Search Results - "Alfoldi, Jessica"

Human genetic variation alters CRISPR-Cas9 on- and off-targeting specificity at therapeutically implicated loci by Lessard, Samuel, Francioli, Laurent, Alfoldi, Jessica, Tardif, Jean-Claude, Ellinor, Patrick T., MacArthur, Daniel G., Lettre, Guillaume, Orkin, Stuart H., Canver, Matthew C.

“…The CRISPR-Cas9 nuclease system holds enormous potential for therapeutic genome editing of a wide spectrum of diseases. Large efforts have been made to further…”
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A comprehensive genomic history of extinct and living elephants by Palkopoulou, Eleftheria, Lipson, Mark, Mallick, Swapan, Nielsen, Svend, Rohland, Nadin, Baleka, Sina, Karpinski, Emil, Ivancevic, Atma M., To, Thu-Hien, Kortschak, R. Daniel, Raison, Joy M., Qu, Zhipeng, Chin, Tat-Jun, Alt, Kurt W., Claesson, Stefan, Dalén, Love, MacPhee, Ross D. E., Meller, Harald, Roca, Alfred L., Ryder, Oliver A., Heiman, David, Young, Sarah, Breen, Matthew, Williams, Christina, Aken, Bronwen L., Ruffier, Magali, Karlsson, Elinor, Johnson, Jeremy, Di Palma, Federica, Alfoldi, Jessica, Adelson, David L., Mailund, Thomas, Munch, Kasper, Lindblad-Toh, Kerstin, Hofreiter, Michael, Poinar, Hendrik, Reich, David

“…Elephantids are the world’s most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14…”
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Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes by Soh, Y Q Shirleen, Alföldi, Jessica, Pyntikova, Tatyana, Brown, Laura G, Graves, Tina, Minx, Patrick J, Fulton, Robert S, Kremitzki, Colin, Koutseva, Natalia, Mueller, Jacob L, Rozen, Steve, Hughes, Jennifer F, Owens, Elaine, Womack, James E, Murphy, William J, Cao, Qing, de Jong, Pieter, Warren, Wesley C, Wilson, Richard K, Skaletsky, Helen, Page, David C

“…We sequenced the MSY (male-specific region of the Y chromosome) of the C57BL/6J strain of the laboratory mouse Mus musculus. In contrast to theories that Y…”
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Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma by Megquier, Kate, Turner-Maier, Jason, Swofford, Ross, Kim, Jong-Hyuk, Sarver, Aaron L, Wang, Chao, Sakthikumar, Sharadha, Johnson, Jeremy, Koltookian, Michele, Lewellen, Mitzi, Scott, Milcah C, Schulte, Ashley J, Borst, Luke, Tonomura, Noriko, Alfoldi, Jessica, Painter, Corrie, Thomas, Rachael, Karlsson, Elinor K, Breen, Matthew, Modiano, Jaime F, Elvers, Ingegerd, Lindblad-Toh, Kerstin

“…Angiosarcoma is a highly aggressive cancer of blood vessel-forming cells with few effective treatment options and high patient mortality. It is both rare and…”
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Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes by Broeckx, Bart J.G., Hitte, Christophe, Coopman, Frank, Verhoeven, Geert E.C., De Keulenaer, Sarah, De Meester, Ellen, Derrien, Thomas, Alfoldi, Jessica, Lindblad-Toh, Kerstin, Bosmans, Tim, Gielen, Ingrid, Van Bree, Henri, Van Ryssen, Bernadette, Saunders, Jimmy H., Van Nieuwerburgh, Filip, Deforce, Dieter

“…By limiting sequencing to those sequences transcribed as mRNA, whole exome sequencing is a cost-efficient technique often used in disease-association studies…”
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The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling by Noh, Hyun Ji, Turner-Maier, Jason, Schulberg, S. Anne, Fitzgerald, Michael L., Johnson, Jeremy, Allen, Kaitlin N., Hückstädt, Luis A., Batten, Annabelle J., Alfoldi, Jessica, Costa, Daniel P., Karlsson, Elinor K., Zapol, Warren M., Buys, Emmanuel S., Lindblad-Toh, Kerstin, Hindle, Allyson G.

“…The Weddell seal ( Leptonychotes weddellii ) thrives in its extreme Antarctic environment. We generated the Weddell seal genome assembly and a high-quality…”
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Progressive Cactus is a multiple-genome aligner for the thousand-genome era by 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

“…New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing…”
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FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome by Wucher, Valentin, Legeai, Fabrice, Hédan, Benoît, Rizk, Guillaume, Lagoutte, Lætitia, Leeb, Tosso, Jagannathan, Vidhya, Cadieu, Edouard, David, Audrey, Lohi, Hannes, Cirera, Susanna, Fredholm, Merete, Botherel, Nadine, Leegwater, Peter A J, Le Béguec, Céline, Fieten, Hille, Johnson, Jeremy, Alföldi, Jessica, André, Catherine, Lindblad-Toh, Kerstin, Hitte, Christophe, Derrien, Thomas

“…Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to…”
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Comparative genomics as a tool to understand evolution and disease by Alfoeldi, J, Lindblad-Toh, K

“…When the human genome project started, the major challenge was how to sequence a 3 billion letter code in an organized and cost-effective manner. When…”
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Genome-wide synteny through highly sensitive sequence alignment: Satsuma by Grabherr, Manfred G., Russell, Pamela, Meyer, Miriah, Mauceli, Evan, Alföldi, Jessica, Di Palma, Federica, Lindblad-Toh, Kerstin

“…Motivation: Comparative genomics heavily relies on alignments of large and often complex DNA sequences. From an engineering perspective, the problem here is to…”
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SETD2 Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma by Sakthikumar, Sharadha, Elvers, Ingegerd, Kim, Jaegil, Arendt, Maja L, Thomas, Rachael, Turner-Maier, Jason, Swofford, Ross, Johnson, Jeremy, Schumacher, Steven E, Alföldi, Jessica, Axelsson, Erik, Couto, C Guillermo, Kisseberth, William C, Pettersson, Mats E, Getz, Gad, Meadows, Jennifer R S, Modiano, Jaime F, Breen, Matthew, Kierczak, Marcin, Forsberg-Nilsson, Karin, Marinescu, Voichita D, Lindblad-Toh, Kerstin

“…Osteosarcoma is a debilitating bone cancer that affects humans, especially children and adolescents. A homologous form of osteosarcoma spontaneously occurs in…”
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Convergent evolution of the genomes of marine mammals by Foote, Andrew D, Liu, Yue, Thomas, Gregg W C, Vinař, Tomáš, Alföldi, Jessica, Deng, Jixin, Dugan, Shannon, van Elk, Cornelis E, Hunter, Margaret E, Joshi, Vandita, Khan, Ziad, Kovar, Christie, Lee, Sandra L, Lindblad-Toh, Kerstin, Mancia, Annalaura, Nielsen, Rasmus, Qin, Xiang, Qu, Jiaxin, Raney, Brian J, Vijay, Nagarjun, Wolf, Jochen B W, Hahn, Matthew W, Muzny, Donna M, Worley, Kim C, Gilbert, M Thomas P, Gibbs, Richard A

“…Andrew Foote and colleagues report the whole-genome sequences and de novo assemblies of three marine mammal species—the walrus, killer whale and manatee—and an…”
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Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators by Bellott, Daniel W., Hughes, Jennifer F., Skaletsky, Helen, Brown, Laura G., Pyntikova, Tatyana, Cho, Ting-Jan, Koutseva, Natalia, Zaghlul, Sara, Graves, Tina, Rock, Susie, Kremitzki, Colin, Fulton, Robert S., Dugan, Shannon, Ding, Yan, Morton, Donna, Khan, Ziad, Lewis, Lora, Buhay, Christian, Wang, Qiaoyan, Watt, Jennifer, Holder, Michael, Lee, Sandy, Nazareth, Lynne, Alföldi, Jessica, Rozen, Steve, Muzny, Donna M., Warren, Wesley C., Gibbs, Richard A., Wilson, Richard K., Page, David C.

“…The human X and Y chromosomes evolved from an ordinary pair of autosomes, but millions of years ago genetic decay ravaged the Y chromosome, and only three per…”
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An Improved microRNA Annotation of the Canine Genome by Penso-Dolfin, Luca, Swofford, Ross, Johnson, Jeremy, Alföldi, Jessica, Lindblad-Toh, Kerstin, Swarbreck, David, Moxon, Simon, Di Palma, Federica

“…The domestic dog, Canis familiaris, is a valuable model for studying human diseases. The publication of the latest Canine genome build and annotation,…”
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Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes by Eckalbar, Walter L, Hutchins, Elizabeth D, Markov, Glenn J, Allen, April N, Corneveaux, Jason J, Lindblad-Toh, Kerstin, Di Palma, Federica, Alföldi, Jessica, Huentelman, Matthew J, Kusumi, Kenro

“…The green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology,…”
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Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background by Elvers, Ingegerd, Turner-Maier, Jason, Swofford, Ross, Koltookian, Michele, Johnson, Jeremy, Stewart, Chip, Zhang, Cheng-Zhong, Schumacher, Steven E, Beroukhim, Rameen, Rosenberg, Mara, Thomas, Rachael, Mauceli, Evan, Getz, Gad, Palma, Federica Di, Modiano, Jaime F, Breen, Matthew, Lindblad-Toh, Kerstin, Alföldi, Jessica

“…Lymphoma is the most common hematological malignancy in developed countries. Outcome is strongly determined by molecular subtype, reflecting a need for new and…”
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The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations by Keane, Michael, Craig, Thomas, Alföldi, Jessica, Berlin, Aaron M, Johnson, Jeremy, Seluanov, Andrei, Gorbunova, Vera, Di Palma, Federica, Lindblad-Toh, Kerstin, Church, George M, de Magalhães, João Pedro

“…The naked mole rat (Heterocephalus glaber) is an exceptionally long-lived and cancer-resistant rodent native to East Africa. Although its genome was previously…”
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Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals by Casewell, Nicholas R., Petras, Daniel, Card, Daren C., Suranse, Vivek, Mychajliw, Alexis M., Richards, David, Koludarov, Ivan, Albulescu, Laura-Oana, Slagboom, Julien, Hempel, Benjamin-Florian, Ngum, Neville M., Kennerley, Rosalind J., Brocca, Jorge L., Whiteley, Gareth, Harrison, Robert A., Bolton, Fiona M. S., Debono, Jordan, Vonk, Freek J., Alföldi, Jessica, Johnson, Jeremy, Karlsson, Elinor K., Lindblad-Toh, Kerstin, Mellor, Ian R., Süssmuth, Roderich D., Fry, Bryan G., Kuruppu, Sanjaya, Hodgson, Wayne C., Kool, Jeroen, Castoe, Todd A., Barnes, Ian, Sunagar, Kartik, Undheim, Eivind A. B., Turveyb, Samuel T.

“…Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model…”
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Acf7 (MACF) is an actin and microtubule linker protein whose expression predominates in neural, muscle, and lung development by Bernier, Gilbert, Pool, Madeline, Kilcup, Michael, Alfoldi, Jessica, De Repentigny, Yves, Kothary, Rashmi

“…Several proteins belonging to the plakin family of cytoskeletal linker proteins have recently been identified, including dystonin/Bpag1 and plectin. These…”
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The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons by Braasch, Ingo, Gehrke, Andrew R, Smith, Jeramiah J, Kawasaki, Kazuhiko, Manousaki, Tereza, Pasquier, Jeremy, Amores, Angel, Desvignes, Thomas, Batzel, Peter, Catchen, Julian, Berlin, Aaron M, Campbell, Michael S, Barrell, Daniel, Martin, Kyle J, Mulley, John F, Ravi, Vydianathan, Lee, Alison P, Nakamura, Tetsuya, Chalopin, Domitille, Fan, Shaohua, Wcisel, Dustin, Cañestro, Cristian, Sydes, Jason, Beaudry, Felix E G, Sun, Yi, Hertel, Jana, Beam, Michael J, Fasold, Mario, Ishiyama, Mikio, Johnson, Jeremy, Kehr, Steffi, Lara, Marcia, Letaw, John H, Litman, Gary W, Litman, Ronda T, Mikami, Masato, Ota, Tatsuya, Saha, Nil Ratan, Williams, Louise, Stadler, Peter F, Wang, Han, Taylor, John S, Fontenot, Quenton, Ferrara, Allyse, Searle, Stephen M J, Aken, Bronwen, Yandell, Mark, Schneider, Igor, Yoder, Jeffrey A, Volff, Jean-Nicolas, Meyer, Axel, Amemiya, Chris T, Venkatesh, Byrappa, Holland, Peter W H, Guiguen, Yann, Bobe, Julien, Shubin, Neil H, Di Palma, Federica, Alföldi, Jessica, Lindblad-Toh, Kerstin, Postlethwait, John H

“…Ingo Braasch, John Postlethwait and colleagues report the genome of the spotted gar ( Lepisosteus oculatus ), whose lineage diverged from teleosts before…”
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