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McHardy, Alice Carolyn, Martin, Hector Garcia, Tsirigos, Aristotelis, Hugenholtz, Philip and Rigoutsos, Isidore (2007) Accurate phylogenetic classification of variable-length DNA fragments. Nature Methods, 4 1: 63-72. doi:10.1038/NMETH976 58   200 Cited 224 times in Scopus224 16
Martín, Héctor García, Kunin, Victor, Ivanova, Natalia, Warnecke, Falk, Peterson, S. B., Barry, Kerrie, McHardy, Alice C., Yeates, Christine, He, Shaomei, Salamov, Asaf, Szeto, Ernest, Dalin, Eileen, Putnam, Nik, Rigoutsos, Isidore, Kyrpides, Nikos C., Blackall, Linda Louise, McMahon, Katherine D. and Hugenholtz, Philip (2006). Metagenomic analysis of phosphorus removing sludge communities. In: ISME Vienna 2006: 11th International Symposium on Microbial Ecology. The hidden powers: Microbial communities in action, Vienna, Austria, (A457-A457). 20-25 August 2006. 151  
Martín, Hector Garcia, Ivanova, Natalia, Kunin, Victor, Warnecke, Falk, Barry, Kerrie W., McHardy, Alice C., Yeates, Christine, He, Shaomei, Salamov, Asaf A., Szeto, Ernest, Dalin, Eileen, Putnam, Nik H., Shapiro, Harris J., Pangilinan, Jasmyn L., Rigoutsos, Isidore, Kyrpides, Nikos C., Blackall, Linda Louise, McMahon, Katherine D. and Hugenholtz, Philip (2006) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature Biotechnology, 24 10: 1263-1269. doi:10.1038/nbt1247 106   251 Cited 308 times in Scopus308 3
Warnecke, Falk, Luginbuehl, Peter, Ivanova, Natalia, Ghassemian, Majid, Richardson, Toby H., Stege, Justin T., Cayouette, Michelle, McHardy, Alice C., Djordjevic, Gordana, Aboushadi, Nahla, Sorek, Rotem, Tringe, Susannah G., Podar, Mircea, Martin, Hector Garcia, Kunin, Victor, Dalevi, Daniel, Madejska, Julita, Kirton, Edward, Platt, Darren, Szeto, Ernest, Salamov, Asaf, Barry, Kerrie, Mikhailova, Natalia, Kyrpides, Nikos C., Matson, Eric G., Ottesen, Elizabeth A., Zhang, Xinning, Hernandez, Myriam, Murillo, Catalina, Acosta, Luis G., Rigoutsos, Isidore, Tamayo, Giselle, Green, Brian D., Chang, Cathy, Rubin, Edward M., Mathur, Eric J., Robertson, Dan E., Hugenholtz, Philip and Leadbetter, Jared R. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature, 450 7169: 560-565. doi:10.1038/nature06269 73   470 Cited 477 times in Scopus477 2
Hoehl, Michael, Rigoutsos, Isidore and Ragan, Mark A. (2006) Pattern-based phylogenetic distance estimation and tree reconstruction. Evolutionary Bioinformatics, 2 359-375. 81   10
Dehal, Paramvir, Satou, Yutaka, Campbell, Robert K., Chapman, Jarrod, Degnan, Bernard, De Tomaso, Anthony, Davidson, Brad, Gregorio, Anna Di, Gelpke, Maarten, Goodstein, David M., Harafuji, Naoe, Hastings, Kenneth E. M., Ho, Isaac, Hotta, Kohji, Huang, Wayne, Kawashima, Takeshi, Lemaire, Patrick, Martinez, Diego, Meinertzhagen, Ian A., Necula, Simona, Nonaka, Masaru, Putnam, Nik, Rash, Sam, Saiga, Hidetoshi, Satake, Masanobu, Terry, Astrid, Yamada, Lixy, Wang, Hong-Gang, Awazu, Satoko, Azumi, Kaoru, Boore, Jeffrey, Branno, Margherita, Chin-bow, Stephen, DeSantis, Rosaria, Doyle, Sharon, Francino, Pilar, Keys, David N., Haga, Shinobu, Hayashi, Hiroko, Hino, Kyosuke, Imai, Kaoru S., Inaba, Kazuo, Kano, Shungo, Kobayashi, Kenji, Kobayashi, Mari, Lee, Byung-In, Makabe, Kazuhiro W., Manohar, Chitra, Matassi, Giorgio, Medina, Monica, Mochizuki, Yasuaki, Mount, Steve, Morishita, Tomomi, Miura, Sachiko, Nakayama, Akie, Nishizaka, Satoko, Nomoto, Hisayo, Ohta, Fumiko, Rigoutsos, Isidore, Sano, Masako, Akane, Sasaki, Sasakura, Yasunori, Shoguchi, Eiichi, Shin-i, Tadasu, Spagnuolo, Antoinetta, Stainier, Didier, Suzuki, Miho M., Tassy, Olivier, Takatori, Naohito, Tokuoka, Miki, Yagi, Kasumi, Yoshizaki, Fumiko, Wada, Shuichi, Zhang, Cindy, Hyatt, P. Douglas, Larimer, Frank, Detter, Chris, Doggett, Norman, Glavina, Tijana, Hawkins, Trevor, Richardson, Paul, Lucas, Susan, Kohara, Yuji, Levine, Michael, Satoh, Nori and Rokhsar, Daniel S. (2002) The draft genome sequence of the ascidian Ciona intestinalis: insights into the evolutionary origins of chordates and vertebrates. Science, 298 5601: 2157-2167. doi:10.1126/science.1080049 245   1000 Cited 976 times in Scopus976 11
Mavromatis, Konstantinos, Ivanova, Natalia, Barry, Kerry, Shapiro, Harris, Goltsman, Eugene, McHardy, Alice C., Rigoutsos, Isidore, Salamov, Asaf, Korzeniewski, Frank, Land, Miriam, Lapidus, Alla, Grigoriev, Igor, Richardson, Paul, Hugenholtz, Philip and Kyrpides, Nikos C. (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods, 4 6: 495-500. doi:10.1038/nmeth1043 70   150 Cited 162 times in Scopus162 21