Chief Financial Officer

0001144204-16-134352.txt : 20161114 0001144204-16-134352.hdr.sgml : 20161111 20161114173032 ACCESSION NUMBER: 0001144204-16-134352 CONFORMED SUBMISSION TYPE: 13F-HR PUBLIC DOCUMENT COUNT: 2 CONFORMED PERIOD OF REPORT: 20160930 FILED AS OF DATE: 20161114 DATE AS OF CHANGE: 20161114 EFFECTIVENESS DATE: 20161114 FILER: COMPANY DATA: COMPANY CONFORMED NAME: BAKER BROS. ADVISORS LP 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: 161996166 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 FORMER COMPANY: FORMER CONFORMED NAME: BAKER BROS ADVISORS LLC DATE OF NAME CHANGE: 20030911 13F-HR 1 primary_doc.xml 13F-HR LIVE false false false 0001263508 XXXXXXXX 09-30-2016 09-30-2016 false BAKER BROS. ADVISORS LP

667 Madison Ave 21st Floor New York NY 10065

13F HOLDINGS REPORT 028-10519 N Alexandra Toohey Chief Financial Officer 212-339-5690 /s/ Alexandra Toohey New York NY 11-14-2016 0 134 11019928 INFORMATION TABLE 2 infotable.xml AbbVie Inc. COM 00287Y109 904636 14343358 SH SOLE 14343358 0 0 Abeona Therapeutics Inc. COM 00289Y107 610 101680 SH SOLE 101680 0 0 ACADIA Pharmaceuticals Inc. COM 004225108 821327 25819768 SH SOLE 25819768 0 0 Acceleron Pharma Inc. COM 00434H108 1041 28765 SH SOLE 28765 0 0 Achaogen, Inc. COM 004449104 479 100000 SH SOLE 100000 0 0 Achillion Pharmaceuticals, Inc. COM 00448Q201 20052 2475515 SH SOLE 2475515 0 0 Acorda Therapeutics, Inc. COM 00484M106 76443 3661082 SH SOLE 3661082 0 0 Adamas Pharmaceuticals, Inc. COM 00548A106 2833 172630 SH SOLE 172630 0 0 Adaptimmune Therapeutics plc SPONSORED ADR 00653A107 705 100000 SH SOLE 600000 0 0 Advanced Accelerator Applications S.A. SPONSORED ADR 00790T100 39194 1029247 SH SOLE 2058494 0 0 Aeglea BioTherapeutics, Inc. COM 00773J103 2591 404230 SH SOLE 404230 0 0 Aerie Pharmaceuticals, Inc. COM 00771V108 11298 299356 SH SOLE 299356 0 0 Affimed N.V. COM N01045108 1112 400000 SH SOLE 400000 0 0 Agios Pharmaceuticals, Inc. COM 00847X104 10982 207915 SH SOLE 207915 0 0 Aimmune Therapeutics, Inc. COM 00900T107 10109 673908 SH SOLE 673908 0 0 Akari Therapeutics plc SPONSORED ADR 00972G108 4229 496901 SH SOLE 49690100 0 0 Alcobra Ltd. SHS M2239P109 5771 2336359 SH SOLE 2336359 0 0 Alder BioPharmaceuticals, Inc. COM 014339105 7122 217328 SH SOLE 217328 0 0 Aldeyra Therapeutics, Inc. COM 01438T106 1110 142000 SH SOLE 142000 0 0 Alexion Pharmaceuticals, Inc. COM 015351109 801815 6543295 SH SOLE 6543295 0 0 Alkermes plc SHS G01767105 11769 250251 SH SOLE 250251 0 0 Alnylam Pharmaceuticals, Inc. COM 02043Q107 769 11340 SH SOLE 11340 0 0 Amarin Corporation plc SPONSORED ADR NEW 023111206 65811 20630477 SH SOLE 20630477 0 0 Aptose Biosciences Inc. COM NEW 03835T200 909 404211 SH SOLE 404211 0 0 Aquinox Pharmaceuticals, Inc. COM 03842B101 140762 10536092 SH SOLE 10536092 0 0 Arbutus Biopharma Corporation COM 03879J100 621 180582 SH SOLE 180582 0 0 Array BioPharma Inc. COM 04269X105 22347 3310666 SH SOLE 3310666 0 0 Arrowhead Pharmaceuticals, Inc. COM 04280A100 13649 1856967 SH SOLE 1856967 0 0 Ascendis Pharma A/S SPONSORED ADR 04351P101 14985 745521 SH SOLE 745521 0 0 Assembly Biosciences, Inc. COM 045396108 1803 250000 SH SOLE 250000 0 0 BeiGene, Ltd. SPONSORED ADR 07725L102 58930 1912680 SH SOLE 24864840 0 0 Bellicum Pharmaceuticals, Inc. COM 079481107 96826 4865647 SH SOLE 4865647 0 0 BioCryst Pharmaceuticals, Inc. COM 09058V103 48351 10963944 SH SOLE 10963944 0 0 BioDelivery Sciences International, Inc. COM 09060J106 567 210021 SH SOLE 210021 0 0 BioMarin Pharmaceutical Inc. COM 09061G101 444696 4806483 SH SOLE 4806483 0 0 BioTime, Inc. *W EXP 10/1/201 09066L162 17 20084 SH SOLE 20084 0 0 bluebird bio, Inc. COM 09609G100 19923 293943 SH SOLE 293943 0 0 Catalyst Pharmaceuticals, Inc. COM 14888U101 5561 5102153 SH SOLE 5102153 0 0 Cellectis S.A. SPONSORED ADS 15117K103 1204 50000 SH SOLE 50000 0 0 Cerus Corporation COM 157085101 81061 13053275 SH SOLE 13053275 0 0 ChemoCentryx, Inc. COM 16383L106 296 49064 SH SOLE 49064 0 0 Chimerix, Inc. COM 16934W106 638 115216 SH SOLE 115216 0 0 CoLucid Pharmaceuticals, Inc. COM 19716T101 1156 30310 SH SOLE 30310 0 0 Concert Pharmaceuticals, Inc. COM 206022105 3205 316976 SH SOLE 316976 0 0 ContraFect Corporation COM 212326102 10034 4045876 SH SOLE 4045876 0 0 Cyclacel Pharmaceuticals, Inc. PFD CONV EX 6% 23254L207 90 13253 SH SOLE 13253 0 0 CytRx Corporation COM PAR $.001 232828509 388 659995 SH SOLE 659995 0 0 DBV Technologies S.A. SPONSORED ADR 23306J101 200162 5509560 SH SOLE 2754780 0 0 Derma Sciences, Inc. COM PAR $.01 249827502 17524 3752390 SH SOLE 3752390 0 0 Dermira, Inc. COM 24983L104 11040 326428 SH SOLE 326428 0 0 Dimension Therapeutics, Inc. COM 25433V105 10003 1251881 SH SOLE 1251881 0 0 Dynavax Technologies Corporation COM NEW 268158201 787 75000 SH SOLE 75000 0 0 Enanta Pharmaceuticals, Inc. COM 29251M106 2005 75357 SH SOLE 75357 0 0 Endocyte, Inc. COM 29269A102 2685 868983 SH SOLE 868983 0 0 Epizyme, Inc. COM 29428V104 2288 232481 SH SOLE 232481 0 0 Exelixis, Inc. COM 30161Q104 63048 4929494 SH SOLE 4929494 0 0 Five Prime Therapeutics, Inc. COM 33830X104 1010 19247 SH SOLE 19247 0 0 Foamix Pharmaceuticals Ltd. SHS M46135105 22842 2466702 SH SOLE 2466702 0 0 Foundation Medicine, Inc. COM 350465100 488 20892 SH SOLE 20892 0 0 Fulgent Genetics, Inc. COM 359664109 1153 125000 SH SOLE 125000 0 0 Galapagos NV SPONSORED ADR 36315X101 16805 259894 SH SOLE 259894 0 0 Genomic Health, Inc. COM 37244C101 398237 13770302 SH SOLE 13770302 0 0 GlycoMimetics, Inc. COM 38000Q102 2726 381235 SH SOLE 381235 0 0 Halozyme Therapeutics, Inc. COM 40637H109 20911 1731057 SH SOLE 1731057 0 0 Heron Therapeutics, Inc. COM 427746102 49230 2857250 SH SOLE 2857250 0 0 Idera Pharmaceuticals, Inc. COM NEW 45168K306 17956 7014015 SH SOLE 7014015 0 0 Ignyta, Inc. COM 451731103 3592 571000 SH SOLE 571000 0 0 Immune Design Corp. COM 45252L103 1129 148937 SH SOLE 148937 0 0 ImmunoGen, Inc. COM 45253H101 8081 3015353 SH SOLE 3015353 0 0 Incyte Corporation COM 45337C102 2215711 23498898 SH SOLE 23498898 0 0 Infinity Pharmaceuticals, Inc. COM 45665G303 905 580400 SH SOLE 580400 0 0 Insmed Incorporated COM PAR $.01 457669307 5808 400000 SH SOLE 400000 0 0 Intellia Therapeutics, Inc. COM 45826J105 18077 1062120 SH SOLE 1062120 0 0 Intra-Cellular Therapies, Inc. COM 46116X101 9284 609166 SH SOLE 609166 0 0 Invitae Corporation COM 46185L103 57422 6554967 SH SOLE 6554967 0 0 InVivo Therapeutics Holdings Corp. COM NEW 46186M209 2720 400000 SH SOLE 400000 0 0 Ionis Pharmaceuticals, Inc. COM 462222100 2094 57140 SH SOLE 57140 0 0 Juno Therapeutics, Inc. COM 48205A109 2401 80000 SH SOLE 80000 0 0 Karyopharm Therapeutics Inc. COM 48576U106 2111 216990 SH SOLE 216990 0 0 La Jolla Pharmaceutical Company COM PAR $.0001 2 503459604 327 13746 SH SOLE 13746 0 0 Ligand Pharmaceuticals Incorporated COM NEW 53220K504 7490 73386 SH SOLE 73386 0 0 Loxo Oncology, Inc. COM 548862101 3606 137735 SH SOLE 137735 0 0 MacroGenics, Inc. COM 556099109 10878 363676 SH SOLE 363676 0 0 Madrigal Pharmaceuticals, Inc. COM 558868105 732 57762 SH SOLE 57762 0 0 Mast Therapeutics, Inc. COM 576314108 944 8584051 SH SOLE 8584051 0 0 Medgenics, Inc. COM NEW 58436Q203 4905 880539 SH SOLE 880539 0 0 MediWound Ltd. ORD SHS M68830104 1740 226000 SH SOLE 226000 0 0 Merus N.V. COM N5749R100 19430 1160014 SH SOLE 1160014 0 0 Minerva Neurosciences, Inc. COM 603380106 3653 258805 SH SOLE 258805 0 0 Mirati Therapeutics, Inc. COM 60468T105 14999 2269198 SH SOLE 2269198 0 0 MyoKardia, Inc. COM 62857M105 1634 100000 SH SOLE 100000 0 0 Nabriva Therapeutics AG SPONSORED ADR 62957M104 2468 350000 SH SOLE 35000 0 0 Natera, Inc. COM 632307104 5000 450000 SH SOLE 450000 0 0 Neurocrine Biosciences, Inc. COM 64125C109 45344 895422 SH SOLE 895422 0 0 NeuroDerm Ltd. ORD SHS M74231107 5639 305000 SH SOLE 305000 0 0 Ophthotech Corporation COM 683745103 1644 35649 SH SOLE 35649 0 0 Osiris Therapeutics, Inc. COM 68827R108 2476 499193 SH SOLE 499193 0 0 Palatin Technologies, Inc. COM PAR $.01 696077403 1289 2050000 SH SOLE 2050000 0 0 Progenics Pharmaceuticals, Inc. COM 743187106 23110 3650808 SH SOLE 3650808 0 0 ProNAi Therapeutics, Inc. COM 74346L101 364 200000 SH SOLE 200000 0 0 ProQR Therapeutics N.V. SHS EURO N71542109 5739 860464 SH SOLE 860464 0 0 Proteon Therapeutics, Inc. COM 74371L109 2786 298591 SH SOLE 298591 0 0 Ritter Pharmaceuticals, Inc. COM 767836109 672 400000 SH SOLE 400000 0 0 Sage Therapeutics, Inc. COM 78667J108 9594 208328 SH SOLE 208328 0 0 Sangamo BioSciences, Inc. COM 800677106 18779 4055876 SH SOLE 4055876 0 0 SCYNEXIS, Inc. COM 811292101 1810 467600 SH SOLE 467600 0 0 Seattle Genetics, Inc. COM 812578102 2381857 44100294 SH SOLE 44100294 0 0 Selecta Biosciences, Inc. COM 816212104 2550 178950 SH SOLE 178950 0 0 Seres Therapeutics, Inc. COM 81750R102 1536 125000 SH SOLE 125000 0 0 Spark Therapeutics, Inc. COM 84652J103 79180 1318341 SH SOLE 1318341 0 0 Stemline Therapeutics, Inc. COM 85858C107 3612 333497 SH SOLE 333497 0 0 Sunesis Pharmaceuticals, Inc. COM PAR 867328700 3241 741665 SH SOLE 741665 0 0 Syros Pharmaceuticals, Inc. COM 87184Q107 2836 204465 SH SOLE 204465 0 0 Tenax Therapeutics, Inc. COM 88032L100 972 420000 SH SOLE 420000 0 0 TG Therapeutics, Inc. COM 88322Q108 15511 2003991 SH SOLE 2003991 0 0 Trevena, Inc. COM 89532E109 3038 450000 SH SOLE 450000 0 0 Trillium Therapeutics Inc. COM NEW 89620X506 6120 413697 SH SOLE 413697 0 0 Ultragenyx Pharmaceutical Inc. COM 90400D108 7094 100000 SH SOLE 100000 0 0 uniQure N.V. SHS N90064101 1760 230000 SH SOLE 230000 0 0 Versartis, Inc. COM 92529L102 26145 2134247 SH SOLE 2134247 0 0 Vitae Pharmaceuticals, Inc. COM 92847N103 13339 637597 SH SOLE 637597 0 0 Windtree Therapeutics, Inc. COM 97382D105 653 254973 SH SOLE 254973 0 0 Xencor, Inc. COM 98401F105 21357 872072 SH SOLE 872072 0 0 Zogenix, Inc. COM NEW 98978L204 11430 1000000 SH SOLE 1000000 0 0 Acorda Therapeutics, Inc. Notes 1.75% 6/15/2021 NOTE 1.75% 6/15/2021 00484MAA4 62830 77083000 PRN SOLE 77083000 0 0 Aegerion Pharmaceuticals, Inc. Notes 2.0% 8/15/2019 NOTE 2.0% 8/15/2019 00767EAB8 17432 26517000 PRN SOLE 26517000 0 0 Array BioPharma Inc. Notes 3.0% 6/1/2020 NOTE 3.0% 6/1/2020 04269XAA3 3561 3000000 PRN SOLE 3000000 0 0 BioMarin Pharmaceutical Inc. Notes 1.875% 4/23/2017 NOTE 1.875% 4/23/2017 09061GAD3 101405 22379000 PRN SOLE 22379000 0 0 BioMarin Pharmaceutical Inc. Notes 0.75% 10/15/2018 NOTE 0.75% 10/15/2018 09061GAE1 14630 12228000 PRN SOLE 12228000 0 0 Clovis Oncology, Inc. 2.5% 9/15/2021 NOTE 2.5% 9/15/2021 189464AB6 69135 72758000 PRN SOLE 72758000 0 0 Incyte Corporation Notes 0.375% 11/15/2018 144A NOTE 0.375% 11/15/2018 45337CAK8 491344 259000000 PRN SOLE 259000000 0 0 Incyte Corporation Notes 1.25% 11/15/2020 144A NOTE 1.25% 11/15/2020 45337CAL6 531244 274500000 PRN SOLE 274500000 0 0 Inotek Pharmaceuticals Corporation Notes 5.75% 8/1/2021 NOTE 5.75% 8/1/2021 45780VAB8 6708 5000000 PRN SOLE 5000000 0 0 Protalix BioTherapeutics, Inc. Notes 4.5% 9/15/18 NOTE 4.5% 9/15/2018 74365AAB7 2294 3423000 PRN SOLE 3423000 0 0