Paired involvement of human-specific Olduvai domains and NOTCH2NL genes in human brain evolution

por Fiddes, Ian T., Pollen, Alex A., Davis, Jonathan M., Sikela, James M.
Publicado 2019

Improved data analysis for the MinION nanopore sequencer

por Jain, Miten, Fiddes, Ian, Miga, Karen H., Olsen, Hugh E., Paten, Benedict, Akeson, Mark
Publicado 2015

scHLAcount: allele-specific HLA expression from single-cell gene expression data

por Darby, Charlotte A, Stubbington, Michael J T, Marks, Patrick J, Martínez Barrio, Álvaro, Fiddes, Ian T
Publicado 2020

Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells

por Tunstall, Tate, Kock, Richard, Vahala, Jiri, Diekhans, Mark, Fiddes, Ian, Armstrong, Joel, Paten, Benedict, Ryder, Oliver A., Steiner, Cynthia C.
Publicado 2018

Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation

por Srivastava, Anuj, Kumar Sarsani, Vishal, Fiddes, Ian, Sheehan, Susan M, Seger, Rita L, Barter, Mary E, Neptune-Bear, Selena, Lindqvist, Charlotte, Korstanje, Ron
Publicado 2019

Incomplete dosage balance and dosage compensation in the ZZ/ZW Gila monster (Heloderma suspectum) revealed by de novo genome assembly

por Webster, Timothy H., Vannan, Annika, Pinto, Brendan J., Denbrock, Grant, Morales, Matheo, Dolby, Greer A., Fiddes, Ian T., DeNardo, Dale F., Wilson, Melissa A.
Publicado 2023

Transcriptional activity and strain-specific history of mouse pseudogenes

por Sisu, Cristina, Muir, Paul, Frankish, Adam, Fiddes, Ian, Diekhans, Mark, Thybert, David, Odom, Duncan T., Flicek, Paul, Keane, Thomas M., Hubbard, Tim, Harrow, Jennifer, Gerstein, Mark
Publicado 2020

A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing

por 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.
Publicado 2019

Author Correction: A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing

por 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.
Publicado 2022

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

por 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
Publicado 2018

Single-cell sequencing of genomic DNA resolves sub-clonal heterogeneity in a melanoma cell line

por 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.
Publicado 2020

Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes

por 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
Publicado 2019

A missense mutation in the proprotein convertase gene furinb causes hepatic cystogenesis during liver development in zebrafish

por Ellis, Jillian L., Evason, Kimberley J., Zhang, Changwen, Fourman, Makenzie N., Liu, Jiandong, Ninov, Nikolay, Delous, Marion, Vanhollebeke, Benoit, Fiddes, Ian, Otis, Jessica P., Houvras, Yariv, Farber, Steven A., Xu, Xiaolei, Lin, Xueying, Stainier, Didier Y. R., Yin, Chunyue
Publicado 2022

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

por Replogle, Joseph M., Norman, Thomas M., Xu, Albert, Hussmann, Jeffrey A., Chen, Jin, Cogan, J. Zachary, 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
Publicado 2020

The Genome of C57BL/6J “Eve”, the Mother of the Laboratory Mouse Genome Reference Strain

por 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.
Publicado 2019

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

por 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
Publicado 2020

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling

por Rice, Edward S., Kohno, Satomi, John, John St., Pham, Son, Howard, Jonathan, Lareau, Liana F., O'Connell, Brendan L., Hickey, Glenn, Armstrong, Joel, Deran, Alden, Fiddes, Ian, Platt, Roy N., Gresham, Cathy, McCarthy, Fiona, Kern, Colin, Haan, David, Phan, Tan, Schmidt, Carl, Sanford, Jeremy R., Ray, David A., Paten, Benedict, Guillette, Louis J., Green, Richard E.
Publicado 2017

The UCSC Genome Browser database: 2018 update

por 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
Publicado 2018

Nanopore sequencing and assembly of a human genome with ultra-long reads

por 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
Publicado 2018

Improved reference genome for the domestic horse increases assembly contiguity and composition

por 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.
Publicado 2018