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Statistical and Machine Learning Scientist, Computational Biology

Maxwell
Konnaris, PhD Candidate

I develop and translate models to improve the reliability and interpretability of insights from limited, high-dimensional, noisy and imperfect data — with a focus on biological systems.

Maxwell Konnaris
Pennsylvania State University

Background & Interests


I am a PhD candidate in Bioinformatics and Genomics at Pennsylvania State University, where I am advised by two statisticans: Prof. Justin Silverman, MD, PhD and Prof. Nicole Lazar, PhD.

I am interested in identifying and solving broad problems at scale. I am motivated by the potential of technology to accelerate scientific discovery and improve human health. My work focuses on a major gap in the rigor of scientific methods for analyzing high-throughput sequencing data. I aim to help close that gap by studying the information content of data, evaluating limitations, and developing robust/practical analytical frameworks to solve these challenges.

Without rigor, flawed methodology can produce findings that do not replicate, waste resources, erode trust in science, and slow the pace of discovery.

I believe scientific modeling requires a deep understanding of both the underlying translational context and the statistical/computational principles involved. I possess a unique combination of the statistical depth, translational understanding, and computational skills essential for building methods that are not only theoretically sound, but also practical for real-world problems guided by a science/medical background.

Open to Postdoctoral & Industry R&D Positions · Expected graduation Spring 2027
Education
PhD · Bioinformatics & Genomics, Statistical Genomics Option Pennsylvania State University
BS · Physiology & Premedicine Ithaca College
Additional Experience
🏥 2+ years hands-on clinical experience 🧪 3 years wet lab & clinical research 🏆 Applied Coaching and Training 📋 Phase II clinical trial work

News & Press


Me with PhD Advisors Justin Silverman and Nicole Lazar
PhD Advisors Justin Silverman (left) and Nicole Lazar (center), with me (right) featured in Eberly magazine.

News Penn State Researchers Announce New Comprehensive Omics Database

Research Areas


Google Scholar
Rigor & Reproducibility: AI for Science
Developing statistically principled approaches to improve reliability and transparency in Biological data analysis. Especially where data is limited, high dimensional, and prone to measurement error.
Methods for Sequence Analysis
Modeling and analyzing biological systems measured with high-throughput sequencing technologies.
Drug Discovery and Development, Biomarker Discovery
Developing computational methods for identifying and validating potential drug targets and biomarkers in biological systems.
Sports Medicine, Rehabilitation, and Human Performance
Investigating the biological and mechanical factors that influence athletic performance and recovery. Identifying candidate biomarkers and therapeutic targets.

Teaching and Mentoring


Graduate Instruction
Undergraduate Instruction and Mentoring
  • Global Code in Ghana: Software Engineering Bootcamp for Undergraduates
  • Mentored 3 undergraduate students through various programs: Hunter college, DREAM, etc.
K-12 Teaching


"Non-Traditional"
"Non-Traditional"
Development, Resources, and Short-Stories
Maxwell A. Konnaris
Click to open the book →
Development, Resources, and Short-Stories
"Non-Traditional"
Maxwell A. Konnaris
Premed → Bioinformatics PhD
Statistical & Probabilistic ML
i
"Non-Traditional" Preface
Preface
About This Book

[ Your preface — to be written ]

ii
"Non-Traditional" Contents
Navigation
Table of Contents
Chapter I Transitioning to a Quantitative Field 1
On identity, self-teaching, and what you already know
Chapter II Forthcoming
Chapter III Forthcoming
Chapter IV Forthcoming
iii
"Non-Traditional" Contents
"The impediment to action advances action. What stands in the way becomes the way." — Marcus Aurelius

Click any entry in the table of contents
to jump directly to that chapter.

iv
Chapter I Transitioning to a Quantitative Field
Chapter One
Transitioning to a Quantitative Field

No one tells you that the transition takes longer on the inside than it does on paper. You can update your CV long before you update your sense of who you are.

This chapter is for anyone arriving at a quantitative field from somewhere else — from physiology, biology, social science, or any domain where the tools of inquiry are not grounded by mathematical rigor. I write from the vantage of a premed-to-bioinformatics-to-quantitative scientist transition, but the shape of the problem is the same across fields: you are not starting from zero, but you do not yet know what you have.

The Identity Is the Last Thing to Change

There is a liminal phase that most people underestimate. You can be genuinely capable at quantitative work and still introduce yourself, for years, with the old credential as a hedge — I'm a biologist, but I do some programming. The hedge is protective. It manages expectations and offers an exit route if the room turns skeptical. It is also a symptom.

The shift — from someone who codes to a statistician, an ML researcher, a computational scientist, whatever the destination label turns out to be — does not happen at a specific moment. It happens in aggregate, through the accumulation of problems you solved with quantitative tools and couldn't have solved any other way. At some point you stop reaching for the old vocabulary to explain yourself. That is the transition completing itself.

The credential hedge is understandable, and for a while it's honest. But at some point it stops describing your uncertainty and starts creating it. Notice when that happens.

1
Chapter I Transitioning to a Quantitative Field
What You Actually Need to Know — and When

The fear of mathematics is almost always disproportionate to what a transition actually requires. The first instinct is to treat it like a prerequisite course: master calculus, then linear algebra, then probability theory, then statistics, then you may begin. This is the wrong order and the wrong model entirely.

What most transitions into quantitative biology or ML require at the outset is narrower than you think: enough calculus to understand what a gradient is doing, enough linear algebra to reason about data as matrices and understand why decompositions matter, and enough probability to understand what a distribution is and why conditioning matters. You do not need proofs. You need intuition about what the operations represent.

The deeper mathematics arrives naturally, and only when a specific problem demands it. I did not properly understand eigendecomposition until I needed to think carefully about PCA on gene expression data. I did not understand the KL divergence until variational inference required it. The problem came first; the understanding followed. This is not a shortcut. It is how mathematical knowledge actually accumulates in practice.

Learn enough to begin. The gaps will announce themselves when they matter. A gap that has not yet blocked you is not your most urgent problem.

Programming Is a Means, Not an Endpoint

Many people transitioning from non-quantitative fields treat programming as the primary skill to acquire. This is understandable — it is the most visible difference between where they are and where they want to be. Syntax is learnable in weeks. Thinking computationally — knowing how to decompose a problem, when to approximate, what to trust in your output — takes years and does not come from syntax.

2
Chapter I Transitioning to a Quantitative Field
Teaching Yourself Without a Roadmap

There is no curriculum designed for the transition you are making, because the transition is different for everyone and the field moves faster than curricula can track. The roadmap does not exist. This is disorienting. It is also, eventually, freeing.

Self-teaching under these conditions is necessarily non-linear. You will pick up linear algebra from a video series when PCA stops making sense, probability from a textbook when a paper's methods section becomes opaque, and statistical modeling from the code of people whose results you are trying to reproduce. None of these will happen in a clean sequence. All of them will happen in response to a specific problem that mattered to you right now — and that is precisely why they will stick.

The failure mode to watch for is the preparation trap: convincing yourself that you must complete some prior body of knowledge before you are permitted to begin the actual work. There is always more prior knowledge. The people who make the transition successfully do not wait until they are ready. They begin, encounter what they don't know, and go learn exactly that thing.

Build the plane while flying it. The alternative — waiting on the ground until you understand aerodynamics — does not produce pilots. It produces people who read a lot about flight.

What Your Background Already Gave You

People trained in quantitative fields learn to optimize functions they do not always understand. People trained in biology and medicine learn what the function is supposed to represent. This asymmetry sounds abstract. Its consequences are concrete.

Domain knowledge is not decoration applied after the real work is done. It is a filter — often the only filter available — against results that are technically correct and scientifically meaningless. The ability to look at a model output and recognize that it is biologically implausible, even when the loss converged and the code ran clean, is a form of intelligence that cannot be derived from data alone.

3
Chapter I Transitioning to a Quantitative Field

This shows up in subtler ways too. A physiologist who learns to build statistical models brings with it an understanding of measurement error — the knowledge that a blood pressure reading is not blood pressure, that a self-report is not a behavior, that a sequencing read is not a transcript. This understanding of the distance between the measurement and the thing measured is hard-earned in experimental science and largely invisible to people who learned statistics on clean benchmark datasets.

Coming from premed specifically: the clinical framing — who does this affect, what decision does this change, what would happen if you were wrong — is not something most quantitative training instills deliberately. Carry it forward. It becomes one of the rarer things you bring to a field that often optimizes metrics without asking what the metric is for.

When You Stop Being a Guest

There will be a period, probably longer than feels fair, when you feel like a visitor in the field. You sit in seminars and follow maybe half of what is said. You read papers and skip the methods. You produce results that you cannot fully defend yet. This is not impostor syndrome in the pejorative sense — it is an accurate read of your current state. The answer to it is not reassurance. It is time and repetition.

You stop being a guest when you begin to have opinions. When you read a methods section and have a reaction — that model choice seems odd given the data structure, that baseline comparison is misleading — rather than just receiving information. Opinions require context. Context requires immersion. There is no shortcut, but there is a direction: do the work, read widely, and be honest about what you don't understand yet.

The transition is complete not when you know everything, but when you know enough to know what you're missing — and can find it.

· · ·
4
"Non-Traditional" Coming Soon
Chapter Two
Forthcoming

[ Next chapter — to be written ]

5
"Non-Traditional" Coming Soon
6
"Non-Traditional" Coming Soon
Chapter Three
Forthcoming

[ Next chapter — to be written ]

7
"Non-Traditional" Coming Soon
✦ ✦ ✦

This is a living document.
Comments and corrections are welcome.

8
Pages i – ii

Community Engagement & Public Service


Letters to a Pre-Scientist
Science Outreach

Letters to a Pre-Scientist

Showcasing STEM for K–12 Students
Letters to a Pre-Scientist

A national pen-pal program pairing professional scientists with middle school students, many from under-resourced communities. Through personal correspondence I help demystify what scientists actually do, and show students that science is a real career path for people who look like them.

prescientist.org
Conference Organization

CCBB Workshop, 2024 & 2026

Conference Organization
Center for Computational Biology & Bioinformatics

Co-organizer of the CCBB Workshop, bringing together researchers developing methods for sequence analysis. I ideated and co-led a panel discussion with professors and students on the gap between method developers and users — focusing on community needs, tool adoption, and barriers to use.

ccbb.psu.edu/wip2024
NYC Marathon volunteering \
Leadership Training

NYRR Volunteer Leadership

Leadership Training
New York Road Runners Volunteer Leadership Program

Selected for a competitive leadership development program with NYRR, the organization behind the NYC Marathon. Training in nonprofit leadership, community engagement, and event management — including organizing and supervising volunteers across races, including the NYC Marathon itself.

nyrr.org/volunteer-leadership-program
Medical Aide Across Borders

Catholic Diocese of Ghana

Medical Aide Across Borders
Catholic Diocese of Ghana

Volunteered as a medical aide, learning firsthand about the barriers to care in a developing country. Assisted in basic healthcare services and health education. This experience deepened my understanding of global health challenges and the importance of accessible healthcare.

GenoMIX at Penn State
Student Leadership

President of GenoMIX, Penn State

Community Development & Student Leadership
President, GenoMIX Graduate Student Organization

Led Penn State's graduate organization for genomics — organizing events, managing communications, mentoring peers. Developed 10 student resources including a graduate school guide, area assimilation handbook, career development guide, and mentorship program framework.

GenoMIX at Penn State
iSTEAM Microbiome Marvels
Science Communication

iSTEAM Microbiome Marvels

Science Communication
iSTEAM Microbiome Marvels: Decoding the Hidden Heroes of Human Health Evaluation

As part of a T32 training grant, I helped develop and deliver a curriculum on microbiome science for high school biology teachers. The curriculum included interactive lessons, hands-on activities, and real-world applications to help teachers introduce big ideas about the small world.

Adventures & Stories


Outside of research, I spend much of my time in endurance sport, exercise, photography, and traveling. Always looking for the next immersive adventure where I can learn something new and connect with people.
Athletics & Competition
Triathlons, Soccer, and What Not
I compete in triathlons and am actively training for a half Ironman. I also build bicycles!

I was a collegiate soccer player and still compete in local leagues and tournaments. Im also a die hard Arsenal fan.
Exploring Cultures
Urban Backpacking
Constantly immersing myself in different cultures, traveling, and learning as much as I can.

Ask me about coffee: I have toured the worlds premier coffee shops and hope to continue learning.
Creative Outlets
Photography and Visual Editing
I like to capture moments and turn them into images that emphasize main characters spotlighting their "cool".

Get in Touch