Difference between pages "Publications" and "Lab Members"

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* '''Identification of predictive cis-regulatory elements using a discriminative objective function and dynamic search spaces.''' Karnik, R, and Beer MA. 2012 (submitted)
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__NOTOC__
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==PI==
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[[Users:Mbeer|Mike Beer (with short hair)]]
  
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* '''kmer-SVM: a Web-based Toolkit for the Computational Identification of Predictive Regulatory Sequence Features in Genomic Datasets.''' Fletez-Brant C*, Lee D*, McCallion AS and Beer MA. 2012. (submitted)
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[[File:Beer_m.gif]] [[File:group_pic.jpg|350px]]
  
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* '''[http://genome.cshlp.org/content/early/2012/09/26/gr.139360.112 Integration of ChIP-seq and Machine Learning Reveals Enhancers and a Predictive Regulatory Sequence Vocabulary in Melanocytes.]''' Gorkin DU, Lee D, Reed X, Fletez-Brant C, Blessling SL, Loftus SK, Beer MA, Pavan WJ, and McCallion AS. 2012. Genome Research (published in advance September 27, 2012)
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==Postdocs==
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* Ayoti Patra
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[[File:Ayoti.png|80x160]]
  
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* '''[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038695 Group Normalization for Genomic Data.]''' Ghandi M, and Beer MA. 2012. PLoS ONE 7:e38695.
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==Graduate students==
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* Dustin Shigaki
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* Wang Xi
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* Jin-Woo Oh
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* Milad Razavi Mohseni
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* Nick Vulpescu (rotation)
  
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/21875935 Discriminative prediction of mammalian enhancers from DNA sequence.]''' Lee D, Karchin R, and Beer MA. 2011. Genome Research 21:2167 –2180.
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==Current Undergraduates==
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* Gary Yang
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* Deepak Manda
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* Alex Chang
  
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/19253296 Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach.]''' Yang Y, Chaerkady R, Beer MA, Mendell JT, and Pandey A. 2009. Proteomics 9:1374–1384.
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==Former graduate students==
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* Paul Michel (summer MD genomics rotation)
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* [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&hl=en Dongwon Lee] (now at Boston Children's Hospital and Harvard Medical School)
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* Kipper Fletez-Brant (HG rotation student, now at 23andMe)
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* Mahmoud Ghandi (now at Third Rock Ventures Newco)
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* [http://www.genebrew.com Rahul Karnik] (now Principal Scientist at Omega Therapeutics)
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* Jun Kyu Rhee (now at Korea Institute of Science and Technology)
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* Donavan Cheng (now Director, Population Genomics at Illumina)
  
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/19211792 Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation.]''' Chang T-C, Zeitels LR, Hwang H-W, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, et al. 2009. PNAS 106:3384–3389.
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==Former Undergraduates==
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* Richard Liu
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/18071029  Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b.]''' McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, and McCallion AS. 2008. Genome Research 18:252 –260.
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* Nico Eng
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* Michael Mudgett
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/17540599 Transactivation of miR-34a by p53 Broadly Influences Gene Expression and Promotes Apoptosis.]''' Chang T-C, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, et al. 2007. Molecular Cell 26: 745–752.
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* Felix Yu
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/15870260 Functional Characterization of a Novel Ku70/80 Pause Site at the H19/Igf2 Imprinting Control Region.]''' Katz DJ, Beer MA, Levorse JM, and Tilghman SM. 2005. Mol Cell Biol 25:3855–3863.
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* Amy Xiao
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* Sunny Thodupunuri
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/14672978 Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation.]''' Pritsker M, Liu Y-C, Beer MA, and Tavazoie S. 2004. Genome Research 14:99–108.
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* Tianyue Ou
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence.]''' Beer MA, Tavazoie S. 2004. Cell 117:185–198.
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* Ganesh Arvapalli
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* Zachary Heiman
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* Gianluca Silva Croso
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* Kendrick Hougen
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* Nole Lin
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* Ashutosh Jindal
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* Kyle Xiong
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* Ben Strober
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* Alessandro Asoni
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* Billy Kang
 +
* John Lee
 +
* Andrew Pao
 +
* Tuo Li
 +
* Peter Li
 +
* Juinting Chiang

Revision as of 22:04, 30 November 2020

PI

Mike Beer (with short hair)

Beer m.gif Group pic.jpg

Postdocs

  • Ayoti Patra

80x160

Graduate students

  • Dustin Shigaki
  • Wang Xi
  • Jin-Woo Oh
  • Milad Razavi Mohseni
  • Nick Vulpescu (rotation)

Current Undergraduates

  • Gary Yang
  • Deepak Manda
  • Alex Chang

Former graduate students

  • Paul Michel (summer MD genomics rotation)
  • Dongwon Lee (now at Boston Children's Hospital and Harvard Medical School)
  • Kipper Fletez-Brant (HG rotation student, now at 23andMe)
  • Mahmoud Ghandi (now at Third Rock Ventures Newco)
  • Rahul Karnik (now Principal Scientist at Omega Therapeutics)
  • Jun Kyu Rhee (now at Korea Institute of Science and Technology)
  • Donavan Cheng (now Director, Population Genomics at Illumina)

Former Undergraduates

  • Richard Liu
  • Nico Eng
  • Michael Mudgett
  • Felix Yu
  • Amy Xiao
  • Sunny Thodupunuri
  • Tianyue Ou
  • Ganesh Arvapalli
  • Zachary Heiman
  • Gianluca Silva Croso
  • Kendrick Hougen
  • Nole Lin
  • Ashutosh Jindal
  • Kyle Xiong
  • Ben Strober
  • Alessandro Asoni
  • Billy Kang
  • John Lee
  • Andrew Pao
  • Tuo Li
  • Peter Li
  • Juinting Chiang
Retrieved from "http://beerlab.org/index.php?title=Publications&oldid=219"