Leung Lab Blog

Genomics/ next-generation sequencing

1. Anders S, Huber W. Differential expression analysis for sequence count data.Genome Biol. 2010;11(10):R106. Epub 2010 Oct 27. PubMed PMID: 20979621.
2. Gresham D, Boer VM, Caudy A, Ziv N, Brandt NJ, Storey JD, Botstein D. System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae. Genetics. 2011 Jan;187(1):299-317. Epub2010 Oct 13. PubMed PMID: 20944018; PubMed Central PMCID: PMC3018308.
3. Inaki K, Hillmer AM, Ukil L, Yao F, Woo XY, Vardy LA, Zawack KF, Lee CW, Ariyaratne PN, Chan YS, Desai KV, Bergh J, Hall P, Putti TC, Ong WL, Shahab A, Cacheux-Rataboul V, Karuturi RK, Sung WK, Ruan X, Bourque G, Ruan Y, Liu ET. Transcriptional consequences of genomic structural aberrations in breast cancer.  Genome Res. 2011 May;21(5):676-87. Epub 2011 Apr 5. PubMed PMID: 21467264.

Gene mapping

1. Chakravarti A. Genomic contributions to Mendelian disease. Genome Res. 2011 May;21(5):643-4. PubMed PMID: 21536725.
2. Erlich Y, Edvardson S, Hodges E, Zenvirt S, Thekkat P, Shaag A, Dor T, Hannon GJ, Elpeleg O. Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. Genome Res. 2011 May;21(5):658-64. Epub 2011 Apr 12. PubMed PMID: 21487076.
3. Lupski JR, Reid JG, Gonzaga-Jauregui C, Rio Deiros D, Chen DC, Nazareth L, Bainbridge M, Dinh H, Jing C, Wheeler DA, McGuire AL, Zhang F, Stankiewicz P, Halperin JJ, Yang C, Gehman C, Guo D, Irikat RK, Tom W, Fantin NJ, Muzny DM, Gibbs RA. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med. 2010 Apr 1;362(13):1181-91. Epub 2010 Mar 10. PubMed PMID: 20220177.
4. Musunuru K, Pirruccello JP, Do R, Peloso GM, Guiducci C, Sougnez C, Garimella KV, Fisher S, Abreu J, Barry AJ, Fennell T, Banks E, Ambrogio L, Cibulskis K, Kernytsky A, Gonzalez E, Rudzicz N, Engert JC, DePristo MA, Daly MJ, Cohen JC, Hobbs HH, Altshuler D, Schonfeld G, Gabriel SB, Yue P, Kathiresan S. Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia. N Engl J Med. 2010 Dec 2;363(23):2220-7. Epub 2010 Oct 13. PubMed PMID: 20942659; PubMed Central PMCID: PMC3008575.

Systems Biology/ gene regulatory network

1. Macneil L, Walhout AJ. Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res. 2011 Feb 4. [Epub ahead of print] PubMed PMID: 21324878.
2. Hakim O, Sung MH, Voss TC, Splinter E, John S, Sabo PJ, Thurman RE, Stamatoyannopoulos JA, de Laat W, Hager GL. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res. 2011 May;21(5):697-706. Epub 2011 Apr 6. PubMed PMID: 21471403.

Stem cells

1. Focus on stem cells. Nat Cell Biol. 2011 May;13(5):489. PubMed PMID: 21540843.
2. Ng HH, Surani MA. The transcriptional and signalling networks of pluripotency. Nat Cell Biol. 2011 May;13(5):490-6. PubMed PMID: 21540844.
3. Wu SM, Hochedlinger K. Harnessing the potential of induced pluripotent stem cells for regenerative medicine. Nat Cell Biol. 2011 May;13(5):497-505. PubMed PMID: 21540845.
4. Jones DL, Rando TA. Emerging models and paradigms for stem cell ageing. NatCell Biol. 2011 May;13(5):506-12. PubMed PMID: 21540846.
5. Fuchs E, Horsley V. Ferreting out stem cells from their niches. Nat Cell Biol.2011 May;13(5):513-8. PubMed PMID: 21540847.
6. Barrero MJ, Izpisua Belmonte JC. iPS cells forgive but do not forget. Nat CellBiol. 2011 May;13(5):523-5. PubMed PMID: 21540851.
7. Ohi Y, Qin H, Hong C, Blouin L, Polo JM, Guo T, Qi Z, Downey SL, Manos PD, Rossi DJ, Yu J, Hebrok M, Hochedlinger K, Costello JF, Song JS, Ramalho-Santos M. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol. 2011 May;13(5):541-9. Epub 2011 Apr 17. PubMedPMID: 21499256.

Eye disease

1. Shu X, Zeng Z, Gautier P, Lennon A, Gakovic M, Cheetham ME, Patton EE, Wright AF. Knockdown of the Zebrafish Ortholog of the Retinitis Pigmentosa 2 (RP2) Gene Results in Retinal Degeneration. Invest Ophthalmol Vis Sci. 2011 May5;52(6):2960-6. Print 2011. PubMed PMID: 21282572.
2. Pinazo-Durán MD, Pons-Vázquez S, Gallego-Pinazo R, Galbis Estrada C, Zanón-Moreno V, Vila Bou V, Sanz Solana P. Thyroid hormone deficiency disrupts rat eye neurodevelopment. Brain Res. 2011 Apr 9. [Epub ahead of print] PubMedPMID: 21529787.

Zebrafish

1. Nava SS, An S, Hamil T. Visual detection of UV cues by adult zebrafish (Danio rerio). J Vis. 2011 May 4;11(6). pii: 2. doi: 10.1167/11.6.2. Print 2011. PubMed PMID: 21543523.