCloudPlatform+GoogleAPIs)</li>
<li><b>Database & Network systems</b> — MySQL, Postgres, Oracle, NoSQL/Cassandra (familiar); ssh
tunneling</li>
<li><b>High-speed algorithms design</b> — O(n) execution time complexity⇢efficiency optimization (sw:
datatype homogeneity, array vectorization, memory cache⇢data locality, just-in-time compilation,
»Cython, Numba, Dask.DataFrame's, Pandas API; hw: »NVIDIA CUDA/GPU’s)</li>
<li><b>Parallelization</b> — concurrent operations (multi-processing, VM-autoscaling);
Hadoop/HDFS/Spark functionality in Python via PyData »Blaze, Dask.Distributed, Dask.Parquet, etc.
(pandas-based asynchronous task mgmt. & binary serialization; low latency autoscheduling);
shell-scripted »GNU Parallel</li>
<li><b>DevOps</b> — version control (»git), unit testing, UI/UX Web/Apps Design (LAMP; »Flask/Django),
Agile development practices, containerization (»Docker/Kubernetes)</li>
</ul><br />
<hr />
<br />
<br />
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<p class="jc-anim-active" id="experience">EXPERIENCE</p>
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<br />
<p class="Basic-Paragraph ParaOverride-11"><span class="CharOverride-67">Bioinformatics Data
Scientist</span></p>
<p class="Basic-Paragraph ParaOverride-12"><span class="Character-Style-8 CharOverride-75">at</span>
<span class="Character-Style-8 CharOverride-76"><a href="https://www.pactpharma.com">PACT Pharma,
Inc.</a></span><span class="Character-Style-8 CharOverride-77">,</span></p>
<p class="ParaOverride-1"><span class="Character-Style-8 CharOverride-79">South San Francisco,
California</span></p>
<p class="Basic-Paragraph ParaOverride-13"><span class="CharOverride-80">Sept 2018—Sept
2020</span></p><br />
<center>
<img src="https://live.staticflickr.com/65535/52216706217_834034bf43_k.jpg" width="90%" />
</center><br />
<p class="Paragraph-Style-10 ParaOverride-14"><span class="CharOverride-81">Supported the bioinformatic
data integration of an incredible interdisciplinary immuno- oncology effort spanning the latest
technology in protein sciences, gene editing, and tumor immunology to create a first-of-its-kind
patient-tailored cancer-targeting T cell therapy applicable to all solid tumor types.</span></p>
<ul>
<li class="Basic-Paragraph ParaOverride-15"><span class="CharOverride-87"><span class=
"CharOverride-92">W</span>as the principal database/lims manager for all R&D teams, leveraging
a cloud platform LIMS/ELN solution called Benchling; including writing custom software using the
Benchling API</span><span class="CharOverride-94">.</span></li>
<li class="Basic-Paragraph ParaOverride-15"><span class="CharOverride-87"><span class=
"CharOverride-92">C</span>reated a custom sanger sequencing web application (90% Python; >10,000
lines source code) which reduced a multi-hour manual QC and analysis process of gene-edited plasmid
sequencing data down to <1 minute fully-automated computation time. Application featured
numerous lab scientist end user- requested UI/UX components, and was architected and deployed with
24/7 reliability and scalability allowing for multiple concurrent users on any number of machines/
browsers and parallelized computationally to allow for hundreds of samples to be processed per user
session</span> <span class="CharOverride-97">.</span></li>
</ul><br />
<div class="underline">
<br />
<p class="Basic-Paragraph ParaOverride-11"><span class="CharOverride-67">Bioinformatics Pipeline
Developer</span></p>
<p class="Basic-Paragraph ParaOverride-12"><span class=
"Character-Style-8 CharOverride-75">at</span> <span class=
"Character-Style-8 CharOverride-76"><a href="https://www.bms.com">Bristol-Myers
Squibb</a></span><span class="Character-Style-8 CharOverride-77">,</span></p>
<p class="ParaOverride-1"><span class="Character-Style-8 CharOverride-79">Redwood City, California
— Biologics Center</span></p>
<p class="Basic-Paragraph ParaOverride-13"><span class="CharOverride-80">2018</span></p>
<p class="Paragraph-Style-10 ParaOverride-14"><span class="CharOverride-81">Contributed new code
and cloud computing infrastructure support to both: 1) supplement existing Python-backend +
RShiny-frontend, wetlab user-facing, internal web apps for protein engineering sequence analysis,
and 2) create from scratch a new NGS pipeline for "Antigen Receptor Repertoire" interpretation, as
part of the Biologics Lead Discovery—Data Science & Bioinformatics team at the Immuno-Oncology
R&D site.</span></p>
<ul>
<li class="Basic-Paragraph ParaOverride-15"><span class="CharOverride-87"><span class=
"CharOverride-92">I</span>ntegrated a combination of open source bioinformatics and data
science tool resources with custom python programming, shell scripting, and
Docker-containerized Linux environment mgmt. for cloud-based, high-performance computing of
V(D)J-gene rearrangement genomics analyses</span><span class="CharOverride-94">.</span></li>
<li class="Basic-Paragraph ParaOverride-15"><span class="CharOverride-87"><span class=
"CharOverride-92">C</span>reated an original implementation of SciKitLearn's "Affinity
Propagation" clustering algorithm with the python-Levenshtein edit-distance metric PyPI
package, for unsupervised classification of large lists of nucleic acid/protein sequences and
identification of exemplar representatives without the need for inputting an ideal number of
clusters</span><span class="CharOverride-97">.</span></li>
</ul><br />
<div class="underline">
<br />
<p class="Basic-Paragraph ParaOverride-11"><span class="CharOverride-67">Bioinformatician
II</span></p>
<p class="Basic-Paragraph ParaOverride-12"><span class="CharOverride-67-sub">—Sequencing
Analysis</span></p>
<p class="Basic-Paragraph ParaOverride-12"><span class=
"Character-Style-8 CharOverride-75">at</span> <span class=
"Character-Style-8 CharOverride-76"><a href=
"http://www.bio-rad.com/en-us/applications-technologies/digital-pcr-next-generation-sequencing-ngs">
Bio-Rad Laboratories</a></span><span class="Character-Style-8 CharOverride-77">,</span></p>
<p class="ParaOverride-1"><span class="Character-Style-8 CharOverride-79">Digital Biology
Center</span></p>
<p class="Basic-Paragraph ParaOverride-13"><span class="CharOverride-80">Ap</span><span class=
"CharOverride-80">ril/May 2017—July 2017</span></p>
<p class="Paragraph-Style-10 ParaOverride-14"><span class="CharOverride-81">Created a working
framework for a secondary and tertiary custom RNA-Seq pipeline for a single-cell, whole
transcriptome, Unique Molecular Identifier-containing (UMI) assay called ddSEQ™ leveraging
Bio-Rad’s Droplet Digital™ technology for individual cell isolation and 3’-end poly(A)-tail
bead-capture along with Illumina’s “tagmentation” technology Nextera™ (adapter
ligation).</span></p>
<ul>
<li class="Basic-Paragraph ParaOverride-15"><span class="CharOverride-87"><span class=
"CharOverride-92">D</span>eveloped a cloud computing network architecture</span>
<span class="CharOverride-94">on</span> <span class="CharOverride-99">Microsoft
Azure</span><span class="CharOverride-100">, and</span> <span class=
"CharOverride-98">genomically mapped samples in parallel</span> <span class=
"CharOverride-97">u</span><span class="CharOverride-97">sing a</span> <span class=
"CharOverride-100">scalable, distributed cluster of highly multi-core, ephemeral VM
instances</span><span class="CharOverride-94">.</span></li>
<li class="Basic-Paragraph ParaOverride-15"><span class="CharOverride-87"><span class=
"CharOverride-92">W</span>rote UMI-barcode deconvolution algorithms</span> <span class=
"CharOverride-100">and integrated database genome-wide “gene” annotations</span>
<span class="CharOverride-97">to</span> <span class="CharOverride-98">transform reads into
digital transcript counts for</span> <span class="CharOverride-98">analysis of differential
gene expression</span><span class="CharOverride-97">.</span></li>
<li class="Basic-Paragraph ParaOverride-16"><span class="CharOverride-87"><span class=
"CharOverride-92">A</span>pplied dimensionality reduction,</span> <span class=
"CharOverride-92">decomposition</span><span class="CharOverride-98">, and</span>
<span class="CharOverride-92">feature enrich</span><span class=
"CharOverride-92">ment</span> <span class="CharOverride-98">to quantitatively and visually
discriminate human and murine immune system cell subpopulations,</span> <span class=
"CharOverride-97">from</span> <span class="CharOverride-98">Python's scikit-learn
library</span><span class="CharOverride-97">, such as</span> <span class=
"CharOverride-100">K-means clustering, PCA,</span> <span class="CharOverride-97">and</span>
<span class="CharOverride-100">t-SNE</span><span class="CharOverride-97">.</span></li>
</ul><br />
<br />
<div class="underline">
<p class="ParaOverride-1"><span class="CharOverride-67">Bioinformatics Analyst</span></p>
<p class="ParaOverride-17"><span class="Character-Style-8 CharOverride-75">at</span>
<span class="Character-Style-8 CharOverride-93"><a href="www.allosure.com">CareDx,
Inc.</a></span></p>
<p class="ParaOverride-14"><span class="CharOverride-96">(RA/Bioinformatician,
2014-2016</span><span class="CharOverride-96">)</span></p>
<p class="ParaOverride-13"><span class="CharOverride-80">November 2014—April
2017</span></p><br />
<center>
<img src="http://jmd.amjpathol.org/cms/attachment/2069108762/2067529109/gr1_lrg.jpg"
width="90%" />
</center><br />
<p class="Paragraph-Style-10 ParaOverride-14"><span class="CharOverride-81">Python-centric
genotyping analysis, rigorous analytical validation, and publication-quality visualization
of a deep coverage targeted SNP panel NGS diagnostic that measures “percent donor-derived
cell-free DNA” (% dd-cfDNA) without prior genotyping of the donor or recipient,
implementing a mix of standard and complex custom software tools with a focus on assay
performance characterization.</span></p>
<ul>
<li class="Basic-Paragraph ParaOverride-15"><span class=
"CharOverride-92">S</span><span class="CharOverride-87">tatistical Python
scripting—pipeline vector-graphics reports</span> <span class=
"CharOverride-104">automated to handle large sample input, generating various evolving
assay-specific metrics critical for pass/fail classification</span> <span class=
"CharOverride-98">such as</span> <span class="CharOverride-100">coverage variability,
error, bias, low DNA input (<3ng), heterozygous genotype %’s,</span> <span class=
"CharOverride-98">and</span> <span class=
"CharOverride-100">contamination</span><span class="CharOverride-98">.</span></li>
<li class="Basic-Paragraph ParaOverride-15"><span class=
"CharOverride-92">U</span><span class="CharOverride-87">ncovering sample handling
error</span> <span class="CharOverride-88">by n</span><span class=
"CharOverride-101">2</span> <span class="CharOverride-88">(pairwise)</span>
<span class="CharOverride-102">correlation of allele frequencies</span> <span class=
"CharOverride-104">as a means of</span> <span class="CharOverride-105">very</span>
<span class="CharOverride-104">high confidence identity verification</span>
<span class="CharOverride-98">(visualized by</span> <span class=
"CharOverride-100">hover-interactive hierarchically clustered matrix-coefficient
heatmaps</span> <span class="CharOverride-106">to reveal correct genomic patient
ID→analyte</span><span class="CharOverride-8">).</span></li>
<li class="Basic-Paragraph ParaOverride-15"><span class=
"CharOverride-92">D</span><span class="CharOverride-87">etermination of Limit of
Quantification</span> <span class="CharOverride-88">by</span> <span class=
"CharOverride-100">nonlinear least squares</span> <span class=
"CharOverride-100">modeling</span> <span class="CharOverride-103">on the</span>
<span class="CharOverride-108">log-transformed CV's of analytical validation spike-in
replicates</span> <span class="CharOverride-103">(measuring 0.2-12%
dd-cfDNA).</span></li>
</ul>
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<p class="jc-anim-active" id="publications">PUBLICATIONS</p><br />
<p class="Paragraph-Style-10 ParaOverride-14"><span class="CharOverride-68">Public sources
of Python-built NGS analytics</span> <span class="CharOverride-81">can be seen in the
figures to the open-access publication below, describing a novel liquid biopsy-like assay
for quantitative surveillance of allograft “genome transplant dynamics.” Published in
the</span> <span class="CharOverride-109">Association for Molecular
Pathology</span><span class="CharOverride-81">’s official journal and selected as the cover
issue presented during 2016's annual meeting.</span></p><br />
<p class="ParaOverride-20"><span class=
"Character-Style-7 CharOverride-110">PUBLICATIONS</span></p>
<p class="ParaOverride-10"><span class="CharOverride-111">Association for Molecular
Pathology—</span></p>
<p class="ParaOverride-10"><span class="CharOverride-112">The Journal of Molecular
Diagnostics</span></p>
<p class="ParaOverride-10"><span class="CharOverride-93">November 2016, Cover
Feature.</span></p><br />
<p class="ParaOverride-22"><span class="CharOverride-90">Grskovic, et al.</span></p>
<p class="ParaOverride-23"><span class="Hyperlink CharOverride-119"><a href=
"http://linkinghub.elsevier.com/retrieve/pii/S1525157816301386">Validation of a
Clinical-Grade Assay to Measure Donor-Derived Cell-Free DNA in Solid Organ Transplant
Patients</a></span></p><br />
<img src="http://jmd.amjpathol.org/cms/attachment/2069108762/2067529105/gr3_lrg.jpg" width=
"70%" /><br />
<br />
<p class="ParaOverride-21"><span class="CharOverride-49">Fig. 3A.</span> <a href=
"http://allosure.com"><span class="CharOverride-115">AlloSure™</span><span class=
"CharOverride-116">’s</span></a> <span class="CharOverride-49">validated Limit of Blank is
precisely</span> <span class="CharOverride-49">0.1% — the 95th percentile of 180 “blank”
sample results (in this case, meaning</span> <span class=
"CharOverride-49">2</span><span class="CharOverride-49">n genomic ploidy; i.e., in which
the total relative fraction of plasma-circulating allogeneic cfDNA has an expected mean
value of zero percent</span><span class="CharOverride-49">)</span><span class=
"CharOverride-49">.</span></p><br />
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<p class="jc-anim-active" id="education">EDUCATION</p><br />
<p class="ParaOverride-9"><span class="CharOverride-120">University of
California</span></p>
<p class="ParaOverride-9"><span class="CharOverride-122">Santa</span> <span class=
"CharOverride-122">Cruz</span></p>
<p class="ParaOverride-25"><span class="CharOverride-123">2013—2014</span></p>
<p class="ParaOverride-25"><span class="CharOverride-42">Master of Science
(M.Sc.),</span></p>
<p class="ParaOverride-25"><span class="CharOverride-124">Biomolecular
Engineering</span></p>
<p class="ParaOverride-25"><span class="CharOverride-124">and</span> <span class=
"CharOverride-124">Bioinformatic</span><span class="CharOverride-124">s</span></p><br />
<p><span class="CharOverride-123">2009—2013</span></p>
<p><span class="CharOverride-42">Bachelor of Science (B.S.),</span></p>
<p><span class="CharOverride-124">Bioengineering</span></p>
<p><span class="CharOverride-80"><small><i>Graduated with Honors in the
Major</i></small></span></p><br />
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