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Mutations of AKT3 are associated with a wide spectrum of developmental disorders including extreme megalencephaly.
Published in:
2017
By:
- Alcantara, Diana;
- Timms, Andrew E.;
- Gripp, Karen;
- Baker, Laura;
- Park, Kaylee;
- Collins, Sarah;
- Chi Cheng;
- Stewart, Fiona;
- Mehta, Sarju G.;
- Saggar, Anand;
- Sztriha, László;
- Zombor, Melinda;
- Caluseriu, Oana;
- Mesterman, Ronit;
- Van Allen, Margot I.;
- Jacquinet, Adeline;
- Ygberg, Sofia;
- Bernstein, Jonathan A.;
- Wenger, Aaron M.;
- Guturu, Harendra
Publication type:
journal article
Approaches to long-read sequencing in a clinical setting to improve diagnostic rate.
Published in:
Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-20113-x
By:
- Sanford Kobayashi, Erica;
- Batalov, Serge;
- Wenger, Aaron M.;
- Lambert, Christine;
- Dhillon, Harsharan;
- Hall, Richard J.;
- Baybayan, Primo;
- Ding, Yan;
- Rego, Seema;
- Wigby, Kristen;
- Friedman, Jennifer;
- Hobbs, Charlotte;
- Bainbridge, Matthew N.
Publication type:
Article
Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals.
Published in:
Nucleic Acids Research, 2018, v. 46, n. 18, p. 9299, doi. 10.1093/nar/gky741
By:
- Berger, Mark J;
- Wenger, Aaron M;
- Guturu, Harendra;
- Bejerano, Gill
Publication type:
Article
Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish.
Published in:
Nucleic Acids Research, 2013, v. 41, n. 15, p. e151, doi. 10.1093/nar/gkt557
By:
- Hiller, Michael;
- Agarwal, Saatvik;
- Notwell, James H.;
- Parikh, Ravi;
- Guturu, Harendra;
- Wenger, Aaron M.;
- Bejerano, Gill
Publication type:
Article
Germline mosaicism of a missense variant in KCNC2 in a multiplex family with autism and epilepsy characterized by long‐read sequencing.
Published in:
American Journal of Medical Genetics. Part A, 2022, v. 188, n. 7, p. 2071, doi. 10.1002/ajmg.a.62743
By:
- Mehinovic, Elvisa;
- Gray, Teddi;
- Campbell, Meghan;
- Ekholm, Jenny;
- Wenger, Aaron;
- Rowell, William;
- Grudo, Ari;
- Grimwood, Jane;
- Korlach, Jonas;
- Gurnett, Christina;
- Constantino, John N.;
- Turner, Tychele N.
Publication type:
Article
Biallelic loss‐of‐function <italic>WNT5A</italic> mutations in an infant with severe and atypical manifestations of Robinow syndrome.
Published in:
American Journal of Medical Genetics. Part A, 2018, v. 176, n. 4, p. 1030, doi. 10.1002/ajmg.a.38636
By:
- Birgmeier, Johannes;
- Esplin, Edward D.;
- Jagadeesh, Karthik A.;
- Guturu, Harendra;
- Wenger, Aaron M.;
- Chaib, Hassan;
- Buckingham, Julia A.;
- Bejerano, Gill;
- Bernstein, Jonathan A.
Publication type:
Article
DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer.
Published in:
Nature Biotechnology, 2023, v. 41, n. 2, p. 232, doi. 10.1038/s41587-022-01435-7
By:
- Baid, Gunjan;
- Cook, Daniel E.;
- Shafin, Kishwar;
- Yun, Taedong;
- Llinares-López, Felipe;
- Berthet, Quentin;
- Belyaeva, Anastasiya;
- Töpfer, Armin;
- Wenger, Aaron M.;
- Rowell, William J.;
- Yang, Howard;
- Kolesnikov, Alexey;
- Ammar, Waleed;
- Vert, Jean-Philippe;
- Vaswani, Ashish;
- McLean, Cory Y.;
- Nattestad, Maria;
- Chang, Pi-Chuan;
- Carroll, Andrew
Publication type:
Article
Curated variation benchmarks for challenging medically relevant autosomal genes.
Published in:
Nature Biotechnology, 2022, v. 40, n. 5, p. 672, doi. 10.1038/s41587-021-01158-1
By:
- Wagner, Justin;
- Olson, Nathan D.;
- Harris, Lindsay;
- McDaniel, Jennifer;
- Cheng, Haoyu;
- Fungtammasan, Arkarachai;
- Hwang, Yih-Chii;
- Gupta, Richa;
- Wenger, Aaron M.;
- Rowell, William J.;
- Khan, Ziad M.;
- Farek, Jesse;
- Zhu, Yiming;
- Pisupati, Aishwarya;
- Mahmoud, Medhat;
- Xiao, Chunlin;
- Yoo, Byunggil;
- Sahraeian, Sayed Mohammad Ebrahim;
- Miller, Danny E.;
- Jáspez, David
Publication type:
Article
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Published in:
Nature Biotechnology, 2019, v. 37, n. 10, p. 1155, doi. 10.1038/s41587-019-0217-9
By:
- Wenger, Aaron M.;
- Peluso, Paul;
- Rowell, William J.;
- Chang, Pi-Chuan;
- Hall, Richard J.;
- Concepcion, Gregory T.;
- Ebler, Jana;
- Fungtammasan, Arkarachai;
- Kolesnikov, Alexey;
- Olson, Nathan D.;
- Töpfer, Armin;
- Alonge, Michael;
- Mahmoud, Medhat;
- Qian, Yufeng;
- Chin, Chen-Shan;
- Phillippy, Adam M.;
- Schatz, Michael C.;
- Myers, Gene;
- DePristo, Mark A.;
- Ruan, Jue
Publication type:
Article
GREAT improves functional interpretation of cis-regulatory regions.
Published in:
Nature Biotechnology, 2010, v. 28, n. 5, p. 495, doi. 10.1038/nbt.1630
By:
- McLean, Cory Y.;
- Bristor, Dave;
- Hiller, Michael;
- Clarke, Shoa L.;
- Schaar, Bruce T.;
- Lowe, Craig B.;
- Wenger, Aaron M.;
- Bejerano, Gill
Publication type:
Article
HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing.
Published in:
Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae042
By:
- Holt, James M;
- Saunders, Christopher T;
- Rowell, William J;
- Kronenberg, Zev;
- Wenger, Aaron M;
- Eberle, Michael
Publication type:
Article
Father-to-offspring transmission of extremely long NOTCH2NLC repeat expansions with contractions: genetic and epigenetic profiling with long-read sequencing.
Published in:
Clinical Epigenetics, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13148-021-01192-5
By:
- Fukuda, Hiromi;
- Yamaguchi, Daisuke;
- Nyquist, Kristofor;
- Yabuki, Yasushi;
- Miyatake, Satoko;
- Uchiyama, Yuri;
- Hamanaka, Kohei;
- Saida, Ken;
- Koshimizu, Eriko;
- Tsuchida, Naomi;
- Fujita, Atsushi;
- Mitsuhashi, Satomi;
- Ohbo, Kazuyuki;
- Satake, Yuki;
- Sone, Jun;
- Doi, Hiroshi;
- Morihara, Keisuke;
- Okamoto, Tomoko;
- Takahashi, Yuji;
- Wenger, Aaron M.
Publication type:
Article
Comprehensive de novo mutation discovery with HiFi long-read sequencing.
Published in:
Genome Medicine, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13073-023-01183-6
By:
- Kucuk, Erdi;
- van der Sanden, Bart P. G. H.;
- O'Gorman, Luke;
- Kwint, Michael;
- Derks, Ronny;
- Wenger, Aaron M.;
- Lambert, Christine;
- Chakraborty, Shreyasee;
- Baybayan, Primo;
- Rowell, William J.;
- Brunner, Han G.;
- Vissers, Lisenka E. L. M.;
- Hoischen, Alexander;
- Gilissen, Christian
Publication type:
Article
Intronic ATTTC repeat expansions in STARD7 in familial adult myoclonic epilepsy linked to chromosome 2.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-12671-y
By:
- Corbett, Mark A.;
- Kroes, Thessa;
- Veneziano, Liana;
- Bennett, Mark F.;
- Florian, Rahel;
- Schneider, Amy L.;
- Coppola, Antonietta;
- Licchetta, Laura;
- Franceschetti, Silvana;
- Suppa, Antonio;
- Wenger, Aaron;
- Mei, Davide;
- Pendziwiat, Manuela;
- Kaya, Sabine;
- Delledonne, Massimo;
- Straussberg, Rachel;
- Xumerle, Luciano;
- Regan, Brigid;
- Crompton, Douglas;
- van Rootselaar, Anne-Fleur
Publication type:
Article
Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-018-08148-z
By:
- Chaisson, Mark J. P.;
- Sanders, Ashley D.;
- Zhao, Xuefang;
- Malhotra, Ankit;
- Porubsky, David;
- Rausch, Tobias;
- Gardner, Eugene J.;
- Rodriguez, Oscar L.;
- Guo, Li;
- Collins, Ryan L.;
- Fan, Xian;
- Wen, Jia;
- Handsaker, Robert E.;
- Fairley, Susan;
- Kronenberg, Zev N.;
- Kong, Xiangmeng;
- Hormozdiari, Fereydoun;
- Lee, Dillon;
- Wenger, Aaron M.;
- Hastie, Alex R.
Publication type:
Article
Human-specific loss of regulatory DNA and the evolution of human-specific traits.
Published in:
Nature, 2011, v. 471, n. 7337, p. 216, doi. 10.1038/nature09774
By:
- McLean, Cory Y.;
- Reno, Philip L.;
- Pollen, Alex A.;
- Bassan, Abraham I.;
- Capellini, Terence D.;
- Guenther, Catherine;
- Indjeian, Vahan B.;
- Lim, Xinhong;
- Menke, Douglas B.;
- Schaar, Bruce T.;
- Wenger, Aaron M.;
- Bejerano, Gill;
- Kingsley, David M.
Publication type:
Article
High-coverage, long-read sequencing of Han Chinese trio reference samples.
Published in:
Scientific Data, 2019, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41597-019-0098-2
By:
- Wang, Ying-Chih;
- Olson, Nathan D.;
- Deikus, Gintaras;
- Shah, Hardik;
- Wenger, Aaron M.;
- Trow, Jonathan;
- Xiao, Chunlin;
- Sherry, Stephen;
- Salit, Marc L.;
- Zook, Justin M.;
- Smith, Melissa;
- Sebra, Robert
Publication type:
Article
Automated Discovery of Tissue-Targeting Enhancers and Transcription Factors from Binding Motif and Gene Function Data.
Published in:
PLoS Computational Biology, 2014, v. 10, n. 1, p. 1, doi. 10.1371/journal.pcbi.1003449
By:
- Tuteja, Geetu;
- Moreira, Karen Betancourt;
- Chung, Tisha;
- Chen, Jenny;
- Wenger, Aaron M.;
- Bejerano, Gill
Publication type:
Article
AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature.
Published in:
Science Translational Medicine, 2020, v. 12, n. 544, p. 1, doi. 10.1126/scitranslmed.aau9113
By:
- Birgmeier, Johannes;
- Haeussler, Maximilian;
- Deisseroth, Cole A.;
- Steinberg, Ethan H.;
- Jagadeesh, Karthik A.;
- Ratner, Alexander J.;
- Guturu, Harendra;
- Wenger, Aaron M.;
- Diekhans, Mark E.;
- Stenson, Peter D.;
- Cooper, David N.;
- Ré, Christopher;
- Beggs, Alan H.;
- Bernstein, Jonathan A.;
- Bejerano, Gill
Publication type:
Article
Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads.
Published in:
Annals of Human Genetics, 2020, v. 84, n. 2, p. 125, doi. 10.1111/ahg.12364
By:
- Vollger, Mitchell R.;
- Logsdon, Glennis A.;
- Audano, Peter A.;
- Sulovari, Arvis;
- Porubsky, David;
- Peluso, Paul;
- Wenger, Aaron M.;
- Concepcion, Gregory T.;
- Kronenberg, Zev N.;
- Munson, Katherine M.;
- Baker, Carl;
- Sanders, Ashley D.;
- Spierings, Diana C.J.;
- Lansdorp, Peter M.;
- Surti, Urvashi;
- Hunkapiller, Michael W.;
- Eichler, Evan E.
Publication type:
Article
Control of pelvic girdle development by genes of the Pbx family and Emx2.
Published in:
Developmental Dynamics, 2011, v. 240, n. 5, p. 1173, doi. 10.1002/dvdy.22617
By:
- Capellini, Terence D.;
- Handschuh, Karen;
- Quintana, Laura;
- Ferretti, Elisabetta;
- Di Giacomo, Giuseppina;
- Fantini, Sebastian;
- Vaccari, Giulia;
- Clarke, Shoa L.;
- Wenger, Aaron M.;
- Bejerano, Gill;
- Sharpe, James;
- Zappavigna, Vincenzo;
- Selleri, Licia
Publication type:
Article
Characterization and visualization of tandem repeats at genome scale.
Published in:
Nature Biotechnology, 2024, v. 42, n. 10, p. 1606, doi. 10.1038/s41587-023-02057-3
By:
- Dolzhenko, Egor;
- English, Adam;
- Dashnow, Harriet;
- De Sena Brandine, Guilherme;
- Mokveld, Tom;
- Rowell, William J.;
- Karniski, Caitlin;
- Kronenberg, Zev;
- Danzi, Matt C.;
- Cheung, Warren A.;
- Bi, Chengpeng;
- Farrow, Emily;
- Wenger, Aaron;
- Chua, Khi Pin;
- Martínez-Cerdeño, Verónica;
- Bartley, Trevor D.;
- Jin, Peng;
- Nelson, David L.;
- Zuchner, Stephan;
- Pastinen, Tomi
Publication type:
Article
The Enhancer Landscape during Early Neocortical Development Reveals Patterns of Dense Regulation and Co-option.
Published in:
PLoS Genetics, 2013, v. 9, n. 8, p. 1, doi. 10.1371/journal.pgen.1003728
By:
- Wenger, Aaron M.;
- Clarke, Shoa L.;
- Notwell, James H.;
- Chung, Tisha;
- Tuteja, Geetu;
- Guturu, Harendra;
- Schaar, Bruce T.;
- Bejerano, Gill
Publication type:
Article
Human Developmental Enhancers Conserved between Deuterostomes and Protostomes.
Published in:
PLoS Genetics, 2012, v. 8, n. 8, p. 1, doi. 10.1371/journal.pgen.1002852
By:
- Clarke, Shoa L.;
- Vandermeer, Julia E.;
- Wenger, Aaron M.;
- Schaar, Bruce T.;
- Ahituv, Nadav;
- Bejerano, Gill
Publication type:
Article
A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/ LMBR1) causes preaxial polydactyly with triphalangeal thumb.
Published in:
Human Mutation, 2012, v. 33, n. 7, p. 1063, doi. 10.1002/humu.22097
By:
- Laurell, Tobias;
- VanderMeer, Julia E.;
- Wenger, Aaron M.;
- Grigelioniene, Giedre;
- Nordenskjöld, Agneta;
- Arner, Marianne;
- Ekblom, Anna Gerber;
- Bejerano, Gill;
- Ahituv, Nadav;
- Nordgren, Ann
Publication type:
Article

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