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Items: 42


Epigenetic activation and memory at a TGFB2 enhancer in systemic sclerosis.

Shin JY, Beckett JD, Bagirzadeh R, Creamer TJ, Shah AA, McMahan Z, Paik JJ, Sampedro MM, MacFarlane EG, Beer MA, Warren D, Wigley FM, Dietz HC.

Sci Transl Med. 2019 Jun 19;11(497). pii: eaaw0790. doi: 10.1126/scitranslmed.aaw0790.


Genome-scale screens identify JNK-JUN signaling as a barrier for pluripotency exit and endoderm differentiation.

Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh CL, Yang D, Crespo M, Shukla A, Xiang Q, Dündar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massagué J, Garippa R, Evans T, Beer MA, Huangfu D.

Nat Genet. 2019 Jun;51(6):999-1010. doi: 10.1038/s41588-019-0408-9. Epub 2019 May 20.


Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.

Shigaki D, Adato O, Adhikari AN, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar DD, Schubach M, Xiong C, Yan Z, Boyle AP, Kreimer A, Kulakovskiy IV, Reid J, Unger R, Yosef N, Shendure J, Ahituv N, Kircher M, Beer MA.

Hum Mutat. 2019 Sep;40(9):1280-1291. doi: 10.1002/humu.23797. Epub 2019 Jun 23.


Local epigenomic state cannot discriminate interacting and non-interacting enhancer-promoter pairs with high accuracy.

Xi W, Beer MA.

PLoS Comput Biol. 2018 Dec 18;14(12):e1006625. doi: 10.1371/journal.pcbi.1006625. eCollection 2018 Dec.


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 J Hum Genet. 2018 Dec 6;103(6):874-892. doi: 10.1016/j.ajhg.2018.10.018. Epub 2018 Nov 29.


Quantifying the unquantifiable: why Hymenoptera, not Coleoptera, is the most speciose animal order.

Forbes AA, Bagley RK, Beer MA, Hippee AC, Widmayer HA.

BMC Ecol. 2018 Jul 12;18(1):21. doi: 10.1186/s12898-018-0176-x.


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 SC, Durand NC, Feng T, De Jager PL, Chang HY, Aiden EL, Benoist C, Beer MA, Ye CJ, Regev A.

Nat Genet. 2018 Aug;50(8):1140-1150. doi: 10.1038/s41588-018-0156-2. Epub 2018 Jul 9.


A small protein probe for correlated microscopy of endogenous proteins.

de Beer MA, Kuipers J, van Bergen En Henegouwen PMP, Giepmans BNG.

Histochem Cell Biol. 2018 Mar;149(3):261-268. doi: 10.1007/s00418-018-1632-6. Epub 2018 Jan 11.


Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X.

Migeon BR, Beer MA, Bjornsson HT.

PLoS One. 2017 Apr 12;12(4):e0170403. doi: 10.1371/journal.pone.0170403. eCollection 2017.


Predicting gene expression in massively parallel reporter assays: A comparative study.

Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Tewhey R, Sabeti PC, Goke J, Mueller NS, Kellis M, Kundaje A, Beer MA, Keles S, Gifford DK, Yosef N.

Hum Mutat. 2017 Sep;38(9):1240-1250. doi: 10.1002/humu.23197. Epub 2017 Mar 9.


The clinical anatomy of the insertion of the rotator cuff tendons.

Vosloo M, Keough N, De Beer MA.

Eur J Orthop Surg Traumatol. 2017 Apr;27(3):359-366. doi: 10.1007/s00590-017-1922-z. Epub 2017 Feb 16.


Predicting enhancer activity and variant impact using gkm-SVM.

Beer MA.

Hum Mutat. 2017 Sep;38(9):1251-1258. doi: 10.1002/humu.23185. Epub 2017 Mar 15.


gkmSVM: an R package for gapped-kmer SVM.

Ghandi M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, Beer MA.

Bioinformatics. 2016 Jul 15;32(14):2205-7. doi: 10.1093/bioinformatics/btw203. Epub 2016 Apr 19.


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, Nathans J.

Elife. 2016 Mar 7;5:e11613. doi: 10.7554/eLife.11613.


Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space.

Karnik R, Beer MA.

PLoS One. 2015 Oct 14;10(10):e0140557. doi: 10.1371/journal.pone.0140557. eCollection 2015.


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.

Nat Genet. 2015 Aug;47(8):955-61. doi: 10.1038/ng.3331. Epub 2015 Jun 15.


Association of HSD11B1 polymorphic variants and adipose tissue gene expression with metabolic syndrome, obesity and type 2 diabetes mellitus: a systematic review.

do Nascimento FV, Piccoli V, Beer MA, von Frankenberg AD, Crispim D, Gerchman F.

Diabetol Metab Syndr. 2015 Apr 28;7:38. doi: 10.1186/s13098-015-0036-1. eCollection 2015.


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 LH, 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 Commun. 2015 Jan 13;6:5903. doi: 10.1038/ncomms6903.


Comparison of the transcriptional landscapes between human and mouse tissues.

Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17224-9. doi: 10.1073/pnas.1413624111. Epub 2014 Nov 20.


A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.


Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis.

Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ.

Genome Res. 2014 Dec;24(12):1932-44. doi: 10.1101/gr.164178.113. Epub 2014 Oct 15.


Enhanced regulatory sequence prediction using gapped k-mer features.

Ghandi M, Lee D, Mohammad-Noori M, Beer MA.

PLoS Comput Biol. 2014 Jul 17;10(7):e1003711. doi: 10.1371/journal.pcbi.1003711. eCollection 2014 Jul. Erratum in: PLoS Comput Biol. 2014 Dec;10(12):e1004035.


Robust k-mer frequency estimation using gapped k-mers.

Ghandi M, Mohammad-Noori M, Beer MA.

J Math Biol. 2014 Aug;69(2):469-500. doi: 10.1007/s00285-013-0705-3. Epub 2013 Jul 17.


kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets.

Fletez-Brant C, Lee D, McCallion AS, Beer MA.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W544-56. doi: 10.1093/nar/gkt519. Epub 2013 Jun 14.


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, Bessling SL, Loftus SK, Beer MA, Pavan WJ, McCallion AS.

Genome Res. 2012 Nov;22(11):2290-301. doi: 10.1101/gr.139360.112. Epub 2012 Sep 27.


Group normalization for genomic data.

Ghandi M, Beer MA.

PLoS One. 2012;7(8):e38695. doi: 10.1371/journal.pone.0038695. Epub 2012 Aug 13.


Discriminative prediction of mammalian enhancers from DNA sequence.

Lee D, Karchin R, Beer MA.

Genome Res. 2011 Dec;21(12):2167-80. doi: 10.1101/gr.121905.111. Epub 2011 Aug 29.


Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome.

Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon WH, Joore J, Beer MA, Cope L, Pandey A.

J Proteomics Bioinform. 2011;4(2):22-35.


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.

Nat Genet. 2009 Jun;41(6):739-45. doi: 10.1038/ng.366. Epub 2009 May 10.


Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach.

Yang Y, Chaerkady R, Beer MA, Mendell JT, Pandey A.

Proteomics. 2009 Mar;9(5):1374-84. doi: 10.1002/pmic.200800551.


Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation.

Chang TC, Zeitels LR, Hwang HW, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, Mendell JT.

Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3384-9. doi: 10.1073/pnas.0808300106. Epub 2009 Feb 11.


Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b.

McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, McCallion AS.

Genome Res. 2008 Feb;18(2):252-60. Epub 2007 Dec 10.


Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis.

Chang TC, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, Mendell JT.

Mol Cell. 2007 Jun 8;26(5):745-52. Epub 2007 May 31.


Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region.

Katz DJ, Beer MA, Levorse JM, Tilghman SM.

Mol Cell Biol. 2005 May;25(10):3855-63.


Predicting gene expression from sequence.

Beer MA, Tavazoie S.

Cell. 2004 Apr 16;117(2):185-98.


The anatomy of the subscapularis tendon insertion as applied to rotator cuff repair.

Boon JM, de Beer MA, Botha D, Maritz NG, Fouche AA.

J Shoulder Elbow Surg. 2004 Mar-Apr;13(2):165-9.


Whole-genome discovery of transcription factor binding sites by network-level conservation.

Pritsker M, Liu YC, Beer MA, Tavazoie S.

Genome Res. 2004 Jan;14(1):99-108. Epub 2003 Dec 12.




J Med Soc N J. 1964 Oct;61:449-53. No abstract available.


Arrhenoblastoma of the ovary.


Am J Obstet Gynecol. 1953 Jan;65(1):208-10. No abstract available.


Pig face fetus, a teratological study.


Am J Obstet Gynecol. 1952 May;63(5):1157-61. No abstract available.


Full-term abdominal pregnancy with living mother and child.


N Y State J Med. 1951 May 1;51(9):1185-6. No abstract available.


Postpartum pelvic hematoma.


N Y State J Med. 1950 Sep 15;50(18):2205-6. No abstract available.


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