================================================================================ UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G (Amendment No. 1) Under the Securities Exchange Act of 1934 Lynx Therapeutics, Inc. -------------------------------------------------------------------------------- (Name of Issuer) Common Stock -------------------------------------------------------------------------------- (Title of Class of Securities) 551812-30-8 -------------------------------------------------------------------------------- (CUSIP Number) December 31, 2002 -------------------------------------------------------------------------------- (Date of Event Which Requires Filing of This Statement) Check the appropriate box to designate the rule pursuant to which this Schedule is filed: [X] Rule 13d-1(c) [ ] Rule 13d-1(d) [ ] Rule 13d-1(b) * The remainder of this cover page shall be filled out for a reporting person's initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page. The information required on the remainder of this cover page shall not be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange Act of 1934 ("Act") or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes). ================================================================================ -------------------------- -------------------------- CUSIP NO. 551812-30-8 SCHEDULE 13G PAGE 2 OF 13 PAGES -------------------------------------------------------------------------------- 1. NAME OF REPORTING PERSON/S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON SENECA CAPITAL, L.P. -------------------------------------------------------------------------------- 2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (A) [ ] (B) [X] -------------------------------------------------------------------------------- 3. SEC USE ONLY -------------------------------------------------------------------------------- 4. CITIZENSHIP OR PLACE OF ORGANIZATION DELAWARE -------------------------------------------------------------------------------- 5. SOLE VOTING POWER 0 NUMBER OF -------------------------------------------------- SHARES 6. SHARED VOTING POWER BENEFICIALLY OWNED BY 761,300 EACH -------------------------------------------------- REPORTING 7. SOLE DISPOSITIVE POWER PERSON WITH: 0 -------------------------------------------------- 8. SHARED DISPOSITIVE POWER 761,300 -------------------------------------------------------------------------------- 9. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 761,300 -------------------------------------------------------------------------------- 10. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* [ ] -------------------------------------------------------------------------------- 11. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 2.50% -------------------------------------------------------------------------------- 12. TYPE OF REPORTING PERSON* PN ================================================================================ -------------------------- -------------------------- CUSIP NO. 551812-30-8 SCHEDULE 13G PAGE 3 OF 13 PAGES -------------------------------------------------------------------------------- 1. NAME OF REPORTING PERSON/S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON SENECA CAPITAL II, L.P. -------------------------------------------------------------------------------- 2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (A) [ ] (B) [X] -------------------------------------------------------------------------------- 3. SEC USE ONLY -------------------------------------------------------------------------------- 4. CITIZENSHIP OR PLACE OF ORGANIZATION DELAWARE -------------------------------------------------------------------------------- 5. SOLE VOTING POWER 0 NUMBER OF -------------------------------------------------- SHARES 6. SHARED VOTING POWER BENEFICIALLY OWNED BY 22,500 EACH -------------------------------------------------- REPORTING 7. SOLE DISPOSITIVE POWER PERSON WITH: 0 -------------------------------------------------- 8. SHARED DISPOSITIVE POWER 22,500 -------------------------------------------------------------------------------- 9. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 22,500 -------------------------------------------------------------------------------- 10. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES* [ ] -------------------------------------------------------------------------------- 11. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 0.07% -------------------------------------------------------------------------------- 12. TYPE OF REPORTING PERSON* PN ================================================================================ -------------------------- -------------------------- CUSIP NO. 551812-30-8 SCHEDULE 13G PAGE 4 OF 13 PAGES -------------------------------------------------------------------------------- 1. NAME OF REPORTING PERSON/S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON SENECA CAPITAL ADVISORS, LLC -------------------------------------------------------------------------------- 2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (A) [ ] (B) [X] -------------------------------------------------------------------------------- 3. SEC USE ONLY -------------------------------------------------------------------------------- 4. CITIZENSHIP OR PLACE OF ORGANIZATION DELAWARE -------------------------------------------------------------------------------- 5. SOLE VOTING POWER 0 NUMBER OF -------------------------------------------------- SHARES 6. SHARED VOTING POWER BENEFICIALLY OWNED BY 783,800 EACH -------------------------------------------------- REPORTING 7. SOLE DISPOSITIVE POWER PERSON WITH: 0 -------------------------------------------------- 8. SHARED DISPOSITIVE POWER 783,800 -------------------------------------------------------------------------------- 9. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 783,800 -------------------------------------------------------------------------------- 10. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES [ ] -------------------------------------------------------------------------------- 11. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 2.57% -------------------------------------------------------------------------------- 12. TYPE OF REPORTING PERSON 00 - LIMITED LIABILITY COMPANY ================================================================================ -------------------------- -------------------------- CUSIP NO. 551812-30-8 SCHEDULE 13G PAGE 5 OF 13 PAGES -------------------------------------------------------------------------------- 1. NAME OF REPORTING PERSON/S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON SENECA CAPITAL INTERNATIONAL, LTD. -------------------------------------------------------------------------------- 2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (A) [ ] (B) [X] -------------------------------------------------------------------------------- 3. SEC USE ONLY -------------------------------------------------------------------------------- 4. CITIZENSHIP OR PLACE OF ORGANIZATION CAYMAN ISLANDS, BRITISH WEST INDIES -------------------------------------------------------------------------------- 5. SOLE VOTING POWER 0 NUMBER OF -------------------------------------------------- SHARES 6. SHARED VOTING POWER BENEFICIALLY OWNED BY 1,781,603 EACH -------------------------------------------------- REPORTING 7. SOLE DISPOSITIVE POWER PERSON WITH: 0 -------------------------------------------------- 8. SHARED DISPOSITIVE POWER 1,781,603 -------------------------------------------------------------------------------- 9. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 1,781,603 -------------------------------------------------------------------------------- 10. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES [ ] -------------------------------------------------------------------------------- 11. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 5.84% -------------------------------------------------------------------------------- 12. TYPE OF REPORTING PERSON CO ================================================================================ -------------------------- -------------------------- CUSIP NO. 551812-30-8 SCHEDULE 13G PAGE 6 OF 13 PAGES -------------------------------------------------------------------------------- 1. NAME OF REPORTING PERSON/S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON SENECA CAPITAL INVESTMENTS, LLC -------------------------------------------------------------------------------- 2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (A) [ ] (B) [X] -------------------------------------------------------------------------------- 3. SEC USE ONLY -------------------------------------------------------------------------------- 4. CITIZENSHIP OR PLACE OF ORGANIZATION DELAWARE -------------------------------------------------------------------------------- 5. SOLE VOTING POWER 0 NUMBER OF -------------------------------------------------- SHARES 6. SHARED VOTING POWER BENEFICIALLY OWNED BY 1,800,003 EACH -------------------------------------------------- REPORTING 7. SOLE DISPOSITIVE POWER PERSON WITH: 0 -------------------------------------------------- 8. SHARED DISPOSITIVE POWER 1,800,003 -------------------------------------------------------------------------------- 9. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 1,800,003 -------------------------------------------------------------------------------- 10. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES [ ] -------------------------------------------------------------------------------- 11. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 5.90% -------------------------------------------------------------------------------- 12. TYPE OF REPORTING PERSON 00 - LIMITED LIABILITY COMPANY ================================================================================ -------------------------- -------------------------- CUSIP NO. 551812-30-8 SCHEDULE 13G PAGE 7 OF 13 PAGES -------------------------------------------------------------------------------- 1. NAME OF REPORTING PERSON/S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON DOUGLAS A. HIRSCH -------------------------------------------------------------------------------- 2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (A) [ ] (B) [X] -------------------------------------------------------------------------------- 3. SEC USE ONLY -------------------------------------------------------------------------------- 4. CITIZENSHIP OR PLACE OF ORGANIZATION USA -------------------------------------------------------------------------------- 5. SOLE VOTING POWER 0 NUMBER OF -------------------------------------------------- SHARES 6. SHARED VOTING POWER BENEFICIALLY OWNED BY 2,583,803 EACH -------------------------------------------------- REPORTING 7. SOLE DISPOSITIVE POWER PERSON WITH: 0 -------------------------------------------------- 8. SHARED DISPOSITIVE POWER 2,583,803 -------------------------------------------------------------------------------- 9. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 2,583,803 -------------------------------------------------------------------------------- 10. CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES [ ] -------------------------------------------------------------------------------- 11. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 8.47% -------------------------------------------------------------------------------- 12. TYPE OF REPORTING PERSON IN ================================================================================ SCHEDULE 13G CUSIP No. 551812-30-8 Page 8 of 13 Pages ----------- --- ---- ITEM 1. (a) Name of Issuer: Lynx Therapeutics, Inc. -------------------------------- (b) Address of Issuer's Principal Executive Offices: 25861 Industrial Boulevard, Hayward, California 94545 --------------------------------------------------------- ITEM 2. (a) Name of Persons Filing: (b) Address or principal business office or, if none, residence: (c) Citizenship: Seneca Capital, L.P. 527 Madison Avenue, 11th Floor New York, NY 10022 (Delaware limited partnership) Seneca Capital II, L.P. 527 Madison Avenue, 11th Floor New York, NY 10022 (Delaware limited partnership) Seneca Capital Advisors, LLC 527 Madison Avenue, 11th Floor New York, NY 10022 (Delaware limited liability company) Seneca Capital International, Ltd. c/o Consolidated Fund Management (BVI) Limited PO Box HM 2257 Par La Ville Place 14 Par La Ville Road Hamilton HMJX, Bermuda (Cayman Islands (BWI) Company) Seneca Capital Investments, LLC 527 Madison Avenue, 11th Floor New York, NY 10022 (Delaware limited liability company) Douglas A. Hirsch c/o Seneca Capital 527 Madison Avenue, 11th Floor New York, NY 10022 (United States Citizen) SCHEDULE 13G CUSIP No. 551812-30-8 Page 9 of 13 Pages ----------- --- ---- ITEM 2(d). Title of Class of Securities: Common stock ------------------- ITEM 2(e). CUSIP Number: 551812-30-8 ------------------- ITEM 3. IF THIS STATEMENT IS FILED PURSUANT TO RULE 13D-1(B), OR 13D-2(B), CHECK WHETHER THE PERSON FILING IS A: (a) [ ] Broker or Dealer registered under Section 15 of the Act (15 U.S.C. 78o). (b) [ ] Bank as defined in section 3(a)(6) of the Act (15 U.S.C. 78c). (c) [ ] Insurance Company as defined in section 3(a)(19) of the Act (15 U.S.C. 78c). (d) [ ] Investment Company registered under section 8 of the Investment Company Act of 1940 (15 U.S.C. 80a-8). (e) [ ] Investment Adviser registered under section 203 of the Investment Advisers Act or under the laws of any State (f) [ ] Employee Benefit Plan, Pension fund which is subject to the provisions of the Employee Retirement Income Security Act of 1974 or Endowment Fund; see Section 240.13d-1(b)(1)(ii)(F) (g) [ ] A Parent Holding Company or control person, in accordance with Section 240.13d-1(b)(ii)(G)(Note: See Item 7) (h) [ ] A Savings Association as defined in Section 3(b) of the Federal Deposit Insurance Act (12 U.S.C. 1813) (i) [ ] A Church Plan that is excluded from the definition of an investment company under Section 3(c)(14) of the Investment Company Act of 1940 (15 U.S.C. 80a-3) (j) [ ] Group, in accordance with Section 240.13d-1(b)(1)(ii)(J) If this statement is filed pursuant to Section 240.13d-1(c), check this box [X]. ITEM 4. OWNERSHIP Provide the following information regarding the aggregate number and percentage of the class of securities of the issuer identified in Item 1. SENECA CAPITAL, L.P. (1) (a) Amount Beneficially Owned: 761,300 ------------------------------------------- (b) Percent of Class: 2.50% ---------------------------------------------------- (c) Number of shares as to which such person has: (i) sole power to vote or to direct the vote: 0 ----------------------- (ii) shared power to vote or to direct the vote: 761,300 --------------------- (iii)sole power to dispose or to direct the disposition of: 0 ---------- (iv) shared power to dispose or to direct the disposition of: 761,300 --------- SENECA CAPITAL II, L.P. (2) (a) Amount Beneficially Owned: 22,500 ------------------------------------------- (b) Percent of Class: 0.07% ---------------------------------------------------- (c) Number of shares as to which such person has: (i) sole power to vote or to direct the vote: 0 ----------------------- (ii) shared power to vote or to direct the vote: 22,500 --------------------- SCHEDULE 13G CUSIP No. 551812-30-8 Page 10 of 13 Pages ----------- ---- ---- (iii)sole power to dispose or to direct the disposition of: 0 ---------- (iv) shared power to dispose or to direct the disposition of: 22,500 --------- SENECA CAPITAL ADVISORS, LLC (3) (a) Amount Beneficially Owned: 783,800 ------------------------------------------- (b) Percent of Class: 2.57% ---------------------------------------------------- (c) Number of shares as to which such person has: (i) sole power to vote or to direct the vote: 0 ----------------------- (ii) shared power to vote or to direct the vote: 783,800 --------------------- (iii)sole power to dispose or to direct the disposition of: 0 ---------- (iv) shared power to dispose or to direct the disposition of: 783,800 --------- SENECA CAPITAL INTERNATIONAL, LTD. (4) (a) Amount Beneficially Owned: 1,781,603 ------------------------------------------- (b) Percent of Class: 5.84% ---------------------------------------------------- (c) Number of shares as to which such person has: (i) sole power to vote or to direct the vote: 0 ----------------------- (ii) shared power to vote or to direct the vote: 1,781,603 --------------------- (iii)sole power to dispose or to direct the disposition of: 0 ----------- (iv) shared power to dispose or to direct the disposition of:1,781,603 --------- SENECA CAPITAL INVESTMENTS, LLC (5) (a) Amount Beneficially Owned: 1,800,003 ------------------------------------------- (b) Percent of Class: 5.90% ---------------------------------------------------- (c) Number of shares as to which such person has: (i) sole power to vote or to direct the vote: 0 ----------------------- (ii) shared power to vote or to direct the vote: 1,800,003 --------------------- (iii)sole power to dispose or to direct the disposition of: 0 ---------- (iv) shared power to dispose or to direct the disposition of:1,800,003 --------- DOUGLAS A. HIRSCH (6) (a) Amount Beneficially Owned: 2,583,803 ------------------------------------------- (b) Percent of Class: 8.47% ---------------------------------------------------- (c) Number of shares as to which such person has: (i) sole power to vote or to direct the vote: 0 ----------------------- (ii) shared power to vote or to direct the vote: 2,583,803 --------------------- (iii)sole power to dispose or to direct the disposition of: 0 ---------- (iv) shared power to dispose or to direct the disposition of:2,583,803 --------- (1) Includes 231,600 shares of common stock which Seneca Capital, L.P. has a right to acquire upon the exercise of warrants. (2) Includes 7,600 shares of common stock which Seneca Capital II, L.P. has a right to acquire upon the exercise of warrants. (3) Shares reported for Seneca Capital Advisors, LLC represent shares beneficially owned by Seneca Capital, L.P. and Seneca Capital II, L.P. Seneca Capital Advisors, LLC is the sole general partner of Seneca Capital, L.P. and of Seneca Capital II, L.P. SCHEDULE 13G CUSIP No. 551812-30-8 Page 11 of 13 Pages ----------- ---- ---- (4) Includes 547,058 shares of common stock which Seneca Capital International, Ltd. has a right to acquire upon the exercise of warrants. (5) Shares reported for Seneca Capital Investments, LLC includes shares beneficially owned by Seneca Capital International, Ltd. and also includes 6,000 shares of common stock which the beneficial owner has a right to acquire upon the exercise of warrants. Seneca Capital Investments, LLC is sole investment manager of Seneca Capital International, Ltd. (6) Shares reported for Douglas A. Hirsch include shares beneficially owned by Seneca Capital, L.P., Seneca Capital II, L.P. and Seneca Capital International, Ltd., which entities may be deemed to be controlled by Mr. Hirsch because he is the Manager of Seneca Capital Advisors, LLC (the sole General Partner of Seneca Capital, L.P. and of Seneca Capital II, L.P.) and the Manager of Seneca Capital Investments, LLC (the investment manager of Seneca Capital International, Ltd.). ITEM 5. OWNERSHIP OF FIVE PERCENT OR LESS OF A CLASS If this statement is being filed to report the fact that as of the date hereof the reporting person has ceased to be the beneficial owner of more than five percent of the class of securities, check the following [ ]. NOT APPLICABLE. ITEM 6. OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER PERSON If any other person is known to have the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, such securities, a statement to that effect should be included in response to this item and, if such interest relates to more than five percent of the class, such person should be identified. A listing of the shareholders of an investment company registered under the Investment Company Act of 1940 or the beneficiaries of employees benefit plan, pension fund or endowment fund is not required. NOT APPLICABLE. ITEM 7. IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH ACQUIRED THE SECURITY BEING REPORTED ON BY THE PARENT HOLDING COMPANY If a parent holding company has filed this schedule, pursuant to Rule 13d-1(b)(ii)(G), so indicate under Item 3(g) and attach an exhibit stating the identity and the Item 3 classification of the relevant subsidiary. If a parent holding company has filed this schedule pursuant to Rule 13d-1(c), attach an exhibit stating the identification of the relevant subsidiary. NOT APPLICABLE. ITEM 8. IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF THE GROUP If a group has filed this schedule pursuant to Rule 13d-1(b)(ii)(J), so indicate under Item 3(h) and attach an exhibit stating the identity and Item 3 classification of each member of the group. If a group has filed this schedule pursuant to Rule 13d-1(d), attach an exhibit stating the identity of each member of the group. NOT APPLICABLE. SCHEDULE 13G CUSIP No. 551812-30-8 Page 12 of 13 Pages ----------- ---- ---- ITEM 9. NOTICE OF DISSOLUTION OF GROUP Notice of dissolution of a group may be furnished as an exhibit stating the date of the dissolution and that all further filings with respect to transactions in the security report on will be filed, if required, by members of the group, in their individual capacity. NOT APPLICABLE. ITEM 10. CERTIFICATION By signing below, I certify that, to the best of my knowledge and belief, the securities referred to above were acquired and are held in the ordinary course of business and were not acquired and are not held for the purpose of and do not have the effect of changing or influencing the control of the issuer of such securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect. SCHEDULE 13G CUSIP No. 551812-30-8 Page 13 of 13 Pages ----------- ---- ---- SIGNATURE After reasonable inquiry and to the best of my knowledge and belief, I hereby certify that the information set forth in this statement is true, complete and correct. Date: February 11, 2003 SENECA CAPITAL, L.P. By Seneca Capital Advisors, LLC, its General Partner By: /S/ Douglas A. Hirsch ----------------------------------------- Douglas A. Hirsch, Its Managing Member SENECA CAPITAL II, L.P. By Seneca Capital Advisors, LLC, its General Partner By: /S/ Douglas A. Hirsch ------------------------------------------ Douglas A. Hirsch, Its Managing Member SENECA CAPITAL ADVISORS, LLC By: /S/ Douglas A. Hirsch ------------------------------------------ Douglas A. Hirsch, Its Managing Member SENECA CAPITAL INTERNATIONAL, LTD. By Seneca Capital Investments, LLC, its Investment Manager By: /S/ Douglas A. Hirsch ------------------------------------------ Douglas A. Hirsch, Its Managing Member SENECA CAPITAL INVESTMENTS, LLC By: /S/ Douglas A. Hirsch ------------------------------------------ Douglas A. Hirsch, Its Managing Member By: /S/ Douglas A. Hirsch ------------------------------------------ Douglas A. Hirsch, Individually