0001144204-12-008784.txt : 20120214 0001144204-12-008784.hdr.sgml : 20120214 20120214161719 ACCESSION NUMBER: 0001144204-12-008784 CONFORMED SUBMISSION TYPE: 13F-HR PUBLIC DOCUMENT COUNT: 1 CONFORMED PERIOD OF REPORT: 20111231 FILED AS OF DATE: 20120214 DATE AS OF CHANGE: 20120214 EFFECTIVENESS DATE: 20120214 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: 12610064 BUSINESS ADDRESS: STREET 1: 667 MADISON AVE STREET 2: 21ST FLOOR CITY: NEW YORK STATE: NY ZIP: 10065 BUSINESS PHONE: 2123395600 MAIL ADDRESS: STREET 1: 667 MADISON AVE STREET 2: 21ST FLOOR CITY: NEW YORK STATE: NY ZIP: 10065 13F-HR 1 v302114_13fhr.txt HOLDINGS REPORT UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 13F FORM 13F COVER PAGE Report for the Calendar Year or Quarter Ended: December 31, 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. February 10, 2012 -------------------------- --------------------------- ------------------- [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: 57 ----------- Form 13F Information Table Entry Value: $3,025,796 ----------- (thousands) List of Other Included Managers: None Baker Brothers Form 13F 12-31-11

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 Adventrx Pharmaceuticals COM 00764X202 38 64,692 SH SOLE 64,692 3 Aegerion Pharmaceuticals COM 00767E102 8,815 526,575 SH SOLE 526,575 4 Amicus Therapeutics COM 03152W109 3,141 913,129 SH SOLE 913,129 5 Anacor Pharmaceuticals COM 32420101 2,902 468,130 SH SOLE 468,130 6 Anthera Pharmaceuticals COM 03674U102 4,652 757,600 SH SOLE 757,600 7 Aradigm Corp. COM 038505301 11 100,000 SH SOLE 100,000 8 Ardea Biosciences Inc. COM 03969P107 101,061 6,011,989 SH SOLE 6,011,989 9 Ariad Pharmaceuticals Inc. COM 04033A100 66,194 5,403,560 SH SOLE 5,403,560 10 Auxilium COM 05334D107 128,775 6,461,354 SH SOLE 6,461,354 11 Avanir Pharmaceuticals COM 05348P401 1,025 500,000 SH SOLE 500,000 12 Biocryst Pharmaceuticals Inc. COM 09058V103 13,742 5,563,615 SH SOLE 5,563,615 13 BioDelivery Sciences Intl. Inc. COM 09060J106 2,089 2,595,044 SH SOLE 2,595,044 14 Biomarin COM 09061G101 16,766 487,679 SH SOLE 487,679 15 Chelsea Therapeutics COM 163428105 5,718 1,114,700 SH SOLE 1,114,700 16 Clovis Oncology COM 189464100 4,932 350,000 SH SOLE 350,000 17 Cyclacel Pharmaceuticals Pfd. Conv. Ex 6% PFD CONV EX 23254L207 60 20,979 SH SOLE 20,979 18 Cumberland Pharmaceuticals COM 230770109 127 23,627 SH SOLE 23,627 19 Dendreon COM 24823Q107 5,180 681,528 SH SOLE 681,528 20 Derma Sciences COM 249827502 3,607 475,807 SH SOLE 475,807 21 Exelixis Inc. COM 30161Q104 6,101 1,288,483 SH SOLE 1,288,483 22 Genomic Health Inc. COM 37244C101 222,959 8,781,344 SH SOLE 8,781,344 23 Gilead Sciences Inc. COM 375558103 118,159 2,886,861 SH SOLE 2,886,861 24 GTX Inc. COM 40052B108 10,363 3,084,156 SH SOLE 3,084,156 25 Halozyme Therapeutics Inc. COM 40637H109 17,019 1,789,595 SH SOLE 1,789,595 26 Idera Pharmaceuticals Inc. COM 45168K108 303 288,252 SH SOLE 288,252 27 Incyte Corp. COM 45337C102 233,392 15,549,112 SH SOLE 15,549,112 28 Inhibitex Inc. COM 45719T103 24,879 2,274,095 SH SOLE 2,274,095 29 Ligand Pharmaceuticals, Inc. COM 53220K504 871 73,401 SH SOLE 73,401 30 Medivation Inc. COM 58501N101 22,285 483,300 SH SOLE 483,300 31 Micromet COM 59509C105 28,605 3,978,438 SH SOLE 3,978,438 32 Onyx COM 683399109 9,429 214,543 SH SOLE 214,543 33 Pharmacyclics Inc. COM 716933106 118,760 8,013,514 SH SOLE 8,013,514 34 Pharmasset Inc. COM 71715N106 201,239 1,569,727 SH SOLE 1,569,727 35 Raptor Pharmaceuticals COM 75382F106 2,829 451,955 SH SOLE 451,955 36 Rigel Pharmaceuticals COM 766559603 894 113,270 SH SOLE 113,270 37 Salix Pharmaceuticals, Inc. COM 795435106 5,138 107,373 SH SOLE 107,373 38 Seattle Genetics Inc. COM 812578102 344,286 20,597,463 SH SOLE 20,597,463 39 Spectrum COM 84763A108 13,312 909,884 SH SOLE 909,884 40 Synageva COM 87159A103 164,668 6,183,574 SH SOLE 6,183,574 41 Targacept Inc. COM 87611R306 1,996 358,416 SH SOLE 358,416 42 Threshold Pharma COM 885807107 4,474 3,667,643 SH SOLE 3,667,643 43 Tranzyme COM 89413J102 5,802 2,007,867 SH SOLE 2,007,867 44 Ventrus Biosciences, Inc. COM 922822101 195 24,300 SH SOLE 24,300 45 Viropharma Inc. COM 928241108 330,013 12,048,664 SH SOLE 12,048,664 46 Xenoport COM 98411C100 3,083 809,112 SH SOLE 809,112 47 Xoma Ltd. SHS G9825R206 460 400,400 SH SOLE 400,400 48 YM Biosciences COM 984238105 13,178 8,035,655 SH SOLE 8,035,655 49 Alere Inc. Conv. Notes 3% 5/15/16 CONV BONDS 01449JAA3 4,247 4,482,000 PRN SOLE 4,482,000 50 Biomarin Pharmaceuticals Notes 1.875% 4/23/2017 CONV BONDS 09061GAD3 14,039 7,898,000 PRN SOLE 7,898,000 51 Dendreon 2.875% 1/15/16 CONV BONDS 24823QAB3 7,362 10,641,000 PRN SOLE 10,641,000 52 Gilead 1.625% 5/1/16 CONV BONDS 375558AP8 24,503 21,500,000 PRN SOLE 21,500,000 53 Incyte Genomics Notes 4.75% 10/1/2015 CONV BONDS 45337CAH5 300,500 160,000,000 PRN SOLE 160,000,000 54 Intermune Inc Notes 2.5% 9/15/18 CONV BONDS 45884XAE3 15,964 21,500,000 PRN SOLE 21,500,000 55 Intermune Inc Notes 5% 3/1/15 CONV BONDS 45884XAD5 18,977 18,801,000 PRN SOLE 18,801,000 56 Salix 5.5% 8/15/28 CONV BONDS 795435AB2 231,650 44,500,000 PRN SOLE 44,500,000 57 Salix 2.75% 5/15/15 CONV BONDS 795435AC0 129,361 100,572,000 PRN SOLE 100,572,000 --------- 3,025,796 =========