Denali Therapeutics Software Engineer Interview Guide

The 60-second brief

As a Software Engineer at Denali Therapeutics, you play a pivotal role in advancing the company’s mission to develop innovative therapies for neurodegenerative diseases. This position is essential for designing, implementing, and maintaining software solutions that drive our research and product development processes. Your contributions will have a direct impact on the efficacy and efficiency of our scientific pursuits, ultimately benefiting patients and healthcare providers. This role is critical due to the complexity and scale of the challenges faced in biotechnology. You will collaborate with cross-functional teams, including researchers, data scientists, and other engineers, to develop applications that support data analysis, modeling, and simulation.

This guide is scoped to a Software Engineer candidate at Denali Therapeutics.

Focus areas

• Quality Assurance (QA)
• Validation Testing
• Software Engineering (General)

The Denali Therapeutics interview process

Denali Therapeutics candidates report 4 rounds over 3-5 weeks. The stages below are what candidates describe, not a published process.

Initial Screening Call

An initial call to assess your background and fit for the role.

What to demonstrate

• An initial call to assess your background and fit for the role
• Depth in Quality Assurance (QA)

How to prepare

• Be able to walk your CV end to end in two minutes, and say why this company specifically.
• Have your salary expectations, notice period and location constraints ready, and ask for the rest of the loop in writing.

Technical Interviews

Multiple interviews focusing on your technical skills and problem-solving abilities.

What to demonstrate

• Multiple interviews focusing on your technical skills and problem-solving abilities
• Depth in Quality Assurance (QA)

How to prepare

• Answer aloud and timed: How do you ensure code quality and maintainability?
• Answer aloud and timed: Explain the principles of object-oriented programming.

Behavioral Assessments

Evaluations aimed at understanding your cultural fit and thought processes.

What to demonstrate

• Evaluations aimed at understanding your cultural fit and thought processes
• Depth in Quality Assurance (QA)

How to prepare

• Prepare three examples from your own work, each with a decision you made and an outcome you can quantify.
• Re-read the description of the behavioral assessments above and write down what you would ask to confirm before it.

Discussions with Senior Leadership

Final discussions to assess alignment with company values and leadership expectations.

What to demonstrate

• Final discussions to assess alignment with company values and leadership expectations
• Depth in Quality Assurance (QA)

How to prepare

• Answer aloud and timed: Describe the considerations you take into account when designing a database schema.
• Answer aloud and timed: Explain the trade-offs between microservices and a monolithic architecture.

Where candidates lose points

Understand the Mission

Familiarize yourself with Denali Therapeutics’ mission and values. Show how your goals align with their commitment to tackling neurodegenerative diseases.

Practice Coding

Use platforms like LeetCode or HackerRank to practice coding problems, particularly those relevant to the languages you’ll be using.

Prepare Questions

Have thoughtful questions ready to ask your interviewers about their work, challenges they face, and the team culture.

Review Past Projects

Be ready to discuss your previous work in detail, including challenges faced, technologies used, and outcomes achieved. This will demonstrate your practical experience and problem-solving abilities.

Questions & practice

Write a function to reverse a linked list.

Medium · Coding / Algorithms

Approach

1. Restate the input: its shape, its size, and what is guaranteed about it.
2. Name the brute-force solution and its complexity before improving on it.
3. Choose the data structure from the access pattern, not from familiarity.
4. State the target complexity and say which constraint rules the naive version out.

Follow-up

• How does this change if the input no longer fits in memory?
• What is the worst case, and how likely is it on real data?

How would you implement a binary search algorithm in your preferred language?

Medium · Coding / Algorithms

Approach

1. Restate the input: its shape, its size, and what is guaranteed about it.
2. Name the brute-force solution and its complexity before improving on it.
3. Choose the data structure from the access pattern, not from familiarity.
4. State the target complexity and say which constraint rules the naive version out.

Follow-up

• How does this change if the input no longer fits in memory?
• What is the worst case, and how likely is it on real data?

Given a dataset, how would you find duplicates efficiently?

Medium · Coding / Algorithms

Approach

1. Restate the input: its shape, its size, and what is guaranteed about it.
2. Name the brute-force solution and its complexity before improving on it.
3. Choose the data structure from the access pattern, not from familiarity.
4. State the target complexity and say which constraint rules the naive version out.

Follow-up

• How does this change if the input no longer fits in memory?
• What is the worst case, and how likely is it on real data?

Explain the differences between depth-first search and breadth-first search.

Medium · Coding / Algorithms

Approach

1. Restate the input: its shape, its size, and what is guaranteed about it.
2. Name the brute-force solution and its complexity before improving on it.
3. Choose the data structure from the access pattern, not from familiarity.
4. State the target complexity and say which constraint rules the naive version out.

Follow-up

• How does this change if the input no longer fits in memory?
• What is the worst case, and how likely is it on real data?

Solve a problem involving dynamic programming and explain your approach.

Medium · Coding / Algorithms

Approach

1. Restate the input: its shape, its size, and what is guaranteed about it.
2. Name the brute-force solution and its complexity before improving on it.
3. Choose the data structure from the access pattern, not from familiarity.
4. State the target complexity and say which constraint rules the naive version out.

Follow-up

• How does this change if the input no longer fits in memory?
• What is the worst case, and how likely is it on real data?

Describe the considerations you take into account when designing a database schema.

Medium · System Design / Architecture

Approach

1. Name the grain you start from and join outward from it.
2. Check whether any join is one-to-many before aggregating, or the sums inflate.
3. Say which index the query would use, and what makes it unusable.
4. Handle the rows that do not match: that is usually the actual question.

Follow-up

• How does the query change if that join becomes one-to-many?
• What happens to this when the table is ten times larger?

Find version gaps and relay lag with window functions

Medium · window functions · event tables · frame semantics

outbox_event holds event_id, aggregate_type, aggregate_id, aggregate_version, event_type, payload, status ('pending','published','dead'), attempts, created_at, published_at. A projection is missing rows and you must decide whether the relay skipped events or the consumer dropped them. Write three queries over the last seven days: one listing every aggregate_id whose published aggregate_version sequence has a hole, one giving per-day counts with a running total, and one returning the newest published event per aggregate. For each, say where the window function is evaluated relative to WHERE and LIMIT. PostgreSQL 16.

Approach

1. Gaps: compute lead(aggregate_version) OVER (PARTITION BY aggregate_id ORDER BY aggregate_version) in a subquery, then filter next_version <> aggregate_version + 1 in the outer query. Window functions are evaluated after WHERE, GROUP BY and HAVING and before the outer ORDER BY and LIMIT, so the predicate cannot sit in the same WHERE clause and PostgreSQL 16 has no QUALIFY.
2. Say what the seven-day filter does to the answer: it truncates every partition, so the first row per aggregate has no predecessor inside the window and a hole spanning the boundary is invisible. Widen the window, or join to resource.version as the authority for the true maximum.
3. Running total: SELECT date_trunc('day', created_at) AS d, count() AS n, sum(count()) OVER (ORDER BY date_trunc('day', created_at) ROWS UNBOUNDED PRECEDING). An aggregate inside a window call is legal because grouping runs before windowing. The grouping key is unique per row here so ROWS and RANGE agree, but write the frame anyway — over ungrouped rows with tied timestamps the default RANGE frame pulls in every peer row and the total jumps.
4. Newest per aggregate: DISTINCT ON (aggregate_id) ... ORDER BY aggregate_id, aggregate_version DESC is the cheap PostgreSQL-only form when an index matches that order; row_number() OVER (PARTITION BY aggregate_id ORDER BY aggregate_version DESC) = 1 is the portable form and needs a subquery for the same evaluation-order reason as the gap query.

Follow-up

• Relay failover redelivers events. Does a duplicate break the gap query, and how would you detect one from this table alone?
• Turn the gap check into a continuous monitor rather than a query someone runs after an incident. What does it watch?

What programming languages are you most proficient in, and why did you choose them?

Medium · Technical / Domain Questions

Approach

1. Clarify what is being asked and what a complete answer contains.
2. State your assumptions explicitly before working the problem.
3. Say what you would check first and why it is the highest-information step.
4. Work from the requirement backwards to the design.

Follow-up

• What assumption would you test first?
• How would you know your answer was wrong?

Describe a challenging software project you have worked on and the technologies you used.

Medium · Technical / Domain Questions

Approach

1. Clarify what is being asked and what a complete answer contains.
2. State your assumptions explicitly before working the problem.
3. Say what you would check first and why it is the highest-information step.
4. Work from the requirement backwards to the design.

Follow-up

• What assumption would you test first?
• How would you know your answer was wrong?

How do you ensure code quality and maintainability?

Medium · Technical / Domain Questions

Approach

1. Clarify what is being asked and what a complete answer contains.
2. State your assumptions explicitly before working the problem.
3. Say what you would check first and why it is the highest-information step.
4. Work from the requirement backwards to the design.

Follow-up

• What assumption would you test first?
• How would you know your answer was wrong?

Explain the principles of object-oriented programming.

Medium · Technical / Domain Questions

Approach

1. Clarify what is being asked and what a complete answer contains.
2. State your assumptions explicitly before working the problem.
3. Say what you would check first and why it is the highest-information step.
4. Work from the requirement backwards to the design.

Follow-up

• What assumption would you test first?
• How would you know your answer was wrong?

What tools do you use for version control, and why are they important?

Medium · Technical / Domain Questions

Approach

1. Clarify what is being asked and what a complete answer contains.
2. State your assumptions explicitly before working the problem.
3. Say what you would check first and why it is the highest-information step.
4. Work from the requirement backwards to the design.

Follow-up

• What assumption would you test first?
• How would you know your answer was wrong?

How would you design a system to handle real-time data processing?

Medium · System Design / Architecture

Approach

1. Fix the scope first: who calls this, how often, and what they do when it fails.
2. Name the read and write paths separately; they rarely have the same bottleneck.
3. Choose a partition key and say what query it makes expensive.
4. State the consistency you need, and where you are willing to be stale.

Follow-up

• What breaks first when traffic grows ten times?
• How does this behave when that dependency is down for an hour?

Explain the trade-offs between microservices and a monolithic architecture.

Medium · System Design / Architecture

Approach

1. Fix the scope first: who calls this, how often, and what they do when it fails.
2. Name the read and write paths separately; they rarely have the same bottleneck.
3. Choose a partition key and say what query it makes expensive.
4. State the consistency you need, and where you are willing to be stale.

Follow-up

• What breaks first when traffic grows ten times?
• How does this behave when that dependency is down for an hour?

How do you approach API design and documentation?

Medium · System Design / Architecture

Approach

1. Fix the scope first: who calls this, how often, and what they do when it fails.
2. Name the read and write paths separately; they rarely have the same bottleneck.
3. Choose a partition key and say what query it makes expensive.
4. State the consistency you need, and where you are willing to be stale.

Follow-up

• What breaks first when traffic grows ten times?
• How does this behave when that dependency is down for an hour?

What strategies do you use for load balancing and high availability?

Medium · System Design / Architecture

Approach

1. Fix the scope first: who calls this, how often, and what they do when it fails.
2. Name the read and write paths separately; they rarely have the same bottleneck.
3. Choose a partition key and say what query it makes expensive.
4. State the consistency you need, and where you are willing to be stale.

Follow-up

• What breaks first when traffic grows ten times?
• How does this behave when that dependency is down for an hour?

Describe your thought process when faced with an unexpected technical challenge.

Medium · Problem-solving / Case Studies

Approach

1. Clarify what is being asked and what a complete answer contains.
2. State your assumptions explicitly before working the problem.
3. Say what you would check first and why it is the highest-information step.
4. Work from the requirement backwards to the design.

Follow-up

• What assumption would you test first?
• How would you know your answer was wrong?

Provide an example of how you optimized a process or system.

Medium · Problem-solving / Case Studies

Approach

1. Clarify what is being asked and what a complete answer contains.
2. State your assumptions explicitly before working the problem.
3. Say what you would check first and why it is the highest-information step.
4. Work from the requirement backwards to the design.

Follow-up

• What assumption would you test first?
• How would you know your answer was wrong?

How would you tackle a project with unclear requirements?

Medium · Problem-solving / Case Studies

Approach

1. Clarify what is being asked and what a complete answer contains.
2. State your assumptions explicitly before working the problem.
3. Say what you would check first and why it is the highest-information step.
4. Work from the requirement backwards to the design.

Follow-up

• What assumption would you test first?
• How would you know your answer was wrong?

How would you approach debugging a production issue?

Medium · Problem-solving / Case Studies

Approach

1. Establish what changed and when, before forming any theory.
2. Pick a bisection that eliminates candidates whichever way it turns out.
3. Check the instrumentation before believing the symptom.
4. Separate the trigger from the cause; the deploy is rarely the bug.

Follow-up

• What would you look at first, and what would it rule out?
• How would you tell a cause from a coincidence here?

Suggested practice checklist

Built from the rounds and topics Denali Therapeutics candidates report.

Day 1 — Map the Denali Therapeutics loop

• Write out the reported sequence: Initial Screening Call, Technical Interviews, Behavioral Assessments, Discussions with Senior Leadership.
• For each round, write one sentence on what it is judging, from the description above, and mark the one you are least ready for.

Deliverable: A one-page map of the 4 reported rounds, with the weakest marked.

Day 2 — Work Quality Assurance (QA)

• Spend the session on Quality Assurance (QA), which Denali Therapeutics candidates report being tested on.
• Write one worked example in Quality Assurance (QA) and time yourself on it.

Deliverable: One timed worked example in Quality Assurance (QA).

Day 3 — Work Validation Testing

• Spend the session on Validation Testing, which Denali Therapeutics candidates report being tested on.
• Write one worked example in Validation Testing and time yourself on it.

Deliverable: One timed worked example in Validation Testing.

Day 4 — Work Software Engineering (General)

• Spend the session on Software Engineering (General), which Denali Therapeutics candidates report being tested on.
• Write one worked example in Software Engineering (General) and time yourself on it.

Deliverable: One timed worked example in Software Engineering (General).

Day 5 — Answer out loud: Technical / Domain Questions

• Answer aloud, timed: What programming languages are you most proficient in, and why did you choose them?
• Answer aloud, timed: Describe a challenging software project you have worked on and the technologies you used.

Deliverable: Spoken answers to 2 reported Technical / Domain Questions question(s), under time.

Day 6 — Answer out loud: System Design / Architecture

• Answer aloud, timed: How would you design a system to handle real-time data processing?
• Answer aloud, timed: Describe the considerations you take into account when designing a database schema.

Deliverable: Spoken answers to 2 reported System Design / Architecture question(s), under time.

Day 7 — Answer out loud: Behavioral / Leadership

• Answer aloud, timed: Describe a time when you had to work with a difficult team member. How did you handle it?
• Answer aloud, timed: How do you prioritize tasks when working on multiple projects?

Deliverable: Spoken answers to 2 reported Behavioral / Leadership question(s), under time.

Behavioural preparation

Behavioural rounds judge the decision you made and what it cost.

Describe a time when you had to work with a difficult team member. How did you handle it?

Medium · Behavioral / Leadership

Approach

1. Pick a story where you made the decision, not one where you watched it.
2. State the situation in two sentences and spend the rest on the reasoning.
3. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?

How do you prioritize tasks when working on multiple projects?

Medium · Behavioral / Leadership

Approach

1. Pick a story where you made the decision, not one where you watched it.
2. State the situation in two sentences and spend the rest on the reasoning.
3. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?

Can you give an example of a time you took the initiative on a project?

Medium · Behavioral / Leadership

Approach

1. Pick a story where you made the decision, not one where you watched it.
2. State the situation in two sentences and spend the rest on the reasoning.
3. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?

How do you handle feedback and criticism?

Medium · Behavioral / Leadership

Approach

1. Pick a story where you made the decision, not one where you watched it.
2. State the situation in two sentences and spend the rest on the reasoning.
3. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?

What does teamwork mean to you, and how do you contribute to a team dynamic?

Medium · Behavioral / Leadership

Approach

1. Pick a story where you made the decision, not one where you watched it.
2. State the situation in two sentences and spend the rest on the reasoning.
3. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?

Discuss a time when you used data to inform a decision.

Medium · Problem-solving / Case Studies

Approach

1. Pick a story where you made the decision, not one where you watched it.
2. State the situation in two sentences and spend the rest on the reasoning.
3. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?