Jay Flatley
Denali TherapeuticsAbout Jay Flatley
Jay Flatley (age 72) has served as an independent director of Denali Therapeutics since 2015, bringing decades of life-sciences leadership as former CEO and Executive Chairman of Illumina and earlier CEO/President of Molecular Dynamics, with degrees in industrial engineering (BS, MS) from Stanford and a BA in economics from Claremont McKenna College . He is currently a member of Denali’s Audit Committee and chairs the Compensation Committee, with documented independence under Nasdaq rules .
Past Roles
| Organization | Role | Tenure | Committees/Impact |
|---|---|---|---|
| Illumina, Inc. | Chairman of the Board; Executive Chairman; CEO; CEO & President | Chairman: Jan 2020–May 2021; Exec Chair: Jul 2016–Jan 2020; CEO: Dec 2013–Jul 2016; CEO & President: Oct 1999–Dec 2013 | Led growth of genomics platform; industry leadership |
| Molecular Dynamics | Co-founder, President, CEO, Director | Jul 1994–Sep 1998 (sale to Amersham Pharmacia Biotech) | Built genetic analysis business; exit via sale |
| Zymergen Inc. | Chairman and Acting CEO | Until acquisition by Ginkgo Bioworks in 2022 | Stewarded transition to acquisition |
External Roles
| Organization | Role | Public/Private/Non-profit | Notes |
|---|---|---|---|
| Wellcome Trust Leap Fund | Chairman | Non-profit | Strategic oversight in biomedical innovation |
| Cellanome | Chairman of the Board | Private | Board leadership |
| Iridia | Chairman of the Board | Private | Board leadership |
| Rivian Automotive | Director | Public | External public company directorship |
| The Salk Institute | Trustee | Non-profit | Scientific institution governance |
| UCSD Moores Cancer Center | Advisory Board Member | Non-profit | Scientific/clinical advisory |
| Prior boards: Zymergen, Juno Therapeutics, Coherent Inc. | Director | Public | Prior public boards |
Board Governance
- Independence: Board determined Flatley is independent; serves on Audit (member) and Compensation (chair) committees, meeting SEC/Nasdaq standards .
- Committee structure and leadership: Audit Committee chaired by Peter Klein; Compensation Committee chaired by Jay Flatley; Flatley on both Audit and Compensation .
- Attendance: Board held 5 meetings in 2024; Flatley attended 100% of board/committee meetings in 2024 vs. 86% in 2023, indicating improved engagement .
- Executive sessions: Board regularly holds independent director sessions without management .
| Item | 2023 | 2024 |
|---|---|---|
| Board meetings held | 5 | 5 |
| Audit Committee meetings | 5 | 5 |
| Compensation Committee meetings | 4 | 3 |
| Corporate Governance & Nominating meetings | 2 | 3 |
| Flatley attendance rate | 86% | 100% |
| Committee memberships | Audit (member) | Audit (member) |
| Committee chair roles | Compensation (chair) | Compensation (chair) |
Fixed Compensation
- Policy rates (outside directors): Board annual retainer increased from $45,000 (2024) to $50,000 (2025); Non-executive Chair retains $35,000. Committee retainers (per 2024/2025): Audit Chair $20,000; Audit member $10,000; Compensation Chair $15,000; Compensation member $7,500; Corporate Governance Chair $10,000; member $5,000; Science & Technology Chair reduced $15,000→$10,000; member $7,500→$5,000 .
| Retainer Component | 2024 Amount | 2025 Amount |
|---|---|---|
| Board annual retainer (all non-employee directors) | $45,000 | $50,000 |
| Non-exec Chair additional retainer | $35,000 | $35,000 |
| Audit Chair | $20,000 | $20,000 |
| Audit member | $10,000 | $10,000 |
| Compensation Chair | $15,000 | $15,000 |
| Compensation member | $7,500 | $7,500 |
| Corp Gov & Nominating Chair | $10,000 | $10,000 |
| Corp Gov & Nominating member | $5,000 | $5,000 |
| Science & Technology Chair | $15,000 | $10,000 |
| Science & Technology member | $7,500 | $5,000 |
- Flatley 2024 director pay: Cash fees $70,000; stock awards grant-date fair value $110,748; option awards grant-date fair value $203,717; total $384,465 .
| Director (2024) | Cash Fees | Stock Awards (grant-date FV) | Option Awards (grant-date FV) | Total |
|---|---|---|---|---|
| Jay Flatley | $70,000 | $110,748 | $203,717 | $384,465 |
Performance Compensation
- Equity structure (outside director policy): Initial onboarding awards ~ $700,000 split 60% options / 40% RSUs; annual awards ~ $400,000 split 60% options / 40% RSUs. Company values RSUs at 1 RSU per 2 option shares to set share counts. Initial Option: 1/4 vest at year 1, then monthly 1/48; Initial RSU: annual tranches over four years; Annual Option/RSU follow similar schedules tied to the annual meeting grant date .
| Award Type | Value Framework | Split | Vesting |
|---|---|---|---|
| Initial director awards | ~$700,000 | 60% options / 40% RSUs | Option: 25% at 1 year, then monthly; RSU: 25% annually over 4 years |
| Annual director awards | ~$400,000 | 60% options / 40% RSUs | Granted at annual meeting; vest per option/RSU schedules |
- Flatley outstanding director equity (as of Dec 31, 2024): Options outstanding 172,154; RSUs unvested 5,967 .
| As of 12/31/2024 | Quantity |
|---|---|
| Options outstanding | 172,154 |
| RSUs unvested | 5,967 |
Other Directorships & Interlocks
- Current public board: Rivian Automotive (director) .
- Prior public boards: Zymergen, Juno Therapeutics, Coherent Inc. .
- Compensation Committee Interlocks: None disclosed; no officers of Denali serving on boards/comp committees of entities with reciprocal executive overlap in 2024 .
- Family relationships: None among directors/executives .
Expertise & Qualifications
- Life-sciences operating leader with genomics commercialization expertise (Illumina), strategic M&A and platform scaling experience (Molecular Dynamics), and governance across public, private, and non-profit biomedical entities .
- Audit Committee member (financial sophistication on committee led by a designated financial expert, Peter Klein) and Compensation Committee chair, indicating governance breadth .
Equity Ownership
- Beneficial ownership (as of March 31, 2025): 500,749 shares; <1% of shares outstanding, consistent with director-level holdings .
- Director stock ownership guidelines: Minimum holdings equal to 3x annual cash retainer; compliance required by April 16, 2026 or 5 years from initial appointment; sales limits apply until guideline met; committee may waive in hardship cases .
- Hedging/pledging: Insider trading policy bars hedging and pledging for directors, officers, and employees .
| Ownership Metric | Value |
|---|---|
| Shares beneficially owned | 500,749 |
| Ownership % | <1% |
| Stock ownership guideline | ≥3x annual cash retainer; deadline 2026 |
| Hedging/pledging policy | Prohibited under insider trading policy |
Fixed Compensation (Policy vs. Practice)
- Policy alignment: Cash retainers plus equity grants (options and RSUs) calibrated against peer and consultant input; outside director policy originally crafted with Aon and amended Jan 2025 .
- Year-over-year structural changes: Increase in base board retainer to $50k for 2025; reduction in Science & Technology Committee retainers, reflecting recalibration of committee workloads/cost .
Governance Assessment
-
Key positives:
- Independence and committee leadership: Independent director; chairs Compensation Committee; member of Audit Committee; no interlocks disclosed .
- Engagement: Attendance improved to 100% in 2024 from 86% in 2023; strong committee participation .
- Pay alignment policies: Equity-heavy director compensation with multi-year vesting; ownership guidelines; anti-hedging/pledging; clawback policy (company-wide) .
- Shareholder sentiment: High say-on-pay approval (~92.2% in 2024; ~93.7% in 2023) indicates overall confidence in compensation governance .
-
Watch items:
- External commitments: Multiple external boards/advisory roles could pose time-allocation risk typical for seasoned directors; 2024 attendance mitigates concern .
- Ownership alignment: Beneficial ownership <1%; policy-based guideline and ongoing annual equity help alignment but absolute ownership is modest relative to total shares .
-
RED FLAGS observed: None disclosed in reviewed sections regarding related-party transactions tied to Flatley, hedging/pledging, excise tax gross-ups, or option repricing; compensation committee interlocks explicitly noted as none .
Implications: Flatley’s governance profile (independence, committee leadership, improved attendance, robust policy framework) generally supports investor confidence. Continued monitoring of ownership guideline compliance by 2026 and external time commitments is prudent .
Notes
- Related-party transactions are overseen by the Audit Committee; no specific Flatley-related transactions are identified in the sections reviewed here .
- Board leadership: Chair transitions to Julian Baker after the 2025 Annual Meeting, maintaining separation of Chair and CEO roles .
