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Items: 1 to 50 of 66

1.

Transcriptome and epigenome landscape of human cortical development modeled in organoids.

Amiri A, Coppola G, Scuderi S, Wu F, Roychowdhury T, Liu F, Pochareddy S, Shin Y, Safi A, Song L, Zhu Y, Sousa AMM; PsychENCODE Consortium, Gerstein M, Crawford GE, Sestan N, Abyzov A, Vaccarino FM.

Science. 2018 Dec 14;362(6420). pii: eaat6720. doi: 10.1126/science.aat6720.

PMID:
30545853
2.
3.

Inferring modes of evolution from colorectal cancer with residual polyp of origin.

Kim M, Druliner BR, Vasmatzis N, Bae T, Chia N, Abyzov A, Boardman LA.

Oncotarget. 2017 Dec 26;9(6):6780-6792. doi: 10.18632/oncotarget.23687. eCollection 2018 Jan 23.

4.

Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations.

Druliner BR, Wang P, Bae T, Baheti S, Slettedahl S, Mahoney D, Vasmatzis N, Xu H, Kim M, Bockol M, O'Brien D, Grill D, Warner N, Munoz-Gomez M, Kossick K, Johnson R, Mouchli M, Felmlee-Devine D, Washechek-Aletto J, Smyrk T, Oberg A, Wang J, Chia N, Abyzov A, Ahlquist D, Boardman LA.

Sci Rep. 2018 Feb 16;8(1):3161. doi: 10.1038/s41598-018-21525-4.

5.

Heterogeneous nucleation on rough surfaces: Generalized Gibbs' approach.

Abyzov AS, Schmelzer JWP, Davydov LN.

J Chem Phys. 2017 Dec 7;147(21):214705. doi: 10.1063/1.5006631.

PMID:
29221413
6.

Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis.

Bae T, Tomasini L, Mariani J, Zhou B, Roychowdhury T, Franjic D, Pletikos M, Pattni R, Chen BJ, Venturini E, Riley-Gillis B, Sestan N, Urban AE, Abyzov A, Vaccarino FM.

Science. 2018 Feb 2;359(6375):550-555. doi: 10.1126/science.aan8690. Epub 2017 Dec 7.

PMID:
29217587
7.

Atomic resolution conformational dynamics of intrinsically disordered proteins from NMR spin relaxation.

Salvi N, Abyzov A, Blackledge M.

Prog Nucl Magn Reson Spectrosc. 2017 Nov;102-103:43-60. doi: 10.1016/j.pnmrs.2017.06.001. Epub 2017 Jul 10. Review.

PMID:
29157493
8.

Beating Homogeneous Nucleation and Tuning Atomic Ordering in Glass-Forming Metals by Nanocalorimetry.

Zhao B, Yang B, Abyzov AS, Schmelzer JWP, Rodríguez-Viejo J, Zhai Q, Schick C, Gao Y.

Nano Lett. 2017 Dec 13;17(12):7751-7760. doi: 10.1021/acs.nanolett.7b03952. Epub 2017 Nov 9.

PMID:
29111758
9.

Analytical Description of NMR Relaxation Highlights Correlated Dynamics in Intrinsically Disordered Proteins.

Salvi N, Abyzov A, Blackledge M.

Angew Chem Int Ed Engl. 2017 Nov 6;56(45):14020-14024. doi: 10.1002/anie.201706740. Epub 2017 Sep 14.

PMID:
28834051
10.

Landscape and variation of novel retroduplications in 26 human populations.

Zhang Y, Li S, Abyzov A, Gerstein MB.

PLoS Comput Biol. 2017 Jun 29;13(6):e1005567. doi: 10.1371/journal.pcbi.1005567. eCollection 2017 Jun.

11.

Patient-reported (EORTC QLQ-CIPN20) versus physician-reported (CTCAE) quantification of oxaliplatin- and paclitaxel/carboplatin-induced peripheral neuropathy in NCCTG/Alliance clinical trials.

Le-Rademacher J, Kanwar R, Seisler D, Pachman DR, Qin R, Abyzov A, Ruddy KJ, Banck MS, Lavoie Smith EM, Dorsey SG, Aaronson NK, Sloan J, Loprinzi CL, Beutler AS.

Support Care Cancer. 2017 Nov;25(11):3537-3544. doi: 10.1007/s00520-017-3780-y. Epub 2017 Jun 20.

12.

Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network.

McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM; Brain Somatic Mosaicism Network.

Science. 2017 Apr 28;356(6336). pii: eaal1641. doi: 10.1126/science.aal1641. Epub 2017 Apr 27. Review.

13.

Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans.

Haraksingh RR, Abyzov A, Urban AE.

BMC Genomics. 2017 Apr 24;18(1):321. doi: 10.1186/s12864-017-3658-x.

14.

Human induced pluripotent stem cells for modelling neurodevelopmental disorders.

Ardhanareeswaran K, Mariani J, Coppola G, Abyzov A, Vaccarino FM.

Nat Rev Neurol. 2017 May;13(5):265-278. doi: 10.1038/nrneurol.2017.45. Epub 2017 Apr 18. Review.

15.

One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin.

Abyzov A, Tomasini L, Zhou B, Vasmatzis N, Coppola G, Amenduni M, Pattni R, Wilson M, Gerstein M, Weissman S, Urban AE, Vaccarino FM.

Genome Res. 2017 Apr;27(4):512-523. doi: 10.1101/gr.215517.116. Epub 2017 Feb 24.

16.

Colorectal Cancer with Residual Polyp of Origin: A Model of Malignant Transformation.

Druliner BR, Rashtak S, Ruan X, Bae T, Vasmatzis N, O'Brien D, Johnson R, Felmlee-Devine D, Washechek-Aletto J, Basu N, Liu H, Smyrk T, Abyzov A, Boardman LA.

Transl Oncol. 2016 Aug;9(4):280-6. doi: 10.1016/j.tranon.2016.06.002. Epub 2016 Jul 9.

17.

Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation.

Salvi N, Abyzov A, Blackledge M.

J Phys Chem Lett. 2016 Jul 7;7(13):2483-9. doi: 10.1021/acs.jpclett.6b00885. Epub 2016 Jun 20.

PMID:
27300592
18.

Elevated variant density around SV breakpoints in germline lineage lends support to error-prone replication hypothesis.

Dhokarh D, Abyzov A.

Genome Res. 2016 Jul;26(7):874-81. doi: 10.1101/gr.205484.116. Epub 2016 May 23.

19.

Identification of Dynamic Modes in an Intrinsically Disordered Protein Using Temperature-Dependent NMR Relaxation.

Abyzov A, Salvi N, Schneider R, Maurin D, Ruigrok RW, Jensen MR, Blackledge M.

J Am Chem Soc. 2016 May 18;138(19):6240-51. doi: 10.1021/jacs.6b02424. Epub 2016 May 6.

PMID:
27112095
20.

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.

21.

Testing of candidate single nucleotide variants associated with paclitaxel neuropathy in the trial NCCTG N08C1 (Alliance).

Boora GK, Kanwar R, Kulkarni AA, Abyzov A, Sloan J, Ruddy KJ, Banck MS, Loprinzi CL, Beutler AS.

Cancer Med. 2016 Apr;5(4):631-9. doi: 10.1002/cam4.625. Epub 2016 Jan 14.

22.

Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors.

Mitra AK, Mukherjee UK, Harding T, Jang JS, Stessman H, Li Y, Abyzov A, Jen J, Kumar S, Rajkumar V, Van Ness B.

Leukemia. 2016 May;30(5):1094-102. doi: 10.1038/leu.2015.361. Epub 2015 Dec 29.

PMID:
26710886
23.

Understanding genome structural variations.

Abyzov A, Li S, Gerstein MB.

Oncotarget. 2016 Feb 16;7(7):7370-1. doi: 10.18632/oncotarget.6485. No abstract available.

24.

The PsychENCODE project.

PsychENCODE Consortium, Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N.

Nat Neurosci. 2015 Dec;18(12):1707-12. doi: 10.1038/nn.4156. Review. No abstract available.

25.

An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.

Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.

26.

Erratum: analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB.

Nat Commun. 2015 Sep 8;6:8389. doi: 10.1038/ncomms9389. No abstract available.

PMID:
26346554
27.

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.

Mariani J, Coppola G, Zhang P, Abyzov A, Provini L, Tomasini L, Amenduni M, Szekely A, Palejev D, Wilson M, Gerstein M, Grigorenko EL, Chawarska K, Pelphrey KA, Howe JR, Vaccarino FM.

Cell. 2015 Jul 16;162(2):375-390. doi: 10.1016/j.cell.2015.06.034.

28.

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB.

Nat Commun. 2015 Jun 1;6:7256. doi: 10.1038/ncomms8256. Erratum in: Nat Commun. 2015;6:8389.

29.

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.

Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY.

Bioinformatics. 2015 Aug 15;31(16):2741-4. doi: 10.1093/bioinformatics/btv204. Epub 2015 Apr 10.

30.

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.

Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY.

Bioinformatics. 2015 May 1;31(9):1469-71. doi: 10.1093/bioinformatics/btu828. Epub 2014 Dec 17.

31.

Heterogeneous nucleation in solutions: generalized Gibbs' approach.

Abyzov AS, Schmelzer JW.

J Chem Phys. 2014 Jun 28;140(24):244706. doi: 10.1063/1.4884395.

PMID:
24985667
32.

Integrative annotation of variants from 1092 humans: application to cancer genomics.

Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M.

Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587.

33.

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division.

Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L; 1000 Genomes Project Consortium, Lee C, Gerstein M.

Genome Res. 2013 Dec;23(12):2042-52. doi: 10.1101/gr.154625.113. Epub 2013 Sep 11.

34.

Temperature of critical clusters in nucleation theory: generalized Gibbs' approach.

Schmelzer JW, Boltachev GSh, Abyzov AS.

J Chem Phys. 2013 Jul 21;139(3):034702. doi: 10.1063/1.4813238.

PMID:
23883047
35.

Generalized Gibbs' approach in heterogeneous nucleation.

Abyzov AS, Schmelzer JW.

J Chem Phys. 2013 Apr 28;138(16):164504. doi: 10.1063/1.4802201.

PMID:
23635154
36.

Size and rate dependence of crystal nucleation in single tin drops by fast scanning calorimetry.

Yang B, Abyzov AS, Zhuravlev E, Gao Y, Schmelzer JW, Schick C.

J Chem Phys. 2013 Feb 7;138(5):054501. doi: 10.1063/1.4789447.

PMID:
23406127
37.

Child development and structural variation in the human genome.

Zhang Y, Haraksingh R, Grubert F, Abyzov A, Gerstein M, Weissman S, Urban AE.

Child Dev. 2013 Jan-Feb;84(1):34-48. doi: 10.1111/cdev.12051. Epub 2013 Jan 13. Review.

PMID:
23311762
38.

Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells.

Abyzov A, Mariani J, Palejev D, Zhang Y, Haney MS, Tomasini L, Ferrandino AF, Rosenberg Belmaker LA, Szekely A, Wilson M, Kocabas A, Calixto NE, Grigorenko EL, Huttner A, Chawarska K, Weissman S, Urban AE, Gerstein M, Vaccarino FM.

Nature. 2012 Dec 20;492(7429):438-42. doi: 10.1038/nature11629. Epub 2012 Nov 18.

39.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

40.

Regulatory element copy number differences shape primate expression profiles.

Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, Lee C.

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12656-61. doi: 10.1073/pnas.1205199109. Epub 2012 Jul 13.

41.

Comment on "Minimum free-energy pathway of nucleation" [J. Chem. Phys. 135, 134508 (2011)].

Schmelzer JW, Abyzov AS.

J Chem Phys. 2012 Mar 14;136(10):107101. doi: 10.1063/1.3692688. No abstract available.

PMID:
22423863
42.

Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms.

Haraksingh RR, Abyzov A, Gerstein M, Urban AE, Snyder M.

PLoS One. 2011;6(11):e27859. doi: 10.1371/journal.pone.0027859. Epub 2011 Nov 30.

43.

Dynamic processes in a silicate liquid from above melting to below the glass transition.

Nascimento ML, Fokin VM, Zanotto ED, Abyzov AS.

J Chem Phys. 2011 Nov 21;135(19):194703. doi: 10.1063/1.3656696.

PMID:
22112093
44.

Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions.

Bhardwaj N, Abyzov A, Clarke D, Shou C, Gerstein MB.

Protein Sci. 2011 Oct;20(10):1745-54. doi: 10.1002/pro.710. Epub 2011 Sep 15.

45.

AlleleSeq: analysis of allele-specific expression and binding in a network framework.

Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M.

Mol Syst Biol. 2011 Aug 2;7:522. doi: 10.1038/msb.2011.54.

46.

Identification of genomic indels and structural variations using split reads.

Zhang ZD, Du J, Lam H, Abyzov A, Urban AE, Snyder M, Gerstein M.

BMC Genomics. 2011 Jul 25;12:375. doi: 10.1186/1471-2164-12-375.

47.

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.

Abyzov A, Urban AE, Snyder M, Gerstein M.

Genome Res. 2011 Jun;21(6):974-84. doi: 10.1101/gr.114876.110. Epub 2011 Feb 7.

48.

Thermodynamic analysis of nucleation in confined space: generalized Gibbs approach.

Schmelzer JW, Abyzov AS.

J Chem Phys. 2011 Feb 7;134(5):054511. doi: 10.1063/1.3548870.

PMID:
21303142
49.

Mapping copy number variation by population-scale genome sequencing.

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project.

Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.

50.

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.

Abyzov A, Gerstein M.

Bioinformatics. 2011 Mar 1;27(5):595-603. doi: 10.1093/bioinformatics/btq713. Epub 2011 Jan 13.

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