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Robert D. Baertsch, Ph.D. - Publications

Affiliations: 
University of California, Santa Cruz, Santa Cruz, CA, United States 
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43 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Nickols NG, Nazarian R, Zhao SG, Tan V, Uzunangelov V, Xia Z, Baertsch R, Neeman E, Gao AC, Thomas GV, Howard L, De Hoedt AM, Stuart J, Goldstein T, Chi K, et al. MEK-ERK signaling is a therapeutic target in metastatic castration resistant prostate cancer. Prostate Cancer and Prostatic Diseases. PMID 30804427 DOI: 10.1038/S41391-019-0134-5  0.653
2017 Newton Y, Novak AM, Swatloski T, McColl DC, Chopra S, Graim K, Weinstein AS, Baertsch R, Salama SR, Ellrott K, Chopra M, Goldstein TC, Haussler D, Morozova O, Stuart JM. TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal. Cancer Research. 77: e111-e114. PMID 29092953 DOI: 10.1158/0008-5472.Can-17-0580  0.775
2017 Doronina L, Churakov G, Kuritzin A, Shi J, Baertsch R, Clawson H, Schmitz J. Speciation network in Laurasiatheria: retrophylogenomic signals. Genome Research. PMID 28298429 DOI: 10.1101/Gr.210948.116  0.474
2016 Schmitz J, Noll A, Raabe CA, Churakov G, Voss R, Kiefmann M, Rozhdestvensky T, Brosius J, Baertsch R, Clawson H, Roos C, Zimin A, Minx P, Montague MJ, Wilson RK, et al. Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. Nature Communications. 7: 12997. PMID 27708261 DOI: 10.1038/Ncomms12997  0.649
2016 Sokolov A, Carlin DE, Paull EO, Baertsch R, Stuart JM. Pathway-Based Genomics Prediction using Generalized Elastic Net. Plos Computational Biology. 12: e1004790. PMID 26960204 DOI: 10.1371/Journal.Pcbi.1004790  0.388
2015 Smith BA, Sokolov A, Uzunangelov V, Baertsch R, Newton Y, Graim K, Mathis C, Cheng D, Stuart JM, Witte ON. A basal stem cell signature identifies aggressive prostate cancer phenotypes. Proceedings of the National Academy of Sciences of the United States of America. PMID 26460041 DOI: 10.1073/Pnas.1518007112  0.312
2015 Doronina L, Churakov G, Shi J, Brosius J, Baertsch R, Clawson H, Schmitz J. Exploring massive incomplete lineage sorting in arctoids (Laurasiatheria, Carnivora). Molecular Biology and Evolution. PMID 26337548 DOI: 10.1093/Molbev/Msv188  0.482
2015 Small EJ, Huang J, Youngren J, Sokolov A, Aggarwal RR, Thomas G, True LD, Zhang L, Foye A, Alumkal JJ, Ryan CJ, Rettig M, Evans CP, Gleave ME, Baertsch R, et al. Characterization of neuroendocrine prostate cancer (NEPC) in patients with metastatic castration resistant prostate cancer (mCRPC) resistant to abiraterone (Abi) or enzalutamide (Enz): Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT). Journal of Clinical Oncology. 33: 5003-5003. DOI: 10.1200/Jco.2015.33.15_Suppl.5003  0.347
2015 Lee JK, Smith BA, Phillips JW, Park J, Stoyanova TI, Baertsch R, Sokolov A, Mathis C, Cheng D, Stuart JM, Huang J, Witte ON. Abstract A28: N-Myc drives small cell neuroendocrine cancer initiated from human prostate basal cells Molecular Cancer Research. 13. DOI: 10.1158/1557-3125.Myc15-A28  0.3
2015 Graim K, Newton Y, Bivol A, Sokolov A, Ellrott K, Baertsch R, Stuart J. Abstract A2-64: A signature catalog to classify tumor mixtures: Application to recognition of metastatic disease in prostate cancer Cancer Research. 75. DOI: 10.1158/1538-7445.Transcagen-A2-64  0.324
2015 Baertsch R, Wong C, Youngren J, Stuart J, Small E, Goldstein T. Abstract A1-46: Using Medbook Workbench to create evidence streams to guide medical decisions Cancer Research. 75. DOI: 10.1158/1538-7445.Transcagen-A1-46  0.749
2015 Woodward J, King C, Coleman D, Lisac R, Schwartzman J, Wang N, Gleave M, Gray J, Thomas G, Beer TM, Hook KV, Baertsch R, Goldstein T, Stuart J, Gao L, et al. Abstract 731: Integrative genomic analysis to identify emergent enzalutamide resistance mechanisms in castration-resistant prostate cancer Cancer Research. 75: 731-731. DOI: 10.1158/1538-7445.Am2015-731  0.728
2014 Small EJ, Youngren J, Alumkal J, Evans C, Ryan CJ, Lara P, Beer T, Witte O, Baertsch R, Stuart J. 760PDNEUROENDOCRINE PROSTATE CANCER (NEPC) IN PATIENTS (PTS) WITH METASTATIC CASTRATION RESISTANT PROSTATE CANCER (MCRPC) RESISTANT TO ABIRATERONE (ABI) OR ENZALUTAMIDE (ENZ): PRELIMINARY RESULTS FROM THE SU2C/PCF/AACR WEST COAST PROSTATE CANCER DREAM TEAM (WCDT). Annals of Oncology : Official Journal of the European Society For Medical Oncology. 25: iv258. PMID 28172078 DOI: 10.1093/Annonc/Mdu336.8  0.357
2014 Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, ... ... Baertsch R, et al. Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Research. 42: D865-72. PMID 24217909 DOI: 10.1093/Nar/Gkt1059  0.693
2014 Alumkal JJ, Heiser L, Beer TM, Small EJ, Baertsch R, Stuart J, King C, Korkola J, Cetnar J, Graff JN, Thomas G, Ryan CW, Toschi A, Youngren J, Tucker E, et al. Identifying enzalutamide resistance mechanisms in men with castration-resistant prostate cancer. Journal of Clinical Oncology. 32. DOI: 10.1200/Jco.2014.32.15_Suppl.Tps5104  0.307
2014 Thomas G, Youngren J, Ryan CJ, Beer TM, Gleave ME, Evans CP, Stuart J, Rettig M, Toschi A, Foye A, Alumkal JJ, Corless CL, Neff T, Baertsch R, Huang J, et al. Molecular profiling of metastatic castration-resistant prostate cancer (mCRPC): Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT). Journal of Clinical Oncology. 32: 5088-5088. DOI: 10.1200/Jco.2014.32.15_Suppl.5088  0.706
2014 Bivol A, Baertsch R, Sokolov A, Paull E, Newton Y, Goldstein TC, Foye A, Pourmand N, Youngren J, Parulkar R, Lopez A, de Vere White R, Alumkal JJ, Toschi A, Beer TM, et al. Pathway-based signature analysis of RNA-seq data to reveal new targetable avenues for metastatic castration-resistant prostate cancer (mCRPC) patients (pts): Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT). Journal of Clinical Oncology. 32: 11078-11078. DOI: 10.1200/Jco.2014.32.15_Suppl.11078  0.666
2014 Bivol A, Graim K, Paull E, Carlin D, Baertsch R, Sokolov A, Stuart J. Abstract 4177: Identification of pathways relevant for metastatic site prediction in prostate cancer Cancer Research. 74: 4177-4177. DOI: 10.1158/1538-7445.Am2014-4177  0.367
2013 Febbo PG, Goldstein TC, Baertsch R, Youngren J, Newton Y, Bivol A, Small EJ, Stuart JM. Identification of polo-like kinase 1 (PLK1) in aggressive prostate cancer by paradigm analysis. Journal of Clinical Oncology. 31: 5006-5006. DOI: 10.1200/Jco.2013.31.15_Suppl.5006  0.723
2013 Goldstein TC, Baertsch R, Febbo PG, Stuart J, Haussler D. Abstract 60: The MedBook network for cancer precision medical care. Cancer Research. 73: 60-60. DOI: 10.1158/1538-7445.Am2013-60  0.686
2009 Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, ... ... Baertsch R, et al. The completion of the Mammalian Gene Collection (MGC). Genome Research. 19: 2324-33. PMID 19767417 DOI: 10.1101/Gr.095976.109  0.725
2009 Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, ... Baertsch R, et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Research. 19: 1316-23. PMID 19498102 DOI: 10.1101/Gr.080531.108  0.699
2009 Churakov G, Kriegs JO, Baertsch R, Zemann A, Brosius J, Schmitz J. Mosaic retroposon insertion patterns in placental mammals. Genome Research. 19: 868-75. PMID 19261842 DOI: 10.1101/Gr.090647.108  0.39
2008 Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J. Retrocopy contributions to the evolution of the human genome. Bmc Genomics. 9: 466. PMID 18842134 DOI: 10.1186/1471-2164-9-466  0.681
2008 Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding Bioinformatics. 24: 637-644. PMID 18218656 DOI: 10.1093/Bioinformatics/Btn013  0.737
2008 Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, et al. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Research. 36: D773-9. PMID 18086701 DOI: 10.1093/Nar/Gkm966  0.852
2007 Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, et al. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research. 17: 1797-808. PMID 17984227 DOI: 10.1101/Gr.6761107  0.856
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Baertsch R, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.836
2007 Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, et al. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Research. 17: 839-51. PMID 17568002 DOI: 10.1101/Gr.5586307  0.653
2007 Zhang Y, Luoh SM, Hon LS, Baertsch R, Wood WI, Zhang Z. GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database. Nucleic Acids Research. 35: W152-8. PMID 17545196 DOI: 10.1093/Nar/Gkm381  0.478
2007 Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, ... ... Baertsch R, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science (New York, N.Y.). 316: 222-34. PMID 17431167 DOI: 10.1126/Science.1139247  0.835
2007 Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, ... ... Baertsch R, et al. The UCSC genome browser database: update 2007. Nucleic Acids Research. 35: D668-73. PMID 17142222 DOI: 10.1093/Nar/Gkl928  0.827
2006 Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, Haussler D. Forces shaping the fastest evolving regions in the human genome. Plos Genetics. 2: e168. PMID 17040131 DOI: 10.1371/Journal.Pgen.0020168  0.818
2006 Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Research. 34: D590-8. PMID 16381938 DOI: 10.1093/Nar/Gkj144  0.817
2006 Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM. The UCSC Archaeal Genome Browser. Nucleic Acids Research.. 34: D407-410. PMID 16381898 DOI: 10.1093/Nar/Gkj134  0.791
2005 Robertson MP, Igel H, Baertsch R, Haussler D, Ares M, Scott WG. The structure of a rigorously conserved RNA element within the SARS virus genome. Plos Biology. 3: e5. PMID 15630477 DOI: 10.1371/Journal.Pbio.0030005  0.595
2004 Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Research. 14: 708-15. PMID 15060014 DOI: 10.1101/Gr.1933104  0.824
2004 Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE. Hotspots of mammalian chromosomal evolution. Genome Biology. 5: R23. PMID 15059256 DOI: 10.1186/Gb-2004-5-4-R23  0.689
2004 Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, ... ... Baertsch R, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/Nature02426  0.856
2003 Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proceedings of the National Academy of Sciences of the United States of America. 100: 11484-9. PMID 14500911 DOI: 10.1073/Pnas.1932072100  0.744
2003 Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Research. 13: 103-7. PMID 12529312 DOI: 10.1101/Gr.809403  0.743
2003 Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ. The UCSC Genome Browser Database. Nucleic Acids Research. 31: 51-4. PMID 12519945 DOI: 10.1093/Nar/Gkg129  0.825
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262  0.816
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