“Nick is an extremely diverse developer. His field of bioinformatics, in its specificity made Nick a unique candidate for a social-network analysis company. I was surprised by how diversified his resume was so early on in his career. Nick did not have much experience in React and JavaScript when we met, but had impressive problem solving (and finding) skills as well as a toolkit of other languages under his belt. We believed that Nick had a unique perspective that would help us immensely. After a couple weeks, Nick was beyond proficient in React and JavaScript. Within a couple months, Nick was responsible for the entire existence of our frontend. He led a team to scrap what we already had, with a much more streamlined interface that they created. With Nick’s ability to immerse himself in a project and manage his time and his team, it was no wonder that he had done so much at such a young age. Every project we put him and his team on was on-time and often early. One of my favorite qualities about Nick was that he blended very well with the design team and backend team to meet their needs as well as integrate different components in a lean, efficiency-focused manner. I would definitely work with Nick again and am confident that his future ventures will be very successful.”
About
Ex-LinkedIn Staff SWE
Ex-Amazon AWS SDE II
M.S. Computer…
Activity
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One of the coolest parts of my role @ Harmonic is working with 100+ investment firms (from two-person emerging managers to multi-B funds), innovation…
One of the coolest parts of my role @ Harmonic is working with 100+ investment firms (from two-person emerging managers to multi-B funds), innovation…
Liked by Nick Bavafa
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After a lot of thought, I’m excited to share that I’ll be starting my MBA at Carnegie Mellon University - Tepper School of Business this fall! This…
After a lot of thought, I’m excited to share that I’ll be starting my MBA at Carnegie Mellon University - Tepper School of Business this fall! This…
Liked by Nick Bavafa
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I am thrilled to share that I have started my position as a Senior Analyst, Financial Data Analytics at Thermo Fisher Scientific on the BioProduction…
I am thrilled to share that I have started my position as a Senior Analyst, Financial Data Analytics at Thermo Fisher Scientific on the BioProduction…
Liked by Nick Bavafa
Experience & Education
Volunteer Experience
Publications
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Activation of Subthalamic Nucleus Stop Circuit Disrupts Cognitive Performance
eNeuro
See publicationMuch evidence supports a fundamental role for the subthalamic nucleus (STN) in rapidly stopping behavior when a stop signal or surprising event occurs, but the extent to which the STN may be involved in stopping cognitive processes is less clear. Here, we used an optogenetic approach to control STN activity in a delayed-match-to-position (DMTP) task where mice had to recall a response location after a delay. We first demonstrated that a surprising event impaired performance by both slowing the…
Much evidence supports a fundamental role for the subthalamic nucleus (STN) in rapidly stopping behavior when a stop signal or surprising event occurs, but the extent to which the STN may be involved in stopping cognitive processes is less clear. Here, we used an optogenetic approach to control STN activity in a delayed-match-to-position (DMTP) task where mice had to recall a response location after a delay. We first demonstrated that a surprising event impaired performance by both slowing the latency to respond and increasing the rate of errors. We next showed that these effects could be mimicked by brief optogenetic activation of the STN. Further, inhibiting STN during surprise blocked surprise-induced slowing, although without changing surprise-induced errors. These data are consistent with the hypothesis that STN is recruited by surprise to slow responding and that this can also interrupt cognitive processes. Under normal conditions STN-mediated stopping of behavior may slow or stop ongoing cognition to facilitate cognitive reorienting and adaptive responses to unexpected sensory information, but when malfunctioning, it could produce pathologies related to over-rigidity or increased distractibility.
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Long-read Amplicon Denoising
Oxford Academic - Nucleic Acids Research
See publicationLong-read next generation amplicon sequencing shows promise for studying complete genes or genomes from complex and diverse populations. Current long-read sequencing technologies have challenging error profiles, hindering data processing and incorporation into downstream analyses. Here we consider the problem of how to reconstruct, free of sequencing error, the true sequence variants and their associated frequencies. Called "amplicon denoising", this problem has been extensively studied for…
Long-read next generation amplicon sequencing shows promise for studying complete genes or genomes from complex and diverse populations. Current long-read sequencing technologies have challenging error profiles, hindering data processing and incorporation into downstream analyses. Here we consider the problem of how to reconstruct, free of sequencing error, the true sequence variants and their associated frequencies. Called "amplicon denoising", this problem has been extensively studied for short-read sequencing technologies, but current solutions do not appear to generalize well to long reads with high indel error rates. We introduce two methods: one that runs nearly instantly and is very accurate for medium length reads (here ~2.6kb) and high template coverage, and another, slower method that is more robust when reads are very long or coverage is lower. On one real dataset with ground truth, and on a number of simulated datasets, we compare our two approaches to each other and to existing algorithms. We outperform all tested methods in accuracy, with competitive run times even for our slower method. Fast Amplicon Denoising (FAD) and Robust Amplicon Denoising (RAD) are implemented purely in the Julia scientific computing language, and are hereby released along with a complete toolkit of functions that allow long-read amplicon sequence analysis pipelines to be constructed in pure Julia. Further, we make available a webserver to dramatically simplify the processing of long-read PacBio sequences.
Courses
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Advanced Bioinformatics Laboratory
CSE 185
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Advanced Data Structures
CSE 100
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Biochemical Energetics and Metabolism
CHEM 114B
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Biochemical Structure and Function
CHEM 114A
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Biological Data Analysis
CSE 182
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Calculus II-III
MATH 20B, MATH 20C
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Computational Linguistics
LIGN 165
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Data Structures
CSE 12
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Design and Analysis of Algorithms
CSE 101
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Discrete Mathematics
CSE 20
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General Chemistry I-III
CHEM 6A, CHEM 6B, CHEM 6C
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Introduction to Object-Oriented Programming
CSE 11
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Introduction to Programming (C)
CSE 5A
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Knowledge-Based Artificial Intelligence
CS 7637
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Mathematics for Algorithms and Systems
CSE 21
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Molecular Sequence Analysis
CSE 181
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Network Security
CS 6262
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Organic Chemistry
CHEM 40A, 40B, 40C
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Physical Biochemistry I: Thermodynamics and Kinetics of Biomolecules
CHEM 126A
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Physics—Mechanics
PHYSICS 2A
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Probability and Statistics for Bioinformatics
MATH 186
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Software Development Process
CS 6300
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Software Tools and Techniques Laboratory
CSE 15L
Projects
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Study Groups
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See projectBuilt a social networking app that allows students (who sign up with a .edu email) to connect with other students at their institution to find study groups. This is achieved by searching by class names and codes, filtering results with a "like/save" feature, and allowing students to create their own study groups. The app allows students to set a time, date, and location for their class study sessions. Other students at the same school are able to view these groups and attend sessions with the…
Built a social networking app that allows students (who sign up with a .edu email) to connect with other students at their institution to find study groups. This is achieved by searching by class names and codes, filtering results with a "like/save" feature, and allowing students to create their own study groups. The app allows students to set a time, date, and location for their class study sessions. Other students at the same school are able to view these groups and attend sessions with the information provided.
Skills used/Aquired
- Firebase backend integration
- Full Stack React Native
- Database field control
- User flow/control with specific accounts
- Redux and API keys
Google Play Store:
//Currently fixing to meet new compliance requirements by Google
iOS App Store:
https://itunes.apple.com/us/app/study-groups/id1435273067?mt=8 -
Tutoring Push Notifications — UC San Diego Mobile Application
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- Worked on a team that designed a full stack API to notify students of upcoming tutoring sessions for their classes
- Client - Server data structures via REST API and reducers -
React-Native Dating App Framework
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See projectThe built the frontend framework for a dating app centered around college students in React Native. I learned and mastered various techniques such as state control, frontend/backend integration, user flow, and object oriented component design. The mechanism is similar to that of Tinder and other various dating apps.
Languages
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English
Native or bilingual proficiency
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Spanish
Limited working proficiency
Recommendations received
1 person has recommended Nick
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