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| Date | Title | Authors |
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| 2009 | Genome Biology: FOXA1 and FOXA3 binding patterns. | Motallebipour M, Ameur A, Reddy Bysani MS, Patra K, Wallerman O, Mangion J, Barker MA, McKernan KJ, Komorowski J, Wadelius C | | 2009 | Bioinformatics and Biology Insights: A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome | Marcin Kierczak, Krzysztof Ginalski, Michal Draminski, Jacek Koronacki, Witold R Rudnicki, Jan Komorowski | | 2009 | Genome Research: Nucleosomes are well positioned in exons and carry characteristic histone modifications. | Robin Andersson, Stefan Enroth, Alvaro Rada-Iglesias, Claes Wadelius, Jan Komorowski | | 2009 | FEBS Journal: Novel genes in cell cycle control and lipid metabolism with dynamically regulated binding sites for sterol regulatory element-binding protein 1 and RNA polymerase II in HepG2 cells detected by chromatin immunoprecipitation with microarray detection. | Mehdi Motallebipour, Stefan Enroth, Tanel Punga, Adam Ameur, Christoph Koch,
Ian Dunham, Jan Komorowski, Johan Ericsson and Claes Wadelius | | 2009 | Nature Physics: Effects of macromolecular crowding and DNA looping on gene regulation kinetics. | Gene-Wei Li, Otto G. Berg, Johan Elf | | 2009 | Epigenetics: Histone H3 lysine 27 trimethylation in adult differentiated colon associated to cancer DNA hypermethylation. | Rada-Iglesias A, Enroth S, Andersson R, Wanders A, Påhlman L, Komorowski J, Wadelius C. | | 2008 | BMC Bioinformatics: Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation | Orzechowski Westholm, Jakub; Xu, Feifei; Ronne, Hans; Komorowski, Jan | | 2008 | BMC Research Notes 2008: Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update. | Freyhult, Eva; Edvardsson Sverker; Tamas, Ivica; Moulton, Vincent; Poole, Anthony M. | | 2008 | Studies in Fuzziness and Soft Computing: Granular Computing: At the Junction of Rough Sets and Fuzzy Sets: Construction of Rough Set-Based Classifiers for Predicting HIV Resistance to Nucleoside Reverse Transcriptase Inhibitors | Kierczak, Marcin;
Rudnicki, Witold R;
Komorowski, Jan | | 2008 | Genome Research: Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. | Rada-Iglesias, Alvaro; Ameur, Adam; Kapranov, Philipp; Enroth, Stefan; Komorowski, Jan; Gingeras, Thomas R; Wadelius, Claes | | 2008 | Human Mutationions: Profiling a copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K: BAC-clone-based array | Díaz de Ståhl, Teresita; Sandgren, Johanna; Piotrowski, Arkadiusz; Nord, Helena; Andersson, Robin; Menzel, Uwe; Bogdan, Adam; Thuresson, Ann-Charlotte; Poplawski, Andrzej; von Tell, Desiree; Hansson, Caisa M; Elshafie, Amir I; ElGhazali, Gehad; Imreh, Stephan; Nordenskjöld, Magnus; Upadhyaya, Meena; Komorowski, Jan; Bruder, Carl EG; Dumanski, Jan P | | 2008 | Am J Med Genet A: Overlapping phenotype of Wolf-Hirschhorn and Beckwith-Wiedemann syndromes in a girl with der(4)t(4;11)(pter;pter). | Mikhail, Fady M; Sathienkijkanchai, Achara; Robin, Nathaniel H; Prucka, Sandra; Biggerstaff, Julie Sanford; Komorowski, Jan; Andersson, Robin; Bruder, Carl E G; Piotrowski, Arkadiusz; de Ståhl, Teresita Diaz; Dumanski, Jan P; Carroll, Andrew J | | 2008 | Bioinformatics: A Segmental Maximum A Posteriori Approach to Genome-wide Copy Number Profiling. | Andersson, Robin; Bruder, Carl E G; Piotrowski, Arkadiusz; Menzel, Uwe; Nord, Helena; Sandgren, Johanna; Hvidsten, Torgeir R; de Ståhl, Teresita Diaz; Dumanski, Jan P; Komorowski, Jan | | 2008 | Bioinformatics: Monte Carlo feature selection for supervised classification. | Draminski, Michal; Rada-Iglesias, Alvaro; Enroth, Stefan; Wadelius, Claes; Koronacki, Jacek; Komorowski, Jan | | 2007 | Journal of Bacteriology: Transient erythromycin resistance phenotype associated with peptidyl-tRNA drop-off on early UGG and GGG codons. | Macvanin, Mirjana; Gonzalez de Valdivia, Ernesto I; Ardell, David H; Isaksson, Leif A | | 2007 | Uppsala University, Dept. of Mathematics: Extremal optimal realizations | Lesser, Alice | | 2007 | Isaac Newton Institute, Cambridge UK: Optimal realizations of generic 5-point metrics | Koolen, Jack; Lesser, Alice; Moulton, Vincent
| | 2007 | Nature: Evolution of genes and genomes on the Drosophila phylogeny. | Clark, Andrew G; Eisen, Michael B; Smith, Douglas R; Bergman, Casey M; Oliver, Brian; Markow, Therese A; Kaufman, Thomas C; Kellis, Manolis; Gelbart, William; Iyer, Venky N; Pollard, Daniel A; Sackton, Timothy B; Larracuente, Amanda M; Singh, Nadia D; Abad, Jose P; Abt, Dawn N; Adryan, Boris; Aguade, Montserrat; Akashi, Hiroshi; Anderson, Wyatt W; Aquadro, Charles F; Ardell, David H; Arguello, Roman; Artieri, Carlo G; Barbash, Daniel A; Barker, Daniel; Barsanti, Paolo; Batterham, Phil; Batzoglou, Serafim; Begun, Dave; Bhutkar, Arjun; Blanco, Enrico; Bosak, Stephanie A; Bradley, Robert K; Brand, Adrianne D; Brent, Michael R; Brooks, Angela N; Brown, Randall H; Butlin, Roger K; Caggese, Corrado; Calvi, Brian R; Bernardo de Carvalho, A; Caspi, Anat; Castrezana, Sergio; Celniker, Susan E; Chang, Jean L; Chapple, Charles; Chatterji, Sourav; Chinwalla, Asif; Civetta, Alberto; Clifton, Sandra W; Comeron, Josep M; Costello, James C; Coyne, Jerry A; Daub, Jennifer; David, Robert G; Delcher, Arthur L; Delehaunty, Kim; Do, Chuong B; Ebling, Heather; Edwards, Kevin; Eickbush, Thomas; Evans, Jay D; Filipski, Alan; Findeiss, Sven; Freyhult, Eva; Fulton, Lucinda; Fulton, Robert; Garcia, Ana C L; Gardiner, Anastasia; Garfield, David A; Garvin, Barry E; Gibson, Greg; Gilbert, Don; Gnerre, Sante; Godfrey, Jennifer; Good, Robert; Gotea, Valer; Gravely, Brenton; Greenberg, Anthony J; Griffiths-Jones, Sam; Gross, Samuel; Guigo, Roderic; Gustafson, Erik A; Haerty, Wilfried; Hahn, Matthew W; Halligan, Daniel L; Halpern, Aaron L; Halter, Gillian M; Han, Mira V; Heger, Andreas; Hillier, LaDeana; Hinrichs, Angie S; Holmes, Ian; Hoskins, Roger A; Hubisz, Melissa J; Hultmark, Dan; Huntley, Melanie A; Jaffe, David B; Jagadeeshan, Santosh; Jeck, William R; Johnson, Justin; Jones, Corbin D; Jordan, William C; Karpen, Gary H; Kataoka, Eiko; Keightley, Peter D; Kheradpour, Pouya; Kirkness, Ewen F; Koerich, Leonardo B; Kristiansen, Karsten; Kudrna, Dave; Kulathinal, Rob J; Kumar, Sudhir; Kwok, Roberta; Lander, Eric; Langley, Charles H; Lapoint, Richard; Lazzaro, Brian P; Lee, So-Jeong; Levesque, Lisa; Li, Ruiqiang; Lin, Chiao-Feng; Lin, Michael F; Lindblad-Toh, Kerstin; Llopart, Ana; Long, Manyuan; Low, Lloyd; Lozovsky, Elena; Lu, Jian; Luo, Meizhong; Machado, Carlos A; Makalowski, Wojciech; Marzo, Mar; Matsuda, Muneo; Matzkin, Luciano; McAllister, Bryant; McBride, Carolyn S; McKernan, Brendan; McKernan, Kevin; Mendez-Lago, Maria; Minx, Patrick; Mollenhauer, Michael U; Montooth, Kristi; Mount, Stephen M; Mu, Xu; Myers, Eugene; Negre, Barbara; Newfeld, Stuart; Nielsen, Rasmus; Noor, Mohamed A F; O'Grady, Patrick; Pachter, Lior; Papaceit, Montserrat; Parisi, Matthew J; Parisi, Michael; Parts, Leopold; Pedersen, Jakob S; Pesole, Graziano; Phillippy, Adam M; Ponting, Chris P; Pop, Mihai; Porcelli, Damiano; Powell, Jeffrey R; Prohaska, Sonja; Pruitt, Kim; Puig, Marta; Quesneville, Hadi; Ram, Kristipati Ravi; Rand, David; Rasmussen, Matthew D; Reed, Laura K; Reenan, Robert; Reily, Amy; Remington, Karin A; Rieger, Tania T; Ritchie, Michael G; Robin, Charles; Rogers, Yu-Hui; Rohde, Claudia; Rozas, Julio; Rubenfield, Marc J; Ruiz, Alfredo; Russo, Susan; Salzberg, Steven L; Sanchez-Gracia, Alejandro; Saranga, David J; Sato, Hajime; Schaeffer, Stephen W; Schatz, Michael C; Schlenke, Todd; Schwartz, Russell; Segarra, Carmen; Singh, Rama S; Sirot, Laura; Sirota, Marina; Sisneros, Nicholas B; Smith, Chris D; Smith, Temple F; Spieth, John; Stage, Deborah E; Stark, Alexander; Stephan, Wolfgang; Strausberg, Robert L; Strempel, Sebastian; Sturgill, David; Sutton, Granger; Sutton, Granger G; Tao, Wei; Teichmann, Sarah; Tobari, Yoshiko N; Tomimura, Yoshihiko; Tsolas, Jason M; Valente, Vera L S; Venter, Eli; Venter, J Craig; Vicario, Saverio; Vieira, Filipe G; Vilella, Albert J; Villasante, Alfredo; Walenz, Brian; Wang, Jun; Wasserman, Marvin; Watts, Thomas; Wilson, Derek; Wilson, Richard K; Wing, Rod A; Wolfner, Mariana F; Wong, Alex; Wong, Gane Ka-Shu; Wu, Chung-I; Wu, Gabriel; Yamamoto, Daisuke; Yang, Hsiao-Pei; Yang, Shiaw-Pyng; Yorke, James A; Yoshida, Kiyohito; Zdobnov, Evgeny; Zhang, Peili; Zhang, Yu; Zimin, Aleksey V; Baldwin, Jennifer; Abdouelleil, Amr; Abdulkadir, Jamal; Abebe, Adal; Abera, Brikti; Abreu, Justin; Acer, St Christophe; Aftuck, Lynne; Alexander, Allen; An, Peter; Anderson, Erica; Anderson, Scott; Arachi, Harindra; Azer, Marc; Bachantsang, Pasang; Barry, Andrew; Bayul, Tashi; Berlin, Aaron; Bessette, Daniel; Bloom, Toby; Blye, Jason; Boguslavskiy, Leonid; Bonnet, Claude; Boukhgalter, Boris; Bourzgui, Imane; Brown, Adam; Cahill, Patrick; Channer, Sheridon; Cheshatsang, Yama; Chuda, Lisa; Citroen, Mieke; Collymore, Alville; Cooke, Patrick; Costello, Maura; D'Aco, Katie; Daza, Riza; De Haan, Georgius; DeGray, Stuart; DeMaso, Christina; Dhargay, Norbu; Dooley, Kimberly; Dooley, Erin; Doricent, Missole; Dorje, Passang; Dorjee, Kunsang; Dupes, Alan; Elong, Richard; Falk, Jill; Farina, Abderrahim; Faro, Susan; Ferguson, Diallo; Fisher, Sheila; Foley, Chelsea D; Franke, Alicia; Friedrich, Dennis; Gadbois, Loryn; Gearin, Gary; Gearin, Christina R; Giannoukos, Georgia; Goode, Tina; Graham, Joseph; Grandbois, Edward; Grewal, Sharleen; Gyaltsen, Kunsang; Hafez, Nabil; Hagos, Birhane; Hall, Jennifer; Henson, Charlotte; Hollinger, Andrew; Honan, Tracey; Huard, Monika D; Hughes, Leanne; Hurhula, Brian; Husby, M Erii; Kamat, Asha; Kanga, Ben; Kashin, Seva; Khazanovich, Dmitry; Kisner, Peter; Lance, Krista; Lara, Marcia; Lee, William; Lennon, Niall; Letendre, Frances; LeVine, Rosie; Lipovsky, Alex; Liu, Xiaohong; Liu, Jinlei; Liu, Shangtao; Lokyitsang, Tashi; Lokyitsang, Yeshi; Lubonja, Rakela; Lui, Annie; MacDonald, Pen; Magnisalis, Vasilia; Maru, Kebede; Matthews, Charles; McCusker, William; McDonough, Susan; Mehta, Teena; Meldrim, James; Meneus, Louis; Mihai, Oana; Mihalev, Atanas; Mihova, Tanya; Mittelman, Rachel; Mlenga, Valentine; Montmayeur, Anna; Mulrain, Leonidas; Navidi, Adam; Naylor, Jerome; Negash, Tamrat; Nguyen, Thu; Nguyen, Nga; Nicol, Robert; Norbu, Choe; Norbu, Nyima; Novod, Nathaniel; O'Neill, Barry; Osman, Sahal; Markiewicz, Eva; Oyono, Otero L; Patti, Christopher; Phunkhang, Pema; Pierre, Fritz; Priest, Margaret; Raghuraman, Sujaa; Rege, Filip; Reyes, Rebecca; Rise, Cecil; Rogov, Peter; Ross, Keenan; Ryan, Elizabeth; Settipalli, Sampath; Shea, Terry; Sherpa, Ngawang; Shi, Lu; Shih, Diana; Sparrow, Todd; Spaulding, Jessica; Stalker, John; Stange-Thomann, Nicole; Stavropoulos, Sharon; Stone, Catherine; Strader, Christopher; Tesfaye, Senait; Thomson, Talene; Thoulutsang, Yama; Thoulutsang, Dawa; Topham, Kerri; Topping, Ira; Tsamla, Tsamla; Vassiliev, Helen; Vo, Andy; Wangchuk, Tsering; Wangdi, Tsering; Weiand, Michael; Wilkinson, Jane; Wilson, Adam; Yadav, Shailendra; Young, Geneva; Yu, Qing; Zembek, Lisa; Zhong, Danni; Zimmer, Andrew; Zwirko, Zac; Jaffe, David B; Alvarez, Pablo; Brockman, Will; Butler, Jonathan; Chin, CheeWhye; Gnerre, Sante; Grabherr, Manfred; Kleber, Michael; Mauceli, Evan; MacCallum, Iain | | 2007 | Biochimie: New computational methods reveal tRNA identity element divergence between Proteobacteria and Cyanobacteria. | Freyhult, Eva; Cui, Yuanyuan; Nilsson, Olle; Ardell, David H | | 2007 | Proteins: Structure, Function and Bioinformatics: Proteochemometric analysis of small cyclic peptides-X interaction with wild-type and chimeric melanocortin receptors | Kontijevskis, Aleksejs; Petrovska, Ramona; Mutule, Ilze; Uhlen, Staffan; Komorowski, Jan; Prusis, Peteris; Wikberg, Jarl | | 2007 | Discrete and Computational Geometry: Concerning the Relationship between Realizations and Tight Spans of Finite Metrics | Koolen, Jack; Lesser, Alice; Moulton, Vincent | | 2007 | Am J Med Genet A: A previously unrecognized microdeletion syndrome on chromosome 22 band q11.2 encompassing the BCR gene. | Mikhail, Fady M; Descartes, Maria; Piotrowski, Arkadiusz; Andersson, Robin; de Ståhl, Teresita Diaz; Komorowski, Jan; Bruder, Carl E G; Dumanski, Jan P; Carroll, Andrew J | | 2007 | Bioinformatics: Boltzmann probability of RNA structural neighbors and riboswitch detection. | Freyhult, Eva; Moulton, Vincent; Clote, Peter | | 2007 | Nucleic Acids Research: RNAbor: a web server for RNA structural neighbors. | Freyhult, Eva; Moulton, Vincent; Clote, Peter | | 2007 | Nucleic Acids Research: TFAM 1.0: an online tRNA function classifier. | Tåquist, Helena; Cui, Yuanyuan; Ardell, David H | | 2007 | Genetics: Increasing the efficiency of variance component quantitative trait loci analysis by using reduced-rank identity-by-descent matrices | Rönnegård, Lars; Mishchenko, Kateryna; Holmgren, Sverker; Carlborg, Örjan | | 2007 | Genome Research: Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes. | Rada-Iglesias, Alvaro; Enroth, Stefan; Ameur, Adam; Koch, Christoph M; Clelland, Gayle K; Respuela-Alonso, Patricia; Wilcox, Sarah; Dovey, Oliver M; Ellis, Peter D; Langford, Cordelia F; Dunham, Ian; Komorowski, Jan; Wadelius, Claes | | 2007 | Nature: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. | Birney, Ewan; Stamatoyannopoulos, John A; Dutta, Anindya; Guiga, Roderic; Gingeras, Thomas R; Margulies, Elliott H; Weng, Zhiping; Snyder, Michael; Dermitzakis, Emmanouil T; Thurman, Robert E; Kuehn, Michael S; Taylor, Christopher M; Neph, Shane; Koch, Christoph M; Asthana, Saurabh; Malhotra, Ankit; Adzhubei, Ivan; Greenbaum, Jason A; Andrews, Robert M; Flicek, Paul; Boyle, Patrick J; Cao, Hua; Carter, Nigel P; Clelland, Gayle K; Davis, Sean; Day, Nathan; Dhami, Pawandeep; Dillon, Shane C; Dorschner, Michael O; Fiegler, Heike; Giresi, Paul G; Goldy, Jeff; Hawrylycz, Michael; Haydock, Andrew; Humbert, Richard; James, Keith D; Johnson, Brett E; Johnson, Ericka M; Frum, Tristan T; Rosenzweig, Elizabeth R; Karnani, Neerja; Lee, Kirsten; Lefebvre, Gregory C; Navas, Patrick A; Neri, Fidencio; Parker, Stephen C J; Sabo, Peter J; Sandstrom, Richard; Shafer, Anthony; Vetrie, David; Weaver, Molly; Wilcox, Sarah; Yu, Man; Collins, Francis S; Dekker, Job; Lieb, Jason D; Tullius, Thomas D; Crawford, Gregory E; Sunyaev, Shamil; Noble, William S; Dunham, Ian; Denoeud, France; Reymond, Alexandre; Kapranov, Philipp; Rozowsky, Joel; Zheng, Deyou; Castelo, Robert; Frankish, Adam; Harrow, Jennifer; Ghosh, Srinka; Sandelin, Albin; Hofacker, Ivo L; Baertsch, Robert; Keefe, Damian; Dike, Sujit; Cheng, Jill; Hirsch, Heather A; Sekinger, Edward A; Lagarde, Julien; Abril, Josep F; Shahab, Atif; Flamm, Christoph; Fried, Claudia; Hackermüller, Jörg; Hertel, Jana; Lindemeyer, Manja; Missal, Kristin; Tanzer, Andrea; Washietl, Stefan; Korbel, Jan; Emanuelsson, Olof; Pedersen, Jakob S; Holroyd, Nancy; Taylor, Ruth; Swarbreck, David; Matthews, Nicholas; Dickson, Mark C; Thomas, Daryl J; Weirauch, Matthew T; Gilbert, James; Drenkow, Jorg; Bell, Ian; Zhao, XiaoDong; Srinivasan, K G; Sung, Wing-Kin; Ooi, Hong Sain; Chiu, Kuo Ping; Foissac, Sylvain; Alioto, Tyler; Brent, Michael; Pachter, Lior; Tress, Michael L; Valencia, Alfonso; Choo, Siew Woh; Choo, Chiou Yu; Ucla, Catherine; Manzano, Caroline; Wyss, Carine; Cheung, Evelyn; Clark, Taane G; Brown, James B; Ganesh, Madhavan; Patel, Sandeep; Tammana, Hari; Chrast, Jacqueline; Henrichsen, Charlotte N; Kai, Chikatoshi; Kawai, Jun; Nagalakshmi, Ugrappa; Wu, Jiaqian; Lian, Zheng; Lian, Jin; Newburger, Peter; Zhang, Xueqing; Bickel, Peter; Mattick, John S; Carninci, Piero; Hayashizaki, Yoshihide; Weissman, Sherman; Hubbard, Tim; Myers, Richard M; Rogers, Jane; Stadler, Peter F; Lowe, Todd M; Wei, Chia-Lin; Ruan, Yijun; Struhl, Kevin; Gerstein, Mark; Antonarakis, Stylianos E; Fu, Yutao; Green, Eric D; Karaöz, UlaÅŸ; Siepel, Adam; Taylor, James; Liefer, Laura A; Wetterstrand, Kris A; Good, Peter J; Feingold, Elise A; Guyer, Mark S; Cooper, Gregory M; Asimenos, George; Dewey, Colin N; Hou, Minmei; Nikolaev, Sergey; Montoya-Burgos, Juan I; Löytynoja, Ari; Whelan, Simon; Pardi, Fabio; Massingham, Tim; Huang, Haiyan; Zhang, Nancy R; Holmes, Ian; Mullikin, James C; Ureta-Vidal, Abel; Paten, Benedict; Seringhaus, Michael; Church, Deanna; Rosenbloom, Kate; Kent, W James; Stone, Eric A; Batzoglou, Serafim; Goldman, Nick; Hardison, Ross C; Haussler, David; Miller, Webb; Sidow, Arend; Trinklein, Nathan D; Zhang, Zhengdong D; Barrera, Leah; Stuart, Rhona; King, David C; Ameur, Adam; Enroth, Stefan; Bieda, Mark C; Kim, Jonghwan; Bhinge, Akshay A; Jiang, Nan; Liu, Jun; Yao, Fei; Vega, Vinsensius B; Lee, Charlie W H; Ng, Patrick; Shahab, Atif; Yang, Annie; Moqtaderi, Zarmik; Zhu, Zhou; Xu, Xiaoqin; Squazzo, Sharon; Oberley, Matthew J; Inman, David; Singer, Michael A; Richmond, Todd A; Munn, Kyle J; Rada-Iglesias, Alvaro; Wallerman, Ola; Komorowski, Jan; Fowler, Joanna C; Couttet, Phillippe; Bruce, Alexander W; Dovey, Oliver M; Ellis, Peter D; Langford, Cordelia F; Nix, David A; Euskirchen, Ghia; Hartman, Stephen; Urban, Alexander E; Kraus, Peter; Van Calcar, Sara; Heintzman, Nate; Kim, Tae Hoon; Wang, Kun; Qu, Chunxu; Hon, Gary; Luna, Rosa; Glass, Christopher K; Rosenfeld, M Geoff; Aldred, Shelley Force; Cooper, Sara J; Halees, Anason; Lin, Jane M; Shulha, Hennady P; Zhang, Xiaoling; Xu, Mousheng; Haidar, Jaafar N S; Yu, Yong; Ruan, Yijun; Iyer, Vishwanath R; Green, Roland D; Wadelius, Claes; Farnham, Peggy J; Ren, Bing; Harte, Rachel A; Hinrichs, Angie S; Trumbower, Heather; Clawson, Hiram; Hillman-Jackson, Jennifer; Zweig, Ann S; Smith, Kayla; Thakkapallayil, Archana; Barber, Galt; Kuhn, Robert M; Karolchik, Donna; Armengol, Lluis; Bird, Christine P; de Bakker, Paul I W; Kern, Andrew D; Lopez-Bigas, Nuria; Martin, Joel D; Stranger, Barbara E; Woodroffe, Abigail; Davydov, Eugene; Dimas, Antigone; Eyras, Eduardo; HallgrÃmsdóttir, Ingileif B; Huppert, Julian; Zody, Michael C; Abecasis, Gonçalo R; Estivill, Xavier; Bouffard, Gerard G; Guan, Xiaobin; Hansen, Nancy F; Idol, Jacquelyn R; Maduro, Valerie V B; Maskeri, Baishali; McDowell, Jennifer C; Park, Morgan; Thomas, Pamela J; Young, Alice C; Blakesley, Robert W; Muzny, Donna M; Sodergren, Erica; Wheeler, David A; Worley, Kim C; Jiang, Huaiyang; Weinstock, George M; Gibbs, Richard A; Graves, Tina; Fulton, Robert; Mardis, Elaine R; Wilson, Richard K; Clamp, Michele; Cuff, James; Gnerre, Sante; Jaffe, David B; Chang, Jean L; Lindblad-Toh, Kerstin; Lander, Eric S; Koriabine, Maxim; Nefedov, Mikhail; Osoegawa, Kazutoyo; Yoshinaga, Yuko; Zhu, Baoli; de Jong, Pieter J | | 2007 | Transactions on Rough Sets VII: Lecture Notes in Computer Science 4400: Rough sets in bioinformatics | Hvidsten, Torgeir R.; Komorowski, Jan | | 2007 | Experimental Cell Research: Endocan is a VEGF-A and PI3K regulated gene with increased expression in human renal cancer. | Rennel, Emma; Mellberg, Sofie; Dimberg, Anna; Petersson, Ludvig; Botling, Johan; Ameur, Adam; Westholm, Jakub Orzechowski; Komorowski, Jan; Lassalle, Philippe; Cross, Michael J; Gerwins, Pär | | 2007 | Proteins: Structure, Function and Bioinformatics: Computational proteomics analysis of HIV-1 protease interactome | Kontijevskis, Aleksejs; Wikberg, Jarl; Komorowski, Jan | | 2007 | PLoS Computational Biology: A Look Inside HIV Resistance through Retroviral Protease Interaction Maps | Kontijevskis, Aleksejs; Prusis, Peteris; Petrovska, Ramona; Yahorava, Sviatlana; Mutulis, Felikss; Mutule, Ilze; Komorowski, Jan; Wikberg, Jarl | | 2007 | J Chem Inf Model: In vitro drug sensitivity-gene expression correlations involve a tissue of origin dependency | Andersson, Claes R; Fryknäs, Mårten; Rickardson, Linda; Larsson, Rolf; Isaksson, Anders; Gustafsson, Mats G | | 2007 | Biology Direct: Intron Evolution and Information processing in the DNA polymerase alpha gene in spirotrichous ciliates: A hypothesis for interconversion between DNA and RNA deletion. | Chang, W.-J.; Addis, V.M.; Li, A.J.; Axelsson, Elin; Ardell, David H.; Landweber, L.F. | | 2007 | Genome Research: Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA | Freyhult, Eva; Bollback, Jonathan P; Gardner, Paul P | | 2007 | BMC Genetics: Separation of base allele and sampling term effects gives new insights in variance component QTL analysis. | Rönnegård, Lars; Carlborg, Örjan | | 2006 | Lecture Notes in Computer Science: Rough Sets and Current Trends in Computing: A Statistical Method for Determining Importance of Variables in an Information System | Rudnicki, Witold R; Kierczak, Marcin;Koronacki, Jacek; Komorowski, Jan | | 2006 | Behavioral Genetics: Epistatic regulation of behavioural and morphological traits in the zebrafish (Danio rerio). | Wright, Dominic; Butlin, Roger K; Carlborg, Orjan | | 2006 | BMC Bioinformatics: Using local gene expression similarities to discover regulatory binding site modules. | Wilczynski, Bartek; Hvidsten, Torgeir R; Kryshtafovych, Andriy; Tiuryn, Jerzy; Komorowski, Jan; Fidelis, Krzysztof | | 2006 | Proteins: Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures. | Strömbergsson, Helena; Kryshtafovych, Andriy; Prusis, Peteris; Fidelis, Krzysztof; Wikberg, Jarl E S; Komorowski, Jan; Hvidsten, Torgeir R | | 2006 | Annals of Combinatorics: Hereditarily Optimal Realizations of Consistent Metrics | Dress, Andreas; Huber, Katharina; Lesser, Alice; Moulton, Vincent | | 2006 | Journal of Molecular Evolution: The coevolution of genes and genetic codes: Crick's frozen accident revisited | Sella, Guy; Ardell, David Herman | | 2006 | Molecular Microbiology: Influences on gene expression in vivo by a Shine-Dalgarno sequence. | Jin, Haining; Zhao, Qing; Gonzalez de Valdivia, Ernesto I; Ardell, David H; Stenström, Magnus; Isaksson, Leif A | | 2006 | Nature Genetics: Epistasis and the release of genetic variation during long-term selection. | Carlborg, Örjan; Jacobsson, Lina; Ahgren, Per; Siegel, Paul; Andersson, Leif | | 2006 | Nucleic Acids Research: Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos. | Freyhult, Eva; Moulton, Vincent; Ardell, David | | 2006 | BIOINFORMATICS: The LCB DataWareHouse | Adam Ameur, Vladimir Yankovski, Stefan Enroth, Ola Spjuth, and Jan Komorowski | | 2006 | BMC Bioinformatics: Bayesian detection of periodic mRNA time profiles without use of training examples | Andersson, Claes; Isaksson, Anders; Gustafsson, Mats G | | 2006 | Nucleic Acids Research: TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA sythetase | Ardell, David H; Andersson, Siv G E | | 2006 | Proteins: Structure, Function, and Bioinformatics: Rough set-based proteochemometrics modeling of G-protein-coupled receptor-ligand interactions | Helena Strömbergsson, Peteris Prusis, Herman Midelfart, Maris Lapinsh, Jarl E.S. Wikberg, Jan Komorowski | | 2005 | Human Molecular Genetics: Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays | Alvaro Rada-Iglesias, Ola Wallerman, Christoph Koch, Adam Ameur, Stefan Enroth, Gayle Clelland, Kenneth Wester, Sarah Wilcox, Oliver M. Dovey, Peter D. Ellis, Vicki L. Wraight, Keith James, Rob Andrews, Cordelia Langford, Pawandeep Dhami, Nigel Carter, David Vetrie, Fredrik Ponte, Jan Komorowski, Ian Dunham and Claes Wadelius | | 2005 | Clin Cancer Res : Markers of adenocarcinoma characteristic of the site of origin: development. | Dennis, Jayne L; Hvidsten, Torgeir R; Wit, Ernst C; Komorowski, Jan; Bell, Alexandra K; Downie, Ian; Mooney, Jacqueline; Verbeke, Caroline; Bellamy, Christopher; Keith, W Nicol, Oien, Karin A | | 2005 | BMC Bioinformatics : Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling.. | Freyhult E, Prusis P, Lapinsh M, Wikberg JE, Moulton V, Gustafsson MG. | | 2005 | Mol Biol Evol : The MinMax Squeeze: guaranteeing a minimal tree for population data.. | Holland, B R; Huber, K T; Penny, D; Moulton, V | | 2005 | Genome Res : Discovering regulatory binding-site modules using rule-based learning.. | Hvidsten, Torgeir R; Wilczynski, Bartosz; Kryshtafovych, Andriy; Tiuryn, Jerzy; Komorowski, Jan; Fidelis, Krzysztof | | 2005 | Genomics : Genome-wide prediction of human VNTRs.. | Näslund, Kalle; Saetre, Peter; von Salomé, Jenny; Bergström, Tomas; Jareborg, Niclas; Jazin, Elena
| | 2004 | PNAS : The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae. | Alsmark, Cecilia; Frank, Carolin; Karlberg, Olof; Legault, Boris-Antoine; Ardell, David; Canbäck, Björn; Eriksson, Ann-Sofie; Handley, Scott; Huvet, Maxime; La Scola, Bernard,La
Holmberg, Martin, Andersson, Siv G E | | 2004 | Bioinformatics : SCANMS: adjusting for multiple comparisons in sliding window neutrality tests.. | Ardell, David H | | 2004 | Molecular Biology and Evolution : Neighbor-Net: An agglomerative method for the construction of phylogenetic networks. | Bryant, D; Moulton, V | | 2004 | Nat Rev Genet : Epistasis: too often neglected in complex trait studies?. | Carlborg, Orjan; Haley, Chris S | | 2004 | Bioinformatics : VisRD--visual recombination detection.. | Forslund, Kristoffer; Huson, Daniel H; Moulton, Vincent | | 2004 | Mol Biol Evol : Using consensus networks to visualize contradictory evidence for species phylogeny.. | Holland, Barbara R; Huber, Katharina T; Moulton, Vincent; Lockhart, Peter J | | 2004 | Discrete Mathematics : Recovering trees from well-separated multi-state characters. | Huber, KT | | 2004 | Discrete & Computational Geometry : The tight span of an antipodal metric space: Part II - Geometrical properties. | Huber, KT; Koolen, JH; Moulton, V | | 2004 | Discrete Applied Mathematics : Replacing cliques by stars in quasi-median graphs. | Huber, KT; Moulton, V; Semple, C | | 2004 | Nature : Chicken genomics: feather-pecking and victim pigmentation.. | Keeling, Linda; Andersson, Leif; Schütz, Karin E; Kerje, Susanne; Fredriksson, Robert; Carlborg, Orjan; Cornwallis, Charles K; Pizzari, Tommaso; Jensen, Per | | 2004 | Journal of Algebraic Combinatorics : There are finitely many triangle-free distance-regular graphs with degree 8, 9 or 10. | Koolen, J. H.; Moulton, V | | 2004 | European Journal of Combinatorics : The structure of spherical graphs. | Koolen, JH; Moulton, V; Stevanovic, D | | 2004 | J Med Virol : Phylogenetic analysis of the full-length SARS-CoV sequences: evidence for phylogenetic. | Magiorkinis, G; Magiorkinis, E; Paraskevis, D; Vandamme, A M; Van Ranst, M; Moulton, V; Hatzakis, A. | | 2004 | Advances in Applied Mathematics : Peeling phylogenetic “oranges” | Moulton, V; Steel, M | | 2004 | Cancer Lett : Gene expression based classification of gastric carcinoma.. | Nørsett, Kristin G; Laegreid, Astrid; Midelfart, Herman; Yadetie, Fekadu; Erlandsen, Sten Even; Falkmer, Sture; Grønbech, Jon E; Waldum, Helge L; Komorowski, Jan; Sandvik, Arne K | | 2004 | Rough Sets and Current Trends in Computing : Feature synthesis and extraction for the construction of generalized properties of amino acids. | Rudnicki, W. R.; Komorowski, J | | 2004 | Proceedings of the German Conference on Bioinformatics: Proteochemometrics Modeling of Receptor-Ligand Interactions Using Rough Sets | Strömbergsson, Helena; Prusis,P; Midelfart, Herman; Wikberg, J. E. S.; Komorowski, Jan. | | 2003 | European Journal of Combinatorics : A bound for the number of columns l((c,a,b)) in the intersection array of a distance-regular graph. | Bang S, Koolen JH, Moulton V | | 2003 | Discrete mathematics : Harmonic graphs with small number of cycles. | Borovicanin B, Grunewald S, Gutman I, Petrovic M | | 2003 | Applied Mathematics Letter : Connectivity calculus. | Cieslik D, Dress A, Huber KT, Moulton V | | 2003 | Ann. Comb. : Fibonacci-Cayley numbers and repetition patterns in genomic DNA. | Dress, Andreas, Giegerich, Robert, Grunewald, Stefan, Wagner, Holger | | 2003 | Applied mathematics letter : Semiharmonic trees and monocyclic graphs. | Dress A, Grunewald S | | 2003 | MATCH-COMMUNICATIONS IN MATHEMATICAL AND IN COMPUTER CHEMISTRY : On the number of walks in trees. | Dress A, Grunewald S, Gutman I, Lepovic M, Vidovic D | | 2003 | Bioinformatics : A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. | Edvardsson S, Gardner PP, Poole AM, Hendy MD, Penny D, Moulton V | | 2003 | Biophysical Journal : Structural modeling extends QSAR analysis of antibody-lysozome interactions to 3D-QSAR. | Freyhult, E K; Andersson, K; Gustafsson, M G | | 2003 | PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES : Optimal alphabets for an RNA world. | Gardner PP, Holland BR, Moulton V, Hendy M, Penny D | | 2003 | Bioinformatics : Learning rule-based models of biological process from gene expression time profiles using gene ontology. | Hvidsten TR, Laegreid A, Komorowski J | | 2003 | Graphs and combinatorics : Maximal energy bipartite graphs. | Koolen JH, Moulton V | | 2003 | Genome research : Predicting gene ontology biological process from temporal gene expression patterns. | Laegreid A, Hvidsten TR, Midelfart H, Komorowski J, Sandvik AK | | 2003 | Journal of Virology : Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses. | Salemi M, De Oliveira T, Courgnaud V, Moulton V, Holland B, Cassol S, Switzer WM, Vandamme AM | | 2003 | Genome Biology : Novel exploratory methods for visual recombination detection. | Strimmer, K., Forslund, K., Holland, B., Moulton, V. | | 2003 | Physiol Genomics : Liver gene expression in rats in response to the peroxisome proliferator-activated. | Yadetie, Fekadu; Laegreid, Astrid; Bakke, Ingunn; Kusnierczyk, Waclaw; Komorowski, Jan; Waldum, Helge L; Sandvik, Arne K | | 2002 | Discrete Applied Mathematics : Quasi-median graphs from sets of partitions. | Bandelt, HJ; Huber, KT; Moulton, V | | 2002 | European Journal of Combinatorics : Antipodal metrics and split systems. | Dress, A; Huber, KT | | 2002 | Advances in Mathematics : An explicit computation of the injective hull of certain finite metric spaces in terms of their associated Buneman complex. | Dress, A; Huber, KT; Moulton, V | | 2002 | European Journal of Combinatorics : On line arrangements in the hyperbolic plane. | Dress, A; Koolen, JH; Moulton, V | | 2002 | Mamm Genome : A large duplication associated with dominant white color in pigs originated. | Giuffra, Elisabetta; Törnsten, Anna; Marklund, Stefan; Bongcam-Rudloff, Erik; Chardon, Patrick; Kijas, James M H; Anderson, Susan I; Archibald, Alan L; Andersson, Leif | | 2002 | Mol Biol Evol : Delta plots: a tool for analyzing phylogenetic distance data.. | Holland, B R; Huber, K T; Dress, A; Moulton, V | | 2002 | Discrete Mathematics : The relation graph. | Huber, K. T.; Moulton, V | | 2002 | Appl Bioinformatics : Spectronet: a package for computing spectra and median networks.. | Huber, Katharina T; Langton, Michael; Penny, David; Moulton, Vincent; Hendy, Michael | | 2002 | European Journal of Combinatorics : Hyperbolic bridged graphs. | Koolen, JH; Moulton, V | | 2002 | European Journal of Combinatorics : On a conjecture of Bannai and Ito: There are finitely many distance-regular graphs with degree 5, 6 or 7. | Koolen, JH; Moulton, V | | 2002 | Exp Cell Res : Menin’s interaction with glial fibrillary acidic protein and vimentinsuggests a role for the intermediate filament network in regulating meninactivity.. | Lopez-Egido, J; Cunningham, J; Berg, M; Oberg, K; Bongcam-Rudloff, E; Gobl, A | | 2002 | Fundamenta Informaticae : Learning rough set classifiers from gene expressions and clinical data. | Midelfart, H; Komorowski, J; Nørsett, K; Yadetie, F; Sandvik, A.K. | | 2001 | Genetics: Statistical epistasis is a generic feature of gene regulatory networks. | Gjuvsland, Arne B; Hayes, Ben J; Omholt, Stig W; Carlborg, Orjan | | 2001 | Mech Dev : A 1.8kb GFAP-promoter fragment is active in specific regions of theembryonic CNS.. | Andrae, J; Bongcam-Rudloff, E; Hansson, I; Lendahl, U; Westermark, B; Nister, M | | 2001 | Genomics : Comparative analysis of a BAC contig of the porcine RN region and the human: implications for the cloning of trait loci.. | Jeon, J T; Amarger, V; Rogel-Gaillard, C; Robic, A; Bongcam-Rudloff, E; Paul, S; Looft, C; Milan, D; Chardon, P; Andersson, L | | 2000 | Int J Cancer : Modulation of phenotype and induction of irregular vessels accompany high tumorigenic potential of clonal human glioma cells xenografted to nude-rat brain.. | Enblad, Per; Hesselager, Göran; Bongcam-Rudloff, Erik; Hallin, Inga; Westermark, Bengt; Nister, Monica |
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