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Brenner Lab Academic Alumni & Awardees

Awards received by Brenner lab researchers during or after their tenure in the research group.

Graduate students

• Andrew Sharo. Apr 2017–December 2021. StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants. Awards: National Science Foundation Postdoctoral Research Fellowship 2021
• Anna Desai. Aug 2011–ongoing. Regulation of pre-mRNA splicing.  Awards: Kosciuzsko Foundation Tuition Scholarship, 2012.
• Courtney French. Apr 2011–Mar 2017. Characterizing nonsense-mediated mRNA decay and alternative splicing throughout eukaryotes with RNA-seq analysis. Awards: National Science Foundation Graduate Research Fellowship Honorable Mention 2011; 3rd Place Student Talks 2011 Computational and Genomic Biology Retreat, UC Berkeley; 3rd place poster 2012 Bay Area RNA Club, UCSF; National Defense Science & Engineering Fellowship, 2012.
• Angela Brooks. Apr 2006–May 2011 (graduate student); May 2011–Aug 2011 (postdoc). Regulation of pre-mRNA splicing. Currently: Postdoctoral researcher, Broad Institute. Awards: Chancellors’ Fellowship for Graduate Studies, 2005; NSF Graduate Research Fellowship, 2007; 1st place poster, Genetics, Genomics & Development retreat, 2007; 1st place poster, Computational and Genomic Biology retreat, 2006; 3rd place poster, Computational and Genomic Biology retreat, 2009; Best Speaker, Bay Area RNA Club conference, 2009; Damon Runyon Fellowship Award, 2012.
• David Soergel. Aug 2004–Dec 2010 (graduate student); Jan 2011–Jun 2011 (postdoc). Interpreting metagenomic data using oligonucleotide signatures. Currently: Postdoctoral researcher, University of Massachusetts, Amherst. Awards: HHMI graduate fellowship, 2003; Tien Scholars graduate fellowship, 2008 & 2009.
• Kasper Daniel Hansen, affiliated graduate student, 2007–2009. Transcriptome sequence analysis of alternative splicing.  (Jointly supervised with Sandrine Dudoit, Biostatistics.) Currently: Postdoctoral researcher, Johns Hopkins University. Awards: 3rd place poster, Computational and Genomic Biology retreat, 2007; 2nd place poster, MGED, 2010.
• Liana Lareau. May 2003–2008 (graduate student); Jun 2008–Dec 2008 (postdoc). The evolutionary relationship of alternative splicing and nonsense-mediated decay. Currently: Postdoctoral researcher, Stanford University. Awards: 1st place poster, Computational and Genomic Biology retreat, 2006 & 2008; NSF postdoctoral fellowship, 2009; Damon Runyon Fellowship, 2009.
• Barbara Engelhardt, affiliated graduate student, Jul 2002–Dec 2007. Inferring protein molecular function by applying Bayesian statistical methods to phylogenomics models. (Supervised with Michael Jordan, EECS.) Currently: Assistant Professor, Duke University. Awards: Fitch Prize for best student presentation, SMBE, 2004; 1st place poster, Computational & Genomic Biology retreat, 2005; Anita Borg Google Scholarship, 2005; Distinguished Departmental Postdoctoral Fellowship, 2008; NIH NHGRI Pathway to Independence (K99/R00), 2011.
• Benjamin Lewis. Jan 2002-Dec 2002. Computational molecular biology of genome expression and regulation. (Jointly supervised with Michael Eisen, MCB.) Currently: Graduate student, MIT (on leave).
• Richard (Ed) Green. Jul 2000–May 2005. Alternative splicing and protein structure. Currently: Assistant Professor, UC Santa Cruz. Awards: 2nd place poster, Computational & Genomic Biology retreat, 2005; NSF postdoctoral fellowship. 2005, 3rd place poster, Computational and Genomic Biology retreat, 2008; Sloan Scholar, 2011; Searle Scholar, 2011; AAAS Newcomb Cleveland Prize, 2011.  

Postdoctoral and visiting researchers

• James Lloyd. May 2014–June 2017. Alternative splicing and nonsense-mediate decay.
• Gang Wei [visiting researcher]. Feb 2010–Mar 2012. Alternative splicing and nonsense-mediated decay. Awards: Tang Distinguished Scholar, 2009.
• Susanna Repo. Sep 2008–Feb 2012. Phylogenomic protein function prediction and metagenomic data. Awards: Research scholarship, Åbo Akademi University Endowment, 2008; Academy of Finland postdoctoral fellowship, 2009; Marie Curie International Outgoing Fellowship, 2009.
• Maxim Shatsky. Jul 2006–Jan 2012. Affiliated scientist, LBL, Feb 2012-ongoing. Protein electron microscopy structure analysis; integrative protein-protein interaction analysis.
• Ameet Talwalker. Aug 2010–Jan 2012. Protein function prediction. Awards: Genentech Fellowship, 2011; NSF Computing Innovation Postdoctoral Fellowship, 2012.
• John-Marc Chandonia [scientist, LBL]. Oct 2005–2007. Affiliated scientist, LBL, Jan 2008-ongoing Structural genomics & astral compendium.
• Neelendu Dey. Jul 2008–Aug 2011. Genomics-based analysis of microbiota of Crohn’s ileitis. Currently: Instructor in Medicine/Gastroenterology, Washington University. Awards: NIH/NIDDK Clinical Loan Repayment Program Award, 2009.
• Gaurav Pandey. Jun 2010–Jun 2011. Protein function prediction.
• Orna Mizrahi-Man. Jul 2008–Dec 2010. Alternative splicing, nonsense-mediated mRNA decay, and ultraconservation. Awards: Sara Lee Schupf Postdoctoral Award, 2008.
• Reece Hart [associate researcher]. Sep 2009–Aug 2010. Genome Commons.
• Robert Edgar [visiting researcher]. Aug 2003-Nov 2005; Feb 2008-ongoing. Alignment algorithms. Awards: Best paper, ISMB, 2004.
• Dan Liang. Sep 2007–Sep 2008. Alternative splicing of SR proteins.
• Degui Zhi. Mar 2006-Feb 2009. Comparison and classification of protein structure. Currently: Assistant professor, University of Alabama, Birmingham. Awards: Best poster, RECOMB 2007; NIH K99/R00 Pathway to Independence grant, 2007.
• Kentaro Tomii. Jun 2000-Mar 2001. Threading for structure prediction. [visiting researcher] Nov 2007-Nov 2008. Metagenomics alignment methodology. Currently: Research Scientist, CBRC, AIST, Japan.
• Dan Liang. Sep 2007-Sep 2008. Alternative splicing of SR proteins.
• Maki Inada. Jul 2005-Jun 2007. Conserved unproductive splicing in the SR protein family. Currently: Assistant professor, Ithaca College.
• Qi Meng. Mar 2005-Jan 2007. Experimental studies of nonsense-mediated mRNA decay. Currently: Associate specialist, Marks lab, UCSF.
• Susan Mashiyama. Jan 2005-Jul 2006. Classification of ancient protein evolution relationships using kernels. Currently: Postdoctoral researcher, McKerrow and Babbitt labs, UCSF. Awards: 1st place poster, Computational & Genomic Biology retreat, 2006; PhRMA postdoctoral fellowship, 2008.
• Marcin Joachimiak. Apr 2003-Jul 2006. Computational prediction of protein and DNA function. Currently: Computational scientist, Arkin Lab, LBNL.
• Donna Hendrix. Jul 2003-Jun 2006. Classification of three-dimensional RNA structure. Currently: Managing Director, QB3, UC Berkeley.
• Emma Hill. Mar 2002–Apr 2005. Structure analysis of Nudix proteins. Currently: Administrative head, Dundee Cancer Centre, University of Dundee.
• Gavin Crooks. Nov 2001–Dec 2004. Threading with experimental restraints. Currently: Senior Scientist, Physical Biosciences, LBNL. Awards: Sloan Postdoctoral Fellowship, 2002; Divisional Fellow, Physical Biosciences, LBNL, 2005; Presidential Early Career  for Scientists and Engineers Award, 2010.
• Rajiv Bhatnagar. Jul 2003-Jul 2004. Biological and medical implications of nonsense-mediated mRNA decay. Currently: Staff physician, Palo Alto Medical Foundation.
• Makio Tamura. May 2001-May 2004. SCOR database. Currently: Researcher, Procter & Gamble.
• David Konerding. Oct 2002-Jul 2003. Structural genomics. Currently: Senior engineer, Google.
• Peter Klosterman. Jun 2000-Sep 2001. RNA structure analysis. Currently: Postdoctoral researcher, UCSF.
• Nigel Walker. May 2000-Dec 2000. ASTRAL database. Currently: Database administrator & web designer at University of Oregon.

Other trainees who have won awards

• Lee Chae, affiliated graduate student, 2003-2008. Awards: 1st place oral presentation, Plant Genomics, 2003; best talk, Plant and Microbial Biology retreat, 2004.
• David Sivak, rotation graduate student, 2003. Awards: DOD/NDSEG fellowship, 2004; NSF fellowship, 2004.
• Tyler Hillman, undergraduate researcher, 2002-2004. Currently: Graduate student, Stanford University. Awards: Nominated for Barry Goldwater Scholarship, 2003; HHMI medical fellow, 2005.
• Daniel Kluesing, undergraduate researcher, 2004-2007. Currently: Graduate student, Stanford University. Awards: URAP Summer Employment Award, 2006.
• Anna Podgornaia, undergraduate researcher, 2008-2009. Currently: Graduate student, MIT. Awards: Kazuo Geral Yanaba & Ting Jung Memorial Fund Prize, 2009.