Document:

Executive Employment Agreement

 EXHIBIT 10.4 
 AVI BIOPHARMA, INC. 
 EXECUTIVE EMPLOYMENT AGREEMENT 

This Employment Agreement (the “Agreement”) is entered into as of March 29, 2011 (the
“Effective Date”) by and between AVI BioPharma, Inc. (the “Company”), and Peter S. Linsley, Ph.D. (“Executive”). 

1. Duties and Scope of Employment. 

(a) Positions and Duties. As of May 1, 2011 (the “Start Date”), Executive will serve as the
Company’s Senior Vice President and Chief Scientific Officer. Executive will render such business and professional services in the performance of his duties as will reasonably be assigned to him by the Company’s Chief Executive Officer.

 (b) Obligations. During the Employment Term, Executive will perform his duties faithfully and to the
best of his ability and will devote his full business efforts and time to the Company. For the duration of the Employment Term, Executive agrees not to actively engage in any other employment, occupation or consulting activity for any direct or
indirect remuneration without the prior approval of the Company’s Board of Directors (the “Board”). 
 2. At-Will Employment. The parties agree that Executive’s employment with the Company will be “at-will” employment and may be terminated at any time with or without Cause or notice.
Executive understands and agrees that neither his job performance nor promotions, commendations, bonuses or the like from the Company give rise to or in any way serve as the basis for modification, amendment, or extension, by implication or
otherwise, of his employment with the Company. However, as described in this Agreement, Executive may be entitled to severance benefits depending on the circumstances of Executive’s termination of employment with the Company. 

3. Term of Agreement. Subject to Section 2 above, this Agreement will have a term of two (2) years,
commencing on the Effective Date (the “Employment Term”). At the end of the Employment Term, the Agreement may be renewed upon mutual agreement in writing by Executive and the Company, otherwise it will expire in accordance with its
terms. Non-renewal at the end of the Employment Term shall not constitute termination without Cause or give Executive an opportunity to terminate his employment for Good Reason, even if a Good Reason event has occurred before the expiration of the
Employment Term under this Agreement. Notwithstanding anything herein to the contrary, if, during the Employment Term, the Company experiences a Change of Control, the Employment Term shall be extended to the end of the Change of Control Period (as
defined in Section 9(b) below). 
 4. Compensation. 

(a) Base Salary. During the Employment Term, the Company will pay Executive an annual salary of $364,000 as
compensation for his services (the “Base Salary”). The Base Salary will be paid periodically in accordance with the Company’s normal payroll practices and be subject 

 
to the usual, required withholdings. Executive’s salary will be subject to review and adjustments will be made based upon the Company’s normal performance review practices. 

(b) Sign-on Bonus. Executive will receive a one-time sign-on bonus of $175,000 (the “Sign-on
Bonus”), less applicable withholdings, payable in cash within thirty (30) days following the Start Date. Notwithstanding the foregoing, if, on or prior to the one (1) year anniversary of the Start Date, Executive terminates his
employment with the Company for any reason, Executive must repay 100% of the Sign-on Bonus to the Company within sixty (60) days of Executive’s termination of employment. 

(c) Target Bonus. Executive will be eligible to receive a target annual bonus of thirty-five
percent (35%) of Executive’s Base Salary, less applicable withholdings, upon achievement of performance objectives to be determined by the Board in its sole discretion (the “Target Bonus”). The maximum bonus Executive will
be eligible to receive is fifty-two and one half percent (52.5%) of his Base Salary. The Target Bonus, or any portion thereof, will be paid as soon as practicable after the Board determines that the Target Bonus has been earned, but in no event
shall the Target Bonus be paid after the later of (i) the fifteenth (15th) day of the third (3rd) month following the close of the Company’s fiscal year in which the Target Bonus is earned or (ii) March 15 following the calendar year in which the Target Bonus is earned.

 (d) Stock Option. Following the Effective Date, it will be recommended that Executive be granted a
stock option to purchase 800,000 shares at an exercise price equal to the fair market value on the date of grant (the “Option”). Subject to the accelerated vesting provisions set forth herein, the Option will vest as to twenty-five
percent (25%) of the shares subject to the Option on the first anniversary of the Start Date, and as to 1/48th of the shares subject to the Option on each monthly anniversary thereafter on the same day of the month as the Start Date (and if
there is no corresponding day, the last day of the month), so that the Option will be fully vested and exercisable four (4) years from the Start Date, subject to Executive continuing to provide services to the Company through the relevant
vesting dates. The Option will be made as an “inducement” grant outside of the Company’s 2002 Equity Incentive Plan and will be subject to the terms, definitions and provisions of a stock option agreement by and between Executive and
the Company (the “Option Agreement”), which document is incorporated herein by reference. 
 5.
Employee Benefits. During the Employment Term, Executive will be entitled to participate in the employee benefit plans currently and hereafter maintained by the Company of general applicability to other executive officers of the Company. The
Company reserves the right to cancel or change the benefit plans and programs it offers to its employees at any time. 
 6. Vacation. Executive will be entitled to four weeks of paid vacation, which vacation shall be fully accrued as of the Start Date. Any additional paid vacation to which Executive may be entitled
will be accrued in accordance with the Company’s vacation policy. For all vacation days, the timing and duration of specific days off shall be mutually and reasonably agreed to by the parties hereto. 

7. Relocation/Corporate Housing. 

  
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 (a) The Company agrees to reimburse Executive up to a total of $30,000 for
his (i) actual corporate housing expenses for housing for Executive and his family in the Seattle, WA metropolitan area and (ii) actual, documented reasonable expenses incurred in moving and relocating his family and household to the
Seattle, WA metropolitan area, which may include any costs or expenses associated with Executive’s (x) sale of his current residence, (y) shipment of personal effects to the Seattle, WA metropolitan area, or (z) the customary
closing costs associated with the purchase of a residence in the Seattle, WA metropolitan area incurred by Executive during the relocation period; provided that any expenses incurred pursuant to Sections 7(a)(i) and (ii) must be incurred within
six months of Executive’s Start Date to be eligible for reimbursement pursuant to this Section 7(a). The Company shall not be responsible for grossing-up any funds received or paid on Executive’s behalf for taxes. Executive will be
responsible for withholding and paying applicable income taxes on taxable relocation funds received from the Company during the course of Executive’s relocation. In addition, Executive agrees that he will submit all such reimbursable expenses
to the Company with appropriate documentation no later than sixty (60) days after such expenses are incurred and the Company shall reimburse Executive promptly thereafter in accordance with the Company’s expense reimbursement policy.
Notwithstanding the prior sentence, to the extent such reimbursements are taxable to Executive under the Code, the Company hereby agrees that it will reimburse Executive for all such expenses by no later than March 15, 2012. 

(b) If, on or prior to the one (1) year anniversary of the Start Date, Executive terminates his employment with the
Company for any reason, Executive must repay 100% of the expense reimbursement paid by the Company to Executive under Section 7(a) above to the Company within sixty (60) days of Executive’s termination of employment. 

8. Business Expenses. The Company will reimburse Executive for reasonable travel, entertainment or other business
expenses incurred by Executive in the furtherance of, or in connection with, the performance of Executive’s duties hereunder, in accordance with the Company’s expense reimbursement policy as in effect from time to time. 

9. Severance. 
 (a) Termination for other than Cause, Death or Disability Apart from a Change of Control. If prior to a Change of Control or after twelve (12) months following a Change of Control, the Company
(or any parent or subsidiary or successor of the Company) terminates Executive’s employment with the Company other than for Cause, death or disability after providing at least thirty (30) days advance notice to Executive, then, subject to
Section 10, Executive will be entitled to 
 (i) receive continuing payments of severance pay at a rate
equal to Executive’s Base Salary, as then in effect, for twelve (12) months from the date of such termination, which will be paid in accordance with the Company’s regular payroll procedures; 

(ii) accelerated vesting as to 50% of Executive’s outstanding and unvested equity awards; and 

(iii) an extension of the post-termination exercise period applicable to Executive’s outstanding options to one
hundred and eighty (180) days following the date of Executive’s termination of employment. 

  
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 (b) Termination for other than Cause, Death or Disability or Resignation
by Executive for Good Reason upon or within Twelve Months Following a Change of Control. If upon or within twelve (12) months following a Change of Control (the “Change of Control Period”), the Company (or any parent or
subsidiary or successor of the Company) terminates Executive’s employment with the Company other than for Cause, death or disability after providing at least thirty (30) days advance notice to Executive, or the Executive resigns from such
employment for Good Reason, then, subject to Section 10, Executive will be entitled to 
 (i) receive
continuing payments of severance pay at a rate equal to Executive’s Base Salary, as then in effect, for twenty-four (24) months from the date of such termination, which will be paid in accordance with the Company’s regular payroll
procedures; 
 (ii) accelerated vesting as to 100% of Executive’s outstanding and unvested equity awards;
and 
 (iii) an extension of the post-termination exercise period applicable to Executive’s outstanding
options to one hundred and eighty (180) days following the date of Executive’s termination of employment. 
 (c) Termination for Cause, Death or Disability; Resignation without Good Reason. If Executive’s employment with the Company (or any parent or subsidiary or successor of the Company) terminates
voluntarily by Executive (except upon resignation for Good Reason during the Change of Control Period), for Cause by the Company or due to Executive’s death or disability, then 

(i) all vesting will terminate immediately with respect to Executive’s outstanding equity awards; 

(ii) all payments of compensation by the Company to Executive hereunder will terminate immediately (except as to amounts
already earned); and 
 (iii) Executive will only be eligible for severance benefits in accordance with the
Company’s established policies, if any, as then in effect. 
 (d) Exclusive Remedy. In the event of
a termination of Executive’s employment with the Company (or any parent or subsidiary or successor of the Company), the provisions of this Section 9 are intended to be and are exclusive and in lieu of any other rights or remedies to which
Executive or the Company may otherwise be entitled, whether at law, tort or contract, in equity, or under this Agreement. Executive will be entitled to no severance or other benefits upon termination of employment with respect to acceleration of
award vesting, extension of the option exercise period, or severance pay other than those benefits expressly set forth in this Section 9. 
 10. Conditions to Receipt of Severance; No Duty to Mitigate. 
 (a) Separation Agreement and Release of Claims. The receipt of any severance pursuant to Section 9(a) or 9(b) will be subject to Executive signing and not revoking a separation agreement and
release of claims in a form reasonably satisfactory to the Company (the “Release”) and provided that such Release becomes effective and irrevocable no later than sixty (60) days

  
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following the termination date (such deadline, the “Release Deadline”). No severance will be paid or provided until the Release becomes effective. If the Release does not become
effective by the Release Deadline, Executive forfeits his right to any severance or similar payment under the Agreement. In the event Executive’s termination of employment occurs at a time during the calendar year where it would be possible for
the Release to become effective in the calendar year following the calendar year in which his termination of employment occurs, then any severance that would be deferred in accordance with the paragraph below will be paid on the first payroll date
to occur during the calendar year following the calendar year in which such termination of employment occurs, or such later time as required by (i) the payment schedule applicable to each payment or benefit, (ii) the date the Release
becomes effective, or (iii) Section 10(c) below. 
 (b) Non-Competition; Non-Solicitation. The
receipt of any severance benefits pursuant to Section 9(a) or 9(b) will be subject to Executive not violating the provisions of Sections 14 and 15. In the event Executive breaches the provisions of Sections 14 and/or 15, or otherwise materially
breaches this Agreement, all continuing payments and benefits to which Executive may otherwise be entitled pursuant to Section 9(a) or 9(b), as applicable, will immediately cease. 

(c) Section 409A. 
 (i) Notwithstanding anything to the contrary in this Agreement, no severance pay or benefits to be paid or provided to Executive, if any, pursuant to this Agreement that, when considered together with any
other severance payments or separation benefits, are considered deferred compensation under Code Section 409A, and the final regulations and any guidance promulgated thereunder (“Section 409A”) (together, the “Deferred
Payments”) will be paid or otherwise provided until Executive has a “separation from service” within the meaning of Section 409A. Similarly, no severance payable to Executive, if any, pursuant to this Agreement that otherwise
would be exempt from Section 409A pursuant to Treasury Regulation Section 1.409A-1(b)(9) will be payable until Executive has a “separation from service” within the meaning of Section 409A. 

(ii) Any severance payments or benefits under this Agreement that would be considered Deferred
Payments will be paid on, or, in the case of installments, will not commence until, the sixtieth (60th) day following Executive’s separation from service, or, if later, such time as required by Section 10(c)(iii). Except as required by Section 10(c)(iii), any installment payments that
would have been made to Executive during the sixty (60) day period immediately following Executive’s separation from service but for the preceding sentence will be paid to Executive on the sixtieth (60th) day following Executive’s separation from service and the
remaining payments shall be made as provided in this Agreement. 
 (iii) Notwithstanding anything to the
contrary in this Agreement, if Executive is a “specified employee” within the meaning of Section 409A at the time of Executive’s termination (other than due to death), then the Deferred Payments that are payable within the first
six (6) months following Executive’s separation from service, will become payable on the first payroll date that occurs on or after the date six (6) months and one (1) day following the date of Executive’s separation from
service. All subsequent Deferred Payments, if any, will be payable in accordance with the payment schedule applicable to each payment or benefit. Notwithstanding anything herein to the contrary, if Executive dies following Executive’s
separation from service, but prior to the six 

  
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(6) month anniversary of the separation from service, then any payments delayed in accordance with this paragraph will be payable in a lump sum as soon as administratively practicable after the
date of Executive’s death and all other Deferred Payments will be payable in accordance with the payment schedule applicable to each payment or benefit. Each payment and benefit payable under this Agreement is intended to constitute a separate
payment for purposes of Section 1.409A-2(b)(2) of the Treasury Regulations. 
 (iv) Any amount paid under
this Agreement that satisfies the requirements of the “short-term deferral” rule set forth in Section 1.409A-1(b)(4) of the Treasury Regulations will not constitute Deferred Payments for purposes of clause (i) above. 

(v) Any amount paid under this Agreement that qualifies as a payment made as a result of an involuntary separation from
service pursuant to Section 1.409A-1(b)(9)(iii) of the Treasury Regulations that does not exceed the Section 409A Limit (as defined below) will not constitute Deferred Payments for purposes of clause (i) above. 

(vi) The foregoing provisions are intended to comply with the requirements of Section 409A so that none of the
severance payments and benefits to be provided hereunder will be subject to the additional tax imposed under Section 409A, and any ambiguities herein will be interpreted to so comply. The Company and Executive agree to work together in good
faith to consider amendments to this Agreement and to take such reasonable actions which are necessary, appropriate or desirable to avoid imposition of any additional tax or income recognition prior to actual payment to Executive under
Section 409A. 
 (d) Confidential Information Agreement. Executive’s receipt of any payments or
benefits under Section 9 will be subject to Executive continuing to comply with the terms of the Confidential Information Agreement (as defined in Section 13). 

(e) No Duty to Mitigate. Executive will not be required to mitigate the amount of any payment contemplated by this
Agreement, nor will any earnings that Executive may receive from any other source reduce any such payment. 

11. Definitions. 
 (a) Cause. For purposes of this Agreement, “Cause” is defined as (i) an act of dishonesty made by Executive in connection with Executive’s responsibilities as an
employee; (ii) Executive’s conviction of, or plea of nolo contendere to, a felony or any crime involving fraud, embezzlement or any other act of moral turpitude; (iii) Executive’s gross misconduct;
(iv) Executive’s unauthorized use or disclosure of any proprietary information or trade secrets of the Company or any other party to whom Executive owes an obligation of nondisclosure as a result of Executive’s relationship with the
Company; (v) Executive’s willful breach of any obligations under any written agreement or covenant with the Company; or (vi) Executive’s continued failure to perform his employment duties after Executive has received a written
demand of performance from the Company which specifically sets forth the factual basis for the Company’s belief that Executive has not substantially performed his duties and has failed to cure such non-performance to the Company’s
satisfaction within ten (10) business days after receiving such notice. 

  
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 (b) Change of Control. For purposes of this Agreement,
“Change of Control” of the Company is defined as: 
 (i) any “person” (as such term
is used in Sections 13(d) and 14(d) of the Securities Exchange Act of 1934, as amended) is or becomes the “beneficial owner” (as defined in Rule 13d-3 under said Act), directly or indirectly, of securities of the Company representing more
than 50% of the total voting power represented by the Company’s then outstanding voting securities; or 

(ii) the date of the consummation of a merger or consolidation of the Company with any other corporation that has been
approved by the shareholders of the Company, other than a merger or consolidation which would result in the voting securities of the Company outstanding immediately prior thereto continuing to represent (either by remaining outstanding or by being
converted into voting securities of the surviving entity or its parent) at least fifty percent (50%) of the total voting power represented by the voting securities of the Company or such surviving entity or its parent outstanding immediately
after such merger or consolidation; or 
 (iii) the date of the consummation of the sale or disposition by the
Company of all or substantially all the Company’s assets. 
 Notwithstanding the foregoing provisions of
this definition, a transaction will not be deemed a Change of Control unless the transaction qualifies as a “change in control event” within the meaning of Section 409A. 

(c) Code. For purposes of this Agreement, “Code” means the Internal Revenue Code of 1986, as
amended. 
 (d) Good Reason. For the purposes of this Agreement, “Good Reason” means the
termination by Executive upon the occurrence of any of the below described events. Executive must provide notice to the Company of the existence of such event within ninety (90) days of the first occurrence of such event, and the Company will
have thirty (30) days to remedy the condition, in which case no Good Reason shall exist. If the Company fails to remedy the condition within such thirty (30) day period, Executive must terminate employment within two (2) years of the
first occurrence of such event. The events which constitute a Good Reason termination are: (i) the assignment of a different title or change that results in a material reduction in Executive’s duties or responsibilities; (ii) a
material reduction by the Company in Executive’s base compensation, other than a reduction in his Base Salary that is part of a general salary reduction affecting employees generally and provided the reduction is not greater, percentage-wise,
than the reduction affecting other employees generally or failure to provide an annual increase in base compensation commensurate with other executives; provided, however, in determining whether to provide an annual increase in base compensation
commensurate with an annual increase provided to other executives, the Company may take into account factors such as market levels of compensation, Executive’s overall performance, and other factors reasonably considered by the Company’s
compensation committee and/or Board, so long as such determination is not made in bad faith with the intent to discriminate against Executive; or (iii) relocation of Executive’s principal place of business of greater than seventy-five
(75) miles from its then location. 

  
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 (e) Section 409A Limit. For purposes of this Agreement,
“Section 409A Limit” will mean two (2) times the lesser of: (i) Executive’s annualized compensation based upon the annual rate of pay paid to Executive during the Executive’s taxable year preceding the
Executive’s taxable year of his or her separation from service as determined under Treasury Regulation Section 1.409A-1(b)(9)(iii)(A)(1) and any Internal Revenue Service guidance issued with respect thereto; and (ii) the maximum
amount that may be taken into account under a qualified plan pursuant to Section 401(a)(17) of the Internal Revenue Code for the year in which Executive’s separation from service occurred. 

12. Limitation on Payments. In the event that the severance and other benefits provided for in this Agreement or
otherwise payable to Executive (i) constitute “parachute payments” within the meaning of Section 280G of the Code and (ii) but for this Section 12, would be subject to the excise tax imposed by Section 4999 of the
Code, then Executive’s severance benefits will be either: 
 (a) delivered in full, or 

(b) delivered as to such lesser extent which would result in no portion of such severance benefits being subject to the
excise tax under Section 4999 of the Code, 
 whichever of the foregoing amounts, taking into account the applicable
federal, state and local income taxes and the excise tax imposed by Section 4999, results in the receipt by Executive on an after-tax basis, of the greatest amount of severance benefits, notwithstanding that all or some portion of such
severance benefits may be taxable under Section 4999 of the Code. If a reduction in the severance and other benefits constituting “parachute payments” is necessary so that no portion of such severance benefits is subject to the excise
tax under Section 4999 of the Code, the reduction shall occur in the following order: (1) reduction of the cash severance payments; (2) cancellation of accelerated vesting of equity awards; and (3) reduction of continued employee
benefits. In the event that acceleration of vesting of equity award compensation is to be reduced, such acceleration of vesting shall be cancelled in the reverse order of the date of grant of Executive’s equity awards. If two or more equity
awards are granted on the same date, each award will be reduced on a pro-rata basis. In no event shall the Executive have any discretion with respect to the ordering of payment reductions. 

Unless the Company and Executive otherwise agree in writing, any determination required under this Section 12 will
be made in writing by the independent public accountants who are primarily used by the Company immediately prior to the Change of Control, the Company’s legal counsel or such other person or entity to which the parties mutually agree (the
“Firm”), whose determination will be conclusive and binding upon Executive and the Company for all purposes. For purposes of making the calculations required by this Section 12, the Firm may make reasonable assumptions and
approximations concerning applicable taxes and may rely on reasonable, good faith interpretations concerning the application of Sections 280G and 4999 of the Code. The Company and Executive will furnish to the Firm such information and documents as
the Firm may reasonably request in order to make a determination under this Section 12. The Company will bear all costs the Firm may reasonably incur in connection with any calculations contemplated by this Section 12. 

  
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 13. Confidential Information. Executive agrees to enter into the
confidential information agreement attached hereto (the “Confidential Information Agreement”) upon commencing employment hereunder. 
 14. Non-Competition. During the term of his employment with the Company and until the later of: the date Executive terminates his employment with the Company and the date Executive no longer
receives the severance benefits provided in Section 9(a)(i) or 9(b)(i), as applicable, Executive will not, either directly or indirectly, (a) serve as an advisor, agent, consultant, director, employee, officer, partner, proprietor or
otherwise of, (b) have any ownership interest in (except for passive ownership of one percent (1%) or less of any entity whose securities have been registered under the Securities Act of 1933, as amended, or Section 12 of the
Securities Exchange Act of 1934, as amended) or (c) participate in the organization, financing, operation, management or control of, any business (i) that is in competition with the Company’s business as conducted by the Company at
any time during the course of Executive’s employment with the Company and (ii) on which Executive worked or about which Executive learned, during his employment, information or knowledge not generally known or available outside the
Company, or information or physical material entrusted to the Company by third parties, including, but not limited to inventions, during Executive’s employment or consultancy with the Company, confidential knowledge, copyrights, product ideas,
techniques, processes, formulas, object codes, biological materials, mask works and/or any other information of any type relating to documentation, laboratory notebooks, data, schematics, algorithms, flow charts, mechanisms, research, manufacture,
improvements, assembly, installation, marketing, forecasts, sales, pricing, customers, the salaries, duties, qualifications, performance levels and terms of compensation of other employees, and/or cost or other financial data concerning any of the
foregoing or the Company and its operations. 
 15. Non-Solicitation. During the term of his employment
with the Company and until the date two (2) years after the termination of Executive’s employment with the Company for any reason, Executive agrees not, either directly or indirectly, to solicit, induce, attempt to solicit, recruit, or
encourage any employee of the Company (or any parent or subsidiary of the Company) to leave his employment either for Executive or for any other entity or person. Executive represents that he (a) is familiar with the foregoing covenant not to
solicit, and (b) is fully aware of his obligations hereunder, including, without limitation, the reasonableness of the length of time, scope and geographic coverage of these covenants. 

16. Assignment. This Agreement will be binding upon and inure to the benefit of (a) the heirs, executors and
legal representatives of Executive upon Executive’s death and (b) any successor of the Company. Any such successor of the Company will be deemed substituted for the Company under the terms of this Agreement for all purposes. For this
purpose, “successor” means any person, firm, corporation or other business entity which at any time, whether by purchase, merger or otherwise, directly or indirectly acquires all or substantially all of the assets or business of the
Company. None of the rights of Executive to receive any form of compensation payable pursuant to this Agreement may be assigned or transferred except by will or the laws of descent and distribution. Any other attempted assignment, transfer,
conveyance or other disposition of Executive’s right to compensation or other benefits will be null and void. 
 17. Notices. All notices, requests, demands and other communications called for hereunder will be in writing and will be deemed given (a) on the date of delivery if delivered

  
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personally, (b) one (1) day after being sent by a well established commercial overnight service, or (c) four (4) days after being mailed by registered or certified mail,
return receipt requested, prepaid and addressed to the parties or their successors at the following addresses, or at such other addresses as the parties may later designate in writing: 

If to the Company: 
 AVI BioPharma, Inc. 
 Attn: Chief Executive Officer

 3450 Monte Villa Parkway, Suite 101 

Bothell, WA 98021 
 If to Executive: 
 at the last residential address known by the
Company. 
 18. Severability. In the event that any provision hereof becomes or is declared by a court of
competent jurisdiction to be illegal, unenforceable or void, this Agreement will continue in full force and effect without said provision. 
 19. Arbitration. 
 (a) General. In consideration of
Executive’s service to the Company, his/her promise to arbitrate all employment related disputes and Executive’s receipt of the compensation, pay raises and other benefits paid to Executive by the Company, at present and in the future,
Executive agrees that any and all controversies, claims, or disputes with anyone (including the Company and any employee, officer, director, shareholder or benefit plan of the Company in their capacity as such or otherwise) arising out of, relating
to, or resulting from Executive’s service to the Company under this Agreement or otherwise or the termination of Executive’s service with the Company, including any breach of this Agreement, shall be subject to binding arbitration under
the Arbitration Rules set forth in the Revised Code of Washington Chapter 7.04 (the “Rules”) and pursuant to Washington law. Disputes which Executive agrees to arbitrate, and thereby agrees to waive any right to a trial by jury,
include any statutory claims under state or federal law, including, but not limited to, claims under Title VII of the Civil Rights Act of 1964, the Americans with Disabilities Act of 1990, the Age Discrimination in Employment Act of 1967, the Older
Workers Benefit Protection Act, claims of harassment, discrimination or wrongful termination. Executive further understands that this Agreement to arbitrate also applies to any disputes that the Company may have with Executive. 

(b) Procedure. Executive agrees that any arbitration will be administered by the American Arbitration Association
(“AAA”) and that a neutral arbitrator will be selected in a manner consistent with its National Rules for the Resolution of Employment Disputes. The arbitration proceedings will allow for discovery according to the rules set forth
in the National Rules for the Resolution of Employment Disputes or the Washington Code of Civil Procedure. Executive agrees that the arbitrator shall have the power to decide any motions brought by any party to the arbitration,
including motions for summary judgment and/or adjudication and motions to dismiss and demurrers, prior to any arbitration hearing. Executive agrees that the arbitrator shall issue a written decision on the merits with findings of fact and
conclusions of law. Executive also agrees that the arbitrator 

  
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shall have the power to award any remedies, including attorneys’ fees and costs, available under applicable law. Executive understands the Company will pay for any administrative or hearing
fees charged by the arbitrator or AAA except that, for any filing fees associated with any arbitration Executive initiates, Executive shall pay an amount equal to the filing fees Executive would have paid had he/she filed a complaint in a court of
law. Executive agrees that the arbitrator shall administer and conduct any arbitration in a manner consistent with the Rules and that to the extent that the AAA’s National Rules for the Resolution of Employment Disputes conflict with the Rules,
the Rules shall take precedence. 
 (c) Remedy. Except as provided by the Rules, arbitration shall be the
sole, exclusive and final remedy for any dispute between Executive and the Company. Accordingly, except as provided for by the Rules, neither Executive nor the Company will be permitted to pursue court action regarding claims that are subject to
arbitration. Notwithstanding, the arbitrator will not have the authority to disregard or refuse to enforce any lawful Company policy, and the arbitrator shall not order or require the Company to adopt a policy not otherwise required by law which the
Company has not adopted. 
 (d) Availability of Injunctive Relief. In addition to the right under the
Rules to petition the court for provisional relief, Executive agrees that any party may also petition the court for injunctive relief where either party alleges or claims a violation of this Agreement or the Confidential Information Agreement or any
other agreement regarding trade secrets, confidential information, non-competition, non-solicitation or non-disparagement. In the event either party seeks injunctive relief, the prevailing party shall be entitled to recover reasonable costs and
attorneys’ fees. 
 (e) Administrative Relief. Executive understands that this Agreement does not
prohibit Executive from pursuing an administrative claim with a local, state or federal administrative body such as the Washington State Human Rights Commission, Equal Employment Opportunity Commission or the workers’ compensation board. This
Agreement does, however, preclude Executive from pursuing court action regarding any such claim. 
 (f)
Voluntary Nature of Agreement. Executive acknowledges and agrees that Executive is executing this Agreement voluntarily and without any duress or undue influence by the Company or anyone else. Executive further acknowledges and agrees that
Executive has carefully read this Agreement and that Executive has asked any questions needed for Executive to understand the terms, consequences and binding effect of this Agreement and fully understands it, including that EXECUTIVE IS
WAIVING EXECUTIVE’S RIGHT TO A JURY TRIAL. Finally, Executive agrees that Executive has been provided an opportunity to seek the advice of an attorney of Executive’s choice before signing this Agreement. 

20. Integration. This Agreement, together with the Option Agreement and the Confidential Information Agreement
represents the entire agreement and understanding between the parties as to the subject matter herein and supersedes all prior or contemporaneous agreements whether written or oral. With respect to stock options or other equity awards granted on or
after the date of this Agreement, the acceleration of vesting provisions provided herein will apply to such stock options and other equity awards except to the extent otherwise explicitly provided in the applicable stock option or equity award
agreement. This Agreement may be modified only by 

  
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agreement of the parties by a written instrument executed by the parties that is designated as an amendment to this Agreement. 

21. Waiver of Breach. The waiver of a breach of any term or provision of this Agreement, which must be in writing,
will not operate as or be construed to be a waiver of any other previous or subsequent breach of this Agreement. 
 22. Headings. All captions and section headings used in this Agreement are for convenient reference only and do not form a part of this Agreement. 

23. Tax Withholding. All payments made pursuant to this Agreement will be subject to withholding of applicable
taxes. 
 24. Governing Law. This Agreement will be governed by the laws of the State of Washington (with
the exception of its conflict of laws provisions). 
 25. Acknowledgment. Executive acknowledges that he
has had the opportunity to discuss this matter with and obtain advice from his private attorney, has had sufficient time to, and has carefully read and fully understands all the provisions of this Agreement, and is knowingly and voluntarily entering
into this Agreement. 
 26. Counterparts. This Agreement may be executed in counterparts, and each
counterpart will have the same force and effect as an original and will constitute an effective, binding agreement on the part of each of the undersigned. 
 [Signature Page Follows] 

  
 -12-

 IN WITNESS WHEREOF, each of the parties has executed this Agreement, in the
case of the Company by their duly authorized officers, as of the day and year first above written. 
  

									
	 COMPANY:
	 		 	
			
	 AVI BIOPHARMA, INC.
	 		 	
					
	 By:
	 	 /s/ Christopher Garabedian
	 		 	 Date:
	 	 March 29, 2011

	 Title:
	 	 Chief Executive Officer
	 		 		 	
			
	 EXECUTIVE:
	 		 	
				
	 /s/ Peter S. Linsley
	 		 	 Date:
	 	 March 29, 2011

	 PETER S. LINSLEY, PH.D.
	 		 		 	

  
  
  

[SIGNATURE PAGE TO EXECUTIVE EMPLOYMENT AGREEMENT] 

  
 -13-Amendment No. 1 to License Agreement

 Exhibit 10.1 

CONFIDENTIAL TREATMENT 
  

 Amendment No. 1 to LICENSE AGREEMENT 

This Amendment No. 1 to License Agreement (this “Amendment No. 1”) is made effective the
5th day of January 2011 (the “Effective
Date”) between Daiichi Sankyo Company, Limited, a Japanese Corporation having a place of business at 5-1, Nihonbashi Honcho 3-Chome, Chuo-ku, Tokyo 103-8426 Japan (“DS”), and Omeros Corporation, a Washington corporation
having a principal place of business at 1420 Fifth Avenue, Suite 2600, Seattle, WA 98101 USA (“Omeros”). 
 WHEREAS Asubio Pharma Co., Ltd. (“Asubio”) and Omeros entered into a license agreement dated February 26, 2010 (“Agreement”) under which Asubio grants Omeros an
exclusive license to certain phosphodiesterase-7 (“PDE7”) inhibitors and related patents and patent applications in the field of movement disorders [†]; 
 WHEREAS Asubio was acquired by DS on April 1, 2010, and DS succeeds all rights and obligations of Asubio under the Agreement in accordance with Section 13.9 thereof; 

WHEREAS Omeros requests DS to expand the Field (as defined in the License Agreement) to include certain central nervous system diseases
and disorders in accordance with Section 2.3 of the Agreement; and 
 WHEREAS DS wishes to accept such Omeros’ request
in consideration of certain payment set forth in this Amendment No. 1. 
 NOW THEREFORE, in consideration for the mutual
covenants and obligations set forth herein as well as other good and valuable consideration, the parties hereby agree as follows: 
  

	1	Definitions 

			
		
	1.1	  	Unless otherwise set forth in this Amendment No. 1, the capitalized terms herein shall have the meaning as defined in the Agreement.
		
	1.2	  	“Asubio” or “Asubio Pharma Co., Ltd.” in the Agreement shall be amended to read “DS” or “Daiichi Sankyo Company, Limited”
respectively.
		
	1.3	  	Section 1.7 of the Agreement is amended and restated in its entirety to read as follows:
		
		  	“ “Field” means (a) all movement disorders described in WHO ICD-10 (G20-G26) and/or in Omeros’ published International PCT Patent Application WO
2008/119057 A2, including, without limitation, Parkinson’s Disease, Restless Legs Syndrome, Post-encephalitic Parkinsonism, Dopamine-Responsive Dystonia, Shy-Drager Syndrome, Periodic Limb Movement Disorder, Periodic Limb Movements in Sleep,
Tourette’s Syndrome, all other movement disorders treatable with a dopamine receptor agonist or a precursor of a dopamine receptor agonist [†] (collectively “Movement Disorder
Indications”) and (b) all addiction and compulsive disorders described in WHO ICD-10 (F10-F19, F40-F48, F50-F59) and/or in Omeros’ pending U.S. Provisional Patent

  

	†	DESIGNATES PORTIONS OF THIS DOCUMENT THAT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT FILED SEPARATELY WITH THE COMMISSION

 CONFIDENTIAL TREATMENT 
  

 
Application 61/411,437 (collectively “Addiction Indications”).” 
  

	2	Milestone Payments 

			
	
	 Sections 3.1 and 3.2 of the Agreement are amended and restated in their entirety to read as
follows:

		
	 3.1
	  	Omeros shall pay DS the following one-time milestone fees (each a “Milestone Fee”) in U.S. dollars following the satisfaction of the following corresponding
milestone events (each a “Milestone”). References below in this Section 3 to a “First Indication” shall mean the initial one of either a Movement Disorder Indication or an Addiction Indication to reach the
corresponding Milestone, and “Second Indication” shall mean the other of a Movement Disorder Indication or an Addiction Indication, e.g., if the initial indication to reach a Phase 1 clinical Milestone is a Movement Disorder
Indication, such Movement Disorder Indication shall trigger the First Indication Phase 1 Clinical Milestone Fee, and thereafter the Second Indication Phase 1 clinical Milestone Fee shall be triggered only upon an Addiction Indication reaching a
Phase 1 clinical Milestone.
		
	 3.1.1.1
	  	Upon execution of this Agreement, Omeros shall pay DS a Milestone Fee of [†].
		
	 3.1.1.2
	  	Upon execution of the Amendment No. 1, Omeros shall pay DS a Milestone Fee of [†].
		
	 3.1.2.1
	  	Upon Omeros’ or its sublicensee(s)’ receipt of positive data from completed toxicology studies, each of three-months minimum duration, of a first Product in a rodent
species and in a non-rodent species, which studies have been conducted in conformance with current good laboratory practice guidance (“GLP”) promulgated by the U.S. Food and Drug Administration (“USFDA”), which data
and studies are sufficient to support the submission by Omeros or its sublicensee(s) to USFDA of an Investigational New Drug Application (“IND”) for a First Indication, Omeros shall pay DS a Milestone Fee of [†].

		
	 3.1.2.2
	  	Should Omeros be required to conduct a second set of toxicology studies to support an IND for a Second Indication, then upon Omeros’ or its sublicensee(s)’ receipt of
positive data from the completed second set of toxicology studies, each of three-months minimum duration, of a first Product in a rodent species and in a non-rodent species, which studies have been conducted in conformance with current GLP
promulgated by the USFDA, which data and studies are sufficient to support the submission by Omeros or its sublicensee(s) to USFDA of an IND for a Second Indication, Omeros shall pay DS a Milestone Fee of [†].
If such second set of toxicology studies is not required, then this Milestone Fee is not payable to DS. If two sets of toxicology studies to support an IND for First Indication and Second Indication respectively are conducted and Milestones
described in Section 3.1.2.1 and this Section 3.1.2.2 are achieved simultaneously, then Milestone Fees in Sections 3.1.2.1 and 3.1.2.2 are payable to DS.

  

	†	DESIGNATES PORTIONS OF THIS DOCUMENT THAT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT FILED SEPARATELY WITH THE COMMISSION

 CONFIDENTIAL TREATMENT 
  

			
	 3.1.3.1
	  	Upon the first dosing of a human subject in the first Phase 1 clinical study for a First Indication sponsored or authorized by Omeros or its sublicensee(s) of a first Product
anywhere in the world, which study has been cleared by USFDA or a corresponding foreign regulatory agency, Omeros shall pay DS a Milestone Fee of [†].
		
	 3.1.3.2
	  	Upon the first dosing of a human subject in the first Phase 1 clinical study for a Second Indication sponsored or authorized by Omeros or its sublicensee(s) of a first Product
anywhere in the world, which study has been cleared by USFDA or a corresponding foreign regulatory agency, Omeros shall pay DS a Milestone Fee of [†].
		
	 3.1.4.1
	  	Upon the first dosing of a human subject in the first Phase 2 clinical study for a First Indication sponsored or authorized by Omeros or its sublicensee(s) of a first Product
anywhere in the world, which study has been cleared by USFDA or a corresponding foreign regulatory agency, Omeros shall pay DS a Milestone Fee of [†].
		
	 3.1.4.2
	  	Upon the first dosing of a human subject in the first Phase 2 clinical study for a Second Indication sponsored or authorized by Omeros or its sublicensee(s) of a first Product
anywhere in the world, which study has been cleared by USFDA or a corresponding foreign regulatory agency, Omeros shall pay DS a Milestone Fee of [†].
		
	 3.1.5.1
	  	Upon the first dosing of a human subject in the first Phase 3 clinical study for a First Indication sponsored or authorized by Omeros or its sublicensee(s) of a first Product
anywhere in the world, which study has been cleared by USFDA or a corresponding foreign regulatory agency, Omeros shall pay DS a Milestone Fee of [†].
		
	 3.1.5.2
	  	Upon the first dosing of a human subject in the first Phase 3 clinical study for a Second Indication sponsored or authorized by Omeros or its sublicensee(s) of a first Product
anywhere in the world, which study has been cleared by USFDA or a corresponding foreign regulatory agency, Omeros shall pay DS a Milestone Fee of [†].
		
	 3.1.6.1
	  	Upon receipt of the first new drug application (“NDA”) marketing approval for a first Product for a First Indication obtained by or on behalf of Omeros or its
sublicensee(s) from USFDA, Omeros shall pay DS a Milestone Fee of [†].
		
	 3.1.6.2
	  	Upon receipt of the first NDA marketing approval for a first Product for a Second Indication obtained by or on behalf of Omeros or its sublicensee(s) from USFDA, Omeros shall pay
DS a Milestone Fee of [†].
		
	 3.1.7.1
	  	Upon receipt of the first marketing authorization for a first Product for a First Indication obtained by or on behalf of Omeros or its sublicensee(s) from an ex-U.S. regulatory
authority corresponding to USFDA, Omeros shall pay DS a Milestone Fee of [†].
		
	 3.1.7.2
	  	Upon receipt of the first marketing authorization for a first Product obtained for a Second Indication by or on behalf of Omeros or its sublicensee(s) from an ex-U.S. regulatory
authority corresponding to USFDA, Omeros shall pay DS a Milestone Fee

  

	†	DESIGNATES PORTIONS OF THIS DOCUMENT THAT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT FILED SEPARATELY WITH THE COMMISSION

 CONFIDENTIAL TREATMENT 
  

			
	 	  	of [†].
		
	 3.1.8
	  	Upon reaching an aggregate of all Net Sales of
[†], Omeros shall pay DS a Milestone Fee of [†].
		
	 3.1.9
	  	Upon reaching an aggregate of all Net Sales of
[†], Omeros shall pay DS a Milestone Fee of [†].
		
	 3.2
	  	If any Milestone above is achieved with respect to a particular Product for a particular First or Second Indication before a prior Milestone has been achieved for such First or
Second Indication, then all prior Milestones for such First or Second Indication that have not previously been paid with respect to that Product shall be deemed achieved upon achievement of the subsequent Milestone, and the corresponding payment
shall become payable; provided, however, that the NDA approval Milestone set forth in Subsections 3.1.6.1 and/or 3.1.6.2 shall not be treated as a “prior Milestone” when the ex-U.S. marketing authorization Milestone set forth in
Subsections 3.1.7.1 and/or 3.1.7.2, respectively, is achieved, and the ex-U.S. marketing authorization Milestone set forth in Subsection 3.1.7.1 and/or Subsection 3.1.7.2 shall not be treated as a “prior Milestone” when the NDA approval
Milestone set forth in Subsection 3.1.6.1 and/or 3.1.6.2, respectively, is achieved. It is understood by the parties that on a certain Measure Date, Movement Disorder Indication would be “a particular First Indication”, and on another
Measure Date, Addiction Indication would be “a particular First Indication” depending on the progress of their development.”

 It is understood by the parties that Omeros has already paid and DS has already received the Milestone Fee of [†] as provided in Section 3.1.1.1 of the Agreement. 

 

	3	Term 

 This Amendment No. 1
shall become effective as of the Effective Date and shall continue to be in effect as long as the Agreement is in effect. 
  

	4	Miscellaneous 

  

	4.1	Section 13.11 of the Agreement is amended and restated in its entirety to read as follows: 

“Any notice required or permitted to be given under the Agreement by either party shall be in writing and shall be (a) delivered
personally, (b) sent by an internationally recognized courier service, charges prepaid, or (c) delivered by facsimile (with the original promptly sent by any of the foregoing manners) to the addresses or facsimile numbers of the other
party set forth below, or at such other addresses as may from time to time be furnished by similar notice by either party. The effective date of any notice hereunder shall be the date of receipt by the receiving party. 

  

	†	DESIGNATES PORTIONS OF THIS DOCUMENT THAT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT FILED SEPARATELY WITH THE COMMISSION

 CONFIDENTIAL TREATMENT 
  

					
	 If to Omeros:
  

Omeros Corporation
 1420 Fifth Avenue, Suite
2600
 Seattle, WA 98101

U.S.A.
	  	 If to DS:
  

Daiichi Sankyo Company, Limited
 5-1, Nihonbashi
Honcho 3-Chome
 Chuo-ku, Tokyo 103-8426

Japan

	  
	  
	  
	  
			
	Attention:	 	Gregory A. Demopulos, M.D.	  	Attention: Noriaki Ishida
			
		 	Chairman & CEO	  	Corporate Officer, Vice President,
		 		  	Business Development & Licensing
		 		  	Department
			
	 And copy to:
	 	Marcia S. Kelbon,	  	
		 	Patent & General Counsel	  	
		
	 Fax: (206) 676.5005
 Phone: (206) 676.5000
	  	 Fax: +81-3-6225-1903
 Phone: +81-3-6225-1008

	  

  

	4.2	This Amendment may be executed in one or more counterparts, each of which will be considered an original, and all of which will constitute the same instrument.

  

	4.3	Except as expressly amended by this Amendment No. 1, all terms and conditions of the Agreement shall continue to be in full force and effect. 

IN WITNESS WHEREOF, DS and Omeros have each acknowledged and accepted this Agreement by causing it to have been signed by their
respective duly authorized officials. 
  

									
	DAIICHI SANKYO COMPANY, LIMITED	  		 	OMEROS CORPORATION
					
	By:	  	 /s/ Noriaki Ishida
	  		 	By:	 	 /s/ Gregory A. Demopulos

					
	Name:	  	Noriaki Ishida	  		 	Name:	 	Gregory A. Demopulos, M.D.
			
	Title: Corporate Officer, Vice President,	  		 	Title: Chairman & CEO
		
	Business Development & Licensing Department	  	
					
	Date:	  	 January 31, 2011
	  		 	Date:	 	 December 28, 2010

  

	†	DESIGNATES PORTIONS OF THIS DOCUMENT THAT HAVE BEEN OMITTED PURSUANT TO A REQUEST FOR CONFIDENTIAL TREATMENT FILED SEPARATELY WITH THE COMMISSION

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