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Items: 32

1.

Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance.

Peshkin L, Gupta M, Ryazanova L, Wühr M.

Mol Cell Proteomics. 2019 Oct;18(10):2108-2120. doi: 10.1074/mcp.TIR119.001317. Epub 2019 Jul 16.

PMID:
31311848
2.

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.

Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM.

Science. 2018 Jun 1;360(6392). pii: eaar5780. doi: 10.1126/science.aar5780. Epub 2018 Apr 26.

3.

Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in the Xenopus egg.

Presler M, Van Itallie E, Klein AM, Kunz R, Coughlin ML, Peshkin L, Gygi SP, Wühr M, Kirschner MW.

Proc Natl Acad Sci U S A. 2017 Dec 12;114(50):E10838-E10847. doi: 10.1073/pnas.1709207114. Epub 2017 Nov 28.

4.

Data on the time of integration of the human mitochondrial pseudogenes (NUMTs) into the nuclear genome.

Gunbin K, Peshkin L, Popadin K, Annis S, Ackermann RR, Khrapko K.

Data Brief. 2017 May 17;13:536-544. doi: 10.1016/j.dib.2017.05.024. eCollection 2017 Aug.

5.

Transcriptomic insights into genetic diversity of protein-coding genes in X. laevis.

Savova V, Pearl EJ, Boke E, Nag A, Adzhubei I, Horb ME, Peshkin L.

Dev Biol. 2017 Apr 15;424(2):181-188. doi: 10.1016/j.ydbio.2017.02.019. Epub 2017 Mar 7.

6.

A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors.

Bryant DM, Johnson K, DiTommaso T, Tickle T, Couger MB, Payzin-Dogru D, Lee TJ, Leigh ND, Kuo TH, Davis FG, Bateman J, Bryant S, Guzikowski AR, Tsai SL, Coyne S, Ye WW, Freeman RM Jr, Peshkin L, Tabin CJ, Regev A, Haas BJ, Whited JL.

Cell Rep. 2017 Jan 17;18(3):762-776. doi: 10.1016/j.celrep.2016.12.063.

7.

Integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A hypothesis.

Gunbin K, Peshkin L, Popadin K, Annis S, Ackermann RR, Khrapko K.

Mitochondrion. 2017 May;34:20-23. doi: 10.1016/j.mito.2016.12.001. Epub 2016 Dec 12.

PMID:
27979772
8.

Luteinizing Hormone is an effective replacement for hCG to induce ovulation in Xenopus.

Wlizla M, Falco R, Peshkin L, Parlow AF, Horb ME.

Dev Biol. 2017 Jun 15;426(2):442-448. doi: 10.1016/j.ydbio.2016.05.028. Epub 2016 Jun 2.

10.

Hemichordate genomes and deuterostome origins.

Simakov O, Kawashima T, Marlétaz F, Jenkins J, Koyanagi R, Mitros T, Hisata K, Bredeson J, Shoguchi E, Gyoja F, Yue JX, Chen YC, Freeman RM Jr, Sasaki A, Hikosaka-Katayama T, Sato A, Fujie M, Baughman KW, Levine J, Gonzalez P, Cameron C, Fritzenwanker JH, Pani AM, Goto H, Kanda M, Arakaki N, Yamasaki S, Qu J, Cree A, Ding Y, Dinh HH, Dugan S, Holder M, Jhangiani SN, Kovar CL, Lee SL, Lewis LR, Morton D, Nazareth LV, Okwuonu G, Santibanez J, Chen R, Richards S, Muzny DM, Gillis A, Peshkin L, Wu M, Humphreys T, Su YH, Putnam NH, Schmutz J, Fujiyama A, Yu JK, Tagawa K, Worley KC, Gibbs RA, Kirschner MW, Lowe CJ, Satoh N, Rokhsar DS, Gerhart J.

Nature. 2015 Nov 26;527(7579):459-65. doi: 10.1038/nature16150. Epub 2015 Nov 18.

11.

On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development.

Peshkin L, Wühr M, Pearl E, Haas W, Freeman RM Jr, Gerhart JC, Klein AM, Horb M, Gygi SP, Kirschner MW.

Dev Cell. 2015 Nov 9;35(3):383-94. doi: 10.1016/j.devcel.2015.10.010.

12.

The Nuclear Proteome of a Vertebrate.

Wühr M, Güttler T, Peshkin L, McAlister GC, Sonnett M, Ishihara K, Groen AC, Presler M, Erickson BK, Mitchison TJ, Kirschner MW, Gygi SP.

Curr Biol. 2015 Oct 19;25(20):2663-71. doi: 10.1016/j.cub.2015.08.047. Epub 2015 Oct 1.

13.

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA, Kirschner MW.

Cell. 2015 May 21;161(5):1187-1201. doi: 10.1016/j.cell.2015.04.044.

14.

A noncanonical Frizzled2 pathway regulates epithelial-mesenchymal transition and metastasis.

Gujral TS, Chan M, Peshkin L, Sorger PK, Kirschner MW, MacBeath G.

Cell. 2014 Nov 6;159(4):844-56. doi: 10.1016/j.cell.2014.10.032.

15.

Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database.

Wühr M, Freeman RM Jr, Presler M, Horb ME, Peshkin L, Gygi S, Kirschner MW.

Curr Biol. 2014 Jul 7;24(13):1467-1475. doi: 10.1016/j.cub.2014.05.044. Epub 2014 Jun 19.

16.

Resveratrol prevents high fat/sucrose diet-induced central arterial wall inflammation and stiffening in nonhuman primates.

Mattison JA, Wang M, Bernier M, Zhang J, Park SS, Maudsley S, An SS, Santhanam L, Martin B, Faulkner S, Morrell C, Baur JA, Peshkin L, Sosnowska D, Csiszar A, Herbert RL, Tilmont EM, Ungvari Z, Pearson KJ, Lakatta EG, de Cabo R.

Cell Metab. 2014 Jul 1;20(1):183-90. doi: 10.1016/j.cmet.2014.04.018. Epub 2014 May 29.

17.

Exploiting polypharmacology for drug target deconvolution.

Gujral TS, Peshkin L, Kirschner MW.

Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):5048-53. doi: 10.1073/pnas.1403080111. Epub 2014 Mar 19.

18.

Accurate multiplexed proteomics at the MS2 level using the complement reporter ion cluster.

Wühr M, Haas W, McAlister GC, Peshkin L, Rad R, Kirschner MW, Gygi SP.

Anal Chem. 2012 Nov 6;84(21):9214-21. doi: 10.1021/ac301962s. Epub 2012 Oct 25.

19.

Vascular disrupting agent drug classes differ in effects on the cytoskeleton.

Kim S, Peshkin L, Mitchison TJ.

PLoS One. 2012;7(7):e40177. doi: 10.1371/journal.pone.0040177. Epub 2012 Jul 24.

20.

A public resource facilitating clinical use of genomes.

Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow MJ, Cano C, Chou MF, Chung WK, Douglas SM, Estep PW, Gore A, Hulick P, Labarga A, Lee JH, Lunshof JE, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters BA, Raman AM, Rienhoff HY, Robasky K, Wheeler MT, Vandewege W, Vorhaus DB, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM.

Proc Natl Acad Sci U S A. 2012 Jul 24;109(30):11920-7. doi: 10.1073/pnas.1201904109. Epub 2012 Jul 13.

21.

Genome sequencing reveals insights into physiology and longevity of the naked mole rat.

Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, Marino SM, Sun X, Turanov AA, Yang P, Yim SH, Zhao X, Kasaikina MV, Stoletzki N, Peng C, Polak P, Xiong Z, Kiezun A, Zhu Y, Chen Y, Kryukov GV, Zhang Q, Peshkin L, Yang L, Bronson RT, Buffenstein R, Wang B, Han C, Li Q, Chen L, Zhao W, Sunyaev SR, Park TJ, Zhang G, Wang J, Gladyshev VN.

Nature. 2011 Oct 12;479(7372):223-7. doi: 10.1038/nature10533.

22.

Toward an unbiased evolutionary platform for unraveling Xenopus developmental gene networks.

Beer R, Wagner F, Grishkevich V, Peshkin L, Yanai I.

Genesis. 2012 Mar;50(3):186-91. doi: 10.1002/dvg.20811. Epub 2012 Jan 5. Review.

PMID:
21956895
23.

Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility.

Yanai I, Peshkin L, Jorgensen P, Kirschner MW.

Dev Cell. 2011 Apr 19;20(4):483-96. doi: 10.1016/j.devcel.2011.03.015.

24.

Remodeling of the metabolome during early frog development.

Vastag L, Jorgensen P, Peshkin L, Wei R, Rabinowitz JD, Kirschner MW.

PLoS One. 2011 Feb 4;6(2):e16881. doi: 10.1371/journal.pone.0016881.

25.

A method and server for predicting damaging missense mutations.

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR.

Nat Methods. 2010 Apr;7(4):248-9. doi: 10.1038/nmeth0410-248. No abstract available.

26.

Effects of temperature on gene expression in embryos of the coral Montastraea faveolata.

Voolstra CR, Schnetzer J, Peshkin L, Randall CJ, Szmant AM, Medina M.

BMC Genomics. 2009 Dec 23;10:627. doi: 10.1186/1471-2164-10-627.

27.

Automated identification of diagnosis and co-morbidity in clinical records.

Cano C, Blanco A, Peshkin L.

Methods Inf Med. 2009;48(6):546-51. doi: 10.3414/ME0615. Epub 2009 Aug 20.

PMID:
19696949
28.

Collaborative text-annotation resource for disease-centered relation extraction from biomedical text.

Cano C, Monaghan T, Blanco A, Wall DP, Peshkin L.

J Biomed Inform. 2009 Oct;42(5):967-77. doi: 10.1016/j.jbi.2009.02.001. Epub 2009 Feb 14.

29.

Resveratrol delays age-related deterioration and mimics transcriptional aspects of dietary restriction without extending life span.

Pearson KJ, Baur JA, Lewis KN, Peshkin L, Price NL, Labinskyy N, Swindell WR, Kamara D, Minor RK, Perez E, Jamieson HA, Zhang Y, Dunn SR, Sharma K, Pleshko N, Woollett LA, Csiszar A, Ikeno Y, Le Couteur D, Elliott PJ, Becker KG, Navas P, Ingram DK, Wolf NS, Ungvari Z, Sinclair DA, de Cabo R.

Cell Metab. 2008 Aug;8(2):157-68. doi: 10.1016/j.cmet.2008.06.011. Epub 2008 Jul 3.

30.

Rapidly retargetable approaches to de-identification in medical records.

Wellner B, Huyck M, Mardis S, Aberdeen J, Morgan A, Peshkin L, Yeh A, Hitzeman J, Hirschman L.

J Am Med Inform Assoc. 2007 Sep-Oct;14(5):564-73. Epub 2007 Jun 28.

31.

Roundup: a multi-genome repository of orthologs and evolutionary distances.

Deluca TF, Wu IH, Pu J, Monaghan T, Peshkin L, Singh S, Wall DP.

Bioinformatics. 2006 Aug 15;22(16):2044-6. Epub 2006 Jun 15.

PMID:
16777906
32.

Segmentation of yeast DNA using hidden Markov models.

Peshkin L, Gelfand MS.

Bioinformatics. 1999 Dec;15(12):980-6.

PMID:
10745987

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