Publications

2015

Agarwal I, Arnold A, Glazer NL, Barasch E, Djousse L, Fitzpatrick AL, Gottdiener JS, Ix JH, Jensen RA, Kizer JR, Rimm EB, Siscovick DS, Tracy RP, Wong  TY, Mukamal KJ. Fibrosis-related biomarkers and large and small vessel disease: the Cardiovascular Health Study. Atherosclerosis. 2015 Apr;239(2):539-46. doi: 10.1016/j.atherosclerosis.2015.02.020. Epub 2015 Feb 16. PubMed PMID: 25725316.

 

Moutsianas L, Agarwala V, Fuchsberger C, Flannick J, Rivas MA, Gaulton KJ, Albers PK; GoT2D Consortium, McVean G, Boehnke M, Altshuler D, McCarthy MI. The power of gene-based rare variant methods to detect disease-associated variation and test hypotheses about complex disease. PLoS Genet. 2015 Apr 23;11(4):e1005165. doi: 10.1371/journal.pgen.1005165. eCollection 2015 Apr. PubMed PMID: 25906071.

 

Andzelm MM, Cherry TJ, Harmin DA, Boeke AC, Lee C, Hemberg M, Pawlyk B, Malik  AN, Flavell SW, Sandberg MA, Raviola E, Greenberg ME. MEF2D Drives Photoreceptor  Development through a Genome-wide Competition for Tissue-Specific Enhancers. Neuron. 2015 Mar 18. pii: S0896-6273(15)00153-1. doi: 10.1016/j.neuron.2015.02.038. [Epub ahead of print] PubMed PMID: 25801704.

 

Roberts AM, Ware JS, Herman DS, Schafer S, Baksi J, Bick AG, Buchan RJ, Walsh  R, John S, Wilkinson S, Mazzarotto F, Felkin LE, Gong S, MacArthur JA, Cunningham F, Flannick J, Gabriel SB, Altshuler DM, Macdonald PS, Heinig M, Keogh AM, Hayward CS, Banner NR, Pennell DJ, O'Regan DP, San TR, de Marvao A, Dawes TJ, Gulati A, Birks EJ, Yacoub MH, Radke M, Gotthardt M, Wilson JG, O'Donnell CJ, Prasad SK, Barton PJ, Fatkin D, Hubner N, Seidman JG, Seidman CE, Cook SA. Integrated allelic, transcriptional, and phenomic dissection of the cardiac effects of titin truncations in health and disease. Sci Transl Med. 2015 Jan 14;7(270):270ra6. doi: 10.1126/scitranslmed.3010134. PubMed PMID: 25589632.

 

Chen AY, Zhong C, Lu TK. Engineering living functional materials. ACS Synth Biol. 2015 Jan 16;4(1):8-11. doi: 10.1021/sb500113b. PubMed PMID: 25592034; PubMed Central PMCID: PMC4304442.

 

D'Gama AM, Geng Y, Couto JA, Martin B, Boyle EA, LaCoursiere CM, Hossain A, Hatem NE, Barry BJ, Kwiatkowski DJ, Vinters HV, Barkovich AJ, Shendure J, Mathern GW, Walsh CA, Poduri A. Mammalian target of rapamycin pathway mutations cause hemimegalencephaly and focal cortical dysplasia. Ann Neurol. 2015 Apr;77(4):720-5. doi: 10.1002/ana.24357. Epub 2015 Feb 26. PubMed PMID: 25599672.

 

Ebina W, Rossi DJ. Transcription factor-mediated reprogramming toward hematopoietic stem cells. EMBO J. 2015 Mar 12;34(6):694-709. doi: 10.15252/embj.201490804. Epub 2015 Feb 20. Review. PubMed PMID: 25712209; PubMed  Central PMCID: PMC4369309.

 

Krönke J, Fink EC, Hollenbach PW, MacBeth KJ, Hurst SN, Udeshi ND, Chamberlain PP, Mani DR, Man HW, Gandhi AK, Svinkina T, Schneider RK, McConkey M, Järås M, Griffiths E, Wetzler M, Bullinger L, Cathers BE, Carr SA, Chopra R, Ebert BL. Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS. Nature. 2015 Jul 9;523(7559):183-8. doi: 10.1038/nature14610. Epub 2015 Jul 1. PubMed PMID: 26131937.

 

Huys QJ, Lally N, Faulkner P, Eshel N, Seifritz E, Gershman SJ, Dayan P, Roiser JP. Interplay of approximate planning strategies. Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3098-103. doi: 10.1073/pnas.1414219112. Epub 2015 Feb 9. PubMed PMID: 25675480; PubMed Central PMCID: PMC4364207.

Evrony GD, Lee E, Mehta BK, Benjamini Y, Johnson RM, Cai X, Yang L, Haseley P, Lehmann HS, Park PJ, Walsh CA. Cell lineage analysis in human brain using endogenous retroelements. Neuron. 2015 Jan 7;85(1):49-59. doi: 10.1016/j.neuron.2014.12.028. PubMed PMID: 25569347.

Lunt SY, Muralidhar V, Hosios AM, Israelsen WJ, Gui DY, Newhouse L, Ogrodzinski M, Hecht V, Xu K, Acevedo PN, Hollern DP, Bellinger G, Dayton TL, Christen S, Elia I, Dinh AT, Stephanopoulos G, Manalis SR, Yaffe MB, Andrechek ER, Fendt SM, Vander Heiden MG. Pyruvate kinase isoform expression alters nucleotide synthesis to impact cell proliferation. Mol Cell. 2015 Jan 8;57(1):95-107. doi: 10.1016/j.molcel.2014.10.027. Epub 2014 Dec 4. PubMed PMID:  25482511; PubMed Central PMCID: PMC4289430

 

 Hatchi E, Skourti-Stathaki K, Ventz S, Pinello L, Yen A, Kamieniarz-Gdula K, Dimitrov S, Pathania S, McKinney KM, Eaton ML, Kellis M, Hill SJ, Parmigiani G,

Proudfoot NJ, Livingston DM. BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair. Mol Cell. 2015 Feb 19;57(4):636-47. doi: 10.1016/j.molcel.2015.01.011. PubMed PMID: 25699710; PubMed Central PMCID: PMC4351672.

 

Bae BI, Jayaraman D, Walsh CA. Genetic Changes Shaping the Human Brain. Dev Cell. 2015 Feb 23;32(4):423-434. doi: 10.1016/j.devcel.2015.01.035. Review.

PubMed PMID: 25710529.

 

Gabel HW, Kinde B, Stroud H, Gilbert CS, Harmin DA, Kastan NR, Hemberg M, Ebert DH, Greenberg ME. Disruption of DNA-methylation-dependent long gene

repression in Rett syndrome. Nature. 2015 Mar 11. doi: 10.1038/nature14319. [Epub ahead of print] PubMed PMID: 25762136.

 

Kinde B, Gabel HW, Gilbert CS, Griffith EC, Greenberg ME. Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation,  and MeCP2. Proc Natl Acad Sci U S A. 2015 Mar 4. pii: 201411269. [Epub ahead of print] PubMed PMID: 25739960.

Choi M, Kwok SJ, Yun SH. In Vivo Fluorescence Microscopy: Lessons From Observing Cell Behavior in Their Native Environment. Physiology (Bethesda). 2015  Jan;30(1):40-49. Review. PubMed PMID: 25559154.

Miao J, Ling AV, Manthena PV, Gearing ME, Graham MJ, Crooke RM, Croce KJ, Esquejo RM, Clish CB; Morbid Obesity Study Group, Vicent D, Biddinger SB. Flavin-containing monooxygenase 3 as a potential player in diabetes-associated atherosclerosis. Nat Commun. 2015 Apr 7;6:6498. doi: 10.1038/ncomms7498. PubMed PMID: 25849138.

 

Liu WW, Mazor O, Wilson RI. Thermosensory processing in the Drosophila brain. Nature. 2015 Mar 4. doi: 10.1038/nature14170. [Epub ahead of print] PubMed PMID: 25739502.

Leshchiner ES, Parkhitko A, Bird GH, Luccarelli J, Bellairs JA, Escudero S, Opoku-Nsiah K, Godes M, Perrimon N, Walensky LD. Direct inhibition of oncogenic KRAS by hydrocarbon-stapled SOS1 helices. Proc Natl Acad Sci U S A. 2015 Feb 10;112(6):1761-6. doi: 10.1073/pnas.1413185112. Epub 2015 Jan 26. PubMed PMID:25624485.

Andzelm MM, Cherry TJ, Harmin DA, Boeke AC, Lee C, Hemberg M, Pawlyk B, Malik  AN, Flavell SW, Sandberg MA, Raviola E, Greenberg ME. MEF2D Drives Photoreceptor  Development through a Genome-wide Competition for Tissue-Specific Enhancers. Neuron. 2015 Mar 18. pii: S0896-6273(15)00153-1. doi: 10.1016/j.neuron.2015.02.038. [Epub ahead of print] PubMed PMID: 25801704.

Malik AN, Gross BA, Rosalind Lai PM, Moses ZB, Du R. Neurogenic Stress Cardiomyopathy After Aneurysmal Subarachnoid Hemorrhage. World Neurosurg. 2015 Feb 2. pii: S1878-8750(15)00035-2. doi: 10.1016/j.wneu.2015.01.013. [Epub ahead of print] PubMed PMID: 25655685

Mayers JR, Vander Heiden MG. Famine versus feast: understanding the metabolism of tumors in vivo. Trends Biochem Sci. 2015 Jan 29. pii: S0968-0004(15)00005-5. doi: 10.1016/j.tibs.2015.01.004. [Epub ahead of print] Review. PubMed PMID: 25639751.

Pattanayak V, Guilinger JP, Liu DR. Determining the specificities of TALENs, Cas9, and other genome-editing enzymes. Methods Enzymol. 2014;546:47-78. doi:
10.1016/B978-0-12-801185-0.00003-9. Review. PubMed PMID: 25398335; PubMed Central PMCID: PMC4440668.

 

Wang LD, Rao TN, Rowe RG, Nguyen PT, Sullivan JL, Pearson DS, Doulatov S, Wu L, Lindsley RC, Zhu H, DeAngelo DJ, Daley GQ, Wagers AJ. The role of Lin28b in myeloid and mast cell differentiation and mast cell malignancy. Leukemia. 2015 Feb 6. doi: 10.1038/leu.2015.19. [Epub ahead of print] PubMed PMID: 25655194.

 

McWilliams JM, Chernew ME, Landon BE, Schwartz AL. Performance Differences in  Year 1 of Pioneer Accountable Care Organizations. N Engl J Med. 2015 Apr 15. [Epub ahead of print] PubMed PMID: 25875195.

 

Scott JW, Sommers BD, Tsai TC, Scott KW, Schwartz AL, Song Z. Dependent coverage provision led to uneven insurance gains and unchanged mortality rates in young adult trauma patients. Health Aff (Millwood). 2015 Jan;34(1):125-33. doi: 10.1377/hlthaff.2014.0880. PubMed PMID: 25561653.

 

Sherry TB. A Note on the Comparative Statics of Pay-for-Performance in Health  Care. Health Econ. 2015 Mar 1. doi: 10.1002/hec.3169. [Epub ahead of print] PubMed PMID: 25728391.

 

Scott JW, Sommers BD, Tsai TC, Scott KW, Schwartz AL, Song Z. Dependent coverage provision led to uneven insurance gains and unchanged mortality rates in

young adult trauma patients. Health Aff (Millwood). 2015 Jan;34(1):125-33. doi: 10.1377/hlthaff.2014.0880. PubMed PMID: 25561653.

 

Lindsley RC, Mar BG, Mazzola E, Grauman PV, Shareef S, Allen SL, Pigneux A, Wetzler M, Stuart RK, Erba HP, Damon LE, Powell BL, Lindeman N, Steensma DP, Wadleigh M, DeAngelo DJ, Neuberg D, Stone RM, Ebert BL. Acute myeloid leukemia ontogeny is defined by distinct somatic mutations. Blood. 2015 Feb 26;125(9):1367-76. doi: 10.1182/blood-2014-11-610543. Epub 2014 Dec 30. PubMed PMID: 25550361; PubMed Central PMCID: PMC4342352.

 

Wang S, Tsun ZY, Wolfson RL, Shen K, Wyant GA, Plovanich ME, Yuan ED, Jones TD, Chantranupong L, Comb W, Wang T, Bar-Peled L, Zoncu R, Straub C, Kim C, Park  J, Sabatini BL, Sabatini DM. Metabolism. Lysosomal amino acid transporter SLC38A9 signals arginine sufficiency to mTORC1. Science. 2015 Jan 9;347(6218):188-94. doi: 10.1126/science.1257132. Epub 2015 Jan 7. PubMed PMID: 25567906.

 

Dryden-Peterson S, Bennett K, Hughes MD, Veres A, John O, Pradhananga R, Boyer M, Brown C, Sakyi B, van Widenfelt E, Keapoletswe K, Mine M, Moyo S, Asmelash A,  Siedner M, Mmalane M, Shapiro RL, Lockman S. An augmented SMS intervention to improve access to antenatal CD4 testing and ART initiation in HIV-infected pregnant women: a cluster randomized trial. PLoS One. 2015 Feb 18;10(2):e0117181. doi: 10.1371/journal.pone.0117181. eCollection 2015. PubMed PMID: 25693050; PubMed Central PMCID: PMC4334487.

 

Wang S, Tsun ZY, Wolfson RL, Shen K, Wyant GA, Plovanich ME, Yuan ED, Jones TD, Chantranupong L, Comb W, Wang T, Bar-Peled L, Zoncu R, Straub C, Kim C, Park  J, Sabatini BL, Sabatini DM. Metabolism. Lysosomal amino acid transporter SLC38A9 signals arginine sufficiency to mTORC1. Science. 2015 Jan 9;347(6218):188-94. doi: 10.1126/science.1257132. Epub 2015 Jan 7. PubMed PMID: 25567906.

Wang S, Tsun ZY, Wolfson RL, Shen K, Wyant GA, Plovanich ME, Yuan ED, Jones TD, Chantranupong L, Comb W, Wang T, Bar-Peled L, Zoncu R, Straub C, Kim C, Park  J, Sabatini BL, Sabatini DM. Metabolism. Lysosomal amino acid transporter SLC38A9 signals arginine sufficiency to mTORC1. Science. 2015 Jan 9;347(6218):188-94. doi: 10.1126/science.1257132. Epub 2015 Jan 7. PubMed PMID: 25567906.

Chantranupong L, Wolfson RL, Sabatini DM. Nutrient-sensing mechanisms across evolution. Cell. 2015 Mar 26;161(1):67-83. doi: 10.1016/j.cell.2015.02.041.Review. PubMed PMID: 25815986; PubMed Central PMCID: PMC4384161

 

Murn J, Zarnack K, Yang YJ, Durak O, Murphy EA, Cheloufi S, Gonzalez DM, Teplova M, Curk T, Zuber J, Patel DJ, Ule J, Luscombe NM, Tsai LH, Walsh CA, Shi Y. Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes Dev. 2015 Mar 1;29(5):501-12. doi: 10.1101/gad.258483.115. PubMed PMID: 25737280; PubMed Central PMCID: PMC4358403.

 

Ran FA*, Cong L*, Yan WX*, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova KS, Koonin EV, Sharp PA, Zhang F. In vivo genome editing using Staphylococcus aureus Cas9. Nature. 2015 Apr 9;520(7546):186-91. doi: 10.1038/nature14299. Epub 2015 Apr 1. PubMed PMID: 25830891; PubMed Central PMCID: PMC4393360 (* co-first authors)