Talk:New York Genome Center

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Please note: Page creator sjbavier is an employee of the New York Genome Center. As am I. Jshatan (talk) 16:03, 22 November 2016 (UTC)

References

Proposed Changes

Would like to add the following citation to the statement that NYGC is a 501(c)(3) nonprofit: http://www.guidestar.org/profile/80-0631734 Thanks. Jshatan (talk) 16:21, 22 November 2016 (UTC)

References

Hi Jshatan, and thanks for your suggestion. Unfortunately, I'm not seeing that statement in the citation given. Do you have another source to show that NYGC is classified 501(c)(3) by the IRS? Altamel (talk) 21:21, 22 November 2016 (UTC)

found it

It is in the 990 PDF, for instance at http://www.guidestar.org/FinDocuments/2014/800/631/2014-800631734-0bd281b6-9.pdf in section I, page 1. In order to access this you need a free login (I got a free account). I'll add a citation based on this later. One thing to consider for tax and financial documents in general - they are self-published and their validity is only as firm as the entity's adherence to laws related to providing truthful disclosures to the government; this applies to all financial disclosure information and it's something I've kind of brushed aside as a minor point for a long time now. --User:Ceyockey (talk to me) 23:40, 22 November 2016 (UTC)

added the citation --User:Ceyockey (talk to me) 23:58, 22 November 2016 (UTC)

Proposed Changes

We would like to request the following edits to the sidebar: Field of Research: Genomics, Bioinformatics, Whole Genome Sequencing

Remove "Staff" and add:

President & COO: Cheryl A. Moore

to reflect all of our affiliations, with the proper names and in alpha order. It should read as follows: Albert Einstein College of Medicine American Museum of Natural History Cold Spring Harbor Laboratory Columbia University in the City of New York Hospital for Special Surgery IBM Icahn School of Medicine at Mount Sinai The Jackson Laboratory Memorial Sloan Kettering Cancer Center NewYork-Presbyterian The New York Stem Cell Foundation Northwell Health NYU School of Medicine Princeton University The Rockefeller University Roswell Park Cancer Institute Stony Brook University Weill Cornell Medicine

Thank you for your consideration. Jshatan (talk) 16:17, 27 March 2017 (UTC)

Please note: I made the changes described above - let us know if there are any objections. Jshatan (talk) 16:30, 4 April 2017 (UTC)

References

Proposed Changes

We would like to move the following text from the opening section to the Founding section, as a second paragraph before the list of 12 founding institutions.

"From November 2012 to December 2016, the Center's President and CEO was Robert B. Darnell.[4][5] During this period, NYGC had a number of major accomplishments[4], including the hiring of 17 full time and part time NYGC faculty,[6] award of a $40 million grant to Dr. Darnell as Principal Investigator from the National Human Genome Research Institute to create a Center for Common Disease focused on autism, Alzheimer's Disease, and Asthma[7], fundraising that included a $55 million grant from New York State to support genomic medicine[8], a $100 million matching grant from the Simons Foundation and Carson Family Charitable Trust[9][10], a $13.5 million contract from NHLBI, a PCORI grant to centralize clinical data in New York[4], and collaborations with IBM to explore and develop the use of Watson for Genomics in glioblastoma[11] and more generally in cancer genomics[12]. As of 2016, though the majority of participating institutions remained New York state-based, two institutions were from outside New York: Jackson lab and Princeton University."

And replace it with the following:

"A collaboration of academic, medical and industry leaders in New York and other partners throughout the country, the New York Genome Center focuses on translating genomic research into clinical solutions for serious diseases. NYGC faculty hold joint academic appointments at its member institutions and lead clinically focused genomic studies in a number of disease areas, including pediatric and adult cancer, asthma, autism, Alzheimer’s disease, ALS and other serious neurodegenerative diseases. NYGC scientists brings a multidisciplinary and in-depth approach to the field of genomics, conducting research in a wide range of areas, including single cell genomics, gene engineering, population and evolutionary genomics, technology and methods development, statistics, computational biology and bioengineering." Jshatan (talk) 21:03, 13 April 2017 (UTC)

Note: I made these changes today. Jshatan (talk) 16:15, 17 April 2017 (UTC)

References

Proposed Changes

We would like to edit the "Publications" section in the following manner:

Remove this text:

Wrzeszczynski KO, Robine N, Vacic V, Emde AK, Chen BJ, Liao W, Arora K, Shah M, Grabowska EA, Felice V, Dikoglu E, Reeves C, Frank M, Jobanputra V, Zody MC, Bloom T, Darnell RB (2016). (not available in source consulted). AACR 2016. Retrieved 22 November 2016.

Add this text:

Genome-wide profiling of heritable and de novo STR variations. Willems T, Zielinski, D, Gordon A, Gymrek M, Erlich Y. Nature Methods. 2017 Apr 24.

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Villani AC, Satija, R, Reynolds, G, Sarkizova S, Shekhar K, Fletcher J, Griesbeck M, Butler A, Zheng S, Lazo S, Jardine L, Dixon D, Stephenson E, Nilsson E, Grundberg I, McDonald D, Filby A, Li W, De Jager PL, Rozenblatt-Rosen O, Lane AA, Haniffa M, Regev A, Hacohen N. Science. 2017 Apr 21.

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Gierahn TM, Wadsworth MH 2nd, Hughes TK, Bryson BD, Butler A, Satija R, Fortune S, Love JC, Shalek AK. Nature Methods. 2017 Apr. 14.

Prostate cancer: Clinical hallmarks in whole cancer genomes. Imielinski M, Rubin MA. Nature Reviews Clinical Oncology. 2017 Apr 4.

Frequent evolution of copy number alterations in CLL following first-line treatment with FC(R) is enriched with TP53 alterations: results from the CLL8 trial. Edelmann J, Tausch E, Landau, DA, Robrecht S, Bahlo J, Fischer K, Fink A, Bloehdorn J, Holzmann K, Böttcher S, Werner L, Kneba M, Gribben JG, Neuberg DS, Wu CJ, Hallek M, Döhner H, Stilgenbauer S. Leukemia. 2017 Mar 31.

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Joung J, Konermann S, Gootenberg JS, Abudayyeh OO, Platt,RJ, Brigham, MD, Sanjana NE & Zhang F. Nature Protocols. 2017 Mar 23.

DNA Compass: a secure, client-side site for navigating personal genetic information. Curnin C, Gordon A, Erlich Y. Bioinformatics. 2017 Mar 11.

DNA Fountain enables a robust and efficient storage architecture. Erlich Y, Zielinski D. Science. 2017 Mar 3.

Genome-scale networks link neurodegenerative disease genes to α-synuclein through specific molecular pathways. Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, Costanzo M, San Luis B-J, Schöndorf DC, Barrasa MI, Ehsani S, Sanjana N, Zhong Q, Gasser T, Bartel DP, Vidal M, Deleidi M, Boone C, Fraenkel E, Berger B, Lindquist S. Cell Systems. 2017 Feb 22.

Genomic complexity of multiple myeloma and its clinical implications. Manier S, Salem KZ, Park J, Landau DA, Getz G, Ghobrial IM. Nature Reviews Clinical Oncology. 2017 Feb 14.

IFI16 is required for DNA sensing in human macrophages by promoting production and function of cGAMP. Jønsson KL, Laustsen A, Krapp C, Skipper KA, Thavachelvam K, Hotter D, Egedal JH, Kjolby M, Mohammadi P, Prabakaran T, Sørensen LK, Sun C, Jensen SB, Holm CK, Lebbink RJ, Johannsen M, Nyegaard M, Mikkelsen JG, Kirchhoff F, Paludan SR, Jakobsen MR. Nature Communications. 2017 Feb 10.

A multi-step transcriptional and chromatin state cascade underlies motor neuron programming from embryonic stem cells Velasco S, Ibrahim MM, Kakumanu A, Garipler G, Aydin B, Al-Sayegh MA, Hirsekorn A, Abdul-Rahman F, Satija R, Ohler U, Mahony S, Mazzoni EO. Cell 2017 Feb 2.

Modeling cancer rearrangement landscapes. Maciejowski J, Imielinski M. Current Opinion in Systems Biology. 2017 Feb.

Case-control association mapping by proxy using family history of disease. Liu JZ, Erlich Y, Pickrell J. Nature Genetics. 2017 Jan 16.   Insertions and Deletions Target Lineage-Defining Genes in Human Cancers. Imielinski M, Giangwu Guo, Meyerson M. Cell. 2017 Jan 12.

Indel variant analysis of short-read sequencing data with Scalpel. Fang H, Bergmann EA, Arora K, Vacic V, Zody MC, Iossifov I, O'Rawe JA, Wu Y, Jimenez Barron LT, Rosenbaum J, Ronemus M, Lee YH, Wang Z, Dikoglu E, Jobanputra V, Lyon GJ, Wigler M, Schatz MC, Narzisi G. Nat Protoc. 2016 Dec;11(12):2529-2548. doi: 10.1038/nprot.2016.150. Epub 2016 Nov 17.

Please let me know if you have any questions.Jshatan (talk) 15:58, 12 May 2017 (UTC)

Note: All of these changes applied, including the change of the section heading to Recent Publications.Jshatan (talk) 20:01, 12 June 2017 (UTC)

References

Proposed Changes

We would like to update the Faculty section from the four names currently listed to a more complete representation, which would be as follows.

Hemali Phatnani, PhD | Director of the Center for Genomics of Neurodegenerative Disease Greg Hannon, PhD | Associate Core Member & Director of Cancer Genomics Marcin Imielinski, MD, PhD | Core Faculty Member, Assistant Investigator Ivan Iossifov, PhD | Core Faculty Member, Assistant Investigator Dan A. Landau, MD, PhD | Core Faculty Member, Assistant Investigator Tuuli Lappalainen, PhD | Core Faculty Member, Assistant Investigator Joe Pickrell, PhD | Core Faculty Member, Assistant Investigator Neville Sanjana, PhD | Core Faculty Member, Assistant Investigator Rahul Satija, PhD | Core Faculty Member, Assistant Investigator Harold E. Varmus, MD | Senior Associate Core Member Michael Wigler, PhD | Senior Associate Core Member David Goldstein, PhD | Associate Jerome B. Posner, MD | Clinical Associate Member Simon Tavaré, PhD | Senior Researcher Yaniv Erlich, PhD | Adjunct Core Member Jshatan (talk) 20:11, 2 November 2017 (UTC)

Note: These changes added. Jshatan (talk) 20:57, 2 November 2017 (UTC)

References