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