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Items: 1 to 20 of 64

1.

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.

PMID:
29988122
2.

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.

3.

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.

4.

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.

5.

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.

6.

Artery Tertiary Lymphoid Organs Control Multilayered Territorialized Atherosclerosis B-Cell Responses in Aged ApoE-/- Mice.

Srikakulapu P, Hu D, Yin C, Mohanta SK, Bontha SV, Peng L, Beer M, Weber C, McNamara CA, Grassia G, Maffia P, Manz RA, Habenicht AJ.

Arterioscler Thromb Vasc Biol. 2016 Jun;36(6):1174-85. doi: 10.1161/ATVBAHA.115.306983. Epub 2016 Apr 21. Erratum in: Arterioscler Thromb Vasc Biol. 2016 Jul;36(7):e62.

7.

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.

8.

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.

9.

Folate Receptor-Targeted Dendrimer-Methotrexate Conjugate for Inflammatory Arthritis.

Qi R, Majoros I, Misra AC, Koch AE, Campbell P, Marotte H, Bergin IL, Cao Z, Goonewardena S, Morry J, Zhang S, Beer M, Makidon P, Kotlyar A, Thomas TP, Baker JR Jr.

J Biomed Nanotechnol. 2015 Aug;11(8):1431-41.

PMID:
26295143
10.

Artery Tertiary Lymphoid Organs Control Aorta Immunity and Protect against Atherosclerosis via Vascular Smooth Muscle Cell Lymphotoxin ╬▓ Receptors.

Hu D, Mohanta SK, Yin C, Peng L, Ma Z, Srikakulapu P, Grassia G, MacRitchie N, Dever G, Gordon P, Burton FL, Ialenti A, Sabir SR, McInnes IB, Brewer JM, Garside P, Weber C, Lehmann T, Teupser D, Habenicht L, Beer M, Grabner R, Maffia P, Weih F, Habenicht AJ.

Immunity. 2015 Jun 16;42(6):1100-15. doi: 10.1016/j.immuni.2015.05.015.

11.

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.

12.

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, Guig├│ R, Gingeras TR.

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

13.

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.

14.

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.

15.

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.

16.

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.

17.

Treatment of biopsy and culture negative Mycobacterium marinum: diagnostic and therapeutic considerations.

Tenbrick P, Beer M, Beer K.

J Drugs Dermatol. 2014 Feb;13(2):204-6.

PMID:
24509973
18.

Advanced basal cell carcinoma: therapeutic options and considerations for patient care. Introduction.

Beer KR, Beer MS.

J Drugs Dermatol. 2013 Oct;12(10 Suppl):s146. No abstract available.

PMID:
24085059
19.

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.

20.

Granuloma annulare masquerading as erythema multiforme.

Beer K, Beer MS, Appelbaum D.

J Drugs Dermatol. 2013 Jun 1;12(6):694-7.

PMID:
23839189

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