corr in DNA (2001)

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2001

JS Almeida, JA Carrico, A Maretzek, PA Noble, M Fletcher (2001), "Analysis of genomic sequences by chaos game representation", Bioinformatics, 17:429-437.
Y Almirantis, A Provata (2001), "An evolutionary model about the origin of non-randomness, long-range order and fractality in the genome", Bioessays, 23:647-656.
D Anastassiou (2001), "Genomic signal processing", IEEE Signal Processing Magazine, 18(4):8-20.
protein

Miguel A. Andrade, Carolina Perez-Iratxeta, Chris P. Ponting (2001), "Protein repeats: structures, functions, and evolution", Journal of Structural Biology, 134(2-3):117-131.
[abstract]
B Audit, C Thermes, C Vaillant, Y d'Aubenton-Carafa, JF Muzy, A Arneodo (2001), "Long-range correlations in genomic DNA: a signature of the nucleosomal structure", Physical Review Letters, 86:2471-2474.
[PDF]
PF Baisnee, P Baldi, S Brunak, AG Pedersen (2001), "Flexibility of the genetic code with respect to DNA structure", Bioinformatics, 17:237-248.
protein

Gill Bejerano, Yevgeny Seldin, Hanah Margalit, Naftali Tishby (2001), "Markovian domain fingerprinting: statistical segmentation of protein sequences", Bioinformatics, 17: 927-934.
Matthew Bellgard, David Schibeci, Edward Trifonov, Takashi Gojobori (2001), "Early detection of G+C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains", Journal of Molecular Evolution, 53:465-468.
Casey M Bergman, Martin Kreitman (2001), "Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences ", Genome Research , 11:1335-1345.
[abstract] [PDF ]
sequence

A Bernal, U Ear, N Kyrpides (2001), "Genomes OnLine Database (GOLD): a monitor of genome projects world-wide", Nucleic Acids Research, 29(1):126-127.
Giorgio Bernardi (2001), "Misunderstandings about isochores. Part I", Gene, 276:3-13.
[PDF]
A Bershadskii (2001), "Multifractal and probabilistic properties of DNA sequences", Physics Letters A, 284(2-3):136-140.
VM Blinov, SI Denisov, DV Saraev, DV Shvetsov, DL Uvarov, N Yu Oparina, LS Sandakhchiev, LL Kisselev (2001), "Structural organization of the human genome: distribution of nucleotides, Alu repeats, and exons in chromosomes 21 and 22", Molecular Biology (Molekulyarnaya Biologiya), 35(6):883-889.
sequence

A Bolotin, P Wincker, S Mauger, O Jaillon, K Malarme, J Weissenbach, SD Ehrlich, A Sorokin (2001), "The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403", Genome Research, 11:731-753.
[abstract]
RJ Boys, DA Henderson (2001), ``A comparison of reversible jump MCMC algorithms for DNA sequence segmentation using hidden Markov models", Computing Science and Statistics, 33:35-49.
sequence

I Chambaud, Heilig R, Ferris S, Barbe V, Samson D, Galisson F, Moszer I, Dybvig K, Wroblewski H, Viari A, Rocha EP, Blanchard A (2001), "The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis", Nucleic Acids Research, 29:2145-2153.
protein

S Chattopadhyay, J Chakrabarti, D Bandyopadhyay, A Som (2001), "Identification of human proteins using the linguist's tools", Indian Journal of Biochemistry and Biophysics, 38(1-2):124-127.
repeats

Francesca Chiaromonte, Shan Yang, Laura Elnitski, Von Bing Yap, Webb Miller, Ross C Hardison (2001), "Association between divergence and interspersed repeats in mammalian noncoding genomic DNA", Proceedings of the National Academy of Sciences, 98(25):14503-14508.
M L Chiusano, L Frappat, P Sorba, A Sciarrino (2001), "Codon usage correlations and crystal basis model of the genetic code", Europhysics Letters, 55:287
[ abstract]
AG Clark (2001), "The search for meaning in noncoding DNA" (insight/outlook), Genome Research , 11:1319-1320.
[html] [PDF ]
O Clay, N Carels, C Douady, G Macaya, G Bernardi (2001), "Compositional heterogeneity within and among isochores in mammalian genomes. I. CsCl and sequence analyses", Gene, 276:15-24.
[PDF ]
O Clay, G Bernardi (2001), "Compositional heterogeneity within and among isochores in mammalian genomes. II. Some general comments", Gene, 276:25-31.
[PDF ]
O Clay, G Bernardi (2001), "The isochores in human chromosomes 21 and 22", Biochemical and Biophysical Research Communications, 285:855-856.
O Clay (2001), "Standard deviations and correlations of GC levels in DNA sequences", Gene, 276:33-38.
[abstract] [PDF ]
sequence

ST Cole, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honore N, Garnier T, Churcher C, Harris D, Mungall K, Basham D, Brown D, Chillingworth T, Connor R, Davies RM, Devlin K, Duthoy S, Feltwell T, Fraser A, Hamlin N, Holroyd S, Hornsby T, Jagels K, Lacroix C, Maclean J, Moule S, Murphy L, Oliver K, Quail MA, Rajandream MA, Rutherford KM, Rutter S, Seeger K, Simon S, Simmonds M, Skelton J, Squares R, Squares S, Stevens K, Taylor K, Whitehead S, Woodward JR, Barrell BG (2001), "Massive gene decay in the leprosy bacillus", Nature, 409:1007-1011.
Josep M Comeron (2001), "What controls the length of noncoding DNA?", Current Opinion in Genetics & Development, 11(6):652-659.
[abstract]
Arkendra De, Michael Ferguson, Suzanne Sindi and Richard Durrett (2001), "The equilibrium distribution for a generalized Sankoff-Ferretti model accurately predicts chromosome size distributions in a wide variety of species", Journal of Applied Probability, 38(2):324-334.
[abstract]
sequence

P Deloukas, Matthews LH, Ashurst J, Burton J, Gilbert JG, Jones M, Stavrides G, Almeida JP, Babbage AK, Bagguley CL, Bailey J, Barlow KF, Bates KN, Beard LM, Beare DM, Beasley OP, Bird CP, Blakey SE, Bridgeman AM, Brown AJ, Buck D, Burrill W, Butler AP, Carder C, Carter NP, Chapman JC, Clamp M, Clark G, Clark LN, Clark SY, Clee CM, Clegg S, Cobley VE, Collier RE, Connor R, Corby NR, Coulson A, Coville GJ, Deadman R, Dhami P, Dunn M, Ellington AG, Frankland JA, Fraser A, French L, Garner P, Grafham DV, Griffiths C, Griffiths MN, Gwilliam R, Hall RE, Hammond S, Harley JL, Heath PD, Ho S, Holden JL, Howden PJ, Huckle E, Hunt AR, Hunt SE, Jekosch K, Johnson CM, Johnson D, Kay MP, Kimberley AM, King A, Knights A, Laird GK, Lawlor S, Lehvaslaiho MH, Leversha M, Lloyd C, Lloyd DM, Lovell JD, Marsh VL, Martin SL, McConnachie LJ, McLay K, McMurray AA, Milne S, Mistry D, Moore MJ, Mullikin JC, Nickerson T, Oliver K, Parker A, Patel R, Pearce TA, Peck AI, Phillimore BJ, Prathalingam SR, Plumb RW, Ramsay H, Rice CM, Ross MT, Scott CE, Sehra HK, Shownkeen R, Sims S, Skuce CD, Smith ML, Soderlund C, Steward CA, Sulston JE, Swann M, Sycamore N, Taylor R, Tee L, Thomas DW, Thorpe A, Tracey A, Tromans AC, Vaudin M, Wall M, Wallis JM, Whitehead SL, Whittaker P, Willey DL, Williams L, Williams SA, Wilming L, Wray PW, Hubbard T, Durbin RM, Bentley DR, Beck S, Rogers J. (2001), "The DNA sequence and comparative analysis of human chromosome 20", Nature, 414(6866):865-871.
[abstract] [PDF]
sequence

S Douglas, S Zauner, M Fraunholz, M Beaton, S Penny, LT Deng, X Wu, M Reith, T Cavalier-Smith, UG Maier UG (2001), "The highly reduced genome of an enslaved algal nucleus", Nature, 410:1091-1096.
IM Dremin, OV Ivanov, VA Nechitailo (2001), "Wavelets and their applications", Uspekhi Fizicheskikh Nauk, 171(5):465-501.
Sean R. Eddy (2001), "Non-coding RNA genes and the modern RNA world", Nature Reviews Genetics, 2:919-929.
[abstract]
Adam Eyre-Walker, Laurence D Hurst (2001), "The evolution of isochores", Nature Reviews Genetics, 2:549-555.
[PDF]
sequence

Ferretti JJ, McShan WM, Ajdic D, Savic DJ, Savic G, Lyon K, Primeaux C, Sezate S, Suvorov AN, Kenton S, Lai HS, Lin SP, Qian Y, Jia HG, Najar FZ, Ren Q, Zhu H, Song L, White J, Yuan X, Clifton SW, Roe BA, McLaughlin R (2001), "Complete genome sequence of an M1 strain of Streptococcus pyogenes", Proceedings of the National Academy of Sciences, 98:4658-4663.
L Frappat, A Sciarrino, P Sorba (2001), "Crystalizing the genetic code", Journal of Biological Physics, 17:1-34.
Robert Friedman, Austin L Hughes (2001), "Gene duplication and the structure of eukaryotic genomes", Genome Research, 11(3):373-381.
[abstract]
SM Fullerton, A Bernardo Carvalho, AG Clark (2001), "Local rates of recombination are positively correlated with GC content in the human genome", Molecular Biology and Evolution, 18(6):1139-1142.
sequence

Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J (2001), "The composite genome of the legume symbiont Sinorhizobium meliloti", Science, 293:668-672.
isochore

N Galtier, G Piganeau, D Mouchiroud, L Duret (2001), "GC-content evolution in mammalian genomes: the biased gene conversion hypothesis", Genetics, 159(2):907-911.
AJ Gentles, S Karlin (2001), "Genome-Scale compositional comparisons in eukaryotes", Genome Research, 11(4):540-546.
[abstract]
sequence

Glaser P, Frangeul L, Buchrieser C, Rusniok C, Amend A, Baquero F, Berche P, Bloecker H, Brandt P, Chakraborty T, Charbit A, Chetouani F, Couve E, de Daruvar A, Dehoux P, Domann E, Dominguez-Bernal G, Duchaud E, Durant L, Dussurget O, Entian KD, Fsihi H, Portillo FG, Garrido P, Gautier L, Goebel W, Gomez-Lopez N, Hain T, Hauf J, Jackson D, Jones LM, Kaerst U, Kreft J, Kuhn M, Kunst F, Kurapkat G, Madueno E, Maitournam A, Vicente JM, Ng E, Nedjari H, Nordsiek G, Novella S, de Pablos B, Perez-Diaz JC, Purcell R, Remmel B, Rose M, Schlueter T, Simoes N, Tierrez A, Vazquez-Boland JA, Voss H, Wehland J, Cossart P (2001), "Comparative genomics of Listeria species", Science, 294:849-852.
G Glocjner, K Szafranski, T Winckler, T Dingerman, MA Quail, E Cox, L Eichinger, AA Noegel, A Rosenthal (2001), "The complex repeats of Dictyostelium discoideum", Genome Research, 11(4):585-594.
[abstract]
sequence

Goodner B, Hinkle G, Gattung S, Miller N, Blanchard M, Qurollo B, Goldman BS, Cao Y, Askenazi M, Halling C, Mullin L, Houmiel K, Gordon J, Vaudin M, Iartchouk O, Epp A, Liu F, Wollam C, Allinger M, Doughty D, Scott C, Lappas C, Markelz B, Flanagan C, Crowell C, Gurson J, Lomo C, Sear C, Strub G, Cielo C, Slater S (2001), "Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58", Science, 294:2323-2328.
Laurent Gueguen (2001), "Segmentation by maximal predictive partitioning according to composition biases", in Lecture Notes in Computer Science , Vol 2066, pp. 32-44 (Computational Biology, eds. O Gascuel, M-F Sagot) (Springer),
[ webpage of the book ]
S Guindon, G Perriere (2001), "Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes", Molecular Biology and Evolution, 18:1838-1840.
Xiaofeng Guo, Milan Randic, Subhash C Basak (2001), "A novel 2-D graphical representation of DNA sequences of low degeneracy", Chemical Physics Letters, 350(1-2):106-112.
JM Gutierrez, MA Rodriguez, G Abramson (2001), "Multifractal analysis of DNA sequences using a novel chaos-game representation", Physica A, 300(1-2):271-284.
[abstract]
D Haring, J Kypr (2001), "No isochores in the human chromosomes 21 and 22?", Biochemical and Biophysical Research Communications, 280(2):567-573.
[PDF]
J Hauck, D Henkel, K Mika (2001), "The evolution processes of DNA sequences, languages and carols", Physica A, 293(3-4):540-548.
sequence

T Hayashi, K Makino, M Ohnishi, K Kurokawa, K Ishii, K Yokoyama, C-G Han, E Ohtsubo, K Nakayama, T Murata, M Tanaka, T Tobe, T Iida, H Takami, T Honda, C Sasakawa, N Ogasawara, T Yasunaga, S Kuhara, T Shiba, M Hattori, and H Shinagawa (2001), "Complete genome sequence of enterohemorrhagic Eschelichia coli O157:H7 and genomic comparison with a laboratory strain K-12", DNA Research, 8(1):11-22. (supplement, 8(1):47-52)
Joachim Hermission (2001), "Four-state quantum chain as a model of sequence evolution", Journal of Statistical Physics, 102(1-2):315-343.
Dirk Holste, Ivo Grosse, and Hanspeter Herzel (2001), "Statistical analysis of the DNA sequence of human chromosome 22", Physical Review E,64(4):041917.
[abstract] [ abstract] [PDF]
sequence

Hoskins J, Alborn WE Jr, Arnold J, Blaszczak LC, Burgett S, DeHoff BS, Estrem ST, Fritz L, Fu DJ, Fuller W, Geringer C, Gilmour R, Glass JS, Khoja H, Kraft AR, Lagace RE, LeBlanc DJ, Lee LN, Lefkowitz EJ, Lu J, Matsushima P, McAhren SM, McHenney M, McLeaster K, Mundy CW, Nicas TI, Norris FH, O'Gara M, Peery RB, Robertson GT, Rockey P, Sun PM, Winkler ME, Yang Y, Young-Bellido M, Zhao G, Zook CA, Baltz RH, Jaskunas SR, Rosteck PR Jr, Skatrud PL, Glass JI (2001), "Genome of the bacterium Streptococcus pneumoniae strain R6", Journal of Bacteriology, 183:5709-5717.
[ abstract]
Gregory D. D. Hurst & John H. Werren (2001), "The role of selfish genetic elements in eukaryotic evolution" Nature Reviews Genetics, 2:597-606.
[abstract]
binding-energy

LD Hurst, AR Merchant (2001), "High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes", Proceedings of the Royal Society of London. B. Biological Sciences, 268:493-497.
sequence

T Kaneko, Y Nakamura, C P Wolk, T Kuritz, S Sasamoto, A Watanabe, M Iriguchi, A Ishikawa, K Kawashima, T Kimura, Y Kishida, M Kohara, M Matsumoto, A Matsuno, A Muraki, N Nakazaki, S Shimpo, M Sugimoto, M Takazawa, M Yamada, M Yasuda, S Tabata (2001), "Complete genomic sequence of the filamentous nitrogen-fixing Cyanobacterium Anabaena sp. strain PCC 7120", DNA Research, 8(5):205-213. (supplement, 8(5):227-253)
repeats

VV Kapitonov, J Jurka (2001), "Rolling-circle transposons in eukaryotes", Proceedings of the National Academy of Sciences, 98(15):8714-8719.
sequence

Katinka MD, Duprat S, Cornillot E, Metenier G, Thomarat F, Prensier G, Barbe V, Peyretaillade E, Brottier P, Wincker P, Delbac F, El Alaoui H, Peyret P, Saurin W, Gouy M, Weissenbach J, Vivares CP (2001), "Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi", Nature, 414:450-453.
sequence

Yutaka Kawarabayasi, Yumi Hino, Hiroshi Horikawa, Koji Jin-no, Mikio Takahashi, Mitsuo Sekine, Sin-ichi Baba, Akiho Ankai, Hiroki Kosugi, Akira Hosoyama, Shigehiro Fukui, Yoshimi Nagai, Keiko Nishijima, Rie Otsuka, Hidekazu Nakazawa, Minako Takamiya, Yumiko Kato, Takio Yoshizawa, Toshihiro Tanaka, Yutaka Kudoh, Jun Yamazaki, Norihiro Kushida, Akio Oguchi, Ken-ichi Aoki, Sayaka Masuda, Masao Yanagii, Masami Nishimura, Akihiko Yamagishi, Tairo Oshima and Hisasi Kikuchi (2001), "Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7", DNA Research, 8(4):123-140.
[abstract]
Margaret G. Kidwell, Damon R. Lisch (2001), "Perspective: Transposable elements, parasitic DNA, and genome evolution", Evolution, 5591):1-24.
OV Kirillova (2001), "Comparative statistical analysis of bacteria genomes in 'word' context", Physica A, 290:453-463.
[abstract]
RM Kliman, BT Rogers, MAF Noor (2001), "Differences in (G+C) content between species: a commentary on Forsdyke's 'chromosomal viewpoint' of speciation ", Journal of Theoretical Biology, 209(2):131-140.
a/symmetry

Robin D Knight, Stephen J Freeland, Laura F Landweber (2001), "A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes", Genome Biology , 2(4): research0010.1-0010.13.
[PDF]
a/symmetry

M Kowalczuk, P Mackiewicz, D Mackiewicz, A Nowicka, M Dudkiewicz, MR Dudek, S Cebrat (2001), "DNA asymmetry and the replicational mutational pressure", Journal of Applied Genetics, 42(4):553-577.
a/symmetry

M Kowalczuk, P Mackiewicz, D Mackiewicz, A Nowicka, M Dudkiewicz, MR Dudek, S Cebrat (2001), "High correlation between the turnover of nucleotides under mutational pressure and the DNA composition", BMC Evolutionary Biology, 1(1):13.
M Kowalczuk, P Mackiewicz, D Szczepanik, A Nowicka, M Dudkiewicz, MR Dudek, S Cebrat (2001), "Multiple base substitution corrections in DNA sequence evolution", International Journal of Modern Physics C, 12(7):1043-1053.
bending

S Kundu, D Bhattacharya, AR Thakur, R Majumdar (2001), "Nucleosomal positioning and genetic divergence study based on DNA flexibility map", Journal of Biomolecular Structure and Dynamics, 18(4):527-533.
sequence

Kuroda M, Ohta T, Uchiyama I, Baba T, Yuzawa H, Kobayashi I, Cui L, Oguchi A, Aoki K, Nagai Y, Lian J, Ito T, Kanamori M, Matsumaru H, Maruyama A, Murakami H, Hosoyama A, Mizutani-Ui Y, Takahashi NK, Sawano T, Inoue R, Kaito C, Sekimizu K, Hirakawa H, Kuhara S, Goto S, Yabuzaki J, Kanehisa M, Yamashita A, Oshima K, Furuya K, Yoshino C, Shiba T, Hattori M, Ogasawara N, Hayashi H, Hiramatsu K (2001), "Whole genome sequencing of meticillin-resistant Staphylococcus aureus", Lancet, 357:1225-1240.
repeats

S Kurtz, JV Choudhuri, E Ohlebusch, C Schleiermacher, J Stoye, R Giegerich (2001), "REPuter: the manifold applications of repeat analysis on a genomic scale", Nucleic Acids Research, 29(22):4633-4642.
sequence

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, Szustakowki J, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ; (International Human Genome Sequencing Consortium) (2001), "Initial sequencing and analysis of the human genome", Nature, 409:860-921.
[PDF]
Andrew A Laskin, Eugene V Korotkov, Nikolai A Kudryashov (2001), "Detection of hidden periodicity in protein sequences and its correlation with structure and function of proteins", in Genome Informatics 2001, eds. H. Matsuda, S. Miyano, T. Takagi, and L. Wong, pp. 343-344.
VG Levitsky, OA Podkolodnaya, NA Kolchanov, NL Podkolodny (2001), "Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis", Bioinformatics, 17(11):998-1010.
VG Levitsky, OA Podkolodnaya, NA Kolchanov, NL Podkolodny (2001), "Nucleosome formation potential of exons, introns, and Alu repeats", Bioinformatics, 17(11):1062-1064.
W Li (2001), "DNA segmentation as a model selection process", Proceedings of the Fifth International Conference on Research in Computational Molecular Biology , pp.204-210 (ACM Press).
[ webpage of RECOMB01]
W Li (2001), "Delineating relative homogeneous G+C domains in DNA sequences", Gene, 276:57-72.
[abstract] [PDF]
W Li (2001), "New stopping criteria for segmenting DNA sequences", Physical Review Letters, 86(25):5815-5818.
[PDF]
Philippe Lopez, Herve Philippe (2001), "Composition strand asymmetries in prokaryotic genomes: mutational bias and biased gene orientation", Comptes Rendus de l'Acad�mie des Sciences - Series III - Sciences de la Vie , 324(3):201-208.
P Mackiewicz, D Mackiewicz, A Gierlik, M Kowalczuk, A Nowicka, M Dudkiewicz, MR Dudek, S Cebrat (2001), "The differential killing of genes by inversions in prokaryotic genomes", Journal of Molecular Evolution, 53(6):615-621.
a/symmetry

P Mackiewicz, D Mackiewicz, M Kowalczuk, S Cebrat (2001), "Flip-flop around the origin and terminus of replication in prokaryotic genomes", Genome Biology, 2(12):interaction1004
Vsevolod Makeev, Vasily Ramensky, Mikhail Gelfand, Mikhail Roytberg, Vladimir Tumanyan (2001), "Bayesian approach to DNA segmentation into regions with different average nucleotide composition", in Lecture Notes in Computer Science , Vol 2066, pp. 57-73 (Computational Biology, eds. O Gascuel, M-F Sagot) (Springer),
[ webpage of the book ]
sequence

BJ May, Q Zhang, LL Li, ML Paustian, TS Whittam, V Kapur (2001), "Complete genomic sequence of Pasteurella multocida Pm70", Proceedings of the National Academy of Sciences, 98:3460-3465.
sequence

McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, Hou S, Layman D, Leonard S, Nguyen C, Scott K, Holmes A, Grewal N, Mulvaney E, Ryan E, Sun H, Florea L, Miller W, Stoneking T, Nhan M, Waterston R, Wilson RK (2001), "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2", Nature, 413:852-856.
Miriam H Meisler (2001), "Evolutionarily conserved noncoding DNA in the human genome: how much and what for? " Genome Research, 11:1617-1618.
[html]
N Nagai, K Kuwata, T Hayashi, H Kuwata, S Era (2001), "Evolution of the periodicity and the self-similarity in DNA sequence: A Fourier transform analysis", Japanese Journal of Physiology, 51(2):159-168.
[abstract]
sequence

Nierman WC, Feldblyum TV, Laub MT, Paulsen IT, Nelson KE, Eisen J, Heidelberg JF, Alley MR, Ohta N, Maddock JR, Potocka I, Nelson WC, Newton A, Stephens C, Phadke ND, Ely B, DeBoy RT, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Kolonay JF, Smit J, Craven MB, Khouri H, Shetty J, Berry K, Utterback T, Tran K, Wolf A, Vamathevan J, Ermolaeva M, White O, Salzberg SL, Venter JC, Shapiro L, Fraser CM (2001), "Complete genome sequence of Caulobacter crescentus", Proceedings of the National Academy of Sciences, 98:4136-4141.
sequence

Nolling J, Breton G, Omelchenko MV, Makarova KS, Zeng Q, Gibson R, Lee HM, Dubois J, Qiu D, Hitti J, Wolf YI, Tatusov RL, Sabathe F, Doucette-Stamm L, Soucaille P, Daly MJ, Bennett GN, Koonin EV, Smith DR (2001), "Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum", Journal of Bacteriology, 183:4823-4838.
[ abstract]
sequence

H Ogata, S Audic, P Renesto-Audiffren, PE Fournier, V Barbe, D Samson, V Roux, P Cossart, J Weissenbach, JM Claverie, D Raoult (2001), "Mechanisms of evolution in Rickettsia conorii and R. prowazekii", Science, 293:2093-2098.
JL Oliver, P Bernaola-Galvan, P Carpena, R Roman-Roldan (2001), "Isochore chromosome maps of eukaryotic genomes", Gene, 276:47-56.
[PDF ]
Igor Ovchinnikov, Andrea B Troxel, Gary D Swergold (2001) "Genomic characterization of recent human LINE-1 insertions: evidence supporting random insertion", Genome Research, 11:2050-2058.
[abstract]
sequence

Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, Sebaihia M, Baker S, Basham D, Brooks K, Chillingworth T, Connerton P, Cronin A, Davis P, Davies RM, Dowd L, White N, Farrar J, Feltwell T, Hamlin N, Haque A, Hien TT, Holroyd S, Jagels K, Krogh A, Larsen TS, Leather S, Moule S, O'Gaora P, Parry C, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG (2001), "Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18", Nature, 413:848-852.
sequence

Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT, Prentice MB, Sebaihia M, James KD, Churcher C, Mungall KL, Baker S, Basham D, Bentley SD, Brooks K, Cerdeno-Tarraga AM, Chillingworth T, Cronin A, Davies RM, Davis P, Dougan G, Feltwell T, Hamlin N, Holroyd S, Jagels K, Karlyshev AV, Leather S, Moule S, Oyston PC, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG (2001), "Genome sequence of Yersinia pestis, the causative agent of plague", Nature, 413:523-527.
sequence

NT Perna, G Plunkett III, V Burland, B Mau, JD Glasner, DJ Rose, GF Mayhew, PS Evans, J Gregor, HA Kirkpatrick, G Posfai, J Hackett, S Klink, A Boutin, Y Shao, L Miller, EJ Grotbeck, NW Davis, A Lim, ET Dimalanta, KD Potamousis, J Apodaca, TS Anantharaman, J Lin, G Yen, DC Schwartz, RA Welch, FR Blattner (2001) "Genome sequence of enterohaemorrhagic Escherichia coli O157:H7", Nature, 409:529-533.
protein

Elisabetta Pizzi, Clara Frontali (2001), "Low-complexity regions in Plasmodium falciparum proteins", Genome Research, 11:218-229.
[abstract] [PDF ]
isochore

L Ponger, L Duret, D Mouchiroud (2001), "Determinants of CpG islands: expression in early embryo and isochore structure", Genome Research, 11(11):1854-1860.
[abstract]
a/symmetry

Dong Qi, A Jamie Cuticchia (2001), "Compositional symmetries in complete genomes", Bioinformatics, 17:557-559.
VE Ramensky, VJ Makeev, MA Roytberg, VG Tumanyan (2001), "Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software", Bioinformatics, 17(11):1065-1066.
William C Ray, Robert S Munson, Jr, Charles J Daniels (2001), "Tricross : using dot-plots in sequence-id space to detect uncataloged intergenic features", Bioinformatics, 17:1105-1112.
S Robin, S Schbath (2001), "Numerical comparison of several approximations of the word count distribution in random sequences", Journal of Computational Biology, 8(4):349-359.
a/symmetry

EP Rocha, A Danchin (2001), "Ongoing evolution of strand composition in bacterial genomes", Molecular Biology and Evolution, 18(9):1789-1799.
Salvatore Saccone, Adam Pavlicek, Concetta Federico, Jan Paces, Giorgio Bernardi (2001), "Genes, isochores and bands in human chromosomes 21 and 22", Chromosome Research, 9(7):533-539.
Rickard Sandberg, G�sta Winberg, Carl-Ivar Br�nden, Alexander Kaske, Ingemar Ernberg, Joakim C�ster (2001), "Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier ", Genome Research, 11(8):1404-1409.
[abstract]
Mary G Schueler, Anne W Higgins, M Katharine Rudd, Karen Gustashaw, Huntington F Willard (2001), "Genomic and genetic definition of a functional human centromere", Science, 294:109-115.
sequence

Q She, Singh RK, Confalonieri F, Zivanovic Y, Allard G, Awayez MJ, Chan-Weiher CC, Clausen IG, Curtis BA, De Moors A, Erauso G, Fletcher C, Gordon PM, Heikamp-de Jong I, Jeffries AC, Kozera CJ, Medina N, Peng X, Thi-Ngoc HP, Redder P, Schenk ME, Theriault C, Tolstrup N, Charlebois RL, Doolittle WF, Duguet M, Gaasterland T, Garrett RA, Ragan MA, Sensen CW, Van der Oost J. (2001), "The complete genome of the crenarchaeon Sulfolobus solfataricus P2", Proceedings of the National Academy of Sciences, 98:7835-7840.
a/symmetry

C Shioiri, N Takahata (2001), "Skew of mononucleotide frequencies, relative abundance of dinucleotides, and DNA strand asymmetry", Journal of Molecular Evolution, 53:364-376.
A Som, S Chattopadhyay, J Chakrabarti (2001), "Codon distributions in DNA", Physica Review E, 63:051908.
[PDF ] [ abstract]
repeats

JE Stenger, KS Lobachev, D Gordenin, TA Darden, J Jurka, MA Resnick (2001), "Biased distribution of inverted and direct Alus in the human genome: implications for insertion, exclusion, and genome stability", Genome Research, 11(1):12-27.
L Stern, L Allison, RL Coppel, TI Dix (2001), "Discovering patterns in plasmodium falciparum genomic DNA", Mol. Biochem. Parasitol., 118(2):175-186.
sequence

G Subramanian, MD Adams, JC Venter, S Broder (2001), "Implications of the human genome for understanding human biology and medicine", JAMA, 286(18):2296-2307.
a/symmetry

D Szczepanik, P Mackiewicz, M Kowalczuk, A Gierlik, A Nowicka, MR Dudek, S Cebrat (2001), "Evolution rates of genes on leading and lagging DNA strands", Journal of Molecular Evolution, 52(5):426-433.
P Szendro, G Vincze, A Szasz (2001), "Pink-noise behaviour of biosystems", European Biophysics Journal with Biophysics Letters, 30(3):227-231.
sequence

Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smith HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM (2001), "Complete genome sequence of a virulent isolate of Streptococcus pneumoniae", Science, 293:498-506.
protein

EN Trifonov, A Kirzhner, VM Kirzhner, IN Berezovsky (2001), "Distinct stages of protein evolution as suggested by protein sequence analysis", Journal of Molecular Evolution, 53(4-5):394-401.
D Ussery, TS Larsen, KT Wilkes, C Friis, P Worning, A Krogh, S Brunak (2001), "Genome Organisation and Chromatin Structure in Escherichia coli", Biochimie, 83:202-212.
sequence

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigo R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X. (2001) "The sequence of the human genome", Science, 291:1304-1351.
[PDF]
A Vinogradov (2001), "Intron length and codon usage", Journal of Molecular Evolution, 52(1):2-5.
[abstract]
A Vinogradov (2001), "Within-intron correlation with base composition of adjacent exons in different genomes", Gene, 276:143-151.
[abstract]
N Volfovsky, BJ Haas, SL Salzberg (2001), "A clustering method for repeat analysis in DNA sequences", Genome Biology, 2(8):research0027.
J Wang, QD Zhang, K Ren, ZS She (2002), "Multi-scaling hierarchical structure analysis on the sequence of E-coli complete genome", Chinese Science Bulletin, 46(23):1988-1992.
bending

J Widom (2001), "Role of DNA sequence in nucleosome stability and dynamics", Quarterly Review of Biophysics, 34:269-324.
Michael J Wise (2001), "0j.py: A software tool for low complexity proteins and protein domains", ISMB (supplement of Bioinformatics ), pp. 288-295.
webpage of ISMB'01.
sequence

Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida NF Jr, Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, Bovee D Sr, Chapman P, Clendenning J, Deatherage G, Gillet W, Grant C, Kutyavin T, Levy R, Li MJ, McClelland E, Palmieri A, Raymond C, Rouse G, Saenphimmachak C, Wu Z, Romero P, Gordon D, Zhang S, Yoo H, Tao Y, Biddle P, Jung M, Krespan W, Perry M, Gordon-Kamm B, Liao L, Kim S, Hendrick C, Zhao ZY, Dolan M, Chumley F, Tingey SV, Tomb JF, Gordon MP, Olson MV, Nester EW (2001), "The genome of the natural genetic engineer Agrobacterium tumefaciens C58", Science, 294:2317-2323.
Tiee-Jian Wu, Ya-Ching Hsieh, Lung-An Li (2001), "Statistical measures of DNA sequence dissimilarity under Markov chain models of base composition", Biometrics, 57:441-448.
Yang Xiang, KY Szeto, JWO Tam (2001), "An Improved Entropic Segmentation Method in Detecting Boundary Between Coding and non-coding DNA Region", Proceeding of the 2001 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS 2001), eds. F.Valafar (CSERA Press), pp.174-177.
Zu-Guo Yu, Vo Ahn (2001), "Time series model based on global structure of complete genome", Chaos, Solitons & Fractals, 12(10):1827-1834.
[abstract]
ZG Yu, V Anh, KS Lau KS (2001), "Multifractal characterisation of length sequences of coding and noncoding segments in a complete genome", Physica A, 301(1-4):351-361.
[abstract]
ZG Yu, VV Ahn, KS Lau (2001), "Measure representation and multifractal analysis of complete genomes", Physical Review E, 64:031903.
[ abstract]
Zu-Guo Yu, V V Ahn, Bin Wang (2001), "Correlation property of length sequences based on global structure of the complete genome", Physical Review E, 63:011903.
[PDF] [ abstract]
ZG Yu, P Jiang (2001), "Distance, correlation and mutual information among portraits of organisms based on complete genomes", Physics Letters A, 286(1):34-46.
[abstract]
ZG Yu, B Wang (2001), "A time series model of CDS sequences in complete genome", Chaos, Solitons & Fractals, 12(3):519-526.
CT Zhang, J Wang, R Zhang (2001), "A novel method to calculate the G+C content of genomic DNA sequences", Journal of Biomolecular Structure and Dynamics, 19(2):333-341.