0001144204-12-029723.txt : 20120515 0001144204-12-029723.hdr.sgml : 20120515 20120515170821 ACCESSION NUMBER: 0001144204-12-029723 CONFORMED SUBMISSION TYPE: 13F-HR PUBLIC DOCUMENT COUNT: 1 CONFORMED PERIOD OF REPORT: 20120331 FILED AS OF DATE: 20120515 DATE AS OF CHANGE: 20120515 EFFECTIVENESS DATE: 20120515 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: 12845858 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 v313469_13f.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: March 31, 2012 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. May 15, 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: 61 ----------- Form 13F Information Table Entry Value: $3,743,364 ----------- (thousands) List of Other Included Managers: None Baker Brothers Form 13F 03-31-12

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 11,280 5,246,312 SH SOLE 5,246,312 2 Aegerion Pharmaceuticals COM 00767E102 7,283 526,575 SH SOLE 526,575 3 Alere COM 01449J105 1,951 75,000 SH SOLE 75,000 4 Amicus Therapeutics COM 03152W109 4,040 765,072 SH SOLE 765,072 5 Anacor Pharmaceuticals COM 32420101 3,346 568,130 SH SOLE 568,130 6 Anthera Pharmaceuticals COM 03674U102 1,674 757,600 SH SOLE 757,600 7 Aradigm Corp. COM 038505301 16 100,000 SH SOLE 100,000 8 Ardea Biosciences Inc. COM 03969P107 150,405 6,911,989 SH SOLE 6,911,989 9 Ariad Pharmaceuticals Inc. COM 04033A100 111,524 6,979,004 SH SOLE 6,979,004 10 Arqule Inc. COM 04269E107 604 86,167 SH SOLE 86,167 11 Array Biopharma Inc. COM 04269X105 3,405 1,000,000 SH SOLE 1,000,000 12 Auxilium COM 05334D107 119,987 6,461,354 SH SOLE 6,461,354 13 Avanir Pharmaceuticals COM 05348P401 1,710 500,000 SH SOLE 500,000 14 Aveo Pharmaceuticals COM 053588109 3,673 296,000 SH SOLE 296,000 15 Biocryst Pharmaceuticals Inc. COM 09058V103 20,220 5,563,615 SH SOLE 5,563,615 16 BioDelivery Sciences Intl. Inc. COM 09060J106 6,280 2,595,044 SH SOLE 2,595,044 17 Chelsea Therapeutics COM 163428105 5,862 2,289,700 SH SOLE 2,289,700 18 Chemocentryx Inc. COM 16383L106 533 50,000 SH SOLE 50,000 19 Clovis Oncology COM 189464100 12,035 472,882 SH SOLE 472,882 20 Cyclacel Pharmaceuticals Pfd. Conv. Ex 6% PFD CONV EX 23254L207 53 20,979 SH SOLE 20,979 21 Cubist Pharmaceuticals Inc. COM 229678107 216 5,000 SH SOLE 5,000 22 Cumberland Pharmaceuticals COM 230770109 177 23,627 SH SOLE 23,627 23 Dendreon COM 24823Q107 4,843 454,528 SH SOLE 454,528 24 Derma Sciences COM 249827502 7,156 743,857 SH SOLE 743,857 25 Discovery Laboratories Inc. COM 254668403 2,747 1,025,000 SH SOLE 1,025,000 26 Exelixis Inc. COM 30161Q104 10,818 2,088,483 SH SOLE 2,088,483 27 Genomic Health Inc. COM 37244C101 316,800 10,349,534 SH SOLE 10,349,534 28 Gilead Sciences Inc. COM 375558103 39,088 800,000 SH SOLE 800,000 29 Halozyme Therapeutics Inc. COM 40637H109 22,835 1,789,595 SH SOLE 1,789,595 30 Idera Pharmaceuticals Inc. COM 45168K108 499 288,252 SH SOLE 288,252 31 Incyte Corp. COM 45337C102 310,865 16,106,976 SH SOLE 16,106,976 32 Infinity Pharmaceuticals Inc. COM 45665303 1,651 138,070 SH SOLE 138,070 33 Ligand Pharmaceuticals Inc. CLASS B 53220K207 1,171 73,401 SH SOLE 73,401 30 Medivation Inc. COM 58501N101 51,056 683,300 SH SOLE 683,300 32 Onyx COM 683399109 8,084 214,543 SH SOLE 214,543 33 Pharmacyclics Inc. COM 716933106 258,932 9,327,514 SH SOLE 9,327,514 35 Raptor Pharmaceuticals COM 75382F106 676 100,000 SH SOLE 100,000 36 Rigel Pharmaceuticals COM 766559603 796 98,919 SH SOLE 98,919 37 Salix Pharmaceuticals, Inc. COM 795435106 5,637 107,375 SH SOLE 107,375 38 Seattle Genetics Inc. COM 812578102 436,335 21,409,963 SH SOLE 21,409,963 39 Sequenom Inc. COM 817337405 2,393 587,850 SH SOLE 587,850 40 Spectrum COM 84763A108 17,483 1,384,255 SH SOLE 1,384,255 41 Synageva Biopharma Corp. COM 87159A103 268,217 7,477,464 SH SOLE 7,477,464 42 Targacept Inc. COM 87611R306 4,226 825,401 SH SOLE 825,401 43 Threshold Pharma COM 885807107 21,072 2,394,469 SH SOLE 2,394,469 44 Tranzyme COM 89413J102 9,842 3,829,730 SH SOLE 3,829,730 45 Ventrus Biosciences, Inc. COM 922822101 789 79,178 SH SOLE 79,178 46 Viropharma Inc. COM 928241108 362,303 12,048,664 SH SOLE 12,048,664 47 Xenoport COM 98411C100 3,641 809,112 SH SOLE 809,112 48 Xoma Ltd. SHS G9825R206 43,079 15,551,915 SH SOLE 15,551,915 49 YM Biosciences COM 984238105 14,946 8,035,655 SH SOLE 8,035,655 50 Ziopharm Oncology Inc. COM 98973P101 2,160 400,000 SH SOLE 400,000 51 Alere Inc. Conv. Notes 3% 5/15/16 CONV BONDS 01449JAA3 4,510 4,482,000 PRN SOLE 4,482,000 52 Biomarin Pharmaceuticals Notes 1.875% 4/23/2017 CONV BONDS 09061GAD3 40,859 22,898,000 PRN SOLE 22,898,000 53 Dendreon 2.875% 1/15/16 CONV BONDS 24823QAB3 5,713 7,141,000 PRN SOLE 7,141,000 54 Gilead 1.625% 5/1/16 CONV BONDS 375558AP8 27,587 21,500,000 PRN SOLE 21,500,000 55 Incyte Genomics Notes 4.75% 10/1/2015 CONV BONDS 45337CAH5 367,800 160,000,000 PRN SOLE 160,000,000 56 Intermune Inc Notes 2.5% 9/15/18 CONV BONDS 45884XAE3 18,530 21,500,000 PRN SOLE 21,500,000 57 Intermune Inc Notes 5% 3/1/15 CONV BONDS 45884XAD5 39,786 33,860,000 PRN SOLE 33,860,000 58 Medivation 2.625% 4/1/17 CONV BONDS 58501NAA9 25,848 24,500,000 PRN SOLE 24,500,000 59 Salix 5.5% 8/15/28 CONV BONDS 795435AB2 128,077 22,250,000 PRN SOLE 22,250,000 60 Salix 2.75% 5/15/15 CONV BONDS 795435AC0 147,890 110,572,000 PRN SOLE 110,572,000 61 Salix 144A 1.5% 3/15/19 CONV BONDS 795435AD8 240,350 230,000,000 PRN SOLE 230,000,000 ---------- 3,743,364 ==========