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Items: 20

1.

Opportunities and obstacles for deep learning in biology and medicine.

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS.

J R Soc Interface. 2018 Apr;15(141). pii: 20170387. doi: 10.1098/rsif.2017.0387. Review.

2.

Sci-Hub provides access to nearly all scholarly literature.

Himmelstein DS, Romero AR, Levernier JG, Munro TA, McLaughlin SR, Greshake Tzovaras B, Greene CS.

Elife. 2018 Mar 1;7. pii: e32822. doi: 10.7554/eLife.32822.

3.

Systematic integration of biomedical knowledge prioritizes drugs for repurposing.

Himmelstein DS, Lizee A, Hessler C, Brueggeman L, Chen SL, Hadley D, Green A, Khankhanian P, Baranzini SE.

Elife. 2017 Sep 22;6. pii: e26726. doi: 10.7554/eLife.26726.

4.

SHH E176/E177-Zn2+ conformation is required for signaling at endogenous sites.

Himmelstein DS, Cajigas I, Bi C, Clark BS, Van Der Voort G, Kohtz JD.

Dev Biol. 2017 Apr 15;424(2):221-235. doi: 10.1016/j.ydbio.2017.02.006. Epub 2017 Mar 2.

5.

Association of HLA Genetic Risk Burden With Disease Phenotypes in Multiple Sclerosis.

Isobe N, Keshavan A, Gourraud PA, Zhu AH, Datta E, Schlaeger R, Caillier SJ, Santaniello A, Lizée A, Himmelstein DS, Baranzini SE, Hollenbach J, Cree BA, Hauser SL, Oksenberg JR, Henry RG.

JAMA Neurol. 2016 Jul 1;73(7):795-802. doi: 10.1001/jamaneurol.2016.0980.

6.

Genetic Association-Guided Analysis of Gene Networks for the Study of Complex Traits.

Greene CS, Himmelstein DS.

Circ Cardiovasc Genet. 2016 Apr;9(2):179-84. doi: 10.1161/CIRCGENETICS.115.001181. Review. No abstract available.

PMID:
27094199
7.

Meta-analysis of genome-wide association studies reveals genetic overlap between Hodgkin lymphoma and multiple sclerosis.

Khankhanian P, Cozen W, Himmelstein DS, Madireddy L, Din L, van den Berg A, Matsushita T, Glaser SL, Moré JM, Smedby KE, Baranzini SE, Mack TM, Lizée A, de Sanjosé S, Gourraud PA, Nieters A, Hauser SL, Cocco P, Maynadié M, Foretová L, Staines A, Delahaye-Sourdeix M, Li D, Bhatia S, Melbye M, Onel K, Jarrett R, McKay JD, Oksenberg JR, Hjalgrim H.

Int J Epidemiol. 2016 Jun;45(3):728-40. doi: 10.1093/ije/dyv364. Epub 2016 Mar 12.

8.

Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology.

Himmelstein DS, Greene CS, Moore JH.

BioData Min. 2016 Feb 3;9:9. doi: 10.1186/s13040-016-0085-5. eCollection 2016.

9.

iCTNet2: integrating heterogeneous biological interactions to understand complex traits.

Wang L, Himmelstein DS, Santaniello A, Parvin M, Baranzini SE.

Version 2. F1000Res. 2015 Aug 5 [revised 2015 Jan 1];4:485. doi: 10.12688/f1000research.6836.2. eCollection 2015.

10.

Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes.

Himmelstein DS, Baranzini SE.

PLoS Comput Biol. 2015 Jul 9;11(7):e1004259. doi: 10.1371/journal.pcbi.1004259. eCollection 2015 Jul.

11.

Understanding multicellular function and disease with human tissue-specific networks.

Greene CS, Krishnan A, Wong AK, Ricciotti E, Zelaya RA, Himmelstein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, Chasman DI, FitzGerald GA, Dolinski K, Grosser T, Troyanskaya OG.

Nat Genet. 2015 Jun;47(6):569-76. doi: 10.1038/ng.3259. Epub 2015 Apr 27.

12.

Lung cancer incidence decreases with elevation: evidence for oxygen as an inhaled carcinogen.

Simeonov KP, Himmelstein DS.

PeerJ. 2015 Jan 13;3:e705. doi: 10.7717/peerj.705. eCollection 2015.

13.

TOC1: a valuable tool in assessing disease progression in the rTg4510 mouse model of tauopathy.

Ward SM, Himmelstein DS, Ren Y, Fu Y, Yu XW, Roberts K, Binder LI, Sahara N.

Neurobiol Dis. 2014 Jul;67:37-48. doi: 10.1016/j.nbd.2014.03.002. Epub 2014 Mar 12.

14.

TOC1: characterization of a selective oligomeric tau antibody.

Ward SM, Himmelstein DS, Lancia JK, Fu Y, Patterson KR, Binder LI.

J Alzheimers Dis. 2013;37(3):593-602. doi: 10.3233/JAD-131235.

15.

Tau oligomers and tau toxicity in neurodegenerative disease.

Ward SM, Himmelstein DS, Lancia JK, Binder LI.

Biochem Soc Trans. 2012 Aug;40(4):667-71. doi: 10.1042/BST20120134. Review.

16.

Tau as a therapeutic target in neurodegenerative disease.

Himmelstein DS, Ward SM, Lancia JK, Patterson KR, Binder LI.

Pharmacol Ther. 2012 Oct;136(1):8-22. doi: 10.1016/j.pharmthera.2012.07.001. Epub 2012 Jul 10. Review.

17.

Evolving hard problems: Generating human genetics datasets with a complex etiology.

Himmelstein DS, Greene CS, Moore JH.

BioData Min. 2011 Jul 7;4(1):21. doi: 10.1186/1756-0381-4-21. Erratum in: BioData Min. 2016;9:9.

18.

Balanced Shh signaling is required for proper formation and maintenance of dorsal telencephalic midline structures.

Himmelstein DS, Bi C, Clark BS, Bai B, Kohtz JD.

BMC Dev Biol. 2010 Nov 29;10:118. doi: 10.1186/1471-213X-10-118.

19.

Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS.

Greene CS, Sinnott-Armstrong NA, Himmelstein DS, Park PJ, Moore JH, Harris BT.

Bioinformatics. 2010 Mar 1;26(5):694-5. doi: 10.1093/bioinformatics/btq009. Epub 2010 Jan 16.

20.

Enabling personal genomics with an explicit test of epistasis.

Greene CS, Himmelstein DS, Nelson HH, Kelsey KT, Williams SM, Andrew AS, Karagas MR, Moore JH.

Pac Symp Biocomput. 2010:327-36.

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