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Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling 期刊论文
BMC BIOINFORMATICS, 2019, 卷号: 20, 页码: 135
Authors:  Wang, C;  Wei, Y;  Zhang, HC;  Kong, LP;  Sun, SW;  Zheng, WM;  Bu, DB
Adobe PDF(1618Kb)  |  Favorite  |  View/Download：46/0  |  Submit date：2019/07/19
TERTIARY STRUCTURES  FRAGMENTS  
FCC-ee: The Lepton Collider: Future Circular Collider Conceptual Design Report Volume 2 期刊论文
EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS, 2019
Authors:  Abada, A;  Abbrescia, M;  AbdusSalam, SS;  Abdyukhanov, I;  Fernandez, JA;  Abramov, A;  Aburaia, M;  Acar, AO;  Adzic, PR;  Agrawal, P;  Aguilar-Saavedra, JA;  Aguilera-Verdugo, JJ;  Aiba, M;  Aichinger, I;  Aielli, G;  Akay, A;  Akhundov, A;  Aksakal, H;  Albacete, JL;  Albergo, S;  Alekou, A;  Aleksa, M;  Aleksan, R;  Fernandez, RMA;  Alexahin, Y;  Alia, RG;  Alioli, S;  Tehrani, NA;  Allanach, BC;  Allport, PP;  Altinli, M;  Altmannshofer, W;  Ambrosio, G;  Amorim, D;  Amstutz, O;  Anderlini, L;  Andreazza, A;  Andreini, M;  Andriatis, A;  Andris, C;  Andronic, A;  Angelucci, M;  Antinori, F;  Antipov, SA;  Antonelli, M;  Antonello, M;  Antonioli, P;  Antusch, S;  Anulli, F;  Apolinario, L;  Apollinari, G;  Apollonio, A;  Appelo, D;  Appleby, RB;  Apyan, A;  Apyan, A;  Arbey, A;  Arbuzov, A;  Arduini, G;  Ari, V;  Arias, S;  Armesto, N;  Arnaldi, R;  Arsenyev, SA;  Arzeo, M;  Asai, S;  Aslanides, E;  Assmann, RW;  Astapovych, D;  Atanasov, M;  Atieh, S;  Attie, D;  Auchmann, B;  Audurier, A;  Aull, S;  Aumon, S;  Aune, S;  Avino, F;  Avrillaud, G;  Aydin, G;  Azatov, A;  Azuelos, G;  Azzi, P;  Azzolini, O;  Azzurri, P;  Bacchetta, N;  Bacchiocchi, E;  Bachacou, H;  Baek, YW;  Baglin, V;  Bai, Y;  Baird, S;  Baker, MJ;  Baldwin, MJ;  Ball, AH;  Ballarino, A;  Banerjee, S;  Barber, DP;  Barducci, D;  Barjhoux, P;  Barna, D;  Barnafoldi, GG;  Barnes, MJ;  Barr, A;  Garcia, JB;  da Costa, JBG;  Bartmann, W;  Baryshevsky, V;  Barzi, E;  Bass, SA;  Bastianin, A;  Baudouy, B;  Bauer, F;  Bauer, M;  Baumgartner, T;  Bautista-Guzman, I;  Bayindir, C;  Beaudette, F;  Bedeschi, F;  Beguin, M;  Bellafont, I;  Bellagamba, L;  Bellegarde, N;  Belli, E;  Bellingeri, E;  Bellini, F;  Bellomo, G;  Belomestnykh, S;  Bencivenni, G;  Benedikt, M;  Bernardi, G;  Bernardi, J;  Bernet, C;  Bernhardt, JM;  Bernini, C;  Berriaud, C;  Bertarelli, A;  Bertolucci, S;  Besana, MI;  Besancon, M;  Beznosov, O;  Bhat, P;  Bhat, C;  Biagini, ME;  Biarrotte, JL;  Chevalier, AB;  Bielert, ER;  Biglietti, M;  Bilei, GM;  Bilki, B;  Biscari, C;  Bishara, F;  Blanco-Garcia, OR;  Blanquez, FR;  Blekman, F;  Blondel, A;  Blumlein, J;  Boccali, T;  Boels, R;  Bogacz, SA;  Bogomyagkov, A;  Boine-Frankenheim, O;  Boland, MJ;  Bologna, S;  Bolukbasi, O;  Bomben, M;  Bondarenko, S;  Bonvini, M;  Boos, E;  Bordini, B;  Bordry, F;  Borghello, G;  Borgonovi, L;  Borowka, S;  Bortoletto, D;  Boscherini, D;  Boscolo, M;  Boselli, S;  Bosley, RR;  Bossu, F;  Botta, C;  Bottura, L;  Boughezal, R;  Boutin, D;  Bovone, G;  Jelisavic, IB;  Bozbey, A;  Bozzi, C;  Bozzini, D;  Braccini, V;  Braibant-Giacomelli, S;  Bramante, J;  Braun-Munzinger, P;  Briffa, JA;  Britzger, D;  Brodsky, SJ;  Brooke, JJ;  Bruce, R;  De Renstrom, PB;  Bruna, E;  Bruning, O;  Brunner, O;  Brunner, K;  Bruzzone, P;  Buffat, X;  Bulyak, E;  Burkart, F;  Burkhardt, H;  Burnet, JP;  Butin, F;  Buttazzo, D;  Butterworth, A;  Caccia, M;  Cai, Y;  Caiffi, B;  Cairo, V;  Cakir, O;  Calaga, R;  Calatroni, S;  Calderini, G;  Calderola, G;  Caliskan, A;  Calvet, D;  Calviani, M;  Camalich, JM;  Camarri, P;  Campanelli, M;  Camporesi, T;  Canbay, AC;  Canepa, A;  Cantergiani, E;  Cantore-Cavalli, D;  Capeans, M;  Cardarelli, R;  Cardella, U;  Cardini, A;  Calame, CMC;  Carra, F;  Carra, S;  Carvalho, A;  Casalbuoni, S;  Casas, J;  Cascella, M;  Castelnovo, P;  Castorina, G;  Catalano, G;  Cavasinni, V;  Cazzato, E;  Cennini, E;  Cerri, A;  Cerutti, F;  Cervantes, J;  Chaikovska, I;  Chakrabortty, J;  Chala, M;  Chamizo-Llatas, M;  Chanal, H;  Chanal, D;  Chance, S;  Chance, A;  Charitos, P;  Charles, J;  Charles, TK;  Chattopadhyay, S;  Chehab, R;  Chekanov, SV;  Chen, N;  Chernoded, A;  Chetvertkova, V;  Chevalier, L;  Chiarelli, G;  Chiarello, G;  Chiesa, M;  Chiggiato, P;  Childers, JT;  Chmielinska, A;  Cholakian, A;  Chomaz, P;  Chorowski, M;  Chou, W;  Chrzaszcz, M;  Chyhyrynets, E;  Cibinetto, G;  Ciftci, AK;  Ciftci, R;  Cimino, R;  Ciuchini, M;  Clark, PJ;  Coadou, Y;  Cobal, M;  Coccaro, A;  Cogan, J;  Cogneras, E;  Collamati, F;  Colldelram, C;  Collier, P;  Collot, J;  Contino, R;  Conventi, F;  Cook, CTA;  Cooley, L;  Corcella, G;  Cornell, AS;  Corral, GH;  Correia-Rodrigues, H;  Costanza, F;  Pinto, PC;  Couderc, F;  Coupard, J;  Craig, N;  Garrido, IC;  Crivellin, A;  Croteau, JF;  Crouch, M;  Alaniz, EC;  Cure, B;  Curti, J;  Curtin, D;  Czech, M;  Dachauer, C;  D'Agnolo, RT;  Daibo, M;  Dainese, A;  Dalena, B;  Daljevec, A;  Dallapiazza, W;  Schwartzentruber, LD;  Dam, M;  D'Ambrosio, G;  Das, SP;  DasBakshi, S;  da Silva, W;  da Silveira, GG;  D'Auria, V;  D'Auria, S;  David, A;  Davidek, T;  Deandrea, A;  de Blas, J;  Debono, CJ;  De Curtis, S;  De Filippis, N;  de Florian, D;  Deghaye, S;  de Jong, SJ;  Del Bo, C;  Del Duca, V;  Delikaris, D;  Deliot, F;  Dell'Acqua, A;  Delle Rose, L;  Delmastro, M;  De Lucia, E;  Demarteau, M;  Denegri, D;  Deniau, L;  Denisov, D;  Denizli, H;  Denner, A;  d'Enterria, D;  de Rijk, G;  De Roeck, A;  Derue, F;  Deschamps, O;  Descotes-Genon, S;  Dev, PSB;  de Regie, JBD;  Dewanjee, RK;  Di Ciaccio, A;  Di Cicco, A;  Dillon, BM;  Di Micco, B;  Di Nezza, P;  Di Vita, S;  Doblhammer, A;  Dominjon, A;  D'Onofrio, M;  Dordei, F;  Drago, A;  Draper, P;  Drasal, Z;  Drewes, M;  Duarte, L;  Dubovyk, I;  Duda, P;  Dudarev, A;  Dudko, L;  Duellmann, D;  Dunser, M;  du Pree, T;  Durante, M;  Yildiz, HD;  Dutta, S;  Duval, F;  Duval, JM;  Dydyshka, Y;  Dziewit, B;  Eisenhardt, S;  Eisterer, M;  Ekelof, T;  El Khechen, D;  Ellis, SA;  Ellis, J;  Ellison, JA;  Elsener, K;  Elsing, M;  Enari, Y;  Englert, C;  Eriksson, H;  Eskola, KJ;  Esposito, LS;  Etisken, O;  Etzion, E;  Fabbricatore, P;  Falkowski, A;  Falou, A;  Faltova, J;  Fan, J;  Fano, L;  Farilla, A;  Farinelli, R;  Farinon, S;  Faroughy, DA;  Fartoukh, SD;  Faus-Golfe, A;  Fawcett, WJ;  Felici, G;  Felsberger, L;  Ferdeghini, C;  Navarro, AMF;  Fernandez-Tellez, A;  Troitino, JF;  Ferrara, G;  Ferrari, R;  Ferreira, L;  da Silva, PF;  Ferrera, G;  Ferro, F;  Fiascaris, M;  Fiorendi, S;  Fiorio, C;  Fischer, O;  Fischer, E;  Flieger, W;  Florio, M;  Fonnesu, D;  Fontanesi, E;  Foppiani, N;  Foraz, K;  Forkel-Wirth, D;  Forte, S;  Fouaidy, M;  Fournier, D;  Fowler, T;  Fox, J;  Francavilla, P;  Franceschini, R;  Franchino, S;  Franco, E;  Freitas, A;  Fuks, B;  Furukawa, K;  Furuseth, SV;  Gabrielli, E;  Gaddi, A;  Galanti, M;  Gallo, E;  Ganjour, S;  Gao, J;  Gao, J;  Diaz, VG;  Perez, MG;  Tabares, LG;  Garion, C;  Garzelli, MV;  Garzia, I;  Gascon-Shotkin, SM;  Gaudio, G;  Gay, P;  Ge, SF;  Gehrmann, T;  Genest, MH;  Gerard, R;  Gerigk, F;  Gerwig, H;  Giacomelli, P;  Giagu, S;  Gianfelice-Wendt, E;  Gianotti, F;  Giffoni, F;  Gilardoni, SS;  Costa, MG;  Giovannetti, M;  Giovannozzi, M;  Giubellino, P;  Giudice, GF;  Giunta, A;  Gladilin, LK;  Glukhov, S;  Gluza, J;  Gobbi, G;  Goddard, B;  Goertz, F;  Golling, T;  Goncalves, VP;  Netto, DG;  Goncalo, R;  Gomez, LAG;  Zadeh, SG;  Gorine, G;  Gorini, E;  Gourlay, SA;  Gouskos, L;  Grancagnolo, F;  Grassellino, A;  Grau, A;  Graverini, E;  Gray, HM;  Greco, M;  Greco, M;  Grenard, JL;  Grimm, O;  Grojean, C;  Gromov, VA;  Grosse-Oetringhaus, JF;  Grudiev, A;  Grzanka, K;  Gu, J;  Guadagnoli, D;  Guidi, V;  Guiducci, S;  Canton, GG;  Gunaydin, YO;  Gupta, R;  Gupta, RS;  Gutierrez, J;  Gutleber, J;  Guyot, C;  Guzey, V;  Gwenlan, C;  Haberstroh, C;  Hacisahinoglu, B;  Haerer, B;  Hahn, K;  Hahn, T;  Hammad, A;  Han, C;  Hance, M;  Hannah, A;  Harris, PC;  Hati, C;  Haug, S;  Hauptman, J;  Haurylavets, V;  He, HJ;  Hegglin, A;  Hegner, B;  Heinemann, K;  Heinemeyer, S;  Helsens, C;  Henriques, A;  Henriques, A;  Hernandez, P;  Hernandez-Pinto, RJ;  Hernandez-Sanchez, J;  Herzig, T;  Hiekkanen, I;  Hillert, W;  Hoehn, T;  Hofer, M;  Hofle, W;  Holdener, F;  Holleis, S;  Holzer, B;  Hong, DK;  Honorato, CG;  Hopkins, SC;  Hrdinka, J;  Hug, F;  Humann, B;  Humer, H;  Hurth, T;  Hutton, A;  Iacobucci, G;  Ibarrola, N;  Iconomidou-Fayard, L;  Ilyina-Brunner, K;  Incandela, J;  Infantino, A;  Ippolito, V;  Ishino, M;  Islam, R;  Ita, H;  Ivanovs, A;  Iwamoto, S;  Iyer, A;  Bermudez, SI;  Jadach, S;  Jamin, DO;  Janot, P;  Jarry, P;  Jeff, A;  Jenny, P;  Jensen, E;  Jensen, M;  Jiang, X;  Jimenez, JM;  Jones, MA;  Jones, OR;  Jowett, JM;  Jung, S;  Kaabi, W;  Kado, M;  Kahle, K;  Kalinovskaya, L;  Kalinowski, J;  Kamenik, JF;  Kannike, K;  Kara, SO;  Karadeniz, H;  Karaventzas, V;  Karpov, I;  Kartal, S;  Karyukhin, A;  Kashikhin, V;  Behr, JK;  Kaya, U;  Keintzel, J;  Keinz, PA;  Keppel, K;  Kersevan, R;  Kershaw, K;  Khanpour, H;  Khatibi, S;  Yanehsari, MK;  Khoze, VV;  Kieseler, J;  Kilic, A;  Kilpinen, A;  Kim, YK;  Kim, DW;  Klein, U;  Klein, M;  Kling, F;  Klinkenberg, N;  Kloppel, S;  Klute, M;  Klyukhin, VI;  Knecht, M;  Kniehl, B;  Kocak, F;  Koeberl, C;  Kolano, AM;  Kollegger, A;  Kolodziej, K;  Kolomiets, AA;  Komppula, J;  Koop, I;  Koppenburg, P;  Koratzinos, M;  Kordiaczynska, M;  Korjik, M;  Kortner, O;  Kostka, P;  Kotlarski, W;  Kotnig, C;  Kottig, T;  Kotwal, AV;  Kovalenko, AD;  Kowalski, S;  Kozaczuk, J;  Kozlov, GA;  Kozub, SS;  Krainer, AM;  Kramer, T;  Kramer, M;  Krammer, M;  Krasnov, AA;  Krauss, F;  Kravalis, K;  Kretzschmar, L;  Kriske, RM;  Kritscher, H;  Krkotic, P;  Kroha, H;  Kucharczyk, M;  Kuday, S;  Kuendig, A;  Kuhlmann, G;  Kulesza, A;  Kumar, M;  Kumar, M;  Kusina, A;  Kuttimalai, S;  Kuze, M;  Kwon, T;  Lackner, F;  Lackner, M;  La Francesca, E;  Laine, M;  Lamanna, G;  La Mendola, S;  Lancon, E;  Landsberg, G;  Langacker, P;  Lange, C;  Langner, A;  Lankford, AJ;  Lansberg, JP;  Lari, T;  Laycock, PJ;  Lebrun, P;  Lechner, A;  Lee, K;  Lee, S;  Lee, R;  Lefevre, T;  Le Guen, P;  Lehtinen, T;  Leith, SB;  Lenzi, P;  Leogrande, E;  Leonidopoulos, C;  Leon-Monzon, I;  Lerner, G;  Leroy, O;  Lesiak, T;  Levai, P;  Leveratto, A;  Levichev, E;  Li, G;  Li, S;  Li, R;  Liberati, D;  Liepe, M;  Lissauer, DA;  Liu, Z;  Lobko, A;  Locci, E;  Agaliotis, EL;  Lombardo, MP;  Long, AJ;  Lorin, C;  Losito, R;  Louzguiti, A;  Low, I;  Lucchesi, D;  Lucchini, MT;  Luciani, A;  Lueckhof, M;  Lunt, AJG;  Luzum, M;  Lyubimtsev, DA;  Maggiora, M;  Magnin, N;  Mahmoud, MA;  Mahmoudi, F;  Maitre, J;  Makarenko, V;  Malagoli, A;  Malcles, J;  Malgeri, L;  Mallon, PJ;  Maltoni, F;  Malvezzi, S;  Malyshev, OB;  Mancinelli, G;  Mandrik, P;  Manfrinetti, P;  Mangano, M;  Manil, P;  Mannelli, M;  Marchiori, G;  Marhauser, F;  Mariani, V;  Marinozzi, V;  Mariotto, S;  Marquard, P;  Marquet, C;  Marriott-Dodington, T;  Martin, R;  Martin, O;  Camalich, JM;  Martinez, T;  Bruzual, HM;  Martinez-Hernandez, MI;  Martins, DE;  Marzani, S;  Marzocca, D;  Marzola, L;  Masciocchi, S;  Masina, I;  Massimiliano, A;  Massironi, A;  Masubuchi, T;  Matveev, VA;  Mazzoni, MA;  McCullough, M;  McIntosh, PA;  Meade, P;  Medina, L;  Meier, A;  Meignan, J;  Mele, B;  Saraiva, JGM;  Menez, F;  Mentink, M;  Meoni, E;  Meridiani, P;  Merk, M;  Mermod, P;  Mertens, V;  Mether, L;  Metral, 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TT;  Yu, F;  Zaborowska, A;  Zadeh, SG;  Zahnd, M;  Zanetti, M;  Zanotto, L;  Zawiejski, L;  Zeiler, P;  Zerlauth, M;  Zernov, SM;  Porta, GZD;  Zhang, Z;  Zhang, Y;  Zhang, C;  Zhang, H;  Zhao, Z;  Zhong, YM;  Zhou, J;  Zhou, D;  Zhuang, P;  Zick, G;  Zimmermann, F;  Zinn-Justin, J;  Zivkovic, L;  Zlobin, AV;  Zobov, M;  Zupan, J;  Zurita, J
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LARGE HADRON COLLIDER  DOUBLE-BETA DECAY  E(+)E(-) COLLISIONS  FLAVOR VIOLATION  ELECTROWEAK MEASUREMENTS  BHABHA SCATTERING  MISSING ENERGY  SINGLE-PHOTON  NEUTRINO MASS  HIGGS-BOSON  
Predicting protein inter-residue contacts using composite likelihood maximization and deep learning 期刊论文
BMC BIOINFORMATICS, 2019, 卷号: 20, 期号: 1, 页码: 537
Authors:  Zhang, Haicang;  Zhang, Qi;  Ju, Fusong;  Zhu, Jianwei;  Gao, Yujuan;  Xie, Ziwei;  Deng, Minghua;  Sun, Shiwei;  Zheng, Wei-Mou;  Bu, Dongbo
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COUPLING ANALYSIS  SEQUENCE  EVOLUTIONARY  INFORMATION  NETWORKS  RANK  
Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling 会议论文
BMC BIOINFORMATICS, Wuhan, PEOPLES R CHINA, JAN 14-16, 2019
Authors:  Wang, C;  Wei, Y;  Zhang, HC;  Kong, LP;  Sun, SW;  Zheng, WM;  Bu, DB
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TERTIARY STRUCTURES  FRAGMENTS  
蛋白质三级结构预测算法综述 期刊论文
计算机学报, 2018, 卷号: 41, 期号: 04, 页码: 760-779
Authors:  王超;  朱建伟;  张海仓;  巩海娥;  郑伟谋;  卜东波
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蛋白质结构  同源建模  归范法  从头预测法  能量函数  动态规划  线性规划  
Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts 期刊论文
BIOINFORMATICS, 2017, 卷号: 33, 期号: 23, 页码: 3749-3757
Authors:  Zhu, JW;  Zhang, HC;  Li, SC;  Wang, C;  Kong, LP;  Sun, SW;  Zheng, WM;  Bu, DB;  Bu, DB (reprint author), Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100190, Peoples R China.;  Zheng, WM (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing 100190, Peoples R China.
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Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis 期刊论文
PLOS GENETICS, 2017, 卷号: 13, 期号: 2, 页码: e1006508
Authors:  Skwark, MJ;  Croucher, NJ;  Puranen, S;  Chewapreecha, C;  Pesonen, M;  Xu, YY;  Turner, P;  Harris, SR;  Beres, SB;  Musser, JM;  Parkhill, J;  Bentley, SD;  Aurell, E;  Corander, J;  Corander, J (reprint author), Wellcome Trust Sanger Inst, Pathogen Gen, Cambridge, England.;  Aurell, E (reprint author), KTH Royal Inst Technol, Dept Computat Biol, Stockholm, Sweden.;  Aurell, E (reprint author), Aalto Univ, Dept Appl Phys & Comp Sci, Espoo, Finland.;  Aurell, E (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing, Peoples R China.;  Corander, J (reprint author), Univ Helsinki, Dept Math & Stat, Helsinki, Finland.;  Corander, J (reprint author), Univ Oslo, Dept Biostat, Oslo, Norway.;  Corander, J (reprint author), Univ Cambridge, Dept Vet Med, Cambridge, England.
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Smoothing potential energy surface of proteins by hybrid coarse grained approach 期刊论文
CHINESE PHYSICS B, 2017, 卷号: 26, 期号: 5, 页码: 50202
Authors:  Lu, YK;  Zhou, X;  OuYang, ZC;  Zhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China.
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Coarse-grained  Hybrid Force Field  Enhanced Sampling  Protein Folding  
FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition 期刊论文
BIOINFORMATICS, 2016, 卷号: 32, 期号: 3, 页码: 462-464
Authors:  Wang, C;  Zhang, HC;  Zheng, WM;  Xu, D;  Zhu, JW;  Wang, B;  Ning, K;  Sun, SW;  Li, SC;  Bu, DB;  Bu, DB (reprint author), Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing, Peoples R China.;  Li, SC (reprint author), City Univ Hong Kong, Dept Comp Sci, Kowloon, Hong Kong, Peoples R China.
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Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins 期刊论文
BIOINFORMATICS, 2015, 卷号: 31, 期号: 23, 页码: 3773-3781
Authors:  Yang, J;  He, BJ;  Jang, R;  Zhang, Y;  Shen, HB;  Zhang, Y (reprint author), Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA.
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