Saved on 7/10/2007 1. Pennacchio LA, Loots GG, Nobrega MA, et al. Predicting tissue-specific enhancers in the human genome GENOME RESEARCH 17 (2): 201-211 FEB 2007 2. Loots G, Ovcharenko I ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes BIOINFORMATICS 23 (1): 122-124 JAN 1 2007 3. Loots GG, Chain PSG, Mabery S, et al. Array2BIO: from microarray expression data to functional annotation of co-regulated genes BMC BIOINFORMATICS 7: Art. No. 307 JUN 16 2006 4. Do Kim J, Hinz AK, Bergmann A, et al. Identification of clustered YY1 binding sites in imprinting control regions GENOME RESEARCH 16 (7): 901-911 JUL 2006 5. Shin JT, Priest JR, Ovcharenko I, et al. Human-zebrafish non-coding conserved elements act in vivo to regulate transcription NUCLEIC ACIDS RESEARCH 33 (17): 5437-5445 2005 6. Loots GG, Ovcharenko I Dcode.org anthology of comparative genomic tools NUCLEIC ACIDS RESEARCH 33: W56-W64 Suppl. S JUL 1 2005 7. Ovcharenko I, Nobrega MA Identifying synonymous regulatory elements in vertebrate genomes NUCLEIC ACIDS RESEARCH 33: W403-W407 Suppl. S JUL 1 2005 8. Loots GG, Ovcharenko I Dcode.org anthology of comparative genomic tools NUCLEIC ACIDS RESEARCH 33: W56-W64 Suppl. 2 JUL 1 2005 9. Ovcharenko I, Nobrega MA Identifying synonymous regulatory elements in vertebrate genomes NUCLEIC ACIDS RESEARCH 33: W403-W407 Suppl. 2 JUL 1 2005 10. Hillier LW, Graves TA, Fulton RS, et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4 NATURE 434 (7034): 724-731 APR 7 2005 11. Ovcharenko I, Loots GG, Nobrega MA, et al. Evolution and functional classification of vertebrate gene deserts GENOME RESEARCH 15 (1): 137-145 JAN 2005 12. Ovcharenko I, Loots GG, Giardine BM, et al. Mulan: Multiple-sequence local alignment and visualization for studying function and evolution GENOME RESEARCH 15 (1): 184-194 JAN 2005 13. Hillier LW, Miller W, Birney E, et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution NATURE 432 (7018): 695-716 DEC 9 2004 14. Wong GKS, Liu B, Wang J, et al. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms NATURE 432 (7018): 717-722 DEC 9 2004 15. Ovcharenko I, Stubbs L, Loots GG Interpreting mammalian evolution using Fugu genome comparisons GENOMICS 84 (5): 890-895 NOV 2004 16. Ovcharenko I, Loots GG Comparative genomic tools for exploring the human genome COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 68: 283-291 2003 17. Loots GG, Ovcharenko I rVISTA 2.0: evolutionary analysis of transcription factor binding sites NUCLEIC ACIDS RESEARCH 32: W217-W221 Suppl. 2 JUL 1 2004 18. Sharan R, Ben-Hur A, Loots GG, et al. CREME: Cis-Regulatory Module Explorer for the human genome NUCLEIC ACIDS RESEARCH 32: W253-W256 Suppl. 2 JUL 1 2004 19. Ovcharenko I, Nobrega MA, Loots GG, et al. ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes NUCLEIC ACIDS RESEARCH 32: W280-W286 Suppl. 2 JUL 1 2004 20. Ovcharenko I, Boffelli D, Loots GG EShadow: A tool for comparing closely related sequences GENOME RESEARCH 14 (6): 1191-1198 JUN 2004 21. Grimwood J, Gordon LA, Olsen A, et al. The DNA sequence and biology of human chromosome 19 NATURE 428 (6982): 529-535 APR 1 2004 22. Ovcharenko I, Loots GG, Hardison RC, et al. zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles GENOME RESEARCH 14 (3): 472-477 MAR 2004 23. Nobrega MA, Ovcharenko I, Afzal V, et al. Scanning human gene deserts for long-range enhancers SCIENCE 302 (5644): 413-413 OCT 17 2003 24. Boffelli D, McAuliffe J, Ovcharenko D, et al. Phylogenetic shadowing of primate sequences to find functional regions of the human genome SCIENCE 299 (5611): 1391-1394 FEB 28 2003 25. Loots GG, Ovcharenko I, Pachter L, et al. rVista for comparative sequence-based discovery of functional transcription factor binding sites GENOME RESEARCH 12 (5): 832-839 MAY 2002 26. Xiao C, Hagelberg F, Ovcharenko I, et al. Geometric structures and stabilities of CuSin clusters (n=8, 10, 12) JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 549: 181-192 Sp. Iss. SI AUG 6 2001 27. Ovcharenko I, Lester WA, Xiao CY, et al. Fixed node diffusion monte carlo characterization of Cu-doped Si clusters. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 221: 271-PHYS Part 2 APR 1 2001 28. Aspuru-Guzik A, Couronne O, Ovcharenko I, et al. Limited fixed sample optimization in quantum Monte Carlo: The challenge of optimizing correlated wavefunctions for large chemical systems. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 221: 275-PHYS Part 2 APR 1 2001 29. Ovcharenko IV, Lester WA, Xiao C, et al. Quantum Monte Carlo characterization of small Cu-doped silicon clusters: CuSi4 and CuSi6 JOURNAL OF CHEMICAL PHYSICS 114 (20): 9028-9032 MAY 22 2001 30. Ovcharenko I, Aspuru-Guzik A, Lester WA Soft pseudopotentials for efficient quantum Monte Carlo calculations: From Be to Ne and Al to Ar JOURNAL OF CHEMICAL PHYSICS 114 (18): 7790-7794 MAY 8 2001 31. Taraban MB, Kruppa AI, Volkova OS, et al. Origin of magnetic field effect in the photolysis of 7-silanorbornadiene derivatives in solution JOURNAL OF PHYSICAL CHEMISTRY A 104 (9): 1811-1816 MAR 9 2000 32. Ovcharenko IV, Shvedenkov YG, Musin RN, et al. Determination of exchange interaction parameters in heterospin exchange clusters JOURNAL OF STRUCTURAL CHEMISTRY 40 (1): 29-34 JAN-FEB 1999 33. Ovcharenko VI, Romanenko GV, Korobkov IV, et al. Crystal structure and magnetic properties of the octahedral complexes of Ni(II) with 3-imidazoline nitroxides JOURNAL OF STRUCTURAL CHEMISTRY 39 (5): 734-746 SEP-OCT 1998 34. Reznikov VA, Ovcharenko IV, Pervukhina NV, et al. Persistent vinylnitroxides CHEMICAL COMMUNICATIONS (6): 539-540 MAR 21 1999 35. Musin RN, Ovcharenko IV, Ohrstrom L, et al. Magnetic properties of Cu(II) bischelate complexes with 3-imidazoline nitroxides. 1. An ab initio analysis of spin density delocalization channels JOURNAL OF STRUCTURAL CHEMISTRY 38 (5): 703-710 SEP-OCT 1997 36. Musin RN, Ovcharenko IV, Ohrstrom L, et al. Magnetic properties of Cu(II) bischelate complexes with 3-imidazoline nitroxides. 2. An ab initio analysis of exchange interaction mechanisms JOURNAL OF STRUCTURAL CHEMISTRY 38 (5): 711-715 SEP-OCT 1997 37. Krupa AA, Gorodov VS, Zyatkevich DP, et al. Stepping up the sintering rate of China through the use of firing wastes treated by a plasma-chemical method GLASS AND CERAMICS 54 (1-2): 63-65 JAN-FEB 1997