Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 47

1.

Single-Cell Transcriptome Analysis of CD34+ Stem Cell-Derived Myeloid Cells Infected With Human Cytomegalovirus.

Galinato M, Shimoda K, Aguiar A, Hennig F, Boffelli D, McVoy MA, Hertel L.

Front Microbiol. 2019 Mar 21;10:577. doi: 10.3389/fmicb.2019.00577. eCollection 2019.

2.

CRISPR-Cas9 interrogation of a putative fetal globin repressor in human erythroid cells.

Chung JE, Magis W, Vu J, Heo SJ, Wartiovaara K, Walters MC, Kurita R, Nakamura Y, Boffelli D, Martin DIK, Corn JE, DeWitt MA.

PLoS One. 2019 Jan 15;14(1):e0208237. doi: 10.1371/journal.pone.0208237. eCollection 2019.

3.

Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells.

DeWitt MA, Magis W, Bray NL, Wang T, Berman JR, Urbinati F, Heo SJ, Mitros T, Muñoz DP, Boffelli D, Kohn DB, Walters MC, Carroll D, Martin DI, Corn JE.

Sci Transl Med. 2016 Oct 12;8(360):360ra134.

4.

Functionally conserved enhancers with divergent sequences in distant vertebrates.

Yang S, Oksenberg N, Takayama S, Heo SJ, Poliakov A, Ahituv N, Dubchak I, Boffelli D.

BMC Genomics. 2015 Oct 30;16:882. doi: 10.1186/s12864-015-2070-7.

5.

piRNA-like small RNAs mark extended 3'UTRs present in germ and somatic cells.

Yamtich J, Heo SJ, Dhahbi J, Martin DI, Boffelli D.

BMC Genomics. 2015 Jun 16;16:462. doi: 10.1186/s12864-015-1662-6.

6.

Deep Sequencing of Serum Small RNAs Identifies Patterns of 5' tRNA Half and YRNA Fragment Expression Associated with Breast Cancer.

Dhahbi JM, Spindler SR, Atamna H, Boffelli D, Martin DI.

Biomark Cancer. 2014 Dec 8;6:37-47. doi: 10.4137/BIC.S20764. eCollection 2014.

7.

Now you see it: genome methylation makes a comeback in Drosophila.

Boffelli D, Takayama S, Martin DI.

Bioessays. 2014 Dec;36(12):1138-44. doi: 10.1002/bies.201400097. Epub 2014 Sep 12.

PMID:
25220261
8.

Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity.

Takayama S, Dhahbi J, Roberts A, Mao G, Heo SJ, Pachter L, Martin DI, Boffelli D.

Genome Res. 2014 May;24(5):821-30. doi: 10.1101/gr.162412.113. Epub 2014 Feb 20.

9.

Deficiency of MIWI2 (Piwil4) induces mouse erythroleukemia cell differentiation, but has no effect on hematopoiesis in vivo.

Jacobs JE, Wagner M, Dhahbi J, Boffelli D, Martin DI.

PLoS One. 2013 Dec 23;8(12):e82573. doi: 10.1371/journal.pone.0082573. eCollection 2013.

10.

Statin-induced changes in gene expression in EBV-transformed and native B-cells.

Bolotin E, Armendariz A, Kim K, Heo SJ, Boffelli D, Tantisira K, Rotter JI, Krauss RM, Medina MW.

Hum Mol Genet. 2014 Mar 1;23(5):1202-10. doi: 10.1093/hmg/ddt512. Epub 2013 Oct 30.

11.

A role for epigenetic inheritance in modern evolutionary theory? A comment in response to Dickins and Rahman.

Suter CM, Boffelli D, Martin DI.

Proc Biol Sci. 2013 Oct 2;280(1771):20130903; discussion 20131820. doi: 10.1098/rspb.2013.0903. Print 2013 Nov 22. No abstract available.

12.

5'-YRNA fragments derived by processing of transcripts from specific YRNA genes and pseudogenes are abundant in human serum and plasma.

Dhahbi JM, Spindler SR, Atamna H, Boffelli D, Mote P, Martin DI.

Physiol Genomics. 2013 Nov 1;45(21):990-8. doi: 10.1152/physiolgenomics.00129.2013. Epub 2013 Sep 10.

PMID:
24022222
13.

Activation-induced cytidine deaminase (AID) is necessary for the epithelial-mesenchymal transition in mammary epithelial cells.

Muñoz DP, Lee EL, Takayama S, Coppé JP, Heo SJ, Boffelli D, Di Noia JM, Martin DI.

Proc Natl Acad Sci U S A. 2013 Aug 6;110(32):E2977-86. doi: 10.1073/pnas.1301021110. Epub 2013 Jul 23.

14.

5' tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction.

Dhahbi JM, Spindler SR, Atamna H, Yamakawa A, Boffelli D, Mote P, Martin DI.

BMC Genomics. 2013 May 2;14:298. doi: 10.1186/1471-2164-14-298.

15.

Deep sequencing identifies circulating mouse miRNAs that are functionally implicated in manifestations of aging and responsive to calorie restriction.

Dhahbi JM, Spindler SR, Atamna H, Yamakawa A, Guerrero N, Boffelli D, Mote P, Martin DI.

Aging (Albany NY). 2013 Feb;5(2):130-41.

16.

Epigenetic inheritance: a contributor to species differentiation?

Boffelli D, Martin DI.

DNA Cell Biol. 2012 Oct;31 Suppl 1:S11-6. doi: 10.1089/dna.2012.1643. Epub 2012 Sep 11. Review.

17.

mRNA-Seq reveals complex patterns of gene regulation and expression in the mouse skeletal muscle transcriptome associated with calorie restriction.

Dhahbi JM, Atamna H, Boffelli D, Martin DI, Spindler SR.

Physiol Genomics. 2012 Mar 19;44(6):331-44. doi: 10.1152/physiolgenomics.00129.2011. Epub 2012 Jan 24.

18.

Identification and correction of systematic error in high-throughput sequence data.

Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L.

BMC Bioinformatics. 2011 Nov 21;12:451. doi: 10.1186/1471-2105-12-451.

19.

Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states.

Martin DI, Singer M, Dhahbi J, Mao G, Zhang L, Schroth GP, Pachter L, Boffelli D.

Genome Res. 2011 Dec;21(12):2049-57. doi: 10.1101/gr.122721.111. Epub 2011 Sep 9.

20.

VISTA Region Viewer (RViewer)--a computational system for prioritizing genomic intervals for biomedical studies.

Lukashin I, Novichkov P, Boffelli D, Paciorkowski AR, Minovitsky S, Yang S, Dubchak I.

Bioinformatics. 2011 Sep 15;27(18):2595-7. doi: 10.1093/bioinformatics/btr440. Epub 2011 Jul 26.

21.

Deep sequencing reveals novel microRNAs and regulation of microRNA expression during cell senescence.

Dhahbi JM, Atamna H, Boffelli D, Magis W, Spindler SR, Martin DI.

PLoS One. 2011;6(5):e20509. doi: 10.1371/journal.pone.0020509. Epub 2011 May 26.

22.

MetMap enables genome-scale Methyltyping for determining methylation states in populations.

Singer M, Boffelli D, Dhahbi J, Schönhuth A, Schroth GP, Martin DI, Pachter L.

PLoS Comput Biol. 2010 Aug 19;6(8):e1000888. doi: 10.1371/journal.pcbi.1000888.

23.

Phylogenetic shadowing: sequence comparisons of multiple primate species.

Boffelli D.

Methods Mol Biol. 2008;453:217-31. doi: 10.1007/978-1-60327-429-6_10.

PMID:
18712305
24.

LPA and PLG sequence variation and kringle IV-2 copy number in two populations.

Crawford DC, Peng Z, Cheng JF, Boffelli D, Ahearn M, Nguyen D, Shaffer T, Yi Q, Livingston RJ, Rieder MJ, Nickerson DA.

Hum Hered. 2008;66(4):199-209. doi: 10.1159/000143403. Epub 2008 Jul 9.

25.

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons.

Wang QF, Prabhakar S, Chanan S, Cheng JF, Rubin EM, Boffelli D.

Genome Biol. 2007;8(1):R1.

26.

Symbiosis insights through metagenomic analysis of a microbial consortium.

Woyke T, Teeling H, Ivanova NN, Huntemann M, Richter M, Gloeckner FO, Boffelli D, Anderson IJ, Barry KW, Shapiro HJ, Szeto E, Kyrpides NC, Mussmann M, Amann R, Bergin C, Ruehland C, Rubin EM, Dubilier N.

Nature. 2006 Oct 26;443(7114):950-5. Epub 2006 Sep 17.

PMID:
16980956
27.

Primate-specific evolution of an LDLR enhancer.

Wang QF, Prabhakar S, Wang Q, Moses AM, Chanan S, Brown M, Eisen MB, Cheng JF, Rubin EM, Boffelli D.

Genome Biol. 2006;7(8):R68. Epub 2006 Aug 2.

28.

Intraspecies sequence comparisons for annotating genomes.

Boffelli D, Weer CV, Weng L, Lewis KD, Shoukry MI, Pachter L, Keys DN, Rubin EM.

Genome Res. 2004 Dec;14(12):2406-11. Epub 2004 Nov 15.

29.

eShadow: a tool for comparing closely related sequences.

Ovcharenko I, Boffelli D, Loots GG.

Genome Res. 2004 Jun;14(6):1191-8.

30.

Comparative genomics at the vertebrate extremes.

Boffelli D, Nobrega MA, Rubin EM.

Nat Rev Genet. 2004 Jun;5(6):456-65. Review. No abstract available.

PMID:
15153998
31.

Obesity in BSB mice is correlated with expression of genes for iron homeostasis and leptin.

Farahani P, Chiu S, Bowlus CL, Boffelli D, Lee E, Fisler JS, Krauss RM, Warden CH.

Obes Res. 2004 Feb;12(2):191-204.

32.

Convergent evolution in primates and an insectivore.

Boffelli D, Cheng JF, Rubin EM.

Genomics. 2004 Jan;83(1):19-23.

PMID:
14667805
33.

Phylogenetic shadowing of primate sequences to find functional regions of the human genome.

Boffelli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM.

Science. 2003 Feb 28;299(5611):1391-4.

34.

Functional annotation of a full-length mouse cDNA collection.

Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schönbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y; RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium.

Nature. 2001 Feb 8;409(6821):685-90.

PMID:
11217851
35.

Genomic interval engineering of mice identifies a novel modulator of triglyceride production.

Zhu Y, Jong MC, Frazer KA, Gong E, Krauss RM, Cheng JF, Boffelli D, Rubin EM.

Proc Natl Acad Sci U S A. 2000 Feb 1;97(3):1137-42.

36.

Estrogen modulation of apolipoprotein(a) expression. Identification of a regulatory element.

Boffelli D, Zajchowski DA, Yang Z, Lawn RM.

J Biol Chem. 1999 May 28;274(22):15569-74.

37.

Identification of a receptor mediating absorption of dietary cholesterol in the intestine.

Hauser H, Dyer JH, Nandy A, Vega MA, Werder M, Bieliauskaite E, Weber FE, Compassi S, Gemperli A, Boffelli D, Wehrli E, Schulthess G, Phillips MC.

Biochemistry. 1998 Dec 22;37(51):17843-50.

PMID:
9922151
38.

Apolipoprotein(a) gene enhancer resides within a LINE element.

Yang Z, Boffelli D, Boonmark N, Schwartz K, Lawn R.

J Biol Chem. 1998 Jan 9;273(2):891-7.

39.

Reconstitution and further characterization of the cholesterol transport activity of the small-intestinal brush border membrane.

Boffelli D, Weber FE, Compassi S, Werder M, Schulthess G, Hauser H.

Biochemistry. 1997 Sep 2;36(35):10784-92.

PMID:
9271510
40.

Molecular cloning of a peroxisomal Ca2+-dependent member of the mitochondrial carrier superfamily.

Weber FE, Minestrini G, Dyer JH, Werder M, Boffelli D, Compassi S, Wehrli E, Thomas RM, Schulthess G, Hauser H.

Proc Natl Acad Sci U S A. 1997 Aug 5;94(16):8509-14.

41.

The uptake of cholesterol at the small-intestinal brush border membrane is inhibited by apolipoproteins.

Boffelli D, Compassi S, Werder M, Weber FE, Phillips MC, Schulthess G, Hauser H.

FEBS Lett. 1997 Jul 7;411(1):7-11.

42.

Comparison of cholesterol and sitosterol uptake in different brush border membrane models.

Compassi S, Werder M, Weber FE, Boffelli D, Hauser H, Schulthess G.

Biochemistry. 1997 Jun 3;36(22):6643-52.

PMID:
9184144
43.

A comparative study of sterol absorption in different small-intestinal brush border membrane models.

Schulthess G, Compassi S, Boffelli D, Werder M, Weber FE, Hauser H.

J Lipid Res. 1996 Nov;37(11):2405-19.

44.

Cholesteryl ester absorption by small intestinal brush border membrane is protein-mediated.

Compassi S, Werder M, Boffelli D, Weber FE, Hauser H, Schulthess G.

Biochemistry. 1995 Dec 19;34(50):16473-82.

PMID:
8845376
45.

Absorption of monoacylglycerols by small intestinal brush border membrane.

Schulthess G, Lipka G, Compassi S, Boffelli D, Weber FE, Paltauf F, Hauser H.

Biochemistry. 1994 Apr 19;33(15):4500-8.

PMID:
8161504
46.

A theoretical method to predict DNA permutation gel electrophoresis from the sequence.

Boffelli D, De Santis P, Palleschi A, Risuleo G, Savino M.

FEBS Lett. 1992 Mar 30;300(2):175-8.

47.

The curvature vector in nucleosomal DNAs and theoretical prediction of nucleosome positioning.

Boffelli D, De Santis P, Palleschi A, Savino M.

Biophys Chem. 1991 Feb;39(2):127-36.

PMID:
1647823

Supplemental Content

Loading ...
Support Center