0001144204-13-029481.txt : 20130515 0001144204-13-029481.hdr.sgml : 20130515 20130515161309 ACCESSION NUMBER: 0001144204-13-029481 CONFORMED SUBMISSION TYPE: 13F-HR PUBLIC DOCUMENT COUNT: 1 CONFORMED PERIOD OF REPORT: 20130331 FILED AS OF DATE: 20130515 DATE AS OF CHANGE: 20130515 EFFECTIVENESS DATE: 20130515 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: 13847191 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 v344943_13f-hr.txt 13F-HR 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, 2013 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 13, 2013 -------------------------- --------------------------- ------------------- [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: 75 ----------- Form 13F Information Table Entry Value: $5,009,281 ----------- (thousands) List of Other Included Managers: None Baker Brothers Form 13F 3-31-13

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 -------------- ----- ------- ------- --- ---- ---------- -------- ---- ------ ---- Acadia Pharmaceuticals Inc. COM 004225108 124,037 15,621,812 SH SOLE 15,621,812 Achillion COM 00448Q201 3,981 455,000 SH SOLE 455,000 Aegerion Pharmaceuticals COM 00767E102 34,843 863,743 SH SOLE 863,743 Amicus Therapeutics COM 03152W109 1,633 515,072 SH SOLE 515,072 Anacor Pharmaceuticals COM 32420101 5,016 776,463 SH SOLE 776,463 Aradigm Corp. COM 038505301 13 100,000 SH SOLE 100,000 Ariad Pharmaceuticals Inc. COM 04033A100 38,872 2,150,000 SH SOLE 2,150,000 Arqule Inc. COM 04269E107 2358 910,267 SH SOLE 910,267 Array Biopharma Inc. COM 04269X105 7,365 1,500,000 SH SOLE 1,500,000 Auxilium COM 05334D107 36,458 2,108,617 SH SOLE 2,108,617 Aveo Pharmaceuticals COM 053588109 3,821 519,833 SH SOLE 519,833 Biocryst Pharmaceuticals Inc. COM 09058V103 6,620 5,563,615 SH SOLE 5,563,615 Biodel Inc. COM 09064M204 1,532 540,000 SH SOLE 540,000 BioDelivery Sciences Intl. Inc. COM 09060J106 7,218 1,714,505 SH SOLE 1,714,505 Biomarin Pharmaceuticals COM 09061G101 48,769 783,311 SH SOLE 783,311 Cerus COM 157085101 28,919 6,542,845 SH SOLE 6,542,845 Chelsea Therapeutics COM 163428105 9,743 4,775,787 SH SOLE 4,775,787 Chemocentryx Inc. COM 16383L106 691 50,000 SH SOLE 50,000 Clovis Oncology COM 189464100 28,703 1,001,163 SH SOLE 1,001,163 Cyclacel Pharmaceuticals Pfd. Conv. Ex 6% PFD CONV EX 23254L207 207 20,979 SH SOLE 20,979 Cytrx Corp. COM 232828509 2,720 1,000,000 SH SOLE 1,000,000 Cubist Pharmaceuticals Inc. COM 229678107 234 5,000 SH SOLE 5,000 Derma Sciences COM 249827502 16,415 1,358,857 SH SOLE 1,358,857 Discovery Laboratories Inc. COM 254668403 1,952 852,617 SH SOLE 852,617 Genomic Health Inc. COM 37244C101 355,686 12,577,272 SH SOLE 12,577,272 Geron Corp. COM 374163103 1,070 1,000,000 SH SOLE 1,000,000 Gilead Sciences Inc. COM 375558103 8,995 183,800 SH SOLE 183,800 Halozyme Therapeutics Inc. COM 40637H109 18,346 3,182,251 SH SOLE 3,182,251 Incyte Corp. COM 45337C102 346,715 14,810,559 SH SOLE 14,810,559 Infinity Pharmaceuticals Inc. COM 45665303 57,121 1,178,485 SH SOLE 1,178,485 Insmed Inc. COM 457669307 5,961 795,803 SH SOLE 795,803 Intercept Pharmaceuticals, Inc. COM 45845P108 14,025 375,000 SH SOLE 375,000 Intermune Inc. COM 45884X103 15,725 1,737,580 SH SOLE 1,737,580 Ironwood Pharmaceuticals COM 46333X108 12,764 698,058 SH SOLE 698,058 Kythera Biopharmaceuticals COM 501570105 4,019 165,000 SH SOLE 165,000 Ligand Pharmaceuticals Inc. CLASS B 53220K207 1,956 73,400 SH SOLE 73,400 Lpath Inc. COM 548910306 1,004 200,000 SH SOLE 200,000 Medivation Inc. COM 58501N101 25,013 534,919 SH SOLE 534,919 MEI Pharma, Inc. COM 55279B103 4,315 500,000 SH SOLE 500,000 Onyx COM 683399109 14,187 159,652 SH SOLE 159,652 Pharmacyclics Inc. COM 716933106 878,385 10,923,830 SH SOLE 10,923,830 Progenics Pharmaceuticals, Inc. COM 743187106 4,842 900,000 SH SOLE 900,000 Prothena Corp. PLC COM G72800108 1,282 191,696 SH SOLE 191,696 QLT, Inc. COM 746927102 13,577 1,535,863 SH SOLE 1,535,863 Questcor Pharmaceuticals, Inc. COM 74835Y101 11,113 341,513 SH SOLE 341,513 Repros Therapeutics COM 76028H209 36,405 2,261,154 SH SOLE 2,261,154 Salix Pharmaceuticals, Inc. COM 795435106 2,245 43,872 SH SOLE 43,872 Seattle Genetics Inc. COM 812578102 686,061 19,322,947 SH SOLE 19,322,947 Stemline Therapeutics Inc. COM 85858C107 5,705 500,000 SH SOLE 500,000 Synageva Biopharma Corp. COM 87159A103 506,536 9,223,182 SH SOLE 9,223,182 Synergy Pharmaceuticals COM 871639308 9,948 1,638,871 SH SOLE 1,638,871 Synta Pharmaceuticals COM 87162T206 12,578 1,462,614 SH SOLE 1,462,614 Tesaro Inc. COM 881569107 686 31,218 SH SOLE 31,218 Threshold Pharma COM 885807107 7,353 1,595,048 SH SOLE 1,595,048 Vanda Pharmaceuticals, Inc. COM 921659108 7,595 1,937,390 SH SOLE 1,937,390 Ventrus Biosciences, Inc. COM 922822101 3,635 1,215,840 SH SOLE 1,215,840 Vertex Pharmaceuticals, Inc. COM 92532F100 13,874 252,400 SH SOLE 252,400 Viropharma Inc. COM 928241108 214,580 8,528,603 SH SOLE 8,528,603 Xenoport COM 98411C100 7,394 1,034,112 SH SOLE 1,034,112 Xoma Corp. COM 98419J107 70,758 20,274,581 SH SOLE 20,274,581 Ziopharm Oncology Inc. COM 98973P101 465 254,199 SH SOLE 254,199 Zogenix, Inc. COM 98978L105 3,602 2,001,000 SH SOLE 2,001,000 Auxilium 1.5% 7/15/2018 CONV BONDS 05334DAA5 110,413 110,000,000 PRN SOLE 110,000,000 Biomarin Pharmaceuticals Notes 1.875% 4/23/2017 CONV BONDS 09061GAD3 70,834 22,898,000 PRN SOLE 22,898,000 Exelisis 4.25% 8/15/2019 CONV BONDS 30161QAC8 18,905 19,000,000 PRN SOLE 19,000,000 Gilead 0.625% 5/1/13 CONV BONDS 375558AH6 64,055 25,000,000 PRN SOLE 25,000,000 Gilead 1.625% 5/1/16 CONV BONDS 375558AP8 46,682 21,500,000 PRN SOLE 21,500,000 Incyte Genomics Notes 4.75% 10/1/2015 CONV BONDS 45337CAH5 425,552 157,758,000 PRN SOLE 157,758,000 Intermune Inc Notes 2.5% 9/15/18 CONV BONDS 45884XAE3 13,740 16,500,000 PRN SOLE 16,500,000 Intermune Inc Notes 5% 3/1/15 CONV BONDS 45884XAD5 17,640 16,860,000 PRN SOLE 16,860,000 Intermune Inc Notes 2.5% 12/15/17 CONV BONDS 45884XAF0 42,589 41,000,000 PRN SOLE 41,000,000 Medivation 2.625% 4/1/17 CONV BONDS 58501NAA9 48,955 39,500,000 PRN SOLE 39,500,000 Salix 2.75% 5/15/15 CONV BONDS 795435AC0 220,383 170,922,000 PRN SOLE 170,922,000 Salix 1.5% 3/15/19 CONV BONDS 795435AE6 107,164 100,860,000 PRN SOLE 100,860,000 United Therapeutics Notes 1% 9/15/16 144A CONV BONDS 91307CAE2 24,728 18,000,000 PRN SOLE 18,000,000