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Saturday, January 17, 2015

Post by Humans of New York.

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Science “Ask Me Anything” by Mike Eisen at Reddit

Wednesday, January 14, 2015

Interesting discussion about open-access publishing.

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2015-01-10 new articles we read this week

Saturday, January 10, 2015

Retinal development

  1. Masuda T, Zhang X, Berlinicke C, Wan J, Yerrabelli A, Conner EA, Kjellstrom S, Bush R, Thorgeirsson SS, Swaroop A, Chen S, Zack DJ. The Transcription Factor GTF2IRD1 Regulates the Topology and Function of Photoreceptors by Modulating Photoreceptor Gene Expression across the Retina. J Neurosci. 2014 Nov 12;34(46):15356-68.
  2. Okabe K, Kobayashi S, Yamada T, Kurihara T, Tai-Nagara I, Miyamoto T,
    Mukouyama YS, Sato TN, Suda T, Ema M, Kubota Y. Neurons limit angiogenesis by titrating VEGF in retina. Cell. 2014 Oct 23;159(3):584-96. doi: 10.1016/j.cell.2014.09.025. PubMed PMID: 25417109.

Retina

  1. Baehr W. Membrane Protein Transport in Photoreceptors: The Function of PDEd.
    Invest Ophthalmol Vis Sci. 2014 Dec 30;55(12):8653-66. doi: 10.1167/iovs.14-16066. PubMed PMID: 25550383.

Genome editing

  1. Auer TO, Duroure K, Concordet JP, Del Bene F. CRISPR/Cas9-mediated conversion of eGFP- into Gal4-transgenic lines in zebrafish. Nat Protoc. 2014 Dec;9(12):2823-40. doi: 10.1038/nprot.2014.187. Epub 2014 Nov 13. PubMed PMID: 25393779.
  2. Yang L, Grishin D, Wang G, Aach J, Zhang CZ, Chari R, Homsy J, Cai X, Zhao Y, Fan JB, Seidman C, Seidman J, Pu W, Church G. Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells. Nat Commun. 2014 Nov 26;5:5507. doi: 10.1038/ncomms6507. PubMed PMID: 25425480.
  3. Nielsen AA, Voigt CA. Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks. Mol Syst Biol. 2014 Nov 24;10:763. doi:
    10.15252/msb.20145735. PubMed PMID: 25422271.
  4. Byrne SM, Ortiz L, Mali P, Aach J, Church GM. Multi-kilobase homozygous
    targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Res. 2014 Nov 20. pii: gku1246. [Epub ahead of print] PubMed PMID: 25414332.
  5. Naito Y, Hino K, Bono H, Ui-Tei K. CRISPRdirect: software for designing
    CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics. 2014 Nov 20. pii: btu743. [Epub ahead of print] PubMed PMID: 25414360.
  6. Doudna JA, Charpentier E. Genome editing. The new frontier of genome
    engineering with CRISPR-Cas9. Science. 2014 Nov 28;346(6213):1258096. doi: 10.1126/science.1258096. PubMed PMID: 25430774.

Imaging

  1. Paquet D, Plucinska G, Misgeld T. In vivo imaging of mitochondria in intact
    zebrafish larvae. Methods Enzymol. 2014;547:151-64. PubMed PMID: 25416357.

Zebrafish

  1. McCluskey BM, Postlethwait JH. Phylogeny of zebrafish, a ‘model species’, within Danio, a ‘model genus’. Mol Biol Evol. 2014 Nov 20. pii: msu325. [Epub ahead of print] PubMed PMID: 25415969.
  2. Magdeldin S, Blaser RE, Yamamoto T, Yates JR 3rd. Behavioral and Proteomic Analysis of Stress Response in Zebrafish (Danio rerio). J Proteome Res. 2014 Nov 26. [Epub ahead of print] PubMed PMID: 25398274.

Stem cells

  1. Byrne SM, Ortiz L, Mali P, Aach J, Church GM. Multi-kilobase homozygous
    targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Res. 2014 Nov 20. pii: gku1246. [Epub ahead of print] PubMed PMID: 25414332.

Development & Disease

  1. The Deciphering Developmental Disorders Study; The Deciphering Developmental Disorders Study. Large-scale discovery of novel genetic causes of developmental disorders. Nature. 2014 Dec 24. doi: 10.1038/nature14135. [Epub ahead of print] PubMed PMID: 25533962.

Genetics

  1. Tan AS, Baty JW, Dong LF, Bezawork-Geleta A, Endaya B, Goodwin J, Bajzikova M, Kovarova J, Peterka M, Yan B, Pesdar EA, Sobol M, Filimonenko A, Stuart S, Vondrusova M, Kluckova K, Sachaphibulkij K, Rohlena J, Hozak P, Truksa J, Eccles D, Haupt LM, Griffiths LR, Neuzil J, Berridge MV. Mitochondrial Genome Acquisition Restores Respiratory Function and Tumorigenic Potential of Cancer Cells without Mitochondrial DNA. Cell Metab. 2015 Jan 6;21(1):81-94. doi: 10.1016/j.cmet.2014.12.003. PubMed PMID: 25565207.

Medicine

  1. Ling LL, Schneider T, Peoples AJ, Spoering AL, Engels I, Conlon BP, Mueller A, Schäberle TF, Hughes DE, Epstein S, Jones M, Lazarides L, Steadman VA, Cohen DR, Felix CR, Fetterman KA, Millett WP, Nitti AG, Zullo AM, Chen C, Lewis K. A new antibiotic kills pathogens without detectable resistance. Nature. 2015 Jan 7. doi: 10.1038/nature14098. [Epub ahead of print] PubMed PMID: 25561178.

Evolution

  1. Yoshida MA, Yura K, Ogura A. Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants. Sci Rep. 2014 Mar 5;4:4256. doi: 10.1038/srep04256. PubMed PMID: 24594543; PubMed Central PMCID: PMC3942700.

 

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Prof. Motokazu Tsujikawa visited the Leung Lab at Purdue University

Sunday, November 16, 2014

Prof. Motokazu Tsujikawa from the Department of Ophthalmology and the Department of Visual Regenerative Medicine at the Osaka University Medical School in Japan visited Leung Lab at Purdue, Indiana University School of Medicine – Lafayette, Bindley Bioscience Center and Drug Discovery Center from 10/22 – 24, 2014. He also gave a departmental seminar on  “Retinal degeneration research using zebrafish – from an ophthalmologist’s perspective” during his visit.

Prof. Motokazu Tsuijikawa interacted with Prof. Gordon Coppoc, Director of the Indiana University School of Medicine — Lafayette, the first year medical students, and pre-med students in the Leung lab. They discussed the differences in health care and medical education between US and Japan.

Prof. Motokazu Tsujikawa and students from the Leung Lab visited Bindley Bioscience Center and Drug Discovery Center.

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2014-11-09 new articles we read … in a while

Sunday, November 9, 2014

Cell cycle

  1. Malumbres M. Cyclin-dependent kinases. Genome Biol. 2014;15(6):122. PubMed PMID: 25180339; PubMed Central PMCID: PMC4097832.

Sequencing/Disease

  1. Gilissen C, Hehir-Kwa JY, Thung DT, van de Vorst M, van Bon BW, Willemsen MH, Kwint M, Janssen IM, Hoischen A, Schenck A, Leach R, Klein R, Tearle R, Bo T, Pfundt R, Yntema HG, de Vries BB, Kleefstra T, Brunner HG, Vissers LE, Veltman JA. Genome sequencing identifies major causes of severe intellectual disability.  Nature. 2014 Jul 17;511(7509):344-7. doi: 10.1038/nature13394. Epub 2014 Jun 4. PubMed PMID: 24896178.

Retina

  1. Labin AM, Safuri SK, Ribak EN, Perlman I. Müller cells separate between wavelengths to improve day vision with minimal effect upon night vision. Nat Commun. 2014 Jul 8;5:4319. doi: 10.1038/ncomms5319. PubMed PMID: 25003477.
  2. Busskamp V, Krol J, Nelidova D, Daum J, Szikra T, Tsuda B, Jüttner J, Farrow K, Scherf BG, Alvarez CP, Genoud C, Sothilingam V, Tanimoto N, Stadler M, Seeliger M, Stoffel M, Filipowicz W, Roska B. miRNAs 182 and 183 Are Necessary to Maintain Adult Cone Photoreceptor Outer Segments and Visual Function. Neuron. 2014 Jul 4. pii: S0896-6273(14)00542-X. doi: 10.1016/j.neuron.2014.06.020. [Epub ahead of print] PubMed PMID: 25002228.
  3. Condition Called Tetrachromacy Allows This Artist To See 100 Million Colors

Neurodegeneration

  1. Games D, Valera E, Spencer B, Rockenstein E, Mante M, Adame A, Patrick C, Ubhi K, Nuber S, Sacayon P, Zago W, Seubert P, Barbour R, Schenk D, Masliah E. Reducing C-terminal-truncated alpha-synuclein by immunotherapy attenuates neurodegeneration and propagation in Parkinson’s disease-like models. J Neurosci. 2014 Jul 9;34(28):9441-54. doi: 10.1523/JNEUROSCI.5314-13.2014. PubMed PMID: 25009275.
  2. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature. 2014 Jul 24;511(7510):421-7. doi: 10.1038/nature13595. Epub 2014 Jul 22. PubMed PMID:25056061; PubMed Central PMCID: PMC4112379.

Neurobiology

  1. Severi KE, Portugues R, Marques JC, O’Malley DM, Orger MB, Engert F. Neural control and modulation of swimming speed in the larval zebrafish. Neuron. 2014 Aug 6;83(3):692-707. doi: 10.1016/j.neuron.2014.06.032. Epub 2014 Jul 24. PubMed PMID: 25066084; PubMed Central PMCID: PMC4126853.
  2. Bruni G, Lakhani P, Kokel D. Discovering novel neuroactive drugs through
    high-throughput behavior-based chemical screening in the zebrafish. Front
    Pharmacol. 2014 Jul 24;5:153. doi: 10.3389/fphar.2014.00153. eCollection 2014. Review. PubMed PMID: 25104936; PubMed Central PMCID: PMC4109429.

Ethical, Social and Legal Issues

  1. Tort AB, Targino ZH, Amaral OB. Rising publication delays inflate journal impact factors. PLoS One. 2012;7(12):e53374. doi: 10.1371/journal.pone.0053374. Epub 2012 Dec 31. PubMed PMID: 23300920; PubMed Central PMCID: PMC3534064.
  2. van Lent M, Overbeke J, Out HJ. Role of editorial and peer review processes in publication bias: analysis of drug trials submitted to eight medical journals. PLoS One. 2014 Aug 12;9(8):e104846. doi: 10.1371/journal.pone.0104846. eCollection 2014. PubMed PMID: 25118182; PubMed Central PMCID: PMC4130599.
  3. Ioannidis JP. How to make more published research true. PLoS Med. 2014 Oct 21;11(10):e1001747. doi: 10.1371/journal.pmed.1001747. eCollection 2014 Oct. PubMed PMID: 25334033; PubMed Central PMCID: PMC4204808.

Stem cells

  1. Pagliuca FW, Millman JR, Gürtler M, Segel M, Van Dervort A, Ryu JH, Peterson QP, Greiner D, Melton DA. Generation of Functional Human Pancreatic β Cells In Vitro. Cell. 2014 Oct 9;159(2):428-39. doi: 10.1016/j.cell.2014.09.040. PubMed PMID: 25303535.
  2. Zhang D, Pekkanen-Mattila M, Shahsavani M, Falk A, Teixeira AI, Herland A. A 3D Alzheimer’s disease culture model and the induction of P21-activated kinase mediated sensing in iPSC derived neurons. Biomaterials. 2014 Feb;35(5):1420-8. doi: 10.1016/j.biomaterials.2013.11.028. Epub 2013 Nov 27. PubMed PMID: 24290439.
  3. Schwartz SD, et al., Human embryonic stem cell-derived retinal pigment
    epithelium in patients with age-related macular degeneration and Stargardt’s macular dystrophy: follow-up of two open-label phase 1/2 studies. Lancet 2014. In press.

Genome editing

  1. Lombardo A, Naldini L. Genome Editing: A Tool For Research and Therapy: Targeted genome editing hits the clinic. Nat Med. 2014 Oct 8;20(10):1101-3. doi: 10.1038/nm.3721. PubMed PMID: 25295939.

Nutrition

  1. Suez J, Korem T, Zeevi D, Zilberman-Schapira G, Thaiss CA, Maza O, Israeli D, Zmora N, Gilad S, Weinberger A, Kuperman Y, Harmelin A, Kolodkin-Gal I, Shapiro H, Halpern Z, Segal E, Elinav E. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature. 2014 Oct 9;514(7521):181-6. doi: 10.1038/nature13793. Epub 2014 Sep 17. PubMed PMID: 25231862.

Molecular biology

  1. Robart AR, Chan RT, Peters JK, Rajashankar KR, Toor N. Crystal structure of a eukaryotic group II intron lariat. Nature. 2014 Oct 9;514(7521):193-7. doi: 10.1038/nature13790. Epub 2014 Sep 24. PubMed PMID: 25252982.

Imaging

  1. Chen BC, Legant WR, Wang K, Shao L, Milkie DE, Davidson MW, Janetopoulos C, Wu XS, Hammer JA 3rd, Liu Z, English BP, Mimori-Kiyosue Y, Romero DP, Ritter AT, Lippincott-Schwartz J, Fritz-Laylin L, Mullins RD, Mitchell DM, Bembenek JN, Reymann AC, Böhme R, Grill SW, Wang JT, Seydoux G, Tulu US, Kiehart DP, Betzig E. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science. 2014 Oct 24;346(6208):1257998. doi:
    10.1126/science.1257998. Epub 2014 Oct 23. PubMed PMID: 25342811.
    Wang K, Milkie DE, Saxena A, Engerer P, Misgeld T, Bronner ME, Mumm J, Betzig E. Rapid adaptive optical recovery of optimal resolution over large volumes. Nat Methods. 2014 Jun;11(6):625-8. doi: 10.1038/nmeth.2925. Epub 2014 Apr 13. PubMed PMID: 24727653; PubMed Central PMCID: PMC4069208.
  2. Amat F, Lemon W, Mossing DP, McDole K, Wan Y, Branson K, Myers EW, Keller PJ. Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data. Nat Methods. 2014 Jul 20. doi: 10.1038/nmeth.3036. [Epub ahead of print] PubMed PMID: 25042785.

Evolution

  1. Rands CM, Meader S, Ponting CP, Lunter G. 8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage. PLoS Genet. 2014 Jul 24;10(7):e1004525. doi:
    10.1371/journal.pgen.1004525. eCollection 2014 Jul. PubMed PMID: 25057982; PubMed Central PMCID: PMC4109858.
  2. News coverage: Only 8.2 % of Human DNA is Functional, Say Genetic Researchers

 

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Gender, Race, Sexuality, and the Neuroscience of Healthy Relationships

Monday, October 13, 2014

The thing that ties each of the following links together is a discussion of the need to incorporate equity, affirmation, and continued learning into social, scientific, and political spheres.  And to recognize that the lines between these spaces is a social construct.

This article offers an explanation of how sexism affects both the oppressed and the oppressor.  While they use a binary gender system in their drawings (male vs. female), it  is easy to understand how this could be applied to people in any gender system: http://imgur.com/gallery/n01WW

This article describes the work of Malala Yousafzai and Kailash Satyarthi who were recently awarded the Nobel Peace Prize for their work on expanding women’s and children’s rights in Pakistan and India, respectively.  Their stories highlight how personal identities are political and politics is personal: http://www.nytimes.com/2014/10/11/world/europe/kailash-satyarthi-and-malala-yousafzai-are-awarded-nobel-peace-prize.html?_r=0

This article goes in depth about African American and AfroCarribean identities in the U.S. as part of a larger history of colonization and slavery – how has this history impacted black Americans now and how is this oppression and the struggle for mutual humanization ongoing: http://www.washingtonpost.com/opinions/ferguson-wasnt-black-rage-against-copsit-was-white-rage-against-progress/2014/08/29/3055e3f4-2d75-11e4-bb9b-997ae96fad33_story.html

This article highlights some of the queer and trans* people of color working on gender, race, and sexuality equity in the U.S.  This is especially important given that the U.S. media (news, movies, t.v., radio, etc) predominately rewards and publicizes white, domestic, heterosexual, and cisgender people: http://www.autostraddle.com/22-badass-qtpoc-couples-that-make-our-hearts-flutter-253889/

Lastly, this article shows some really interesting research being done about children’s responsiveness and understanding of human emotions and interactions.  It has incredible implications for understanding the impacts of trauma, domestic violence, and healthy or unhealthy relationships on children as young as 15 months old!  http://www.huffingtonpost.com/2014/10/10/toddlers-angry-behave-study-video_n_5959482.html?ncid=fcbklnkushpmg00000063

 

Best,

Skye

 

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Ig Nobel prize 2014

Tuesday, September 23, 2014

Wonderful studies as usual!

http://www.improbable.com/ig/winners/#ig2014

The 2014 Ig Nobel Winners: Banana Peels to Nasal Pork

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Autism, The Politics of “Normal”, and Thinking Fast and Slow (the book)

Friday, September 19, 2014

A Cognitive Defense of Stimming (or Why “Quiet Hands” Makes Math Harder)

In the last decade or so, autism spectrum disorders (ASDs) have been in the forefront of the news and research.  Originally, the people thought autism was a psychological disorder and that it was similar to schitzophrenia.  There was a complete lack of understanding about what autism was, how it affected those with it, and how people who were not autistic could relate to people with autism.  People assumed the behaviors of autistic children or adults were just “bad behaviors” that needed to be corrected, often through electroshock therapies, LSD, and other harmful (pain-based) “treatments”.  All of this was administered under the philosphy that “normal” = healthy.

In the 80’s, the genetic and biological basis of behavior started to become a focus in research and health practitioner skills, propelled in part by discoveries about the genetic basis of circadian rhythms.  Behavioral therapy began and the new focus for autistic children was to help the mask the biological basis of their behaviors and confirm to “normal” social behavior so that they could have “normal” lives.  At some point, researchers and parents began to realize that a lot of autistic behaviors were a response to stimulation – over and under stimulation – and research began focusing on the neurobiology and neurogenetics of autism.

The idea that difference is “abnormal” and that “abnormal” = unhealthy is the basis of a LOT of oppression, violence, and harm caused and maintained in communities and cultures across the world at every time in history.  White colonists believed black, brown, yellow, and red people were lesser than and qualified this with “science”, suggesting that white was normal and non-white was abnormal (and of course this thinking continues to dictate structures and communities in colonized spaces today).  This raises larger questions: Who gets to determine what is normal or healthy?  When does normal = healthy?  How does society use standards of “normal” to force marginalized communities out of power?

In 2005 an organization named Autism Speaks was formed (but non-autistic people) to support research that would find a “cure” for autism spectrum disorders.  The organizations viewpoint then and now is that autism is a devastating health crisis that causes children to be lesser than and results in a poor quality of life.  As an autistic person, I find this not only offensive, but hugely damaging (in too many ways to describe here) to parents with autistic children, to autistic children and adults, and to prospective support systems that could be formed for autistic people.  “Curing” autism is similar to the argument about “curing” queerness.  Should we “fix” queer people so that they are all straight and cisgender, or should we support and embrace diverse experiences and lives for what they bring to the table?

As the recognition of autism and the number of autistic children has grown and continues to grow drastically, it is very important to address these questions.  One of the more visible effects of most autism spectrum disabilities is stimming, a word that is short for “self stimulation”.  Researchers now understand the the neurological systems of autistic people are different than those of most “neurotypical” people, making autistic individuals extra sensitive to some sensation and under-sensitive to others (as defined by neurotypical standards).  For example, many autistic people find that repetitive movements are calming (perhaps movement sensory input channels are chronically under-stimulated), so they may stim by tapping fingers or feet, flapping their hands, rocking, or doing something similar.  There is a big divide currently in the world of working with autistic children – should adults teach children to repress their stims or should they be accepted as supportive of childhood development?

I recently found a wonderfully written article on this topic and it refers to Thinking Fast and Slow.  I need to read this book soon (and maybe post on it later), but in the mean time, enjoy this article!  What are your thoughts on this or the other articles at the end of this one?

~Skye

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Spider Dog – for some humor

Wednesday, September 10, 2014

Since we all need to laugh more than we do:

Best,

Skye  🙂

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2014-07-20 new articles we read this week

Sunday, July 20, 2014

Nature’s special on “Challenges in irreproducible research”

Human Behaviour/Psychology

  1. Kramer AD, Guillory JE, Hancock JT. Experimental evidence of massive-scale emotional contagion through social networks. Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):8788-90. doi: 10.1073/pnas.1320040111. Epub 2014 Jun 2. PubMed PMID: 24889601.

Retinal development

  1. Hoon M, Okawa H, Della Santina L, Wong RO. Functional Architecture of the Retina: Development and Disease. Prog Retin Eye Res. 2014 Jun 28. pii: S1350-9462(14)00038-X. doi: 10.1016/j.preteyeres.2014.06.003. [Epub ahead of print] Review. PubMed PMID: 24984227.

Stem cells

  1. Ksander BR, Kolovou PE, Wilson BJ, Saab KR, Guo Q, Ma J, McGuire SP, Gregory MS, Vincent WJ, Perez VL, Cruz-Guilloty F, Kao WW, Call MK, Tucker BA, Zhan Q, Murphy GF, Lathrop KL, Alt C, Mortensen LJ, Lin CP, Zieske JD, Frank MH, Frank NY. ABCB5 is a limbal stem cell gene required for corneal development and repair. Nature. 2014 Jul 17;511(7509):353-7. doi: 10.1038/nature13426. Epub 2014 Jul 2. PubMed PMID: 25030174.
  2. Tsai SQ, Joung JK. What’s Changed with Genome Editing? Cell Stem Cell. 2014 Jul 3;15(1):3-4. doi: 10.1016/j.stem.2014.06.017. PubMed PMID: 24996161.
  3. Veres A, Gosis BS, Ding Q, Collins R, Ragavendran A, Brand H, Erdin S, Talkowski ME, Musunuru K. Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing. Cell Stem Cell. 2014 Jul 3;15(1):27-30. doi: 10.1016/j.stem.2014.04.020. PubMed PMID: 24996167; PubMed Central PMCID: PMC4082799.
  4. Smith C, Gore A, Yan W, Abalde-Atristain L, Li Z, He C, Wang Y, Brodsky RA, Zhang K, Cheng L, Ye Z. Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs. Cell Stem Cell. 2014 Jul 3;15(1):12-3. doi: 10.1016/j.stem.2014.06.011. PubMed PMID: 24996165.
  5. Suzuki K, Yu C, Qu J, Li M, Yao X, Yuan T, Goebl A, Tang S, Ren R, Aizawa E, Zhang F, Xu X, Soligalla RD, Chen F, Kim J, Kim NY, Liao HK, Benner C, Esteban CR, Jin Y, Liu GH, Li Y, Izpisua Belmonte JC. Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. Cell Stem Cell. 2014 Jul 3;15(1):31-6. doi: 10.1016/j.stem.2014.06.016. PubMed PMID: 24996168.
  6. Kiskinis E, Sandoe J, Williams LA, Boulting GL, Moccia R, Wainger BJ, Han S, Peng T, Thams S, Mikkilineni S, Mellin C, Merkle FT, Davis-Dusenbery BN, Ziller M, Oakley D, Ichida J, Di Costanzo S, Atwater N, Maeder ML, Goodwin MJ, Nemesh J, Handsaker RE, Paull D, Noggle S, McCarroll SA, Joung JK, Woolf CJ, Brown RH, Eggan K. Pathways Disrupted in Human ALS Motor Neurons Identified through Genetic Correction of Mutant SOD1. Cell Stem Cell. 2014 Jun 5;14(6):781-95. doi: 10.1016/j.stem.2014.03.004. Epub 2014 Apr 3. PubMed PMID: 24704492.

Eye disease treatment

  1. Jepson LH, Hottowy P, Weiner GA, Dabrowski W, Litke AM, Chichilnisky EJ. High-fidelity reproduction of spatiotemporal visual signals for retinal prosthesis. Neuron. 2014 Jul 2;83(1):87-92. doi: 10.1016/j.neuron.2014.04.044. Epub 2014 Jun 5. PubMed PMID: 24910077.
    • Trenholm S, Roska B. Cell-type-specific electric stimulation for vision restoration. Neuron. 2014 Jul 2;83(1):1-2. doi: 10.1016/j.neuron.2014.06.012. PubMed PMID: 24991948.

Funding

  1. Resnick A. Systemic addiction to research funding. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):E2634. doi: 10.1073/pnas.1407369111. Epub 2014 Jun 11. PubMed PMID: 24920596.
  2. Alberts B, Kirschner MW, Tilghman S, Varmus H. Rescuing US biomedical research from its systemic flaws. Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5773-7. doi: 10.1073/pnas.1404402111. Epub 2014 Apr 14. PubMed PMID: 24733905; PubMed Central PMCID: PMC4000813.

Research Career

  1. Smaglik P. Employment: PhD overdrive. Nature. 2014 Jul 10;511(7508):255-6. PubMed PMID: 25013890.

Systems Biology

  1. Bruggner RV, Bodenmiller B, Dill DL, Tibshirani RJ, Nolan GP. Automated identification of stratifying signatures in cellular subpopulations. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):E2770-7. doi: 10.1073/pnas.1408792111. Epub 2014 Jun 16. PubMed PMID: 24979804.

Genomics/ Sequencing

  1. Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. IVT-seq reveals extreme bias in RNA-sequencing. Genome Biol. 2014 Jun 30;15(6):R86. [Epub ahead of print] PubMed PMID: 24981968.
  2. Tilgner H, Grubert F, Sharon D, Snyder MP. Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9869-74. doi: 10.1073/pnas.1400447111. Epub 2014 Jun
    24. PubMed PMID: 24961374.

Genome editing

  1. Sheridan C. First CRISPR-Cas patent opens race to stake out intellectual property. Nat Biotechnol. 2014 Jul 8;32(7):599-601. doi: 10.1038/nbt0714-599. PubMed PMID: 25004207.
  2. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol. 2014 Jul;32(7):670-6. doi: 10.1038/nbt.2889. Epub 2014 Apr 20. PubMed PMID: 24752079.
  3. Kuscu C, Arslan S, Singh R, Thorpe J, Adli M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol. 2014 Jul;32(7):677-83. doi: 10.1038/nbt.2916. Epub 2014 May 18. PubMed PMID: 24837660.
  4. Tsai SQ, Joung JK. What’s Changed with Genome Editing? Cell Stem Cell. 2014 Jul 3;15(1):3-4. doi: 10.1016/j.stem.2014.06.017. PubMed PMID: 24996161.
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