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 server for identifying predictive regulatory sequence features in genomic datasets.''' Fletez-Brant C<sup>*</sup>, Lee D<sup>*</sup>, McCallion AS and Beer MA. 2013. Nucleic Acids Research Web Server Issue (accepted)
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[[File:Beer_m.gif]] [[File:group_pic.jpg|350px]]
  
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* '''Robust k-mer Frequency Estimation Using Gapped k-mers.''' Ghandi M, Mohammad-Noori M, and Beer MA. 2012. Journal of Mathematical Biology. (accepted)
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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.horizonpress.com/genomeanalysis Mammalian Enhancer Prediction.]''' Lee D, Beer MA. 2014. Genome Analysis: Current Procedures and Applications (in press)
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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/23019145 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 22:2290-2301.
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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/22912661 Group Normalization for Genomic Data.]''' Ghandi M, and Beer MA. 2012. PLoS ONE 7:e38695.
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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/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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==Former Undergraduates==
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* Richard Liu
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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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* Nico Eng
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* Michael Mudgett
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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, Thomas-Tikhonenko A, and Mendell JT. 2009. PNAS 106:3384-3389.
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* Felix Yu
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* Amy Xiao
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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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* Sunny Thodupunuri
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* Tianyue Ou
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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,  Arking DE, Beer MA, Maitra A, and Mendell JT. 2007. Molecular Cell 26: 745-752.
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* Ganesh Arvapalli
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* Zachary Heiman
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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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* Gianluca Silva Croso
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* Kendrick Hougen
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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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* Nole Lin
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* Ashutosh Jindal
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence.]''' Beer MA and Tavazoie S. 2004. Cell 117:185-198.
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* Kyle Xiong
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* Ben Strober
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* Alessandro Asoni
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* Billy Kang
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* John Lee
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* Andrew Pao
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* Tuo Li
 +
* Peter Li
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* 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"