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Using Anthropology, Biology, and Physics to Decrease Infant Mortality

Monday, May 26, 2014

Here is an excellent article about the progress that can be made when disciplines work together.

http://ideas.ted.com/2013/12/18/mother-knows-best-re-making-the-embrace-baby-warmer-for-moms/

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2014-05-25 new articles we read this week

Sunday, May 25, 2014

Gene regulatory network

  1. Barsi JC, Tu Q, Davidson E. General approach for in vivo recovery of cell type specific effector gene sets. Genome Res. 2014 Mar 6. [Epub ahead of print] PubMed PMID: 24604781.

Medicine

  1. Project to Improve Poor Children’s Intellect Led to Better Health, Data Show
  2. Begley CG, Ellis LM. Drug development: Raise standards for preclinical cancer research. Nature. 2012 Mar 28;483(7391):531-3. doi: 10.1038/483531a. PubMed PMID: 22460880.

Neuroscience

  1. Portugues R, Feierstein CE, Engert F, Orger MB. Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior. Neuron. 2014 Mar 19;81(6):1328-43. doi: 10.1016/j.neuron.2014.01.019. PubMed PMID: 24656252.
  2. Lancaster MA, Renner M, Martin CA, Wenzel D, Bicknell LS, Hurles ME, Homfray T, Penninger JM, Jackson AP, Knoblich JA. Cerebral organoids model human brain development and microcephaly. Nature. 2013 Sep 19;501(7467):373-9. doi: 10.1038/nature12517. Epub 2013 Aug 28. PubMed PMID: 23995685; PubMed Central
    PMCID: PMC3817409.

    • Brüstle O. Developmental neuroscience: Miniature human brains. Nature. 2013
      Sep 19;501(7467):319-20. doi: 10.1038/nature12552. Epub 2013 Aug 28. PubMed PMID: 23995687.

Genome editing

  1. Auer TO, Del Bene F. CRISPR/Cas9 and TALEN-mediated knock-in approaches in zebrafish. Methods. 2014 Apr 1. pii: S1046-2023(14)00129-7. doi: 10.1016/j.ymeth.2014.03.027. [Epub ahead of print] PubMed PMID: 24704174.
  2. Zhou Y, Zhu S, Cai C, Yuan P, Li C, Huang Y, Wei W. High-throughput screening
    of a CRISPR/Cas9 library for functional genomics in human cells. Nature. 2014 Apr
    9. doi: 10.1038/nature13166. [Epub ahead of print] PubMed PMID: 24717434.
  3. Yin H, Xue W, Chen S, Bogorad RL, Benedetti E, Grompe M, Koteliansky V, Sharp
    PA, Jacks T, Anderson DG. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat Biotechnol. 2014 Mar 30. doi: 10.1038/nbt.2884. [Epub ahead of print] PubMed PMID: 24681508.

Stem cells

  1. Becker S, Jayaram H, Limb GA. Recent Advances towards the Clinical Application of Stem Cells for Retinal Regeneration. Cells. 2012 Oct 18;1(4):851-73. doi: 10.3390/cells1040851. PubMed PMID: 24710533.
  2. Assawachananont J et al., Transplantation of Embryonic and Induced Pluripotent Stem Cell-Derived 3D Retinal Sheets into Retinal Degenerative Mice. Stem Cell Reports. 2014; 2: 662-674.

Retinal degeneration

  1. Wasfy MM, Matsui JI, Miller J, Dowling JE, Perkins BD. myosin 7aa(-/-) mutant zebrafish show mild photoreceptor degeneration and reduced electroretinographic responses. Exp Eye Res. 2014 Apr 1. pii: S0014-4835(14)00083-9. doi: 10.1016/j.exer.2014.03.007. [Epub ahead of print] PubMed PMID: 24698764.

Retinal development

  1. Weber IP, Ramos AP, Strzyz PJ, Leung LC, Young S, Norden C. Mitotic Position and Morphology of Committed Precursor Cells in the Zebrafish Retina Adapt to Architectural Changes upon Tissue Maturation. Cell Rep. 2014 Apr 2. pii: S2211-1247(14)00192-2. doi: 10.1016/j.celrep.2014.03.014. [Epub ahead of print] PubMed PMID: 24703843.
  2. Almeida AD, Boije H, Chow RW, He J, Tham J, Suzuki SC, Harris WA. Spectrum of Fates: a new approach to the study of the developing zebrafish retina. Development. 2014 Apr 9. [Epub ahead of print] PubMed PMID: 24718991.
  3. Yoshimatsu T, Williams PR, D’Orazi FD, Suzuki SC, Fadool JM, Allison WT, Raymond PA, Wong RO. Transmission from the dominant input shapes the stereotypic ratio of photoreceptor inputs onto horizontal cells. Nat Commun. 2014 May 15;5:3699. doi: 10.1038/ncomms4699. PubMed PMID: 24832361.

Development

  1. Bianchi E, Doe B, Goulding D, Wright GJ. Juno is the egg Izumo receptor and is essential for mammalian fertilization. Nature. 2014 Apr 24;508(7497):483-7. doi: 10.1038/nature13203. Epub 2014 Apr 16. PubMed PMID: 24739963; PubMed Central PMCID: PMC3998876.

Genetics/Synthetic biology

  1. Malyshev DA, Dhami K, Lavergne T, Chen T, Dai N, Foster JM, Corrêa IR Jr, Romesberg FE. A semi-synthetic organism with an expanded genetic alphabet. Nature. 2014 May 15;509(7500):385-8. doi: 10.1038/nature13314. Epub 2014 May 7. PubMed PMID: 24805238.
    • Commentary: Thyer R, Ellefson J. Synthetic biology: New letters for life’s alphabet. Nature. 2014 May 15;509(7500):291-2. doi: 10.1038/nature13335. Epub 2014 May 7. PubMed PMID: 24805244.
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2014-03-23 New articles we read this week

Sunday, March 23, 2014

Genomics

  1. Venter’s New Goal: World’s Largest Sequencing Operation
  2. Clinical Whole Genome Sequencing: Not Quite Ready for Prime Time?

Genetics

  1. Vanderperre B, Lucier JF, Bissonnette C, Motard J, Tremblay G, Vanderperre S, Wisztorski M, Salzet M, Boisvert FM, Roucou X. Direct detection of alternative open reading frames translation products in human significantly expands the proteome. PLoS One. 2013 Aug 12;8(8):e70698. doi: 10.1371/journal.pone.0070698. eCollection 2013. PubMed PMID: 23950983; PubMed Central PMCID: PMC3741303.

Stem cells

  1. Acid-bath stem-cell study under investigation.

Genome-editing

  1. Tebas P, Stein D, Tang WW, Frank I, Wang SQ, Lee G, Spratt SK, Surosky RT, Giedlin MA, Nichol G, Holmes MC, Gregory PD, Ando DG, Kalos M, Collman RG, Binder-Scholl G, Plesa G, Hwang WT, Levine BL, June CH. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N Engl J Med. 2014 Mar 6;370(10):901-10. doi: 10.1056/NEJMoa1300662. PubMed PMID: 24597865.
    • Editorial commentary: Kay MA, Walker BD. Engineering cellular resistance to HIV. N Engl J Med. 2014
      Mar 6;370(10):968-9. doi: 10.1056/NEJMe1400593. PubMed PMID: 24597871.
    • News coverage: Editing Genes May Make Cells Resist HIV.

Philosophy

How Academia and Publishing are Destroying Scientific Innovation: A Conversation with Sydney Brenner

Medicine

  1. Flannick J, Thorleifsson G, Beer NL, Jacobs SB, Grarup N, Burtt NP, Mahajan A, Fuchsberger C, Atzmon G, Benediktsson R, Blangero J, Bowden DW, Brandslund I, Brosnan J, Burslem F, Chambers J, Cho YS, Christensen C, Douglas DA, Duggirala R, Dymek Z, Farjoun Y, Fennell T, Fontanillas P, Forsén T, Gabriel S, Glaser B, Gudbjartsson DF, Hanis C, Hansen T, Hreidarsson AB, Hveem K, Ingelsson E, Isomaa  B, Johansson S, Jørgensen T, Jørgensen ME, Kathiresan S, Kong A, Kooner J, Kravic J, Laakso M, Lee JY, Lind L, Lindgren CM, Linneberg A, Masson G, Meitinger T, Mohlke KL, Molven A, Morris AP, Potluri S, Rauramaa R, Ribel-Madsen R, Richard AM, Rolph T, Salomaa V, Segrè AV, Skärstrand H, Steinthorsdottir V, Stringham HM, Sulem P, Tai ES, Teo YY, Teslovich T, Thorsteinsdottir U, Trimmer JK, Tuomi T, Tuomilehto J, Vaziri-Sani F, Voight BF, Wilson JG, Boehnke M, McCarthy MI, Njølstad PR, Pedersen O, Groop L, Cox DR, Stefansson K, Altshuler D. Loss-of-function mutations in SLC30A8 protect against type 2 diabetes. Nat Genet. 2014 Mar 2. doi: 10.1038/ng.2915. [Epub ahead of print] PubMed PMID: 24584071.
  2. Mapstone M, Cheema AK, Fiandaca MS, Zhong X, Mhyre TR, Macarthur LH, Hall WJ, Fisher SG, Peterson DR, Haley JM, Nazar MD, Rich SA, Berlau DJ, Peltz CB, Tan MT, Kawas CH, Federoff HJ. Plasma phospholipids identify antecedent memory impairment in older adults. Nat Med. 2014 Mar 9. doi: 10.1038/nm.3466. [Epub ahead of print]
    PubMed PMID: 24608097.

Imaging

  1. Foldscope: Origami-based paper microscope

Zebrafish

  1. Cressey D. Fish-kill method questioned. Nature. 2014 Feb 27;506(7489):419-20. doi: 10.1038/506419a. PubMed PMID: 24572404.

 

Eye disease

  1. Fernandez de Castro J, Scott PA, Fransen JW, Demas J, Demarco PJ, Kaplan HJ, McCall MA. Cone Photoreceptors Develop Normally in the Absence of Functional Rod Photoreceptors in a Transgenic Swine Model of Retinitis Pigmentosa. Invest Ophthalmol Vis Sci. 2014 Mar 11. pii: iovs.13-13724v1. doi: 10.1167/iovs.13-13724. [Epub ahead of print] PubMed PMID: 24618325.

Vision

  1. Partridge JC, Douglas RH, Marshall NJ, Chung WS, Jordan TM, Wagner HJ. Reflecting optics in the diverticular eye of a deep-sea barreleye fish (Rhynchohyalus natalensis). Proc Biol Sci. 2014 Mar 19;281(1782):20133223. doi: 10.1098/rspb.2013.3223. Print 2014. PubMed PMID: 24648222.

Evolution

  1. Gassmann AJ, Petzold-Maxwell JL, Clifton EH, Dunbar MW, Hoffmann AM, Ingber DA, Keweshan RS. Field-evolved resistance by western corn rootworm to multiple Bacillus thuringiensis toxins in transgenic maize. Proc Natl Acad Sci U S A. 2014 Mar 17. [Epub ahead of print] PubMed PMID: 24639498.

Neuroscience

  1. Bushdid C, Magnasco MO, Vosshall LB, Keller A. Humans can discriminate more than 1 trillion olfactory stimuli. Science. 2014 Mar 21;343(6177):1370-2. doi: 10.1126/science.1249168. PubMed PMID: 24653035.
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A collection of videos for discussion of ethical and social issues in human embryonic stem cells research

Thursday, March 6, 2014

This is a collection of the videos that I used in lab discussion section of the ethical issues in human embryonic stem cells research in the 2014 BIOL36701 Principles Development at Purdue University.

1. An introduction to stem cell – A stem cell story

2. Are embryos persons?

3. A question of balance?

4. How patients may be exploited – Stem cell fraud

5. hESCs alternative I – Stem cells – the future: an introduction to iPS cells

6. hESCs alternative II – STAP cells

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2012-02-26 New articles we read this week

Thursday, February 27, 2014

Genome editing

  1. Kim JM, Kim D, Kim S, Kim JS. Genotyping with CRISPR-Cas-derived RNA-guided endonucleases. Nat Commun. 2014 Jan 20;5:3157. doi: 10.1038/ncomms4157. PubMed PMID: 24445736.
  2. Bae S, Park J, Kim JS. Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics. 2014 Jan 24. [Epub ahead of print] PubMed PMID: 24463181.
  3. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol. 2014 Jan 26. doi: 10.1038/nbt.2808. [Epub ahead of print] PubMed PMID: 24463574.
  4. Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA. Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation.
    Science. 2014 Feb 6. [Epub ahead of print] PubMed PMID: 24505130.
  5. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature. 2014 Jan 29. doi: 10.1038/nature13011. [Epub ahead of print] PubMed PMID: 24476820.
  6. Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O. Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA. Cell. 2014 Feb 12. pii: S0092-8674(14)00156-1. doi: 10.1016/j.cell.2014.02.001. [Epub ahead of print] PubMed PMID: 24529477.
  7. Niu Y, Shen B, Cui Y, Chen Y, Wang J, Wang L, Kang Y, Zhao X, Si W, Li W, Xiang AP, Zhou J, Guo X, Bi Y, Si C, Hu B, Dong G, Wang H, Zhou Z, Li T, Tan T, Pu X, Wang F, Ji S, Zhou Q, Huang X, Ji W, Sha J. Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos. Cell. 2014 Jan 30;. [Epub ahead of print]
  8. Hai T, Teng F, Guo R, Li W, Zhou Q. One-step generation of knockout pigs by zygote injection of CRISPR/Cas system. Cell Res. 2014 Jan 31;. [Epub ahead of print]
  9. Heigwer F, Kerr G, Boutros M. E-CRISP: fast CRISPR target site identification. Nat Methods. 2014 Jan 30;11(2):122-3.
  10. Nakagawa Y, Yamamoto T, Suzuki K, Araki K, Takeda N, Ohmuraya M, Sakuma T. Screening Methods to Identify TALEN-Mediated Knockout Mice. Exp Anim. 2014;63(1):79-84. PubMed PMID: 24521866.

Development

  1. Simões-Costa M, Tan-Cabugao J, Antoshechkin I, Sauka-Spengler T, Bronner ME. Transcriptome analysis reveals novel players in the cranial neural crest gene regulatory network. Genome Res. 2014 Jan 3. [Epub ahead of print] PubMed PMID: 24389048.
  2. Umulis DM, Othmer HG. Mechanisms of scaling in pattern formation. Development. 2013 Dec;140(24):4830-43. doi: 10.1242/dev.100511. Review. PubMed PMID: 24301464; PubMed Central PMCID: PMC3848184.
  3. Pauli A, Norris ML, Valen E, Chew GL, Gagnon JA, Zimmerman S, Mitchell A, Ma J, Dubrulle J, Reyon D, Tsai SQ, Joung JK, Saghatelian A, Schier AF. Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors. Science. 2014 Jan 9. [Epub ahead of print] PubMed PMID: 24407481.
  4. Dias AS, de Almeida I, Belmonte JM, Glazier JA, Stern CD. Somites without a clock. Science. 2014 Feb 14;343(6172):791-5. doi: 10.1126/science.1247575. Epub 2014 Jan 9. PubMed PMID: 24407478.
    • Kondo S. Developmental biology. Self-organizing somites. Science. 2014 Feb 14;343(6172):736-7. doi: 10.1126/science.1250245. PubMed PMID: 24531958.

Genomics

  1. Zhang Y, Vastenhouw NL, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF, Liu XS. Canonical nucleosome organization at promoters forms during genome activation. Genome Res. 2014 Jan 8. [Epub ahead of print] PubMed PMID:
    24285721.

Retinal degeneration/regeneration

  1. Sherpa T, Lankford T, McGinn TE, Hunter SS, Frey RA, Sun C, Ryan M, Robison BD, Stenkamp DL. Retinal regeneration is facilitated by the presence of surviving neurons. Dev Neurobiol. 2014 Feb 1. doi: 10.1002/dneu.22167. [Epub ahead of print] PubMed PMID: 24488694.
  2. Cruz NM, Yuan Y, Leehy BD, Baid R, Kompella U, Deangelis MM, Escher P, Haider NB. Modifier genes as therapeutics: the nuclear hormone receptor rev erb alpha (nr1d1) rescues nr2e3 associated retinal disease. PLoS One. 2014;9(1):e87942.

Zebrafish

  1. Mueller KP, Neuhauss SC. Sunscreen for Fish: Co-Option of UV Light Protection for Camouflage. PLoS One. 2014 Jan 29;9(1):e87372. doi: 10.1371/journal.pone.0087372. eCollection 2014. PubMed PMID: 24489905.

Stem cells

  1. Stress-Induced Stem Cell Method Questioned

 

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Leung Lab Comic 1

Saturday, February 22, 2014

A fun comic about everyday happenings in the Leung lab.












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My visit to the Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, China

Tuesday, February 18, 2014

In January, I visited the Center for Human Molecular Biology & Genetics at the Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China [Chinese website of the Institute]. It is a large provincial hospital in Sichuan Province with a population of 80.8 million. The hospital served approximately 3.6 million outpatient and emergency cases, and carried out almost 75,000 surgeries in 2011. With this number of patients, the Center for Human Molecular Biology & Genetics collected extensive human samples and has been a leader in genetics study in China.

Prof. Zhengli Yang, the vice president of the hospital and the director of Center for Human Molecular Biology & Genetics, invited both me and a renowned eye geneticist Prof. Shomi Bhattacharya to discuss our current research on eye disease therapy. I discussed how my lab is setting up the foundation to use zebrafish to screen eye drugs at Purdue. Prof. Bhattacharya discussed his work on gene therapy and stem cell therapy. It was a great experience to interact with a world leader in genetics whom discovered many of the key genes in retinal degeneration, and a top notch research institution in China.

Yuk Fai Leung lectured at the Center for Human Molecular Biology & Genetics, the Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China

 

Prof. Shomi Bhattacharya lectured at the Center for Human Molecular Biology & Genetics, the Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China. Prof. Zhenglin Yang (right) hosted the symposium.

 

Audience from the Center for Human Molecular Biology & Genetics, the Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China.

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Leung Lab’s Christmas Party 2013

Saturday, February 1, 2014

The members of the Leung Lab gathered to celebrate the Christmas and New Year holidays on 12/6/2013. Here are some pictures (Courtesy of Lue Xiang).

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When you are away from your office for a little while …

Friday, January 31, 2014

you may get a pleasant surprise when you come back!

It looks like that a Christmas/New Year ritual has been established in the lab….

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2014-01-30 New articles we read this week

Thursday, January 30, 2014

Stem cells

A young scientist in Japan has found a simple approach to make totipotent stem cells by lowering the pH.

Stimulus-triggered fate conversion of somatic cells into pluripotency. Nature

Bidirectional developmental potential in reprogrammed cells with acquired pluripotency. Nature

Retina

  1. Raymond PA, Colvin SM, Jabeen Z, Nagashima M, Barthel LK, Hadidjojo J, Popova L, Pejaver VR, Lubensky DK. Patterning the cone mosaic array in zebrafish retina requires specification of ultraviolet-sensitive cones. PLoS One. 2014 Jan 21;9(1):e85325. doi: 10.1371/journal.pone.0085325. eCollection 2014 Jan 21. PubMed PMID: 24465536.
  2. Centanin L, Wittbrodt J. Retinal neurogenesis. Development. 2014 Jan;141(2):241-4. doi: 10.1242/dev.083642. PubMed PMID: 24381194.
  3. Lenkowski JR, Raymond PA. Müller glia: Stem cells for generation and regeneration of retinal neurons in teleost fish. Prog Retin Eye Res. 2014 Jan 8.  pii: S1350-9462(14)00002-0. doi: 10.1016/j.preteyeres.2013.12.007. [Epub ahead of
    print] PubMed PMID: 24412518.

Genome-editing

  1. Hruscha A, Krawitz P, Rechenberg A, Heinrich V, Hecht J, Haass C, Schmid B. Efficient CRISPR/Cas9 genome editing with low off-target effects in zebrafish. Development. 2013 Dec;140(24):4982-7. doi: 10.1242/dev.099085. Epub 2013 Nov 20. PubMed PMID: 24257628.
  2. Roberts JA, Miguel-Escalada I, Slovik KJ, Walsh KT, Hadzhiev Y, Sanges R, Stupka E, Marsh EK, Balciuniene J, Balciunas D, Müller F. Targeted transgene integration overcomes variability of position effects in zebrafish. Development. 2014 Feb;141(3):715-24. doi: 10.1242/dev.100347. PubMed PMID: 24449846.
  3. Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science. 2014 Jan 3;343(6166):80-4. doi: 10.1126/science.1246981. Epub 2013 Dec 12. PubMed PMID: 24336569.
  4. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014 Jan 3;343(6166):84-7. doi: 10.1126/science.1247005. Epub 2013 Dec 12. PubMed PMID: 24336571.
  5. Wu Y, Liang D, Wang Y, Bai M, Tang W, Bao S, Yan Z, Li D, Li J. Correction of a genetic disease in mouse via use of CRISPR-Cas9. Cell Stem Cell. 2013 Dec 5;13(6):659-62. doi: 10.1016/j.stem.2013.10.016. PubMed PMID: 24315440.

Neuroscience

  1. Dias BG, Ressler KJ. Parental olfactory experience influences behavior and neural structure in subsequent generations. Nat Neurosci. 2014 Jan;17(1):89-96. doi: 10.1038/nn.3594. Epub 2013 Dec 1. PubMed PMID: 24292232.

Gene therapy

  1. Maclaren RE, Groppe M, Barnard AR, Cottriall CL, Tolmachova T, Seymour L, Clark KR, During MJ, Cremers FP, Black GC, Lotery AJ, Downes SM, Webster AR, Seabra MC. Retinal gene therapy in patients with choroideremia: initial findings from a phase 1/2 clinical trial. Lancet. 2014 Jan 15. pii: S0140-6736(13)62117-0. doi: 10.1016/S0140-6736(13)62117-0. [Epub ahead of print] PubMed PMID: 24439297.

 

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