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Items: 22

1.

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C.

Nat Commun. 2019 Apr 16;10(1):1784. doi: 10.1038/s41467-018-08148-z.

2.

exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.

Rozowsky J, Kitchen RR, Park JJ, Galeev TR, Diao J, Warrell J, Thistlethwaite W, Subramanian SL, Milosavljevic A, Gerstein M.

Cell Syst. 2019 Apr 24;8(4):352-357.e3. doi: 10.1016/j.cels.2019.03.004. Epub 2019 Apr 4.

3.

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.

Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A.

Cell. 2019 Apr 4;177(2):463-477.e15. doi: 10.1016/j.cell.2019.02.018.

4.

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci.

Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A.

Science. 2018 Sep 28;361(6409). pii: eaar3146. doi: 10.1126/science.aar3146. Epub 2018 Aug 23.

5.

FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods.

Becker T, Lee WP, Leone J, Zhu Q, Zhang C, Liu S, Sargent J, Shanker K, Mil-Homens A, Cerveira E, Ryan M, Cha J, Navarro FCP, Galeev T, Gerstein M, Mills RE, Shin DG, Lee C, Malhotra A.

Genome Biol. 2018 Mar 20;19(1):38. doi: 10.1186/s13059-018-1404-6.

6.

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.

Kaczor-Urbanowicz KE, Kim Y, Li F, Galeev T, Kitchen RR, Gerstein M, Koyano K, Jeong SH, Wang X, Elashoff D, Kang SY, Kim SM, Kim K, Kim S, Chia D, Xiao X, Rozowsky J, Wong DTW.

Bioinformatics. 2018 Jan 1;34(1):1-8. doi: 10.1093/bioinformatics/btx504.

7.

Corrigendum: Diverse human extracellular RNAs are widely detected in human plasma.

Freedman JE, Gerstein M, Mick E, Rozowsky J, Levy D, Kitchen R, Das S, Shah R, Danielson K, Beaulieu L, Navarro FC, Wang Y, Galeev TR, Holman A, Kwong RY, Murthy V, Tanriverdi SE, Koupenova M, Mikhalev E, Tanriverdi K.

Nat Commun. 2016 Jun 3;7:11902. doi: 10.1038/ncomms11902. No abstract available.

8.

Diverse human extracellular RNAs are widely detected in human plasma.

Freedman JE, Gerstein M, Mick E, Rozowsky J, Levy D, Kitchen R, Das S, Shah R, Danielson K, Beaulieu L, Navarro FC, Wang Y, Galeev TR, Holman A, Kwong RY, Murthy V, Tanriverdi SE, Koupenova-Zamor M, Mikhalev E, Tanriverdi K.

Nat Commun. 2016 Apr 26;7:11106. doi: 10.1038/ncomms11106. Erratum in: Nat Commun. 2016 Jun 03;7:11902.

9.

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.

Chen J, Rozowsky J, Galeev TR, Harmanci A, Kitchen R, Bedford J, Abyzov A, Kong Y, Regan L, Gerstein M.

Nat Commun. 2016 Apr 18;7:11101. doi: 10.1038/ncomms11101.

10.

Reads meet rotamers: structural biology in the age of deep sequencing.

Sethi A, Clarke D, Chen J, Kumar S, Galeev TR, Regan L, Gerstein M.

Curr Opin Struct Biol. 2015 Dec;35:125-34. doi: 10.1016/j.sbi.2015.11.003. Epub 2015 Dec 1. Review.

11.

Geometric and electronic factors in the rational design of transition-metal-centered boron molecular wheels.

Romanescu C, Galeev TR, Li WL, Boldyrev AI, Wang LS.

J Chem Phys. 2013 Apr 7;138(13):134315. doi: 10.1063/1.4798935.

PMID:
23574235
12.

Solid state adaptive natural density partitioning: a tool for deciphering multi-center bonding in periodic systems.

Galeev TR, Dunnington BD, Schmidt JR, Boldyrev AI.

Phys Chem Chem Phys. 2013 Apr 14;15(14):5022-9. doi: 10.1039/c3cp50350j.

PMID:
23443061
13.

Photoelectron spectroscopy and ab initio study of boron-carbon mixed clusters: CB9- and C2B8-.

Galeev TR, Li WL, Romanescu C, Cernusák I, Wang LS, Boldyrev AI.

J Chem Phys. 2012 Dec 21;137(23):234306. doi: 10.1063/1.4770231.

PMID:
23267485
14.

Transition-metal-centered monocyclic boron wheel clusters (M©Bn): a new class of aromatic borometallic compounds.

Romanescu C, Galeev TR, Li WL, Boldyrev AI, Wang LS.

Acc Chem Res. 2013 Feb 19;46(2):350-8. doi: 10.1021/ar300149a. Epub 2012 Dec 5.

PMID:
23210660
15.

Observation of the highest coordination number in planar species: decacoordinated Ta©B10(-) and Nb©B10(-) anions.

Galeev TR, Romanescu C, Li WL, Wang LS, Boldyrev AI.

Angew Chem Int Ed Engl. 2012 Feb 27;51(9):2101-5. doi: 10.1002/anie.201107880. Epub 2012 Feb 1. No abstract available.

PMID:
22298320
16.

Transition-metal-centered nine-membered boron rings: MⓒB9 and MⓒB9(-) (M = Rh, Ir).

Li WL, Romanescu C, Galeev TR, Piazza ZA, Boldyrev AI, Wang LS.

J Am Chem Soc. 2012 Jan 11;134(1):165-8. doi: 10.1021/ja209808k. Epub 2011 Dec 16.

PMID:
22148745
17.

Valence isoelectronic substitution in the B8(-) and B9(-) molecular wheels by an Al dopant atom: umbrella-like structures of AlB7(-) and AlB8(-).

Galeev TR, Romanescu C, Li WL, Wang LS, Boldyrev AI.

J Chem Phys. 2011 Sep 14;135(10):104301. doi: 10.1063/1.3625959.

PMID:
21932887
18.

Aromatic metal-centered monocyclic boron rings: Co©B8- and Ru©B9-.

Romanescu C, Galeev TR, Li WL, Boldyrev AI, Wang LS.

Angew Chem Int Ed Engl. 2011 Sep 26;50(40):9334-7. doi: 10.1002/anie.201104166. Epub 2011 Aug 31. No abstract available.

PMID:
21882323
19.

Planarity takes over in the C(x)H(x)P(6-x) (x = 0-6) series at x = 4.

Galeev TR, Boldyrev AI.

Phys Chem Chem Phys. 2011 Dec 14;13(46):20549-56. doi: 10.1039/c1cp21959f. Epub 2011 Aug 24.

PMID:
21869975
20.

Aluminum avoids the central position in AlB9- and AlB10-: photoelectron spectroscopy and ab initio study.

Li WL, Romanescu C, Galeev TR, Wang LS, Boldyrev AI.

J Phys Chem A. 2011 Sep 29;115(38):10391-7. doi: 10.1021/jp205873g. Epub 2011 Sep 1.

PMID:
21800920
21.

Deciphering the mystery of hexagon holes in an all-boron graphene α-sheet.

Galeev TR, Chen Q, Guo JC, Bai H, Miao CQ, Lu HG, Sergeeva AP, Li SD, Boldyrev AI.

Phys Chem Chem Phys. 2011 Jun 28;13(24):11575-8. doi: 10.1039/c1cp20439d. Epub 2011 May 20.

PMID:
21603683
22.

Molecular wheel to monocyclic ring transition in boron-carbon mixed clusters C2B6⁻ and C3B5⁻.

Galeev TR, Ivanov AS, Romanescu C, Li WL, Bozhenko KV, Wang LS, Boldyrev AI.

Phys Chem Chem Phys. 2011 May 21;13(19):8805-10. doi: 10.1039/c1cp20359b. Epub 2011 Apr 12.

PMID:
21487619

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