0001144204-11-064355.txt : 20111114 0001144204-11-064355.hdr.sgml : 20111111 20111114161849 ACCESSION NUMBER: 0001144204-11-064355 CONFORMED SUBMISSION TYPE: 13F-HR PUBLIC DOCUMENT COUNT: 1 CONFORMED PERIOD OF REPORT: 20110930 FILED AS OF DATE: 20111114 DATE AS OF CHANGE: 20111114 EFFECTIVENESS DATE: 20111114 FILER: COMPANY DATA: COMPANY CONFORMED NAME: BAKER BROS ADVISORS LLC CENTRAL INDEX KEY: 0001263508 IRS NUMBER: 134093645 STATE OF INCORPORATION: DE FISCAL YEAR END: 1231 FILING VALUES: FORM TYPE: 13F-HR SEC ACT: 1934 Act SEC FILE NUMBER: 028-10519 FILM NUMBER: 111202803 BUSINESS ADDRESS: STREET 1: 667 MADISON AVENUE STREET 2: 17TH FLOOR CITY: NEW YORK STATE: NY ZIP: 10021 BUSINESS PHONE: 2125212418 13F-HR 1 v240520_13fhr.txt UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 13F FORM 13F COVER PAGE Report for the Calendar Year or Quarter Ended: September 30, 2011 Check here if Amendment [ ]; Amendment Number: _____ This Amendment (Check only one.): [ ] is a restatement. [ ] adds new holdings entries. Institutional Investment Manager Filing this Report: Name: Baker Bros. Advisors, LLC -------------------------------------------- Address: 667 Madison Avenue, 21st Floor -------------------------------------------- New York, NY 10065-8029 -------------------------------------------- Form 13F File Number: 28-10519 The institutional investment manager filing this report and the person by whom it is signed hereby represent that the person signing the report is authorized to submit it, that all information contained herein is true, correct and complete, and that it is understood that all required items, statements, schedules, lists, and tables, are considered integral parts of this form. Person Signing this Report on Behalf of Reporting Manager: Name: Leo Kirby -------------------------------------------- Title: Chief Financial Officer -------------------------------------------- Phone: 212-339-5633 -------------------------------------------- Signature, Place, and Date of Signing: /s/ Leo Kirby New York, N.Y. November 14, 2011 -------------------------- --------------------------- ------------------- [Signature] [City, State] [Date] Report Type (Check only one.): [X] 13F HOLDINGS REPORT. (Check here if all holdings of this reporting manager are reported in this report.) [_] 13F NOTICE. (Check here if no holdings reported are in this report, and all holdings are reported by other reporting manager(s).) [_] 13F COMBINATION REPORT. (Check here if a portion of the holdings for this reporting manager are reported in this report and a portion are reported by other reporting manager(s).) List of Other Managers Reporting for this Manager: None FORM 13F SUMMARY PAGE Report Summary: Number of Other Included Managers: 0 ----------- Form 13F Information Table Entry Total: 52 ----------- Form 13F Information Table Entry Value: $2,348,486 ----------- (thousands) List of Other Included Managers: None Baker Brothers Form 13F 9-30-11

COLUMN 1 COLUMN 2 COLUMN 3 COLUMN 4 COLUMN 5 COLUMN 6 COLUMN 7 COLUMN 8 VALUE SHRS OR SH/ PUT/ INVESTMENT OTHER VOTING AUTHORITY Name of Issuer CUSIP (x1000) PRN AMT PRN CALL DISCRETION MANAGERS SOLE SHARED NONE -------------- ----- ------- ------- --- ---- ---------- -------- ---- ------ ---- 1 Acadia Pharmaceuticals Inc. COM 004225108 5,666 5,246,312 SH SOLE 5,246,312 2 Adolor Corp. COM 00724X102 11,949 6,947,343 SH SOLE 6,947,343 3 Aegerion Pharmaceuticals Inc. COM 00767E102 6,143 484,847 SH SOLE 484,847 4 Amicus Therapeutics COM 03152W109 3,465 902,386 SH SOLE 902,386 5 Anacor Pharmaceuticals COM 32420101 3,069 538,493 SH SOLE 538,493 6 Anthera Pharmaceuticals COM 03674U102 3,871 811,516 SH SOLE 811,516 7 Aradigm Corp. COM 038505301 15 100,000 SH SOLE 100,000 8 Ardea Biosciences Inc. COM 03969P107 93,907 6,011,989 SH SOLE 6,011,989 9 Ariad Pharmaceuticals Inc. COM 04033A100 11,224 1,276,960 SH SOLE 1,276,960 10 Auxilium COM 05334D107 96,856 6,461,354 SH SOLE 6,461,354 11 Avanir Pharmaceuticals COM 05348P401 1,428 500,000 SH SOLE 500,000 12 Biocryst Pharmaceuticals Inc. COM 09058V103 15,356 5,563,615 SH SOLE 5,563,615 13 BioDelivery Sciences Intl. Inc. COM 09060J106 2,620 2,403,848 SH SOLE 2,403,848 14 Biomarin COM 09061G101 10,751 337,353 SH SOLE 337,353 15 Chelsea Therapeutics COM 163428105 4,058 1,114,700 SH SOLE 1,114,700 16 Cyclacel Pharmaceuticals Pfd. Conv. Ex 6% PFD CONV EX 23254L207 63 20,979 SH SOLE 20,979 17 Cumberland Pharmaceuticals COM 230770109 132 23,627 SH SOLE 23,627 18 Dendreon COM 24823Q107 23,520 2,613,306 SH SOLE 2,613,306 19 Derma Sciences COM 249827502 2,647 339,743 SH SOLE 339,743 20 Exelixis Inc. COM 30161Q104 7,035 1,288,483 SH SOLE 1,288,483 21 Genomic Health Inc. COM 37244C101 172,836 7,863,337 SH SOLE 7,863,337 22 GTX Inc. COM 40052B108 9,159 2,734,110 SH SOLE 2,734,110 23 Halozyme Therapeutics Inc. COM 40637H109 18,007 2,932,812 SH SOLE 2,932,812 24 Idenix Pharmaceuticals Inc. COM 45166R204 2,857 572,576 SH SOLE 572,576 25 Idera Pharmaceuticals Inc. COM 45168K108 340 288,252 SH SOLE 288,252 26 Incyte Corp. COM 45337C102 154,795 11,080,56 SH SOLE 11,080,561 27 Ligand Pharmaceuticals Inc. CLASS B 53220K207 1,004 73,401 SH SOLE 73,401 28 Medivation Inc. COM 58501N101 8,206 483,300 SH SOLE 483,300 29 Micromet COM 59509C105 17,011 3,543,932 SH SOLE 3,543,932 30 Onyx COM 683399109 5,088 169,543 SH SOLE 169,543 31 Pharmacyclics Inc. COM 716933106 83,177 7,031,016 SH SOLE 7,031,016 32 Pharmasset Inc. COM 71715N106 337,188 4,093,582 SH SOLE 4,093,582 33 Raptor Pharmaceuticals COM 75382F106 2,038 451,955 SH SOLE 451,955 34 Rigel Pharmaceuticals COM 766559603 834 113,270 SH SOLE 113,270 35 Salix Pharmaceuticals, Inc. COM 795435106 1,535 51,843 SH SOLE 51,843 36 Seattle Genetics Inc. COM 812578102 392,176 20,597,46 SH SOLE 20,597,463 37 Threshold Pharma COM 885807107 5,282 3,667,644 SH SOLE 3,667,644 38 Tranzyme COM 89413J102 5,035 1,906,982 SH SOLE 1,906,982 39 Trimeris Inc. COM 896263100 8,758 3,475,475 SH SOLE 3,475,475 40 Via Pharmaceuticals COM 92554T103 2 102,881 SH SOLE 102,881 41 Viropharma Inc. COM 928241108 198,125 10,964,30 SH SOLE 10,964,303 42 Xoma Ltd. COM G9825R206 701 400,400 SH SOLE 400,400 43 YM Biosciences COM 984238105 16,018 8,611,799 SH SOLE 8,611,799 44 Ziopharm Oncology Inc. COM 98973P101 3,746 849,500 SH SOLE 849,500 45 Alere Inc. Conv. Notes 3% 5/15/16 CONV BONDS 01449JAA3 3,899 4,482,000 PRN SOLE 4,482,000 46 Biomarin Pharmaceuticals Notes 1.875% 4/23/2017 CONV BONDS 09061GAD3 13,070 7,898,000 PRN SOLE 7,898,000 47 Dendreon 2.875% 1/15/16 CONV BONDS 24823QAB3 9,800 13,641,000 PRN SOLE 13,641,000 48 Incyte Genomics Notes 4.75% 10/1/2015 CONV BONDS 45337CAH5 283,600 160,000,00 PRN SOLE 160,000,000 49 Intermune Inc Notes 2.5% 9/15/18 CONV BONDS 45884XAE3 19,639 21,500,000 PRN SOLE 21,500,000 50 Intermune Inc Notes 5% 3/1/15 CONV BONDS 45884XAD5 25,158 18,801,000 PRN SOLE 18,801,000 51 Salix 5.5% 8/15/28 CONV BONDS 795435AB2 144,903 44,500,000 PRN SOLE 44,500,000 52 Salix 2.75% 5/15/15 CONV BONDS 795435AC0 100,724 101,741,00 PRN SOLE 101,741,000 --------- 2,348,486 =========

Report Type X 13F Holdings Report List of Other Managers NONE Report Summary Number of other Included Managers 0 Form 13F Information Table Entry Total 52 Form 13F Information Table Entry Value 2,348,486