Year | Publication |
2022 | Stankunas labDev Dyn, 2022 Apr 10; Coordinated patterning of zebrafish caudal fin symmetry by a central and two peripheral organizers.Desvignes T, Robbins AE, Carey AZ, Bailon-Zambrano R, Nichols JT, Postlethwait JH, Stankunas K |
2022 | Noma labNucleic Acids Res, 2022 Apr 22;50(7):3799-3816 Rec8 Cohesin-mediated Axis-loop chromatin architecture is required for meiotic recombination.Sakuno T, Tashiro S, Tanizawa H, Iwasaki O, Ding DQ, Haraguchi T, Noma KI, Hiraoka Y |
2022 | Selker labElife, 2022 Mar 8;11 The ACF chromatin-remodeling complex is essential for Polycomb repression.Wiles ET, Mumford CC, McNaught KJ, Tanizawa H, Selker EU |
2022 | Garcia labEpigenomes, 2022 Jan 25;6(1) Biochemical Principles in Prion-Based Inheritance.Dennis EM, Garcia DM |
2022 | von Hippel labJ Chem Phys, 2022 Jan 28;156(4):045101 Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded-double-stranded DNA junctions by 2D fluorescence spectroscopy.Heussman D, Kittell J, von Hippel PH, Marcus AH |
2021 | Libuda labG3 (Bethesda), 2021 Oct 19;11(11) Conditional immobilization for live imaging Caenorhabditis elegans using auxin-dependent protein depletion.Cahoon CK, Libuda DE |
2021 | Libuda labSTAR Protoc, 2021 Sep 17;2(3):100801 Detection of homolog-independent meiotic DNA repair events in C. elegans with the intersister/intrachromatid repair assay.Toraason E, Glover M, Horacek A, Libuda DE |
2021 | Garcia labElife, 2021 Sep 15;10 A prion accelerates proliferation at the expense of lifespan.Garcia DM, Campbell EA, Jakobson CM, Tsuchiya M, Shaw EA, DiNardo AL, Kaeberlein M, Jarosz DF |
2021 | Barkan labPlant Physiol, 2021 Sep 4;187(1):59-72 Ribosome profiling elucidates differential gene expression in bundle sheath and mesophyll cells in maize.Chotewutmontri P, Barkan A |
2021 | Stankunas labDev Biol, 2021 Sep;477:177-190 Basal epidermis collective migration and local Sonic hedgehog signaling promote skeletal branching morphogenesis in zebrafish fins.Braunstein JA, Robbins AE, Stewart S, Stankunas K |
2021 | von Hippel labJ Phys Chem B, 2021 Aug 26;125(33):9426-9440 Submillisecond Conformational Transitions of Short Single-Stranded DNA Lattices by Photon Correlation Single-Molecule Förster Resonance Energy Transfer.Israels B, Albrecht CS, Dang A, Barney M, von Hippel PH, Marcus AH |
2021 | Stankunas labStem Cell Reports, 2021 Jul 13;16(7):1718-1734 Sequential regulation of hemogenic fate and hematopoietic stem and progenitor cell formation from arterial endothelium by Ezh1/2.Soto RA, Najia MAT, Hachimi M, Frame JM, Yette GA, Lummertz da Rocha E, Stankunas K, Daley GQ, North TE |
2021 | Barkan labNucleic Acids Res, 2021 Jun 4;49(10):5985-5997 In vivo stabilization of endogenous chloroplast RNAs by customized artificial pentatricopeptide repeat proteins.Manavski N, Mathieu S, Rojas M, Méteignier LV, Brachmann A, Barkan A, Hammani K |
2021 | Stankunas labDevelopment, 2021 Jun 1;148(11) longfin causes cis-ectopic expression of the kcnh2a ether-a-go-go K+ channel to autonomously prolong fin outgrowth.Stewart S, Le Bleu HK, Yette GA, Henner AL, Robbins AE, Braunstein JA, Stankunas K |
2021 | McKnight labSTAR Protoc, 2021 Jun 18;2(2):100486 Rapid and inexpensive preparation of genome-wide nucleosome footprints from model and non-model organisms.McKnight LE, Crandall JG, Bailey TB, Banks OGB, Orlandi KN, Truong VN, Donovan DA, Waddell GL, Wiles ET, Hansen SD, Selker EU, McKnight JN |
2021 | Libuda labCurr Biol, 2021 Apr 12;31(7):1508-1514.e5 Meiotic DNA break repair can utilize homolog-independent chromatid templates in C. elegans.Toraason E, Horacek A, Clark C, Glover ML, Adler VL, Premkumar T, Salagean A, Cole F, Libuda DE |
2021 | Libuda labGenetics, 2021 Mar 31;217(3) Automated and customizable quantitative image analysis of whole Caenorhabditis elegans germlines.Toraason E, Adler VL, Kurhanewicz NA, DiNardo A, Saunders AM, Cahoon CK, Libuda DE |
2021 | Barkan labPlant J, 2021 Feb;105(3):639-648 CFM1, a member of the CRM-domain protein family, functions in chloroplast group II intron splicing in Setaria viridis.Feiz L, Asakura Y, Mao L, Strickler SR, Fei Z, Rojas M, Barkan A, Stern DB |
2021 | Johnson labSyst Biol, 2021 Feb 10;70(2):203-218 Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent.Poelstra JW, Salmona J, Tiley GP, Schüßler D, Blanco MB, Andriambeloson JB, Bouchez O, Campbell CR, Etter PD, Hohenlohe PA, Hunnicutt KE, Iribar A, Johnson EA, Kappeler PM, Larsen PA, Manzi S, Ralison JM, Randrianambinina B, Rasoloarison RM, Rasolofoson DW, Stahlke AR, Weisrock DW, Williams RC, Chikhi L, Louis EE, Radespiel U, Yoder AD |
2021 | McKnight labElife, 2021 Feb 12;10 Basis of specificity for a conserved and promiscuous chromatin remodeling protein.Donovan DA, Crandall JG, Truong VN, Vaaler AL, Bailey TB, Dinwiddie D, Banks OG, McKnight LE, McKnight JN |
2021 | von Hippel labNucleic Acids Res, 2021 Feb 26;49(4):1872-1885 Dinucleotides as simple models of the base stacking-unstacking component of DNA 'breathing' mechanisms.Beyerle ER, Dinpajooh M, Ji H, von Hippel PH, Marcus AH, Guenza MG |
2021 | von Hippel labNucleic Acids Res, 2021 Jan 25;49(2):916-927 Mapping DNA conformations and interactions within the binding cleft of bacteriophage T4 single-stranded DNA binding protein (gp32) at single nucleotide resolution.Camel BR, Jose D, Meze K, Dang A, von Hippel PH |
2020 | Libuda labCurr Biol, 2020 Dec 21;30(24):5007-5017.e4 Elevated Temperatures Cause Transposon-Associated DNA Damage in C. elegans Spermatocytes.Kurhanewicz NA, Dinwiddie D, Bush ZD, Libuda DE |
2020 | Barkan labPlant Physiol, 2020 Dec;184(4):2011-2021 The PPR-SMR Protein ATP4 Is Required for Editing the Chloroplast rps8 mRNA in Rice and Maize.Zhang J, Guo Y, Fang Q, Zhu Y, Zhang Y, Liu X, Lin Y, Barkan A, Zhou F |
2020 | Selker labGenetics, 2020 Nov;216(3):671-688 Selection and Characterization of Mutants Defective in DNA Methylation in Neurospora crassa.Klocko AD, Summers CA, Glover ML, Parrish R, Storck WK, McNaught KJ, Moss ND, Gotting K, Stewart A, Morrison AM, Payne L, Hatakeyama S, Selker EU |
2020 | Selker labNucleic Acids Res, 2020 Oct 9;48(18):10199-10210 LSD1 prevents aberrant heterochromatin formation in Neurospora crassa.Storck WK, Bicocca VT, Rountree MR, Honda S, Ormsby T, Selker EU |
2020 | Barkan labProc Natl Acad Sci U S A, 2020 Sep 1;117(35):21775-21784 Light-induced psbA translation in plants is triggered by photosystem II damage via an assembly-linked autoregulatory circuit.Chotewutmontri P, Barkan A |
2020 | Libuda labPLoS Genet, 2020 Sep;16(9):e1009001 Excess crossovers impede faithful meiotic chromosome segregation in C. elegans.Hollis JA, Glover ML, Schlientz AJ, Cahoon CK, Bowerman B, Wignall SM, Libuda DE |
2020 | Selker labGenetics, 2020 Jul;215(3):569-578 A Light-Inducible Strain for Genome-Wide Histone Turnover Profiling in Neurospora crassa.Storck WK, Abdulla SZ, Rountree MR, Bicocca VT, Selker EU |
2020 | Selker labMol Cell Biol, 2020 May 14;40(11) Identification of a PRC2 Accessory Subunit Required for Subtelomeric H3K27 Methylation in Neurospora crassa.McNaught KJ, Wiles ET, Selker EU |
2020 | Selker labProc Natl Acad Sci U S A, 2020 May 26;117(21):11614-11623 Evolutionarily ancient BAH-PHD protein mediates Polycomb silencing.Wiles ET, McNaught KJ, Kaur G, Selker JML, Ormsby T, Aravind L, Selker EU |
2020 | Barkan labPlant J, 2020 Apr;102(2):369-382 Exploring the proteome associated with the mRNA encoding the D1 reaction center protein of Photosystem II in plant chloroplasts.Watkins KP, Williams-Carrier R, Chotewutmontri P, Friso G, Teubner M, Belcher S, Ruwe H, Schmitz-Linneweber C, van Wijk KJ, Barkan A |
2020 | Barkan labPLoS Genet, 2020 Apr;16(4):e1007881 Dynamic localization of SPO11-1 and conformational changes of meiotic axial elements during recombination initiation of maize meiosis.Ku JC, Ronceret A, Golubovskaya I, Lee DH, Wang C, Timofejeva L, Kao YH, Gomez Angoa AK, Kremling K, Williams-Carrier R, Meeley R, Barkan A, Cande WZ, Wang CR |
2020 | Barkan labPlants (Basel), 2020 Feb 6;9(2) Functional Analysis of PSRP1, the Chloroplast Homolog of a Cyanobacterial Ribosome Hibernation Factor.Swift K, Chotewutmontri P, Belcher S, Williams-Carrier R, Barkan A |
2020 | Noma labNat Commun, 2020 Feb 13;11(1):877 Epigenetic specifications of host chromosome docking sites for latent Epstein-Barr virus.Kim KD, Tanizawa H, De Leo A, Vladimirova O, Kossenkov A, Lu F, Showe LC, Noma KI, Lieberman PM |
2020 | Barkan labPlants (Basel), 2020 Jan 25;9(2) Exploring the Link between Photosystem II Assembly and Translation of the Chloroplast psbA mRNA.Chotewutmontri P, Williams-Carrier R, Barkan A |
2020 | Garcia labMol Cell, 2020 Jan 16;77(2):251-265.e9 A Non-amyloid Prion Particle that Activates a Heritable Gene Expression Program.Chakravarty AK, Smejkal T, Itakura AK, Garcia DM, Jarosz DF |
2019 | von Hippel labBiophys J, 2019 Dec 3;117(11):2043-2046 The Many Roles of Binding Cooperativity in the Control of DNA Replication.von Hippel PH, Marcus AH |
2019 | Noma labNat Commun, 2019 Dec 12;10(1):5688 Involvement of condensin in cellular senescence through gene regulation and compartmental reorganization.Iwasaki O, Tanizawa H, Kim KD, Kossenkov A, Nacarelli T, Tashiro S, Majumdar S, Showe LC, Zhang R, Noma KI |
2019 | McKnight labCell Rep, 2019 Nov 19;29(8):2520-2535.e4 Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning.Donovan DA, Crandall JG, Banks OGB, Jensvold ZD, Truong V, Dinwiddie D, McKnight LE, McKnight JN |
2019 | Libuda labGenetics, 2019 Oct;213(2):395-409 Synaptonemal Complex Central Region Proteins Promote Localization of Pro-crossover Factors to Recombination Events During Caenorhabditis elegans Meiosis.Cahoon CK, Helm JM, Libuda DE |
2019 | Libuda labChromosoma, 2019 Sep;128(3):199-214 Leagues of their own: sexually dimorphic features of meiotic prophase I.Cahoon CK, Libuda DE |
2019 | von Hippel labBiophys J, 2019 Sep 17;117(6):1101-1115 Local DNA Base Conformations and Ligand Intercalation in DNA Constructs Containing Optical Probes.Ji H, Johnson NP, von Hippel PH, Marcus AH |
2019 | Barkan labPlant Cell, 2019 Aug;31(8):1723-1733 Ribonucleoprotein Capture by in Vivo Expression of a Designer Pentatricopeptide Repeat Protein in Arabidopsis.McDermott JJ, Watkins KP, Williams-Carrier R, Barkan A |
2019 | von Hippel labFaraday Discuss, 2019 Jul 11;216(0):211-235 Measuring local conformations and conformational disorder of (Cy3)2 dimer labeled DNA fork junctions using absorbance, circular dichroism and two-dimensional fluorescence spectroscopy.Heussman D, Kittell J, Kringle L, Tamimi A, von Hippel PH, Marcus AH |
2019 | Selker labGenetics, 2019 Jul;212(3):691-710 Control of Development, Secondary Metabolism and Light-Dependent Carotenoid Biosynthesis by the Velvet Complex of Neurospora crassa.Bayram ÖS, Dettmann A, Karahoda B, Moloney NM, Ormsby T, McGowan J, Cea-Sánchez S, Miralles-Durán A, Brancini GTP, Luque EM, Fitzpatrick DA, Cánovas D, Corrochano LM, Doyle S, Selker EU, Seiler S, Bayram Ö |
2019 | Barkan labPlant J, 2019 Jul;99(1):56-66 The Arabidopsis pentatricopeptide repeat protein LPE1 and its maize ortholog are required for translation of the chloroplast psbJ RNA.Williams-Carrier R, Brewster C, Belcher SE, Rojas M, Chotewutmontri P, Ljungdahl S, Barkan A |
2019 | Barkan labPlant Cell, 2019 Jun;31(6):1308-1327 An RNA Chaperone-Like Protein Plays Critical Roles in Chloroplast mRNA Stability and Translation in Arabidopsis and Maize.Jiang J, Chai X, Manavski N, Williams-Carrier R, He B, Brachmann A, Ji D, Ouyang M, Liu Y, Barkan A, Meurer J, Zhang L, Chi W |
2019 | Barkan labNat Plants, 2019 May;5(5):486-490 Engineered RNA-binding protein for transgene activation in non-green plastids.Yu Q, Barkan A, Maliga P |
2019 | Libuda labElife, 2019 May 14;8 Painting chromosomes in the nucleus.Cahoon CK, Libuda DE |
2019 | Barkan labNat Plants, 2019 May;5(5):505-511 Engineered PPR proteins as inducible switches to activate the expression of chloroplast transgenes.Rojas M, Yu Q, Williams-Carrier R, Maliga P, Barkan A |
2019 | Noma labSci Adv, 2019 May;5(5):eaaw5294 ARID1A spatially partitions interphase chromosomes.Wu S, Fatkhutdinov N, Rosin L, Luppino JM, Iwasaki O, Tanizawa H, Tang HY, Kossenkov AV, Gardini A, Noma KI, Speicher DW, Joyce EF, Zhang R |
2019 | Noma labNat Cell Biol, 2019 Mar;21(3):397-407 NAD+ metabolism governs the proinflammatory senescence-associated secretome.Nacarelli T, Lau L, Fukumoto T, Zundell J, Fatkhutdinov N, Wu S, Aird KM, Iwasaki O, Kossenkov AV, Schultz D, Noma KI, Baur JA, Schug Z, Tang HY, Speicher DW, David G, Zhang R |
2019 | Selker labGenetics, 2019 Feb;211(2):563-578 Nucleosome Positioning by an Evolutionarily Conserved Chromatin Remodeler Prevents Aberrant DNA Methylation in Neurospora.Klocko AD, Uesaka M, Ormsby T, Rountree MR, Wiles ET, Adhvaryu KK, Honda S, Selker EU |
2019 | McKnight labMol Cell, 2019 Feb 7;73(3):533-546.e4 Condensin-Dependent Chromatin Compaction Represses Transcription Globally during Quiescence.Swygert SG, Kim S, Wu X, Fu T, Hsieh TH, Rando OJ, Eisenman RN, Shendure J, McKnight JN, Tsukiyama T |
2019 | Barkan labPLoS Genet, 2019 Jan;15(1):e1007907 Correction: Multilevel effects of light on ribosome dynamics in chloroplasts program genome-wide and psbA-specific changes in translation.Chotewutmontri P, Barkan A |
2018 | Barkan labPlant Physiol, 2018 Dec;178(4):1643-1656 Efficient Replication of the Plastid Genome Requires an Organellar Thymidine Kinase.Le Ret M, Belcher S, Graindorge S, Wallet C, Koechler S, Erhardt M, Williams-Carrier R, Barkan A, Gualberto JM |
2018 | Selker labElife, 2018 Nov 23;7 ASH1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin.Bicocca VT, Ormsby T, Adhvaryu KK, Honda S, Selker EU |
2018 | Barkan labNucleic Acids Res, 2018 Nov 2;46(19):10448-10459 Unexpected functional versatility of the pentatricopeptide repeat proteins PGR3, PPR5 and PPR10.Rojas M, Ruwe H, Miranda RG, Zoschke R, Hase N, Schmitz-Linneweber C, Barkan A |
2018 | Libuda labPLoS Genet, 2018 Sep;14(9):e1007649 2018 PLOS Genetics Research Prize: Bundling, stabilizing, organizing-The orchestration of acentriolar spindle assembly by microtubule motor proteins.Barsh GS, Bhalla N, Cole F, Copenhaver GP, Lacefield S, Libuda DE |
2018 | Barkan labPLoS Genet, 2018 Aug;14(8):e1007555 Multilevel effects of light on ribosome dynamics in chloroplasts program genome-wide and psbA-specific changes in translation.Chotewutmontri P, Barkan A |
2018 | Barkan labPlant J, 2018 Apr;94(1):8-21 Stabilization and translation of synthetic operon-derived mRNAs in chloroplasts by sequences representing PPR protein-binding sites.Legen J, Ruf S, Kroop X, Wang G, Barkan A, Bock R, Schmitz-Linneweber C |
2018 | Barkan labNucleic Acids Res, 2018 Mar 16;46(5):2613-2623 RNA-binding specificity landscapes of designer pentatricopeptide repeat proteins elucidate principles of PPR-RNA interactions.Miranda RG, McDermott JJ, Barkan A |
2018 | Johnson labNat Ecol Evol, 2018 Mar;2(3):491-498 A southern African origin and cryptic structure in the highly mobile plains zebra.Pedersen CT, Albrechtsen A, Etter PD, Johnson EA, Orlando L, Chikhi L, Siegismund HR, Heller R |
2018 | Selker labElife, 2018 Jan 3;7 Telomere repeats induce domains of H3K27 methylation in Neurospora.Jamieson K, McNaught KJ, Ormsby T, Leggett NA, Honda S, Selker EU |
2018 | Barkan labPLoS One, 2018;13(12):e0209713 Effects of RNA structure and salt concentration on the affinity and kinetics of interactions between pentatricopeptide repeat proteins and their RNA ligands.McDermott JJ, Civic B, Barkan A |
2018 | Barkan labMethods Mol Biol, 2018;1676:165-183 Ribosome Profiling in Maize.Chotewutmontri P, Stiffler N, Watkins KP, Barkan A |
2017 | Noma labAnnu Rev Genet, 2017 Nov 27;51:23-44 The Yeast Genomes in Three Dimensions: Mechanisms and Functions.Noma KI |
2017 | Noma labNat Struct Mol Biol, 2017 Nov;24(11):965-976 Architectural alterations of the fission yeast genome during the cell cycle.Tanizawa H, Kim KD, Iwasaki O, Noma KI |
2017 | Selker labProc Natl Acad Sci U S A, 2017 Nov 7;114(45):E9598-E9607 Induction of H3K9me3 and DNA methylation by tethered heterochromatin factors in Neurospora crassa.Gessaman JD, Selker EU |
2017 | Barkan labPlant Physiol, 2017 Jul;174(3):1850-1862 PSA3, a Protein on the Stromal Face of the Thylakoid Membrane, Promotes Photosystem I Accumulation in Cooperation with the Assembly Factor PYG7.Shen J, Williams-Carrier R, Barkan A |
2017 | Stankunas labDev Biol, 2017 Jun 1;426(1):84-96 Histone demethylases Kdm6ba and Kdm6bb redundantly promote cardiomyocyte proliferation during zebrafish heart ventricle maturation.Akerberg AA, Henner A, Stewart S, Stankunas K |
2017 | von Hippel labProc Natl Acad Sci U S A, 2017 May 2;114(18):E3612-E3621 Using microsecond single-molecule FRET to determine the assembly pathways of T4 ssDNA binding protein onto model DNA replication forks.Phelps C, Israels B, Jose D, Marsh MC, von Hippel PH, Marcus AH |
2017 | Selker labProc Natl Acad Sci U S A, 2017 Apr 4;114(14):E2816-E2825 Recurrent rewiring and emergence of RNA regulatory networks.Wilinski D, Buter N, Klocko AD, Lapointe CP, Selker EU, Gasch AP, Wickens M |
2017 | Selker labCurr Opin Genet Dev, 2017 Apr;43:31-37 H3K27 methylation: a promiscuous repressive chromatin mark.Wiles ET, Selker EU |
2017 | Barkan labRNA, 2017 Apr;23(4):586-599 RNA-binding specificity landscape of the pentatricopeptide repeat protein PPR10.Miranda RG, Rojas M, Montgomery MP, Gribbin KP, Barkan A |
2017 | Stankunas labDevelopment, 2017 Apr 1;144(7):1165-1176 Shh promotes direct interactions between epidermal cells and osteoblast progenitors to shape regenerated zebrafish bone.Armstrong BE, Henner A, Stewart S, Stankunas K |
2017 | McKnight labBioessays, 2017 Jan;39(1):1-8 Sequence-specific targeting of chromatin remodelers organizes precisely positioned nucleosomes throughout the genome.Bowman GD, McKnight JN |
2017 | Barkan labFront Plant Sci, 2017;8:385 Translation and Co-translational Membrane Engagement of Plastid-encoded Chlorophyll-binding Proteins Are Not Influenced by Chlorophyll Availability in Maize.Zoschke R, Chotewutmontri P, Barkan A |
2016 | von Hippel labNucleic Acids Res, 2016 Dec 15;44(22):10691-10710 Single-molecule FRET studies of the cooperative and non-cooperative binding kinetics of the bacteriophage T4 single-stranded DNA binding protein (gp32) to ssDNA lattices at replication fork junctions.Lee W, Gillies JP, Jose D, Israels BA, von Hippel PH, Marcus AH |
2016 | von Hippel labJ Phys Chem B, 2016 Dec 29;120(51):13003-13016 Using Multiorder Time-Correlation Functions (TCFs) To Elucidate Biomolecular Reaction Pathways from Microsecond Single-Molecule Fluorescence Experiments.Phelps C, Israels B, Marsh MC, von Hippel PH, Marcus AH |
2016 | Selker labProc Natl Acad Sci U S A, 2016 Dec 27;113(52):15048-15053 Normal chromosome conformation depends on subtelomeric facultative heterochromatin in Neurospora crassa.Klocko AD, Ormsby T, Galazka JM, Leggett NA, Uesaka M, Honda S, Freitag M, Selker EU |
2016 | Noma labJ Cell Biol, 2016 Nov 7;215(3):325-334 HMGB2 orchestrates the chromatin landscape of senescence-associated secretory phenotype gene loci.Aird KM, Iwasaki O, Kossenkov AV, Tanizawa H, Fatkhutdinov N, Bitler BG, Le L, Alicea G, Yang TL, Johnson FB, Noma KI, Zhang R |
2016 | von Hippel labBiophys J, 2016 Nov 1;111(9):1817-1820 Changing the Stability of Macromolecular Surfaces by Manipulating the Aqueous Environment.von Hippel PH |
2016 | Noma labCurr Genet, 2016 Nov;62(4):739-743 Condensin-mediated chromosome organization in fission yeast.Iwasaki O, Noma KI |
2016 | Noma labNat Genet, 2016 Oct;48(10):1242-52 Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast.Kim KD, Tanizawa H, Iwasaki O, Noma K |
2016 | Selker labProc Natl Acad Sci U S A, 2016 Oct 11;113(41):E6135-E6144 Dual chromatin recognition by the histone deacetylase complex HCHC is required for proper DNA methylation in Neurospora crassa.Honda S, Bicocca VT, Gessaman JD, Rountree MR, Yokoyama A, Yu EY, Selker JM, Selker EU |
2016 | Barkan labPlant Physiol, 2016 Sep;172(1):62-77 Codon Optimization to Enhance Expression Yields Insights into Chloroplast Translation.Kwon KC, Chan HT, León IR, Williams-Carrier R, Barkan A, Daniell H |
2016 | Selker labGenome Res, 2016 Aug;26(8):1069-80 Neurospora chromosomes are organized by blocks of importin alpha-dependent heterochromatin that are largely independent of H3K9me3.Galazka JM, Klocko AD, Uesaka M, Honda S, Selker EU, Freitag M |
2016 | Barkan labPLoS Genet, 2016 Jul;12(7):e1006106 Dynamics of Chloroplast Translation during Chloroplast Differentiation in Maize.Chotewutmontri P, Barkan A |
2016 | Johnson labBMC Genomics, 2016 Jun 14;17:464 High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq).Preston JL, Royall AE, Randel MA, Sikkink KL, Phillips PC, Johnson EA |
2016 | McKnight labGenome Res, 2016 May;26(5):693-704 Sequence-targeted nucleosome sliding in vivo by a hybrid Chd1 chromatin remodeler.McKnight JN, Tsukiyama T, Bowman GD |
2016 | Noma labNucleic Acids Res, 2016 May 5;44(8):3618-28 Involvement of condensin-directed gene associations in the organization and regulation of chromosome territories during the cell cycle.Iwasaki O, Corcoran CJ, Noma K |
2016 | Barkan labNucleic Acids Res, 2016 May 19;44(9):4278-88 A PPR protein in the PLS subfamily stabilizes the 5'-end of processed rpl16 mRNAs in maize chloroplasts.Hammani K, Takenaka M, Miranda R, Barkan A |
2016 | Barkan labPlant J, 2016 Mar;85(5):594-606 The PPR-SMR protein PPR53 enhances the stability and translation of specific chloroplast RNAs in maize.Zoschke R, Watkins KP, Miranda RG, Barkan A |
2016 | Johnson labPediatr Cardiol, 2016 Mar;37(3):593-600 Surgical Quality Predicts Length of Stay in Patients with Congenital Heart Disease.Johnson EA, Zubair MM, Armsby LR, Burch GH, Good MK, Lasarev MR, Hohimer AR, Muralidaran A, Langley SM |
2016 | Noma labPLoS Genet, 2016 Mar;12(3):e1005943 Swi1Timeless Prevents Repeat Instability at Fission Yeast Telomeres.Gadaleta MC, Das MM, Tanizawa H, Chang YT, Noma K, Nakamura TM, Noguchi E |
2016 | Stankunas labDevelopment, 2016 Mar 15;143(6):1041-54 Wnt/β-catenin signaling enables developmental transitions during valvulogenesis.Bosada FM, Devasthali V, Jones KA, Stankunas K |
2016 | Selker labGenome Res, 2016 Jan;26(1):97-107 Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin.Jamieson K, Wiles ET, McNaught KJ, Sidoli S, Leggett N, Shao Y, Garcia BA, Selker EU |
2016 | Noma labMethods Enzymol, 2016;574:167-180 An IF-FISH Approach for Covisualization of Gene Loci and Nuclear Architecture in Fission Yeast.Kim KD, Iwasaki O, Noma K |
2016 | Stankunas labPLoS One, 2016;11(8):e0159277 A MultiSite Gateway Toolkit for Rapid Cloning of Vertebrate Expression Constructs with Diverse Research Applications.Fowler DK, Stewart S, Seredick S, Eisen JS, Stankunas K, Washbourne P |
2015 | McKnight labGenom Data, 2015 Dec;6:245-8 The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae.McKnight JN, Tsukiyama T |
2015 | Stankunas labBMC Genomics, 2015 Dec 23;16:1100 Transcriptomes of post-mitotic neurons identify the usage of alternative pathways during adult and embryonic neuronal differentiation.Tallafuss A, Kelly M, Gay L, Gibson D, Batzel P, Karfilis KV, Eisen J, Stankunas K, Postlethwait JH, Washbourne P |
2015 | Johnson labCell, 2015 Dec 3;163(6):1539-54 The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan.Valenzano DR, Benayoun BA, Singh PP, Zhang E, Etter PD, Hu CK, Clément-Ziza M, Willemsen D, Cui R, Harel I, Machado BE, Yee MC, Sharp SC, Bustamante CD, Beyer A, Johnson EA, Brunet A |
2015 | Stankunas labDev Biol, 2015 Nov 1;407(1):158-72 Endocardial Brg1 disruption illustrates the developmental origins of semilunar valve disease.Akerberg BN, Sarangam ML, Stankunas K |
2015 | von Hippel labJ Phys Chem B, 2015 Oct 8;119(40):12798-807 Sequence-Dependent Conformational Heterogeneity and Proton-Transfer Reactivity of the Fluorescent Guanine Analogue 6-Methyl Isoxanthopterin (6-MI) in DNA.Johnson NP, Ji H, Steinberg TH, von Hippel PH, Marcus AH |
2015 | von Hippel labNucleic Acids Res, 2015 Oct 30;43(19):9291-305 Mapping the interactions of the single-stranded DNA binding protein of bacteriophage T4 (gp32) with DNA lattices at single nucleotide resolution: polynucleotide binding and cooperativity.Jose D, Weitzel SE, Baase WA, Michael MM, von Hippel PH |
2015 | von Hippel labNucleic Acids Res, 2015 Oct 30;43(19):9276-90 Mapping the interactions of the single-stranded DNA binding protein of bacteriophage T4 (gp32) with DNA lattices at single nucleotide resolution: gp32 monomer binding.Jose D, Weitzel SE, Baase WA, von Hippel PH |
2015 | McKnight labMol Cell, 2015 Sep 3;59(5):732-43 Global Promoter Targeting of a Conserved Lysine Deacetylase for Transcriptional Shutoff during Quiescence Entry.McKnight JN, Boerma JW, Breeden LL, Tsukiyama T |
2015 | Johnson labMol Biol Evol, 2015 Sep;32(9):2338-50 Phylogeographic Analyses of American Black Bears (Ursus americanus) Suggest Four Glacial Refugia and Complex Patterns of Postglacial Admixture.Puckett EE, Etter PD, Johnson EA, Eggert LS |
2015 | Noma labMol Cell, 2015 Sep 3;59(5):755-67 Interaction between TBP and Condensin Drives the Organization and Faithful Segregation of Mitotic Chromosomes.Iwasaki O, Tanizawa H, Kim KD, Yokoyama Y, Corcoran CJ, Tanaka A, Skordalakes E, Showe LC, Noma K |
2015 | Barkan labBiochim Biophys Acta, 2015 Sep;1847(9):1004-16 Large-scale genetic analysis of chloroplast biogenesis in maize.Belcher S, Williams-Carrier R, Stiffler N, Barkan A |
2015 | Barkan labProc Natl Acad Sci U S A, 2015 Jul 14;112(28):8529-36 Redesigning photosynthesis to sustainably meet global food and bioenergy demand.Ort DR, Merchant SS, Alric J, Barkan A, Blankenship RE, Bock R, Croce R, Hanson MR, Hibberd JM, Long SP, Moore TA, Moroney J, Niyogi KK, Parry MA, Peralta-Yahya PP, Prince RC, Redding KE, Spalding MH, van Wijk KJ, Vermaas WF, von Caemmerer S, Weber AP, Yeates TO, Yuan JS, Zhu XG |
2015 | von Hippel labProc Natl Acad Sci U S A, 2015 Jun 2;112(22):6776-7 John Schellman and the birth of protein folding.Baldwin RL, von Hippel PH |
2015 | Barkan labNew Phytol, 2015 May;206(3):1024-1037 ZmpTAC12 binds single-stranded nucleic acids and is essential for accumulation of the plastid-encoded polymerase complex in maize.Pfalz J, Holtzegel U, Barkan A, Weisheit W, Mittag M, Pfannschmidt T |
2015 | Selker labPLoS Genet, 2015 Mar;11(3):e1005083 Neurospora importin α is required for normal heterochromatic formation and DNA methylation.Klocko AD, Rountree MR, Grisafi PL, Hays SM, Adhvaryu KK, Selker EU |
2015 | Barkan labProc Natl Acad Sci U S A, 2015 Mar 31;112(13):E1678-87 Genome-wide analysis of thylakoid-bound ribosomes in maize reveals principles of cotranslational targeting to the thylakoid membrane.Zoschke R, Barkan A |
2015 | Johnson labBMC Genomics, 2015 Feb 14;16:83 Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis.Pan L, Shah AN, Phelps IG, Doherty D, Johnson EA, Moens CB |
2015 | Barkan labNucleic Acids Res, 2015 Feb 18;43(3):1918-26 The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA.Gully BS, Cowieson N, Stanley WA, Shearston K, Small ID, Barkan A, Bond CS |
2015 | Selker labEukaryot Cell, 2015 Jan;14(1):25-8 The cullin-4 complex DCDC does not require E3 ubiquitin ligase elements to control heterochromatin in Neurospora crassa.Adhvaryu KK, Gessaman JD, Honda S, Lewis ZA, Grisafi PL, Selker EU |
2015 | von Hippel labPLoS One, 2015;10(5):e0126420 A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation.Zhao H, Ghirlando R, Alfonso C, Arisaka F, Attali I, Bain DL, Bakhtina MM, Becker DF, Bedwell GJ, Bekdemir A, Besong TM, Birck C, Brautigam CA, Brennerman W, Byron O, Bzowska A, Chaires JB, Chaton CT, Cölfen H, Connaghan KD, Crowley KA, Curth U, Daviter T, Dean WL, Díez AI, Ebel C, Eckert DM, Eisele LE, Eisenstein E, England P, Escalante C, Fagan JA, Fairman R, Finn RM, Fischle W, de la Torre JG, Gor J, Gustafsson H, Hall D, Harding SE, Cifre JG, Herr AB, Howell EE, Isaac RS, Jao SC, Jose D, Kim SJ, Kokona B, Kornblatt JA, Kosek D, Krayukhina E, Krzizike D, Kusznir EA, Kwon H, Larson A, Laue TM, Le Roy A, Leech AP, Lilie H, Luger K, Luque-Ortega JR, Ma J, May CA, Maynard EL, Modrak-Wojcik A, Mok YF, Mücke N, Nagel-Steger L, Narlikar GJ, Noda M, Nourse A, Obsil T, Park CK, Park JK, Pawelek PD, Perdue EE, Perkins SJ, Perugini MA, Peterson CL, Peverelli MG, Piszczek G, Prag G, Prevelige PE, Raynal BD, Rezabkova L, Richter K, Ringel AE, Rosenberg R, Rowe AJ, Rufer AC, Scott DJ, Seravalli JG, Solovyova AS, Song R, Staunton D, Stoddard C, Stott K, Strauss HM, Streicher WW, Sumida JP, Swygert SG, Szczepanowski RH, Tessmer I, Toth RT 4th, Tripathy A, Uchiyama S, Uebel SF, Unzai S, Gruber AV, von Hippel PH, Wandrey C, Wang SH, Weitzel SE, Wielgus-Kutrowska B, Wolberger C, Wolff M, Wright E, Wu YS, Wubben JM, Schuck P |
2015 | McKnight labCell Cycle, 2015;14(23):3667-8 A molecular off switch for transcriptional quiescence.McKnight JN, Breeden LL, Tsukiyama T |
2015 | Johnson labPeerJ, 2015;3:e1527 Genome-wide identification of hypoxia-induced enhancer regions.Kamps-Hughes N, Preston JL, Randel MA, Johnson EA |
2015 | Noma labCell Cycle, 2015;14(13):2160-70 A novel role for the condensin II complex in cellular senescence.Yokoyama Y, Zhu H, Zhang R, Noma K |
2015 | Noma labMethods Mol Biol, 2015;1300:169-86 Chromatin immunoprecipitation to detect DNA replication and repair factors.Gadaleta MC, Iwasaki O, Noguchi C, Noma K, Noguchi E |
2014 | von Hippel labProc Natl Acad Sci U S A, 2014 Dec 9;111(49):17344-5 Increased subtlety of transcription factor binding increases complexity of genome regulation.von Hippel PH |
2014 | Barkan labPlant J, 2014 Dec;80(5):862-9 A protein with an inactive pterin-4a-carbinolamine dehydratase domain is required for Rubisco biogenesis in plants.Feiz L, Williams-Carrier R, Belcher S, Montano M, Barkan A, Stern DB |
2014 | Stankunas labDevelopment, 2014 Dec;141(23):4500-12 The sinus venosus contributes to coronary vasculature through VEGFC-stimulated angiogenesis.Chen HI, Sharma B, Akerberg BN, Numi HJ, Kivelä R, Saharinen P, Aghajanian H, McKay AS, Bogard PE, Chang AH, Jacobs AH, Epstein JA, Stankunas K, Alitalo K, Red-Horse K |
2014 | McKnight labCurr Protoc Mol Biol, 2014 Oct 1;108:21.28.1-16 Genome-Wide Analysis of Nucleosome Positions, Occupancy, and Accessibility in Yeast: Nucleosome Mapping, High-Resolution Histone ChIP, and NCAM.Rodriguez J, McKnight JN, Tsukiyama T |
2014 | Barkan labJ Biol Chem, 2014 Oct 31;289(44):30657-30667 A thylakoid membrane protein harboring a DnaJ-type zinc finger domain is required for photosystem I accumulation in plants.Fristedt R, Williams-Carrier R, Merchant SS, Barkan A |
2014 | Libuda labGenetics, 2014 Sep;198(1):193-207 DNA helicase HIM-6/BLM both promotes MutSγ-dependent crossovers and antagonizes MutSγ-independent interhomolog associations during caenorhabditis elegans meiosis.Schvarzstein M, Pattabiraman D, Libuda DE, Ramadugu A, Tam A, Martinez-Perez E, Roelens B, Zawadzki KA, Yokoo R, Rosu S, Severson AF, Meyer BJ, Nabeshima K, Villeneuve AM |
2014 | von Hippel labNucleic Acids Res, 2014 May;42(9):5967-77 Internally labeled Cy3/Cy5 DNA constructs show greatly enhanced photo-stability in single-molecule FRET experiments.Lee W, von Hippel PH, Marcus AH |
2014 | Barkan labNucleic Acids Res, 2014 Apr;42(8):5033-42 An mTERF domain protein functions in group II intron splicing in maize chloroplasts.Hammani K, Barkan A |
2014 | Stankunas labCell Rep, 2014 Feb 13;6(3):482-98 Sequential and opposing activities of Wnt and BMP coordinate zebrafish bone regeneration.Stewart S, Gomez AW, Armstrong BE, Henner A, Stankunas K |
2014 | Stankunas labNat Protoc, 2014 Feb;9(2):410-20 Applying thiouracil tagging to mouse transcriptome analysis.Gay L, Karfilis KV, Miller MR, Doe CQ, Stankunas K |
2014 | Barkan labPlant Physiol, 2014 Jan;164(1):239-48 A major role for the plastid-encoded RNA polymerase complex in the expression of plastid transfer RNAs.Williams-Carrier R, Zoschke R, Belcher S, Pfalz J, Barkan A |
2014 | Stankunas labPLoS One, 2014;9(3):e92217 Spatial and temporal control of transgene expression in zebrafish.Akerberg AA, Stewart S, Stankunas K |
2014 | Barkan labAnnu Rev Plant Biol, 2014;65:415-42 Pentatricopeptide repeat proteins in plants.Barkan A, Small I |