SC 13G/A 1 sc13ga.txt NUVELO INC. SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 ---------------- SCHEDULE 13G/A (Rule 13d-102) ---------------- INFORMATION TO BE INCLUDED IN STATEMENTS PURSUANT TO RULES 13d-1(b), (c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2 UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 2)* NUVELO INC. (Name of Issuer) Common Stock, $.01 par value (Title of Class of Securities) 67072M103 (CUSIP Number) December 14, 2005 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant to which this Schedule is filed: [ ] Rule 13d-1(b) [X] Rule 13d-1(c) [ ] Rule 13d-1(d) ----------- * 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 the disclosures provided in a prior cover page. The information required in 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). Schedule 13G/A PAGE 2 OF 15 CUSIP No. 67072M103 ----------------------------------------------------------------------------- (1) NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON CLSP, 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 ----------------------------------------------------------------------------- NUMBER OF (5) SOLE VOTING POWER 0 SHARES ______________________________________________________________ BENEFICIALLY (6) SHARED VOTING POWER 234,375 OWNED BY ______________________________________________________________ EACH (7) SOLE DISPOSITIVE POWER 0 REPORTING ______________________________________________________________ PERSON WITH (8) SHARED DISPOSITIVE POWER 234,375 ----------------------------------------------------------------------------- (9) AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 234,375 ----------------------------------------------------------------------------- (10) CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES [ ] ----------------------------------------------------------------------------- (11) PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 0.6% ----------------------------------------------------------------------------- (12) TYPE OF REPORTING PERSON PN ----------------------------------------------------------------------------- Schedule 13G/A PAGE 3 OF 15 CUSIP No. 67072M103 ----------------------------------------------------------------------------- (1) NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON CLSP 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 ----------------------------------------------------------------------------- NUMBER OF (5) SOLE VOTING POWER 0 SHARES ______________________________________________________________ BENEFICIALLY (6) SHARED VOTING POWER 275,884 OWNED BY ______________________________________________________________ EACH (7) SOLE DISPOSITIVE POWER 0 REPORTING ______________________________________________________________ PERSON WITH (8) SHARED DISPOSITIVE POWER 275,884 ----------------------------------------------------------------------------- (9) AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 275,884 ----------------------------------------------------------------------------- (10) CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES [ ] ----------------------------------------------------------------------------- (11) PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 0.7% ----------------------------------------------------------------------------- (12) TYPE OF REPORTING PERSON PN ----------------------------------------------------------------------------- Schedule 13G/A PAGE 4 OF 15 CUSIP No. 67072M103 ----------------------------------------------------------------------------- (1) NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON CLSP/SBS I, 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 ----------------------------------------------------------------------------- NUMBER OF (5) SOLE VOTING POWER 0 SHARES ______________________________________________________________ BENEFICIALLY (6) SHARED VOTING POWER 0 OWNED BY ______________________________________________________________ EACH (7) SOLE DISPOSITIVE POWER 0 REPORTING ______________________________________________________________ PERSON WITH (8) SHARED DISPOSITIVE POWER 0 ----------------------------------------------------------------------------- (9) AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 0 ----------------------------------------------------------------------------- (10) CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES [ ] ----------------------------------------------------------------------------- (11) PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 0.0% ----------------------------------------------------------------------------- (12) TYPE OF REPORTING PERSON PN ----------------------------------------------------------------------------- Schedule 13G/A PAGE 5 OF 15 CUSIP No. 67072M103 ----------------------------------------------------------------------------- (1) NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON CLSP/SBS 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 ----------------------------------------------------------------------------- NUMBER OF (5) SOLE VOTING POWER 0 SHARES ______________________________________________________________ BENEFICIALLY (6) SHARED VOTING POWER 34,067 OWNED BY ______________________________________________________________ EACH (7) SOLE DISPOSITIVE POWER 0 REPORTING ______________________________________________________________ PERSON WITH (8) SHARED DISPOSITIVE POWER 34,067 ----------------------------------------------------------------------------- (9) AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 34,067 ----------------------------------------------------------------------------- (10) CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES [ ] ----------------------------------------------------------------------------- (11) PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 0.1% ----------------------------------------------------------------------------- (12) TYPE OF REPORTING PERSON PN ----------------------------------------------------------------------------- Schedule 13G/A PAGE 6 OF 15 CUSIP No. 67072M103 ----------------------------------------------------------------------------- (1) NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Cooper Hill Partners, 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 ----------------------------------------------------------------------------- NUMBER OF (5) SOLE VOTING POWER 0 SHARES ______________________________________________________________ BENEFICIALLY (6) SHARED VOTING POWER 209,379 OWNED BY ______________________________________________________________ EACH (7) SOLE DISPOSITIVE POWER 0 REPORTING ______________________________________________________________ PERSON WITH (8) SHARED DISPOSITIVE POWER 209,379 ----------------------------------------------------------------------------- (9) AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 209,379 ----------------------------------------------------------------------------- (10) CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES [ ] ----------------------------------------------------------------------------- (11) PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 0.5% ----------------------------------------------------------------------------- (12) TYPE OF REPORTING PERSON PN ----------------------------------------------------------------------------- Schedule 13G/A PAGE 7 OF 15 CUSIP No. 67072M103 ----------------------------------------------------------------------------- (1) NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Cooper Hill Partners, 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 ----------------------------------------------------------------------------- NUMBER OF (5) SOLE VOTING POWER 0 SHARES ______________________________________________________________ BENEFICIALLY (6) SHARED VOTING POWER 544,326 OWNED BY ______________________________________________________________ EACH (7) SOLE DISPOSITIVE POWER 0 REPORTING ______________________________________________________________ PERSON WITH (8) SHARED DISPOSITIVE POWER 544,326 ----------------------------------------------------------------------------- (9) AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 544,326 ----------------------------------------------------------------------------- (10) CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES [ ] ----------------------------------------------------------------------------- (11) PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 1.3% ----------------------------------------------------------------------------- (12) TYPE OF REPORTING PERSON OO ----------------------------------------------------------------------------- Schedule 13G/A PAGE 8 OF 15 CUSIP No. 67072M103 --------------------------------------------------------------------------- (1) NAME OF REPORTING PERSON S.S. OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Casdin Capital, 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 ----------------------------------------------------------------------------- NUMBER OF (5) SOLE VOTING POWER 0 SHARES ______________________________________________________________ BENEFICIALLY (6) SHARED VOTING POWER 753,705 OWNED BY ______________________________________________________________ EACH (7) SOLE DISPOSITIVE POWER 0 REPORTING ______________________________________________________________ PERSON WITH (8) SHARED DISPOSITIVE POWER 753,705 ----------------------------------------------------------------------------- (9) AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 753,705 ----------------------------------------------------------------------------- (10) CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES [ ] ----------------------------------------------------------------------------- (11) PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (9) 1.8% ----------------------------------------------------------------------------- (12) TYPE OF REPORTING PERSON OO ----------------------------------------------------------------------------- Schedule 13G/A PAGE 9 OF 15 CUSIP No. 67072M103 ITEM 1(a). NAME OF ISSUER: NUVELO INC. ITEM 1(b). ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES: 204 Industrial Road, Suite 310, San Carlos, CA 94070-6211 ITEM 2(a). NAME OF PERSON FILING: This statement is filed by: (i) CLSP, L.P. ("CLSP"), a Delaware limited partnership, with respect to the Securities owned by it; (ii) CLSP II, L.P. ("CLSP II") a Delaware limited partnership, with respect to the Securities owned by it; (iii) CLSP/SBS I, L.P. ("CLSP/SBS I") a Delaware limited partnership, with respect to the Securities owned by it; (iv) CLSP/SBS II, L.P. ("CLSP/SBS II") a Delaware limited partnership, with respect to the Securities owned by it; (v) Cooper Hill Partners, L.P., a Delaware limited partnership with respect to the Securities held for CLSP Overseas, Ltd. ("CLSP Overseas"), a Cayman Islands exempted company; (vi) Cooper Hill Partners, LLC ("Cooper, LLC "), a Delaware limited liability company and the sole general partner of CLSP, CLSP II, CLSP/SBS I AND CLSP/SBS II with respect to the Securities owned by CLSP, CLSP II, CLSP/SBS I AND CLSP/SBS II; (vii) Casdin Capital, L.L.C. ("Casdin, LLC"), a Delaware limited liability company and the sole general partner of Cooper Hill Partners, L.P. and the managing member to Cooper, LLC with respect to the Securities owned by CLSP, CLSP II, CLSP/SBS I and CLSP/SBS II and CLSP Overseas; and The foregoing persons (other than CLSP Overseas) are hereinafter sometimes collectively referred to as the "Reporting Persons." Any disclosures herein with respect to persons other than the Reporting Persons are made on information and belief after making inquiry to the appropriate party. Schedule 13G/A PAGE 10 OF 15 CUSIP No. 67072M103 ITEM 2(b). ADDRESS OF PRINCIPAL OFFICE OR, IF NONE, RESIDENCE: The business address of each of the Reporting Persons is 767 Third Avenue, New York, New York 10017. The business address of CLSP Overseas is c/o Goldman Sachs (Cayman) Trust, Limited P.O. Box 896 G.T. Harbour Centre, Second Floor North Church Street George Town, Grand Cayman Cayman Islands, B.W.I. ITEM 2(c). CITIZENSHIP: Cooper, LLC and Casdin, LLC are Delaware limited liability Companies and CLSP, CLSP II, CLSP/SBS I, CLSP/SBS II and Cooper Hill Partners, L.P. are each a Delaware limited partnership. CLSP Overseas is a Cayman Islands exempted company. The late Jeffrey Casdin was a citizen of the United States. ITEM 2(d). TITLE OF CLASS OF SECURITIES: Common Stock, $.01 par value ITEM 2(e). CUSIP NUMBER: 67072M103 ITEM 3. IF THIS STATEMENT IS FILED PURSUANT TO 13d-1(b) OR 13d-2(b) OR (c), CHECK WHETHER THE PERSON FILING IS A: (a) [ ] Broker or dealer registered under Section 15 of the Act (b) [ ] Bank as defined in Section 3(a)(6) of the Act (c) [ ] Insurance Company as defined in Section 3(a)(19) of the Act (d) [ ] Investment Company registered under Section 8 of the Investment Company Act of 1940 (e) [ ] Investment Adviser registered under Section 203 of the Investment Advisers Act of 1940: see Rule 13d- 1(b)(1)(ii)(E) (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 Rule 13d- 1(b)(1)(ii)(F) (g) [ ] Parent Holding Company, in accordance with Rule 13d- 1(b)(ii)(G); (h) [ ] Savings Associations as defined in Section 3(b) of the Federal Deposit Insurance Act; (i) [ ] Church Plan that is excluded from the definition of an investment company under Section 3(c)(14) of the Investment Company Act of 1940; Schedule 13G/A PAGE 11 OF 15 CUSIP No. 67072M103 (j) [ ] Group, in accordance with Rule 13d-1(b)(1)(ii)(J). IF THIS STATEMENT IS FILED PURSUANT TO Rule 13d-1(c), CHECK THIS BOX. [x] ITEM 4. OWNERSHIP. A. CLSP (a) Amount beneficially owned: 234,375 (b) Percent of class: 0.6% (All percentages herein are based on 42,288,782 shares of Common Stock reported to be outstanding as of October 8, 2005, as reflected in the Company's quarterly report on Form 10-Q filed with the Securities and Exchange Commission by the Company for the quarter ended September 30, 2005). (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 234,375 (iii) sole power to dispose or to direct the disposition of 0 (iv) shared power to dispose or to direct the disposition of 234,375 B. CLSP II (a) Amount beneficially owned: 275,884 (b) Percent of class: 0.7% (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 275,884 (iii) sole power to dispose or to direct the disposition of 0 (iv) shared power to dispose or to direct the disposition of 275,884 C. CLSP/SBS I (a) Amount beneficially owned: 0 (b) Percent of class: 0.0% (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 0 (iii) sole power to dispose or to direct the disposition of 0 Schedule 13G/A PAGE 12 OF 15 CUSIP No. 67072M103 (iv) shared power to dispose or to direct the disposition of 0 D. CLSP/SBS II (a) Amount beneficially owned: 34,067 (b) Percent of class: 0.1% (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 34,067 (iii) sole power to dispose or to direct the disposition of 0 (iv) shared power to dispose or to direct the disposition of 34,067 E. Cooper Hill Partners, L.P. (a) Amount beneficially owned: 209,379 (b) Percent of class: 0.5% (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 209,379 (iii) sole power to dispose or to direct the disposition of 0 (iv) shared power to dispose or to direct the disposition of 209,379 F. Cooper Hill Partners, LLC (a) Amount beneficially owned: 544,326 (b) Percent of class: 1.3% (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 544,326 (iii) sole power to dispose or to direct the disposition of 0 (iv) shared power to dispose or to direct the disposition of 544,326 G. Casdin Capital, LLC (a) Amount beneficially owned: 753,705 (b) Percent of class: 1.8% (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 753,705 (iii) sole power to dispose or to direct the disposition Schedule 13G/A PAGE 13 OF 15 CUSIP No. 67072M103 of 0 (iv) shared power to dispose or to direct the disposition of 753,705 Schedule 13G/A PAGE 14 OF 15 CUSIP No. 67072M103 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 5% OF THE CLASS OF SECURITIES CHECK THE FOLLOWING [ X ]. ITEM 6. OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER PERSON. CLSP, CLSP II, CLSP/SBS I, and CLSP/SBS II are each private investment partnerships, the sole general partner of which is Cooper, LLC. As the sole general partner of CLSP, CLSP II, CLSP/SBS I, and CLSP/SBS II, Cooper, LLC has the power to vote and dispose of the Securities owned by each of CLSP, CLSP II, CLSP/SBS I, and CLSP/SBS II and, accordingly, may be deemed the "beneficial owner" of such Securities. The managing member of Cooper, LLC is Casdin, LLC of which Jeffrey Casdin was the managing member. Jeffrey Casdin passed away in October of 2005 and an authorized signatory of the Estate of Jeffrey Casdin has yet to be determined. Pursuant to an investment advisory contract, Cooper Hill Partners, L.P. currently has the power to vote and dispose of the Securities held for the account of CLSP Overseas and, accordingly, may be deemed the "beneficial owner" of such Securities. Schedule 13G/A PAGE 15 OF 15 CUSIP No. 67072M103 ITEM 7. IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH ACQUIRED THE SECURITY BEING REPORTED ON BY THE PARENT HOLDING COMPANY. Not applicable. ITEM 8. IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF THE GROUP. Not applicable. ITEM 9. NOTICE OF DISSOLUTION OF GROUP. Not applicable. ITEM 10. CERTIFICATION. (if filing pursuant to Rule 13d-1(c)) Each of the Reporting Persons and CLSP Overseas, Ltd. hereby make the following certification: By signing below each Reporting Person certifies that, to the best of its knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the Securities and were not acquired and not held in connection with or as a participant in any transaction having that purpose or effect. SIGNATURES After reasonable inquiry and to the best of our knowledge and belief, the undersigned certify that the information set forth in this statement is true, complete and correct. DATED: January 17, 2006 /s/ Peter Freer, On behalf of CLSP, L.P., CLSP II, L.P., CLSP/SBS I, L.P., and CLSP/SBS II, L.P. and Cooper Hill Partners, L.P. /s/ Peter Freer, On behalf of Cooper Hill Partners, L.L.C.