Difference between revisions of "Publications"

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Full publication list on '''[https://scholar.google.com/citations?hl=en&user=9aH8_eEAAAAJ google scholar]'''.
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* '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''
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* '''[https://www.nature.com/articles/s41467-024-50708-z Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals.]''' Oh JW and Beer MA. Nature Communications 2024.
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* '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023 '''[https://beerlab.org/papers/2023%20NG.pdf pdf]'''
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* '''[https://www.nature.com/articles/s41467-021-21368-0 Loop competition and extrusion model predicts CTCF interaction specificity.]''' Xi W, Beer MA.  Nature Comms. 2021.
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* '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D.  Ann. Rev. Genomics and Human Genetics 2020.
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* '''[https://www.nature.com/articles/s41586-020-2493-4 Expanded encyclopaedias of DNA elements in the human and mouse genomes.]''' ENCODE Project Consortium.  Nature 2020.
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* '''[https://www.jci.org/articles/view/126726 Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer.]''' Xing M, Ooi WF, Tan J, Qamra A, Lee PH, Li Z, Xu C, Padmanabhan N, Lim JQ, Guo YA, Yao X, Amit M, Ng LM, Sheng T, Wang J, Huang KK, Anene-Nzelu CG, Ho SWT, Ray M, Ma L, Fazzi G, Lim KJ, Wijaya GC, Zhang S, Nandi T, Yan T, Chang MM, Das K, Isa ZFA, Wu J, Yean PPS, Lam YN, Lin JS, Tay ST, Lee M, Keng ATL, Ong X, White K, Rozen SG, Beer MA, Foo RSY, Grabsch H, Skanderup AJ, Li S, Teh BT, Tan P. J. Clin. Invest. 2020
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* '''[https://www.nature.com/articles/s41588-019-0408-9 Genome-scale screens uncover JNK/JUN signaling as a key barrier from pluripotency to human endoderm differentiation.]''' Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh C-L, Yang D, Crespo M, Shukla A, Xiang Q, Dundar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massague J, Garippa R, Evans T, Beer MA, and Huangfu D. Nature Genetics 2019.
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* '''[https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, Adato O, Adhikar A, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar D, Schubach M, Xiong C, Yan Z, Boyle A, Kreimer A, Kulakovskiy IV, Reid J, Unger R, Yosef N, Shendure J, Ahituv N, Kircher M, and Beer MA.  Human Mutation 2019.  [http://www.beerlab.org/deltasvm_models (models)]
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* '''[https://stm.sciencemag.org/content/11/497/eaaw0790.abstract Epigenetic activation and memory at a novel TGFβ2 enhancer in systemic sclerosis fibroblasts.]''' Shin JY, Beckett JD, Shah A, McMahan Z, Paik J, Sampedro MM, MacFarlane EG, Beer MA, Warren D, Wigley FM, and Dietz HC.  Science Translational Medicine 2019.
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* '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy.]''' Xi, W and Beer, MA.  PLOS Comp Biol 2018.
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* '''[https://www.sciencedirect.com/science/article/pii/S0002929718303707 Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons.]''' McClymont SA, Hook PW, Soto AI, Reed X, Law WD, Kerans SJ, Waite EL, Briceno NJ, Thole JF, Heckman MG, Diehl NN, Wszolek  ZK, Moore CD, Zhu H, Akiyama JA, Dickel DE, Visel A, Pennacchio LA, Ross OA, Beer MA, & McCallion AS. Am. Jour. Human Genetics 2018
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* '''[https://www.nature.com/articles/s41588-018-0156-2 Genetic determinants of co-accessible chromatin regions in activated T cells across humans.]''' Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang S-C, Durand NC, Feng T, De Jager PL, Chang HY, Lieberman Aiden E, Benoist C, Beer MA, Ye CJ & Regev A.  Nature Genetics 2018.
  
 
* '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23185/full Predicting enhancer activity and variant impact using gkm-SVM.]''' Beer, MA.  Human Mutation 2017.
 
* '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23185/full Predicting enhancer activity and variant impact using gkm-SVM.]''' Beer, MA.  Human Mutation 2017.
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* '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170403 Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X.]''' Migeon BR, Beer MA, and Bjornsson HT. Plos ONE 2017.
 
* '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170403 Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X.]''' Migeon BR, Beer MA, and Bjornsson HT. Plos ONE 2017.
  
* '''[http://bioinformatics.oxfordjournals.org/content/early/2016/05/05/bioinformatics.btw203 gkmSVM: an R package for gapped-kmer SVM.]''' [[Media:Bioinformatics-2016-Ghandi-bioinformatics-btw203.pdf|pdf]] [[Media:Tutorial.pdf|tutorial]] Ghandi, M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, and Beer MA. Bioinformatics 2016.
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* '''[http://bioinformatics.oxfordjournals.org/content/early/2016/05/05/bioinformatics.btw203 gkmSVM: an R package for gapped-kmer SVM.]''' [[Media:Bioinformatics-2016-Ghandi-bioinformatics-btw203.pdf|pdf]] [[tutorial]] Ghandi, M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, and Beer MA. Bioinformatics 2016.
  
 
* '''[http://elifesciences.org/content/5/e11613v1 Epigenomic landscapes of retinal rods and cones.]''' Mo, A, Luo, C, Davis, FP, Mukamel, EA, Henry, GL, Nery JR, Urich, MA, Picard, S, Lister, R, Eddy, SR, Beer, MA, Ecker, JR, and Nathans, J. eLife 2016.
 
* '''[http://elifesciences.org/content/5/e11613v1 Epigenomic landscapes of retinal rods and cones.]''' Mo, A, Luo, C, Davis, FP, Mukamel, EA, Henry, GL, Nery JR, Urich, MA, Picard, S, Lister, R, Eddy, SR, Beer, MA, Ecker, JR, and Nathans, J. eLife 2016.
  
* '''[http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3331.html A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.
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* '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.
  
 
* '''[http://www.ncbi.nlm.nih.gov/pubmed/25582907 Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.]''' Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin, A, Tanzer A, Lagarde J, Zaleski C, See L-H, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Nat. Comm 2015.
 
* '''[http://www.ncbi.nlm.nih.gov/pubmed/25582907 Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.]''' Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin, A, Tanzer A, Lagarde J, Zaleski C, See L-H, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Nat. Comm 2015.

Latest revision as of 15:19, 1 August 2024

Full publication list on google scholar.

  • Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer. Xing M, Ooi WF, Tan J, Qamra A, Lee PH, Li Z, Xu C, Padmanabhan N, Lim JQ, Guo YA, Yao X, Amit M, Ng LM, Sheng T, Wang J, Huang KK, Anene-Nzelu CG, Ho SWT, Ray M, Ma L, Fazzi G, Lim KJ, Wijaya GC, Zhang S, Nandi T, Yan T, Chang MM, Das K, Isa ZFA, Wu J, Yean PPS, Lam YN, Lin JS, Tay ST, Lee M, Keng ATL, Ong X, White K, Rozen SG, Beer MA, Foo RSY, Grabsch H, Skanderup AJ, Li S, Teh BT, Tan P. J. Clin. Invest. 2020
  • A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies. Khanna H, Davis EE, Murga-Zamalloa CA, Estrada-Cuzcano A, Lopez I, den Hollander AI, Zonneveld MN, Othman MI, Waseem N, Chakarova CF, Maubaret C, Diaz-Font A, MacDonald I, Muzny DM, Wheeler DA, Morgan M, Lewis LR, Logan CV, Tan PL, Beer MA, Inglehearn CF, Lewis RA, Jacobson SG, Bergmann C, Beales PL, Attié-Bitach T, Johnson CA, Otto EA, Bhattacharya SS, Hildebrandt F, Gibbs RA, Koenekoop RK, Swaroop A, Katsanis N. 2009. Nat Genet. 41:739-45.



For a full list including my prior work in simulations of plasma turbulence, see my google scholar page.