BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.

BMC Evol. Biol.     Rahul Satija , Adám Novák , István Miklós , Rune Lyngsø , Jotun Hein

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.

Bioinformatics     Rahul Satija , Lior Pachter , Jotun Hein

Evolution of genes and genomes on the Drosophila phylogeny.

Nature     Drosophila 12 Genomes Consortium , Andrew G Clark , Michael B Eisen , Douglas R Smith , Casey M Bergman , Brian Oliver , Therese A Markow , Thomas C Kaufman , Manolis Kellis , William Gelbart , Venky N Iyer , Daniel A Pollard , Timothy B Sackton , Amanda M Larracuente , Nadia D Singh , Jose P Abad , Dawn N Abt , Boris Adryan , Montserrat Aguade , Hiroshi Akashi , Wyatt W Anderson , Charles F Aquadro , David H Ardell , Roman Arguello , Carlo G Artieri , Daniel A Barbash , Daniel Barker , Paolo Barsanti , Phil Batterham , Serafim Batzoglou , Dave Begun , Arjun Bhutkar , Enrico Blanco , Stephanie A Bosak , Robert K Bradley , Adrianne D Brand , Michael R Brent , Angela N Brooks , Randall H Brown , Roger K Butlin , Corrado Caggese , Brian R Calvi , A Bernardo de Carvalho , Anat Caspi , Sergio Castrezana , Susan E Celniker , Jean L Chang , Charles Chapple , Sourav Chatterji , Asif Chinwalla , Alberto Civetta , Sandra W Clifton , Josep M Comeron , James C Costello , Jerry A Coyne , Jennifer Daub , Robert G David , Arthur L Delcher , Kim Delehaunty , Chuong B Do , Heather Ebling , Kevin Edwards , Thomas Eickbush , Jay D Evans , Alan Filipski , Sven Findeiss , Eva Freyhult , Lucinda Fulton , Robert Fulton , Ana C L Garcia , Anastasia Gardiner , David A Garfield , Barry E Garvin , Greg Gibson , Don Gilbert , Sante Gnerre , Jennifer Godfrey , Robert Good , Valer Gotea , Brenton Gravely , Anthony J Greenberg , Sam Griffiths-Jones , Samuel Gross , Roderic Guigo , Erik A Gustafson , Wilfried Haerty , Matthew W Hahn , Daniel L Halligan , Aaron L Halpern , Gillian M Halter , Mira V Han , Andreas Heger , LaDeana Hillier , Angie S Hinrichs , Ian Holmes , Roger A Hoskins , Melissa J Hubisz , Dan Hultmark , Melanie A Huntley , David B Jaffe , Santosh Jagadeeshan , William R Jeck , Justin Johnson , Corbin D Jones , William C Jordan , Gary H Karpen , Eiko Kataoka , Peter D Keightley , Pouya Kheradpour , Ewen F Kirkness , Leonardo B Koerich , Karsten Kristiansen , Dave Kudrna , Rob J Kulathinal , Sudhir Kumar , Roberta Kwok , Eric Lander , Charles H Langley , Richard Lapoint , Brian P Lazzaro , So-Jeong Lee , Lisa Levesque , Ruiqiang Li , Chiao-Feng Lin , Michael F Lin , Kerstin Lindblad-Toh , Ana Llopart , Manyuan Long , Lloyd Low , Elena Lozovsky , Jian Lu , Meizhong Luo , Carlos A Machado , Wojciech Makalowski , Mar Marzo , Muneo Matsuda , Luciano Matzkin , Bryant McAllister , Carolyn S McBride , Brendan McKernan , Kevin McKernan , Maria Mendez-Lago , Patrick Minx , Michael U Mollenhauer , Kristi Montooth , Stephen M Mount , Xu Mu , Eugene Myers , Barbara Negre , Stuart Newfeld , Rasmus Nielsen , Mohamed A F Noor , Patrick O'Grady , Lior Pachter , Montserrat Papaceit , Matthew J Parisi , Michael Parisi , Leopold Parts , Jakob S Pedersen , Graziano Pesole , Adam M Phillippy , Chris P Ponting , Mihai Pop , Damiano Porcelli , Jeffrey R Powell , Sonja Prohaska , Kim Pruitt , Marta Puig , Hadi Quesneville , Kristipati Ravi Ram , David Rand , Matthew D Rasmussen , Laura K Reed , Robert Reenan , Amy Reily , Karin A Remington , Tania T Rieger , Michael G Ritchie , Charles Robin , Yu-Hui Rogers , Claudia Rohde , Julio Rozas , Marc J Rubenfield , Alfredo Ruiz , Susan Russo , Steven L Salzberg , Alejandro Sanchez-Gracia , David J Saranga , Hajime Sato , Stephen W Schaeffer , Michael C Schatz , Todd Schlenke , Russell Schwartz , Carmen Segarra , Rama S Singh , Laura Sirot , Marina Sirota , Nicholas B Sisneros , Chris D Smith , Temple F Smith , John Spieth , Deborah E Stage , Alexander Stark , Wolfgang Stephan , Robert L Strausberg , Sebastian Strempel , David Sturgill , Granger Sutton , Granger G Sutton , Wei Tao , Sarah Teichmann , Yoshiko N Tobari , Yoshihiko Tomimura , Jason M Tsolas , Vera L S Valente , Eli Venter , J Craig Venter , Saverio Vicario , Filipe G Vieira , Albert J Vilella , Alfredo Villasante , Brian Walenz , Jun Wang , Marvin Wasserman , Thomas Watts , Derek Wilson , Richard K Wilson , Rod A Wing , Mariana F Wolfner , Alex Wong , Gane Ka-Shu Wong , Chung-I Wu , Gabriel Wu , Daisuke Yamamoto , Hsiao-Pei Yang , Shiaw-Pyng Yang , James A Yorke , Kiyohito Yoshida , Evgeny Zdobnov , Peili Zhang , Yu Zhang , Aleksey V Zimin , Jennifer Baldwin , Amr Abdouelleil , Jamal Abdulkadir , Adal Abebe , Brikti Abera , Justin Abreu , St Christophe Acer , Lynne Aftuck , Allen Alexander , Peter An , Erica Anderson , Scott Anderson , Harindra Arachi , Marc Azer , Pasang Bachantsang , Andrew Barry , Tashi Bayul , Aaron Berlin , Daniel Bessette , Toby Bloom , Jason Blye , Leonid Boguslavskiy , Claude Bonnet , Boris Boukhgalter , Imane Bourzgui , Adam Brown , Patrick Cahill , Sheridon Channer , Yama Cheshatsang , Lisa Chuda , Mieke Citroen , Alville Collymore , Patrick Cooke , Maura Costello , Katie D'Aco , Riza Daza , Georgius De Haan , Stuart DeGray , Christina DeMaso , Norbu Dhargay , Kimberly Dooley , Erin Dooley , Missole Doricent , Passang Dorje , Kunsang Dorjee , Alan Dupes , Richard Elong , Jill Falk , Abderrahim Farina , Susan Faro , Diallo Ferguson , Sheila Fisher , Chelsea D Foley , Alicia Franke , Dennis Friedrich , Loryn Gadbois , Gary Gearin , Christina R Gearin , Georgia Giannoukos , Tina Goode , Joseph Graham , Edward Grandbois , Sharleen Grewal , Kunsang Gyaltsen , Nabil Hafez , Birhane Hagos , Jennifer Hall , Charlotte Henson , Andrew Hollinger , Tracey Honan , Monika D Huard , Leanne Hughes , Brian Hurhula , M Erii Husby , Asha Kamat , Ben Kanga , Seva Kashin , Dmitry Khazanovich , Peter Kisner , Krista Lance , Marcia Lara , William Lee , Niall Lennon , Frances Letendre , Rosie LeVine , Alex Lipovsky , Xiaohong Liu , Jinlei Liu , Shangtao Liu , Tashi Lokyitsang , Yeshi Lokyitsang , Rakela Lubonja , Annie Lui , Pen MacDonald , Vasilia Magnisalis , Kebede Maru , Charles Matthews , William McCusker , Susan McDonough , Teena Mehta , James Meldrim , Louis Meneus , Oana Mihai , Atanas Mihalev , Tanya Mihova , Rachel Mittelman , Valentine Mlenga , Anna Montmayeur , Leonidas Mulrain , Adam Navidi , Jerome Naylor , Tamrat Negash , Thu Nguyen , Nga Nguyen , Robert Nicol , Choe Norbu , Nyima Norbu , Nathaniel Novod , Barry O'Neill , Sahal Osman , Eva Markiewicz , Otero L Oyono , Christopher Patti , Pema Phunkhang , Fritz Pierre , Margaret Priest , Sujaa Raghuraman , Filip Rege , Rebecca Reyes , Cecil Rise , Peter Rogov , Keenan Ross , Elizabeth Ryan , Sampath Settipalli , Terry Shea , Ngawang Sherpa , Lu Shi , Diana Shih , Todd Sparrow , Jessica Spaulding , John Stalker , Nicole Stange-Thomann , Sharon Stavropoulos , Catherine Stone , Christopher Strader , Senait Tesfaye , Talene Thomson , Yama Thoulutsang , Dawa Thoulutsang , Kerri Topham , Ira Topping , Tsamla Tsamla , Helen Vassiliev , Andy Vo , Tsering Wangchuk , Tsering Wangdi , Michael Weiand , Jane Wilkinson , Adam Wilson , Shailendra Yadav , Geneva Young , Qing Yu , Lisa Zembek , Danni Zhong , Andrew Zimmer , Zac Zwirko , David B Jaffe , Pablo Alvarez , Will Brockman , Jonathan Butler , CheeWhye Chin , Sante Gnerre , Manfred Grabherr , Michael Kleber , Evan Mauceli , Iain MacCallum

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome.

Genome Biol.     Casey M Bergman , Barret D Pfeiffer , Diego E Rincón-Limas , Roger A Hoskins , Andreas Gnirke , Chris J Mungall , Adrienne M Wang , Brent Kronmiller , Joanne Pacleb , Soo Park , Mark Stapleton , Kenneth Wan , Reed A George , Pieter J de Jong , Juan Botas , Gerald M Rubin , Susan E Celniker