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Progressive Cactus is a multiple-genome aligner for the thousand-genome era
Armstrong, Joel, Hickey, Glenn, Diekhans, Mark, Fiddes, Ian T., Novak, Adam M., Deran, Alden, Fang, Qi, Xie, Duo, Feng, Shaohong, Stiller, Josefin, Genereux, Diane, Johnson, Jeremy, Marinescu, Voichita Dana, Alföldi, Jessica, Harris, Robert S., Lindblad-Toh, Kerstin, Haussler, David, Karlsson, Elinor, Jarvis, Erich D., Zhang, Guojie, Paten, Benedict
Published in Nature (London) (12.11.2020)
Published in Nature (London) (12.11.2020)
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Journal Article
Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing
Replogle, Joseph M., Norman, Thomas M., Xu, Albert, Hussmann, Jeffrey A., Chen, Jin, Cogan, J. Zachery, Meer, Elliott J., Terry, Jessica M., Riordan, Daniel P., Srinivas, Niranjan, Fiddes, Ian T., Arthur, Joseph G., Alvarado, Luigi J., Pfeiffer, Katherine A., Mikkelsen, Tarjei S., Weissman, Jonathan S., Adamson, Britt
Published in Nature biotechnology (01.08.2020)
Published in Nature biotechnology (01.08.2020)
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Journal Article
The UCSC Genome Browser database: 2018 update
Casper, Jonathan, Zweig, Ann S, Villarreal, Chris, Tyner, Cath, Speir, Matthew L, Rosenbloom, Kate R, Raney, Brian J, Lee, Christopher M, Lee, Brian T, Karolchik, Donna, Hinrichs, Angie S, Haeussler, Maximilian, Guruvadoo, Luvina, Navarro Gonzalez, Jairo, Gibson, David, Fiddes, Ian T, Eisenhart, Christopher, Diekhans, Mark, Clawson, Hiram, Barber, Galt P, Armstrong, Joel, Haussler, David, Kuhn, Robert M, Kent, W James
Published in Nucleic acids research (04.01.2018)
Published in Nucleic acids research (04.01.2018)
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Journal Article
Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
Pollen, Alex A., Bhaduri, Aparna, Andrews, Madeline G., Nowakowski, Tomasz J., Meyerson, Olivia S., Mostajo-Radji, Mohammed A., Di Lullo, Elizabeth, Alvarado, Beatriz, Bedolli, Melanie, Dougherty, Max L., Fiddes, Ian T., Kronenberg, Zev N., Shuga, Joe, Leyrat, Anne A., West, Jay A., Bershteyn, Marina, Lowe, Craig B., Pavlovic, Bryan J., Salama, Sofie R., Haussler, David, Eichler, Evan E., Kriegstein, Arnold R.
Published in Cell (07.02.2019)
Published in Cell (07.02.2019)
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Journal Article
A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing
Petti, Allegra A., Williams, Stephen R., Miller, Christopher A., Fiddes, Ian T., Srivatsan, Sridhar N., Chen, David Y., Fronick, Catrina C., Fulton, Robert S., Church, Deanna M., Ley, Timothy J.
Published in Nature communications (14.08.2019)
Published in Nature communications (14.08.2019)
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Journal Article
Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
Fiddes, Ian T., Armstrong, Joel, Diekhans, Mark, Nachtweide, Stefanie, Kronenberg, Zev N., Underwood, Jason G., Gordon, David, Earl, Dent, Keane, Thomas, Eichler, Evan E., Haussler, David, Stanke, Mario, Paten, Benedict
Published in Genome research (01.07.2018)
Published in Genome research (01.07.2018)
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Journal Article
Paired involvement of human-specific Olduvai domains and NOTCH2NL genes in human brain evolution
Fiddes, Ian T., Pollen, Alex A., Davis, Jonathan M., Sikela, James M.
Published in Human genetics (01.07.2019)
Published in Human genetics (01.07.2019)
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Journal Article
The Genome of C57BL/6J “Eve”, the Mother of the Laboratory Mouse Genome Reference Strain
Sarsani, Vishal Kumar, Raghupathy, Narayanan, Fiddes, Ian T, Armstrong, Joel, Thibaud-Nissen, Francoise, Zinder, Oraya, Bolisetty, Mohan, Howe, Kerstin, Hinerfeld, Doug, Ruan, Xiaoan, Rowe, Lucy, Barter, Mary, Ananda, Guruprasad, Paten, Benedict, Weinstock, George M, Churchill, Gary A, Wiles, Michael V, Schneider, Valerie A, Srivastava, Anuj, Reinholdt, Laura G
Published in G3 : genes - genomes - genetics (01.06.2019)
Published in G3 : genes - genomes - genetics (01.06.2019)
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Journal Article
Author Correction: A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing
Petti, Allegra A., Williams, Stephen R., Miller, Christopher A., Fiddes, Ian T., Srivatsan, Sridhar N., Chen, David Y., Fronick, Catrina C., Fulton, Robert S., Church, Deanna M., Ley, Timothy J.
Published in Nature communications (21.07.2022)
Published in Nature communications (21.07.2022)
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Journal Article
Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes
Field, Andrew R., Jacobs, Frank M.J., Fiddes, Ian T., Phillips, Alex P.R., Reyes-Ortiz, Andrea M., LaMontagne, Erin, Whitehead, Lila, Meng, Vincent, Rosenkrantz, Jimi L., Olsen, Mari, Hauessler, Max, Katzman, Sol, Salama, Sofie R., Haussler, David
Published in Stem cell reports (12.02.2019)
Published in Stem cell reports (12.02.2019)
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Journal Article
Improved data analysis for the MinION nanopore sequencer
Jain, Miten, Fiddes, Ian T, Miga, Karen H, Olsen, Hugh E, Paten, Benedict, Akeson, Mark
Published in Nature methods (01.04.2015)
Published in Nature methods (01.04.2015)
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Journal Article
Nanopore sequencing and assembly of a human genome with ultra-long reads
Jain, Miten, Koren, Sergey, Miga, Karen H, Quick, Josh, Rand, Arthur C, Sasani, Thomas A, Tyson, John R, Beggs, Andrew D, Dilthey, Alexander T, Fiddes, Ian T, Malla, Sunir, Marriott, Hannah, Nieto, Tom, O'Grady, Justin, Olsen, Hugh E, Pedersen, Brent S, Rhie, Arang, Richardson, Hollian, Quinlan, Aaron R, Snutch, Terrance P, Tee, Louise, Paten, Benedict, Phillippy, Adam M, Simpson, Jared T, Loman, Nicholas J, Loose, Matthew
Published in Nature biotechnology (01.04.2018)
Published in Nature biotechnology (01.04.2018)
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Journal Article
Resolving the full spectrum of human genome variation using Linked-Reads
Marks, Patrick, Garcia, Sarah, Barrio, Alvaro Martinez, Belhocine, Kamila, Bernate, Jorge, Bharadwaj, Rajiv, Bjornson, Keith, Catalanotti, Claudia, Delaney, Josh, Fehr, Adrian, Fiddes, Ian T., Galvin, Brendan, Heaton, Haynes, Herschleb, Jill, Hindson, Christopher, Holt, Esty, Jabara, Cassandra B., Jett, Susanna, Keivanfar, Nikka, Kyriazopoulou-Panagiotopoulou, Sofia, Lek, Monkol, Lin, Bill, Lowe, Adam, Mahamdallie, Shazia, Maheshwari, Shamoni, Makarewicz, Tony, Marshall, Jamie, Meschi, Francesca, O'Keefe, Christopher J., Ordonez, Heather, Patel, Pranav, Price, Andrew, Royall, Ariel, Ruark, Elise, Seal, Sheila, Schnall-Levin, Michael, Shah, Preyas, Stafford, David, Williams, Stephen, Wu, Indira, Xu, Andrew Wei, Rahman, Nazneen, MacArthur, Daniel, Church, Deanna M.
Published in Genome research (01.04.2019)
Published in Genome research (01.04.2019)
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Journal Article
Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis
Fiddes, Ian T., Lodewijk, Gerrald A., Mooring, Meghan, Bosworth, Colleen M., Ewing, Adam D., Mantalas, Gary L., Novak, Adam M., van den Bout, Anouk, Bishara, Alex, Rosenkrantz, Jimi L., Lorig-Roach, Ryan, Field, Andrew R., Haeussler, Maximilian, Russo, Lotte, Bhaduri, Aparna, Nowakowski, Tomasz J., Pollen, Alex A., Dougherty, Max L., Nuttle, Xander, Addor, Marie-Claude, Zwolinski, Simon, Katzman, Sol, Kriegstein, Arnold, Eichler, Evan E., Salama, Sofie R., Jacobs, Frank M.J., Haussler, David
Published in Cell (31.05.2018)
Published in Cell (31.05.2018)
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Journal Article
scHLAcount: allele-specific HLA expression from single-cell gene expression data
Darby, Charlotte A, Stubbington, Michael J T, Marks, Patrick J, Martínez Barrio, Álvaro, Fiddes, Ian T
Published in Bioinformatics (01.06.2020)
Published in Bioinformatics (01.06.2020)
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Journal Article
A high-quality bonobo genome refines the analysis of hominid evolution
Mao, Yafei, Catacchio, Claudia R., Hillier, LaDeana W., Porubsky, David, Li, Ruiyang, Sulovari, Arvis, Fernandes, Jason D., Montinaro, Francesco, Gordon, David S., Storer, Jessica M., Haukness, Marina, Fiddes, Ian T., Murali, Shwetha Canchi, Dishuck, Philip C., Hsieh, PingHsun, Harvey, William T., Audano, Peter A., Mercuri, Ludovica, Piccolo, Ilaria, Antonacci, Francesca, Munson, Katherine M., Lewis, Alexandra P., Baker, Carl, Underwood, Jason G., Hoekzema, Kendra, Huang, Tzu-Hsueh, Sorensen, Melanie, Walker, Jerilyn A., Hoffman, Jinna, Thibaud-Nissen, Françoise, Salama, Sofie R., Pang, Andy W. C., Lee, Joyce, Hastie, Alex R., Paten, Benedict, Batzer, Mark A., Diekhans, Mark, Ventura, Mario, Eichler, Evan E.
Published in Nature (London) (03.06.2021)
Published in Nature (London) (03.06.2021)
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Journal Article
Benchmarking challenging small variants with linked and long reads
Wagner, Justin, Olson, Nathan D., Harris, Lindsay, Khan, Ziad, Farek, Jesse, Mahmoud, Medhat, Stankovic, Ana, Kovacevic, Vladimir, Yoo, Byunggil, Miller, Neil, Rosenfeld, Jeffrey A., Ni, Bohan, Zarate, Samantha, Kirsche, Melanie, Aganezov, Sergey, Schatz, Michael C., Narzisi, Giuseppe, Byrska-Bishop, Marta, Clarke, Wayne, Evani, Uday S., Markello, Charles, Shafin, Kishwar, Zhou, Xin, Sidow, Arend, Bansal, Vikas, Ebert, Peter, Marschall, Tobias, Lansdorp, Peter, Hanlon, Vincent, Mattsson, Carl-Adam, Barrio, Alvaro Martinez, Fiddes, Ian T., Xiao, Chunlin, Fungtammasan, Arkarachai, Chin, Chen-Shan, Wenger, Aaron M., Rowell, William J., Sedlazeck, Fritz J., Carroll, Andrew, Salit, Marc, Zook, Justin M.
Published in Cell genomics (11.05.2022)
Published in Cell genomics (11.05.2022)
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Journal Article
Improved reference genome for the domestic horse increases assembly contiguity and composition
Kalbfleisch, Theodore S., Rice, Edward S., DePriest, Michael S., Walenz, Brian P., Hestand, Matthew S., Vermeesch, Joris R., O′Connell, Brendan L., Fiddes, Ian T., Vershinina, Alisa O., Saremi, Nedda F., Petersen, Jessica L., Finno, Carrie J., Bellone, Rebecca R., McCue, Molly E., Brooks, Samantha A., Bailey, Ernest, Orlando, Ludovic, Green, Richard E., Miller, Donald C., Antczak, Douglas F., MacLeod, James N.
Published in Communications biology (01.01.2018)
Published in Communications biology (01.01.2018)
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Journal Article
Lack of Dosage Balance and Incomplete Dosage Compensation in the ZZ/ZW Gila Monster (Heloderma suspectum) Revealed by De Novo Genome Assembly
Webster, Timothy H, Vannan, Annika, Pinto, Brendan J, Denbrock, Grant, Morales, Matheo, Dolby, Greer A, Fiddes, Ian T, DeNardo, Dale F, Wilson, Melissa A
Published in Genome biology and evolution (02.03.2024)
Published in Genome biology and evolution (02.03.2024)
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Journal Article
Single-cell sequencing of genomic DNA resolves sub-clonal heterogeneity in a melanoma cell line
Velazquez-Villarreal, Enrique I., Maheshwari, Shamoni, Sorenson, Jon, Fiddes, Ian T., Kumar, Vijay, Yin, Yifeng, Webb, Michelle G., Catalanotti, Claudia, Grigorova, Mira, Edwards, Paul A., Carpten, John D., Craig, David W.
Published in Communications biology (25.06.2020)
Published in Communications biology (25.06.2020)
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Journal Article