Top Ten Papers in Regulatory and Systems Genomics 2011

On November 12, 2012, organizers of the 5th Annual RECOMB Conference on Regulatory and Systems Genomics, with DREAM Challenges, and the International Society for Molecular Biology's Special Interest Group on Regulatory Genomics (RegGenSIG) announced the following list of the most influential papers of 2011 in the fields of systems biology and regulatory genomics. The announcement was made by Saurabh Sinha (University of Illinois, Urbana-Champaign) and Manolis Kellis (MIT).


The top ten papers were nominated by researchers within the regulatory genomics and systems biology communities. The final decisions were made following voting by speakers at the 5th Annual RECOMB Conference on Regulatory and Systems Genomics, with DREAM Challenges, and keynote speakers of past conferences in this series.


A high-resolution map of human evolutionary constraint using 29 mammals

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.
Nature. 2011 Oct 12;478(7370):476-82.


Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK.
Genome Res. 2011 Mar;21(3):447-55.


An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma
Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A.
Cell. 2011 Oct 14;147(2):370-81.


Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project
Mu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB.
Nucleic Acids Res. 2011 Sep 1;39(16):7058-76.


Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins
Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS
Cell. 2011 Dec 9;147(6):1270-82.


Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
Rhee HS, Pugh BF.
Cell. 2011 Dec 9;147(6):1408-19.


Discriminative prediction of mammalian enhancers from DNA sequence
Lee D, Karchin R, Beer MA.
Genome Res. Dec;21(12):2167-80.


Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism
Voss TC, Schiltz RL, Sung MH, Yen PM, Stamatoyannopoulos JA, Biddie SC, Johnson TA, Miranda TB, John S, Hager GL.
Cell. 2011 Aug 19;146(4):544-54.


Mapping and analysis of chromatin state dynamics in nine human cell types
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE.
Nature. 2011 May 5;473(7345):43-9.


Prioritizing candidate disease genes by network-based boosting of genome-wide association data
Lee I, Blom UM, Wang PI, Shim JE, Marcotte EM.
Genome Res. 2011 Jul;21(7):1109-21.