|Assigning protein functions by comparative genome analysis: protein phylogenetic profiles|
M Pellegrini, EM Marcotte, MJ Thompson, D Eisenberg, TO Yeates
Proceedings of the National Academy of Sciences 96 (8), 4285-4288, 1999
|Detecting protein function and protein-protein interactions from genome sequences|
EM Marcotte, M Pellegrini, HL Ng, DW Rice, TO Yeates, D Eisenberg
Science 285 (5428), 751-753, 1999
|Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning|
SJ Cokus, S Feng, X Zhang, Z Chen, B Merriman, CD Haudenschild, ...
Nature 452 (7184), 215, 2008
|Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis|
X Zhang, J Yazaki, A Sundaresan, S Cokus, SWL Chan, H Chen, ...
Cell 126 (6), 1189-1201, 2006
|A combined algorithm for genome-wide prediction of protein function|
EM Marcotte, M Pellegrini, MJ Thompson, TO Yeates, D Eisenberg
Nature 402 (6757), 83, 1999
|Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures|
MH Chin, MJ Mason, W Xie, S Volinia, M Singer, C Peterson, ...
Cell Stem Cell 5 (1), 111-123, 2009
|Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency|
C Popp, W Dean, S Feng, SJ Cokus, S Andrews, M Pellegrini, ...
Nature 463 (7284), 1101, 2010
|Conservation and divergence of methylation patterning in plants and animals|
S Feng, SJ Cokus, X Zhang, PY Chen, M Bostick, MG Goll, J Hetzel, J Jain, ...
Proceedings of the National Academy of Sciences 107 (19), 8689-8694, 2010
|Relationship between nucleosome positioning and DNA methylation|
RK Chodavarapu, S Feng, YV Bernatavichute, PY Chen, H Stroud, Y Yu, ...
Nature 466 (7304), 388, 2010
|Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis|
X Zhang, O Clarenz, S Cokus, YV Bernatavichute, M Pellegrini, ...
PLoS biology 5 (5), e129, 2007
|Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation|
SD Fouse, Y Shen, M Pellegrini, S Cole, A Meissner, L Van Neste, ...
Cell stem cell 2 (2), 160-169, 2008
|A census of protein repeats|
EM Marcotte, M Pellegrini, TO Yeates, D Eisenberg
Journal of molecular biology 293 (1), 151-160, 1999
|Genome-wide analysis of mono-, di-and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana|
X Zhang, YV Bernatavichute, S Cokus, M Pellegrini, SE Jacobsen
Genome biology 10 (6), R62, 2009
|Prolinks: a database of protein functional linkages derived from coevolution|
PM Bowers, M Pellegrini, MJ Thompson, J Fierro, TO Yeates, D Eisenberg
Genome biology 5 (5), R35, 2004
|Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas|
NR Boyle, MD Page, B Liu, IK Blaby, D Casero, J Kropat, SJ Cokus, ...
Journal of Biological Chemistry 287 (19), 15811-15825, 2012
|Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana|
YV Bernatavichute, X Zhang, S Cokus, M Pellegrini, SE Jacobsen
PloS one 3 (9), e3156, 2008
|Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming|
A Soufi, MF Garcia, A Jaroszewicz, N Osman, M Pellegrini, KS Zaret
Cell 161 (3), 555-568, 2015
|Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli|
S Atsumi, TY Wu, IMP Machado, WC Huang, PY Chen, M Pellegrini, ...
Molecular systems biology 6 (1), 449, 2010
|DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees|
S Foret, R Kucharski, M Pellegrini, S Feng, SE Jacobsen, GE Robinson, ...
Proceedings of the National Academy of Sciences 109 (13), 4968-4973, 2012
|BS Seeker: precise mapping for bisulfite sequencing|
PY Chen, SJ Cokus, M Pellegrini
BMC bioinformatics 11 (1), 203, 2010