Publications

FEATURED


Proteogenomics connects somatic mutations to signalling in breast cancer
Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA; NCI CPTAC


GENOME ENGINEERING. The Genome Project-Write.
Boeke JD
, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L.


Multi-reporter selection for the design of active and more specific zinc-finger nucleases for genome editing
Benjamin L. Oakes, Danny F. Xia, Elizabeth F. Rowland, Denise J. Xu, Irina Ankoudinova, Jennifer S. Borchardt, Lei Zhang, Patrick Li, Jeffrey C. Miller, Edward J. Rebar & Marcus B. Noyes


Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo.
Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer A, Kaul R, Stamatoyannopoulos JA


Much ado about zero.
Boeke JD, Fenyo D


Role of DNA Methylation in Modulating Transcription Factor Occupancy.
Maurano MT, Wang H, John S, Shafer A, Canfield T, Lee K, Stamatoyannopoulos JA.


Taking Stock of Regulatory Variation.
Matthew T. Maurano, John A. Stamatoyannopoulos


Genomic discovery of potent chromatin insulators for human gene therapy.
Liu M, Maurano MT, Wang H, Qi H, Song CZ, Navas PA, Emery DW, Stamatoyannopoulos JA, Stamatoyannopoulos G


Dr. Jef Boeke - Executive Director - Publications 2014 - Present

1. GENOME ENGINEERING. The Genome Project-Write.
Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L. Science. 2016 Jul 8;353(6295):126-7. PMID: 27256881 

2. Barcode Sequencing Screen Identifies SUB1 as a Regulator of Yeast Pheromone Inducible Genes.
​Sliva A, Kuang Z, Meluh PB, Boeke JD. 2016. G3 (Bethesda). pii: g3.115.026757. PMCID: PMC4825658
 

3. How retrotransposons shape genome regulation
Mita P, Boeke JD. Curr Opin Genet Dev. 2016 37:90-100. PMCID: PMC4914423
 

4. SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes
Shen Y, Stracquadanio G, Wang Y, Yang K, Mitchell L, Xue Y, Cai Y, Chen T, Dymond JS, Kang K, Zhang Y, Gong J, Li Y, Wang J, Yang H, Boeke JD, Bader JS. 2015 Genome Res. 26:36-49 PMCID: PMC4691749

5. Characterization of L1-Ribonucleoprotein Particles.
Taylor MS, LaCava J, Dai L , Mita P, Burns KH, Rout MP, Boeke JD. 2015. Meth. Molec. Biol. 1400:311-38. PMID: 26895062
 

6. Much ado about zero
​Boeke JD and Fenyö D. 2015. Cell, 163:534-5. PMID: 26496595
 

7. BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts.
Yang K, Stracquadanio, G, Luo, J., Boeke JD, Bader JS. 2015. Bioinformatics. 2016 Mar 15;32(6):937-9. PMCID: PMC4803390

8. Development of a tightly controlled off switch for Saccharomyces cerevisiae regulated by camphor, a low-cost natural product.
​Ikushima S,  Zhao Y, Boeke JD. 2015. G3, 5:1983-90. PMCID: PMC4592980

9. Mechanistic Analysis of Ghrelin-O-Acyltransferase Using Substrate.
Taylor MS, Dempsey DR, Hwang Y, Chen Z, Chu N, Boeke JD, Cole PA. 2015. Biorg. Chem. 62:64-73. PMCID: PMC4567917
 

10. Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma.
​Rodić N, Steranka JP, Makohon-Moore A, Moyer A, Shen P, Sharma R, Huang CRL, Ahn D, Mita P, Taylor MS, Hruban R, Iacobuzio-Donahue CA, Boeke JD, Burns KH.  2015. Nature Med. 21:1060-4. PMCID: PMC4775273

11. H3K36 methylation promotes longevity by enhancing transcriptional fidelity
Sen P, Dang W, Donahue G , Dai J, Dorsey J, Cao X, Liu W, Cao K, Perry R, Lee JY, Wagner J, Gregory BD, Wasko BM, Carr DT, Kaeberlein M, Kennedy B, Boeke JD, and Berger SB. 2015. Genes Dev. 29:1362-76. PMCID: PMC4511212

12. Freedom and Responsibility in Synthetic Genomics: The Sc2.0 Project.
*Sliva A, Yang H, Boeke JD, Mathews D. 2015. Genetics 200:1021-1028. PMCID: PMC4574254

13. Versatile Genetic Assembly System (VEGAS) to assemble pathways for expression in S. cerevisiae.
Mitchell LA, Chuang J, Agmon N, Khunsriraksakul C, Phillips NA, Cai Y, Truong DM, Veerakumar A, Wang Y, Mayorga M, Blomquist P, Sadda P, Trueheart J, Boeke JD. 2015. Nucl Acids Res 43:6620-6630. PMCID: PMC4513848

14. Yeast Golden Gate (yGG) for efficient assembly of Saccharomyces cerevisiae transcription units.
​Agmon N, Mitchell LA, Cai Y, Ikushima S, Chuang J, Zheng A, Choi WJ, Martin JA, Caravelli K, Stracquadanio G, Boeke JD. 2015. ACS Synth Biol 4(7):853-859. PMID: 25756291
 

15. Interplay between histone H3 lysine 56 deacetylation and chromatin modifiers in the response to replicative DNA damage.
​Simoneau A, Delgoshaie N, Celic I, Dai J, Costantino S, Boeke JD, Verreault A, Wurtele H. 2015, Genetics 200:185-205. PMCID: PMC4423362

16. High throughput PCRTagging - a real time PCR genotyping assay for Sc2.0
Mitchell LA, Phillips N, Lafont A, Cutting R, Martin JA, Boeke JD. 2015. J Vis Exp, (99):e52941. PMID: 26067760

17. Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes.
Cai Y, Agmon N, Choi WC, Ubide A, Stracquadanio G, Caravelli K, Hao H, Bader JS, Boeke JD.  2015 Proc Natl Acad Sci USA 112:1803-8. PMCID: PMC4330768

18. Human Genomics. Sleeping dogs of the genome. 
​Gorbunova V, Boeke JD, Helfand SL, Sedivy JM. Human Genomics. Science. 2014 Dec 5;346(6214):1187-8 PMCID: PMC4312280

19. Circular permutation of a synthetic eukaryotic chromosome with the telomerator.
Mitchell LA and Boeke JD, 2014 Proc Natl Acad Sci USA 111:17003-10. PMCID: PMC4260612

20. High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast.
Kuang Z, Cai L, Zhang X, Ji HK, Tu BJ, Boeke JD. 2014, Nature Struct Molec Biol, 21:854-863. PMCID: PMC4190017

21. Expression and detection of LINE-1ORF-encoded proteins.
Dai L, LaCava J, Taylor MS, Boeke JD. 2014 Mob Genet Elements. 4:e29319. eCollection 2014. PMCID: PMC4091050

22. Mobile DNA: an evolving field.
​Belfort M, Marraffini L, Macfarlan T, Boeke J, Slotkin K, Malik H, Maquat L.  2014. Mob DNA. 5:16. PubMed PMID: 24904692; PMCID: PMC4046146

23. RADOM, an Efficient In Vivo Method for Assembling Designed DNA Fragments up to 10 kb Long in Saccharomyces cerevisiae.
Lin Q, Jia B, Mitchell LA, Luo J, Yang K, Zeller KI, Zhang W, Xu Z, Stracquadanio G, Bader JS, Boeke JD, Yuan YJ. 2014, ACS Synth Biol. PMID: 24895839
 

24. Characterization of cytoplasmic DNA complementary to non-retroviral RNA viruses in human cells.
Shimizu A, Nakatani Y, Nakamura T, Jinno-Oue A, Ishikawa O, Boeke JD, Takeuchi Y, Hoshino H. Sci Rep. 2014 4:5074. PMCID: PMC4038843

25. Long interspersed element-1 protein expression is a hallmark of many human cancers.
​Rodić N, Sharma R, Sharma R, Zampella J, Dai L, Taylor MS, Hruban RH, Iacobuzio-Donahue CA, Maitra A, Torbenson MS, Goggins M, Shih IeM, Duffield AS, Montgomery EA, Gabrielson E, Netto GJ, Lotan TL, De Marzo AM, Westra W, Binder ZA, Orr BA, Gallia GL, Eberhart CG, Boeke JD, Harris CR, Burns KH. 2014 Am J Pathol. 184:1280-6. PMCID: PMC4005969

26. Total Synthesis of a Functional Designer Eukaryotic Chromosome.
​Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Scheifele LZ, Cooper EM, Cai Y, Zeller K, Agmon N, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo Z, London V, Yeluru A, Murugan S, Kandavelou K, Yang K, JMartin JA, Bilgel M,  Bohutski P,  Boulier KM,  Capaldo BJ,  Chang J,  Charoen K,  Choi WJ, Deng P,  DiCarlo JE,  Doong J,  Dunn J, Feinberg JI,  Fernandez C,  Floria CE,  Gladowski D,  Hadidi P,  Ishizuka I,  Jabbari J, Lau CYL,  Lee PA,  Li S,  Lin D,  Linder ME,  Ling J,  Liu Ja,  Liu Jo,  London M,  Ma H,  Mao J,  McDade JE,  McMillan A,  Moore AM, Oh WC,  Ouyang C,  Patel R,  Paul M,  Paulsen LC,  Qiu J,  Rhee A,  Rubashkin MG,  Soh IY,  Sotuyo NE,  Srinivas V,  Suarez A,  Wong A,  Wong R,  Xie WR,  Xu Y, Yu AT, Koszul R, Bader JS, Boeke JD† and Chandrasegaran S†. 2014 Science, 344: 55-8. PMCID: PMC4033833

27. Synthetic Genomes and the Bioeconomy.
​Boeke, J.D. 2014. In: Pan-European Networks Science and Technology 8:222-223.
 

ALL PUBLICATIONS


Dr. David Fenyo - Professor - Publications 2014 - Present

1. Quantitative data sharing from hyperpeaks to global ion chromatograms (GICs).
​Askenazi M, Fenyo D. OpenSlice: Proteomics. 2016 Jul 19. PMID: 27436706
 

2. HIV-host interactome revealed directly from infected cells.
Luo Y, Jacobs EY, Greco TM, Mohammed KD, Tong T, Keegan S, Binley JM, Cristea IM, Fenyö D, Rout MP, Chait BT, Muesing MA. Nat Microbiol. 2016 Jul;1(7). pii: 16068. Epub 2016 May 23. PMCID: PMC4928716
 

3. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell.
Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu KH, Tabb DL, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih IM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD; CPTAC Investigators. 2016, Cell Jun 28. pii: S0092-8674(16)30673-0. doi: 10.1016/j.cell.2016.05.069. PMID: 27372738
 

4. NCI CPTAC. Proteogenomics connects somatic mutations to signalling in breast cancer.
​Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA; Nature. 2016 May 25;534(7605):55-62. doi: 10.1038/nature18003. PMID: 27251275
 

5. A Complex Systems Approach to Causal Discovery in Psychiatry.
​Saxe GN, Statnikov A, Fenyo D, Ren J, Li Z, Prasad M, Wall D, Bergman N, Briggs EC, Aliferis C. PLoS One. 2016 Mar 30;11(3):e0151174. PMCID: PMC4814084

6. Erratum: Nanoscale visualization of functional adhesion/excitability nodes at the intercalated disc.
Leo-Macias A, Agullo-Pascual E, Sanchez-Alonso JL, Keegan S, Lin X, Arcos T, Feng-Xia-Liang, Korchev YE, Gorelik J, Fenyö D, Rothenberg E, Delmar M. Nat Commun. 2016 Feb 22;7:10919. PMCID: PMC4764909

7. Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays.
​Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Boja E, Carr SA, Chan DW, Chen X, Chen J, Davies SR, Ellis MJ, Fenyö D, Hiltke T, Ketchum KA, Kinsinger C, Kuhn E, Liebler DC, Liu T, Loss M, MacCoss MJ, Qian WJ, Rivers R, Rodland KD, Ruggles KV, Scott MG, Smith RD, Thomas S, Townsend RR, Whiteley G, Wu C, Zhang H, Zhang Z, Rodriguez H, Paulovich AG. Methods Mol Biol. 2016;1410:223-36. PMID: 26867747
 

8. A Database Mapping Protein Post-Translational Modifications to Genomic Coordinates.
Keegan S, Cortens JP, Beavis RC, Fenyö D. g2pDB: J Proteome Res. 2016 Mar 4;15(3):983-90. PMID: 26842767
 

9. Nanoscale visualization of functional adhesion/excitability nodes at the intercalated disc.
Leo-Macias A, Agullo-Pascual E, Sanchez-Alonso JL, Keegan S, Lin X, Arcos T, Feng-Xia-Liang, Korchev YE, Gorelik J, Fenyö D, Rothenberg E, Rothenberg E, Delmar M. Nat Commun. 2016 Jan 20;7:10342. Erratum in: Nat Commun. 2016;7:10919. PMCID: PMC4735805

10. Optimizing selection of large animals for antibody production by screening immune response to standard vaccines.
Thompson MK, Fridy PC, Keegan S, Chait BT, Fenyö D, Rout MP. J Immunol Methods. 2016 Mar;430:56-60. Epub 2016 Jan 9. PMID: 26775851
 

11. Separable roles for Mycobacterium tuberculosis ESX-3 effectors in iron acquisition and virulence.
​Tufariello JM, Chapman JR, Kerantzas CA, Wong KW, Vilchèze C, Jones CM, Cole LE, Tinaztepe E, Thompson V, Fenyö D, Niederweis M, Ueberheide B, Philips JA, Jacobs WR Jr. Proc Natl Acad Sci U S A. 2016 Jan 19;113(3):E348-57. Epub 2016 Jan 4. PMCID: PMC4725510

12. Selenocysteine: Wherefore Art Thou?
​Fenyö D, Beavis RC. J Proteome Res. 2016 Feb 5;15(2):677-8. doi: 10.1021/acs.jproteome.5b01028. Epub 2015 Dec 22. PMID: 26680273
 

13. Proteogenomics from a bioinformatics angle: A growing field.
​Menschaert G, Fenyö D. Mass Spectrom Rev. 2015 Dec 15. doi: 10.1002/mas.21483. [Epub ahead of print] Review. PMID: 26670565
 

14. PGx: Putting Peptides to BED.
​Askenazi M, Ruggles KV, Fenyö D.J Proteome Res. 2016 Mar 4;15(3):795-9. Epub 2015 Dec 18. PMCID: PMC4782174

15. An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.
​Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, Xie L, Liu T, Zhou JY, Sun S, Hoadley KA, Perou CM, Chen X, Davies SR, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Payne S, Ellis MJ, Fenyő D. Mol Cell Proteomics. 2016 Mar;15(3):1060-71. Epub 2015 Dec 2. PMCID: PMC4813688

16. Integrated Bottom-Up and Top-Down Proteomics of Patient-Derived Breast Tumor Xenografts.
​Ntai I, LeDuc RD, Fellers RT, Erdmann-Gilmore P, Davies SR, Rumsey J, Early BP, Thomas PM, Li S, Compton PD, Ellis MJ, Ruggles KV, Fenyö D, Boja ES, Rodriguez H, Townsend RR, Kelleher NL. Mol Cell Proteomics. 2016 Jan;15(1):45-56. Epub 2015 Oct 26. PMCID: PMC4762530

17. Much ado about zero.
​Boeke JD, Fenyo D. Cell. 2015 Oct 22;163(3):534-5. Epub 2015 Oct 22. PMID: 26496595
 

18. Organization and dynamics of the nonhomologous end-joining machinery during DNA double-strand break repair.
Reid DA, Keegan S, Leo-Macias A, Watanabe G, Strande NT, Chang HH, Oksuz BA, Fenyo D, Lieber MR, Ramsden DA, Rothenberg E. Proc Natl Acad Sci U S A. 2015 May 19;112(20):E2575-84. Epub 2015 May 4. PMCID: PMC4443322

19. Rapid, optimized interactomic screening.
​Hakhverdyan Z, Domanski M, Hough LE, Oroskar AA, Oroskar AR, Keegan S, Dilworth DJ, Molloy KR, Sherman V, Aitchison JD, Fenyö D, Chait BT, Jensen TH, Rout MP, LaCava J. Nat Methods. 2015 Jun;12(6):553-60. Epub 2015 May 4. PMCID: PMC4449307

20. The GPMDB REST interface.
​Fenyö D, Beavis RC. Bioinformatics. 2015 Jun 15;31(12):2056-8.. Epub 2015 Feb 19. PMID: 25697819
 

21. Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study.
Sun J, Zhang GL, Li S, Ivanov AR, Fenyo D, Lisacek F, Murthy SK, Karger BL, Brusic V. BMC Genomics. 2014;15 Suppl 9:S1. Epub 2014 Dec 8. PMCID: PMC4290587

22. Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome.
Nilsson CL, Mostovenko E, Lichti CF, Ruggles K, Fenyö D, Rosenbloom KR, Hancock WS, Paik YK, Omenn GS, LaBaer J, Kroes RA, Uhlén M, Hober S, Végvári Á, Andrén PE, Sulman EP, Lang FF, Fuentes M, Carlsohn E, Emmett MR, Moskal JR, Berven FS, Fehniger TE, Marko-Varga G. J Proteome Res. 2015 Feb 6;14(2):603-8. Epub 2014 Nov 26. PMID: 25369122
 

23. A robust pipeline for rapid production of versatile nanobody repertoires.
​Fridy PC, Li Y, Keegan S, Thompson MK, Nudelman I, Scheid JF, Oeffinger M, Nussenzweig MC, Fenyö D, Chait BT, Rout MP. Nat Methods. 2014 Dec;11(12):1253-60. Epub 2014 Nov 2. PMCID: PMC4272012

24. Super-resolution imaging reveals that loss of the C-terminus of connexin43 limits microtubule plus-end capture and NaV1.5 localization at the intercalated disc.
Agullo-Pascual E, Lin X, Leo-Macias A, Zhang M, Liang FX, Li Z, Pfenniger A, Lübkemeier I, Keegan S, Fenyö D, Willecke K, Rothenberg E, Delmar M. Cardiovasc Res. 2014 Nov 1;104(2):371-81. Epub 2014 Aug 18. PMCID: PMC4296112

25. schemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels.
​Mertins P, Yang F, Liu T, Mani DR, Petyuk VA, Gillette MA, Clauser KR, Qiao JW, Gritsenko MA, Moore RJ, Levine DA, Townsend R, Erdmann-Gilmore P, Snider JE, Davies SR, Ruggles KV, Fenyo D, Kitchens RT, Li S, Olvera N, Dao F, Rodriguez H, Chan DW, Liebler D, White F, Rodland KD, Mills GB, Smith RD, Paulovich AG, Ellis M, Carr SA. Mol Cell Proteomics. 2014 Jul;13(7):1690-704. Epub 2014 Apr 9. PMCID: PMC4083109 

 

26. Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines.
Lichti CF, Liu H, Shavkunov AS, Mostovenko E, Sulman EP, Ezhilarasan R, Wang Q, Kroes RA, Moskal JC, Fenyö D, Oksuz BA, Conrad CA, Lang FF, Berven FS, Végvári A, Rezeli M, Marko-Varga G, Hober S, Nilsson CL.
J Proteome Res. 2014 Jan 3;13(1):191-9. Epub 2013 Dec 3. PMID: 24266786
 

ALL PUBLICATIONS


Dr. Liam Holt - Assistant Professor - All Publications

1. GENOME ENGINEERING. The Genome Project-Write.
​Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L. Science. 2016 Jul 8;353(6295):126-7. Epub 2016 Jun 2. PMID: 27256881
 

2. A glucose-starvation response regulates the diffusion of macromolecules.
Joyner RP, Tang JH, Helenius J, Dultz E, Brune C, Holt LJ, Huet S, Müller DJ, Weis K. Elife. 2016 Mar 22;5. PMCID: PMC4811765

3. Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity.
Howard CJ, Hanson-Smith V, Kennedy KJ, Miller CJ, Lou HJ, Johnson AD, Turk BE, Holt LJ. Elife. 2014 Oct 13;3. PMCID: PMC4228266

4. Cell-cycle regulation of formin-mediated actin cable assembly.
​Miao Y, Wong CC, Mennella V, Michelot A, Agard DA, Holt LJ, Yates JR 3rd, Drubin DG. Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):E4446-55. PMCID: PMC3839727

5. The Giardia cell cycle progresses independently of the anaphase-promoting complex.
​Gourguechon S, Holt LJ, Cande WZ. J Cell Sci. 2013 May 15;126(Pt 10):2246-55. PMCID: PMC3672939

6. Coupling protein stability to phopshoregulation during cell division.
Holt LJ. Regulatory modules: FEBS Lett. 2012 Aug 14;586(17):2773-7. doi: 10.1016/j.febslet.2012.05.045. PMID: 22664379
 

7. Phase transitions in biogenic amorphous calcium carbonate.
Gong YU, Killian CE, Olson IC, Appathurai NP, Amasino AL, Martin MC, Holt LJ, Wilt FH, Gilbert PU. Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6088-93. PMCID: PMC3341025

8. Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.
Holt LJ, Tuch BB, Villén J, Johnson AD, Gygi SP, Morgan DO. Science. 2009 Sep 25;325(5948):1682-6. PMCID: PMC2813701

9. The class I bHLH factors E2-2A and E2-2B regulate EMT.
​Sobrado VR, Moreno-Bueno G, Cubillo E, Holt LJ, Nieto MA, Portillo F, Cano A. J Cell Sci. 2009 Apr 1;122(Pt 7):1014-24. PMID: 19295128
 

10. Cyclin-specific control of ribosomal DNA segregation.
Sullivan M, Holt L, Morgan DO. Mol Cell Biol. 2008 Sep;28(17):5328-36. PMCID: PMC2519743

11. Positive feedback sharpens the anaphase switch.
Holt LJ, Krutchinsky AN, Morgan DO. Nature. 2008 Jul 17;454(7202):353-7. PMCID: PMC2636747


Dr. Timothee lionnet - Assistant Professor - Publications 2014 - Present

1. TRICK: A Single-Molecule Method for Imaging the First Round of Translation in Living Cells and Animals 
Halstead, JM, Wilbertz JH, Wippich F, Lionnet T, Ephrussi A, Chao JA (2016) Science Direct dx.doi.org/10.1016/bs.mie.2016.02.027

2. Bright photoactivatable fluorophores for single-molecule Imaging. 
Grimm JB, English BP, Choi H, Muthusamy AK, Mehl BP, Dong P, Brown TA, Lippincott-Schwartz J, Liu Z, Lionnet T, Lavis LD* (2016) Nature Methods doi:10.1038/nmeth.4034 Bioarxiv   |  PMC

3. Supplementary Materials for Real-time quantification of single RNA translation dynamics in living cells
​Morisaki T, Lyon K, DeLuca KF, DeLuca JG, English BP, Zhang Z, Lavis LD, Grimm JB, Viswanathan S, Looger LL, Lionnet T, Stasevich TJ (2016)  Science doi:10.1126/science.aaf0899

4. RNA Polymerase II cluster dynamics predicts mRNA ouput in living cells.
Cho WK, Jayanth N, English BP, Inoue T, Andrews JO, Conway W, Grimm JB, Spille JH, Lavis LD, Lionnet T, Cisse II* (2016) eLife PMC

5. Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging
Abrahamsson S, Ilic R, Wisniewski J, Mehl B, Yu L, Chen L, Davanco M, Oudjedi L, Fiche JB, Hajj B, Jin X, Pulupa J, Cho C, Mir M, Beheiry ME, Darzacq X, Nollmann M, Dahan M, Wu C, Lionnet T, Liddle JA, and Bargmann CI (2016) Biomedical Optics Express doi.org/10.1364/BOE.7.000855

6. Imaging Transcription: Past, Present, and Future
Coleman RA, Liu Z,Darzacq X, Tjian R, Singer RH and Lionnet T (2016) Cold Spring Harbor Symposia on Quantitative Biology PMCID: PMC4915995

7. Mapping translation'hot-spots' in live cells by tracking single molecules of mRNA and ribosomes
Katz ZB, English BP, Lionnet T, Yoon YJ, Monnier N, Ovryn B, Bathe M, Singer RH (2016) eLIFE doi: 10.7554/eLife.10415

8. Quantitative mRNA Imaging Throughout the Entire Drosophila Brain
Long X, Colonell J, Wong AM, Singer RH, Lionnet T (2016) ioRxiv doi: 10.1101/096388

9. Bright photoactivatable fluorophores for single-molecule imaging
Lavis LD, Grimm JB, English BP, Muthusamy AK, Mehl BP, Dong P, Brown TA, Liu Z,  Lionnet T (2016) Nature Methods doi:10.1038/nmeth.4034

10. CASFISH : CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells. 
Deng W, Shi X, Tjian R, Lionnet T, Singer RH. (2015)  Proc. Natl. Acad. Sci., 112 (38), 11870-11875 PMC

11. Drosophila germ granules are structured and contain homotypic mRNA clusters
Trcek T, Grosch M, York A, Shroff H, Lionnet T, and Lehmann R (2015) Nature Communications doi:10.1038/ncomms8962

    12. Cellular Levels of Signaling Factors Are Sensed by β-actin Alleles to Modulate Transcriptional Pulse Intensity. 
    Kalo A, Kanter I, Shraga A, Sheinberger J, Tzemach H, Kinor N, Singer RH, Lionnet T, Shav-Tal Y. (2015) Cell Reports 11(3) 419-32 PMC
     

    13. An RNA biosensor for imaging the first round of translation from single cells to living animals. 
    Halstead JM**, Lionnet T, Wilbertz JH**, Wippich F**, Ephrussi A, Singer RH, Chao JA. (2015) Science 347(6228) 1367-671 PMC
     

    14. A general method to improve fluorophores for live-cell and single-molecule microscopy.
    Grimm JB, English BP, Chen J, Slaughter JP, Zhang Z, Revyakin A, Patel R, Macklin JJ, Normanno D, Singer RH, Lionnet T, Lavis LD.* (2015) Nature Methods 12(3) 244-50 PMC
     

    15. Single-molecule dynamics of enhanceosome assembly in embryonic stem cells. 
    Chen J, Zhang Z, Li L, Chen BC, Revyakin A, Hajj B, Legant W, Dahan M, Lionnet T, Betzig E, Tjian R, Liu Z. (2014)  Cell 156 (6) 1274-85 PMC
     

    ALL PUBLICATIONS


    Dr. Matthew Maurano - Assistant Professor - All Publications

    1. GENOME ENGINEERING. The Genome Project-Write.
    Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L. Science. 2016 Jul 8;353(6295):126-7. PMID: 27256881
     

    2. Taking Stock of Regulatory Variation.
    ​Maurano MT, Stamatoyannopoulos JA. Cell Syst. 2015 Jul 29;1(1):18-21. PMID: 27135686
     

    3. Erratum: Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo.
    ​Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer A, Kaul R, Stamatoyannopoulos JA. Nat Genet. 2016 Jan;48(1):101. PMID: 26711113
     

    4. Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo.
    ​Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer A, Kaul R, Stamatoyannopoulos JA. Nat Genet. 2015 Dec;47(12):1393-401. PMCID: PMC4666772

    5. Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture.
    ​Zheng HF, Forgetta V, Hsu YH, Estrada K, Rosello-Diez A, Leo PJ, Dahia CL, Park-Min KH, Tobias JH, Kooperberg C, Kleinman A, Styrkarsdottir U, Liu CT, Uggla C, Evans DS, Nielson CM, Walter K, Pettersson-Kymmer U, McCarthy S, Eriksson J, Kwan T, Jhamai M, Trajanoska K, Memari Y, Min J, Huang J, Danecek P, Wilmot B, Li R, Chou WC, Mokry LE, Moayyeri A, Claussnitzer M, Cheng CH, Cheung W, Medina-Gómez C, Ge B, Chen SH, Choi K, Oei L, Fraser J, Kraaij R, Hibbs MA, Gregson CL, Paquette D, Hofman A, Wibom C, Tranah GJ, Marshall M, Gardiner BB, Cremin K, Auer P, Hsu L, Ring S, Tung JY, Thorleifsson G, Enneman AW, van Schoor NM, de Groot LC, van der Velde N, Melin B, Kemp JP, Christiansen C, Sayers A, Zhou Y, Calderari S, van Rooij J, Carlson C, Peters U, Berlivet S, Dostie J, Uitterlinden AG, Williams SR, Farber C, Grinberg D, LaCroix AZ, Haessler J, Chasman DI, Giulianini F, Rose LM, Ridker PM, Eisman JA, Nguyen TV, Center JR, Nogues X, Garcia-Giralt N, Launer LL, Gudnason V, Mellström D, Vandenput L, Amin N, van Duijn CM, Karlsson MK, Ljunggren Ö, Svensson O, Hallmans G, Rousseau F, Giroux S, Bussière J, Arp PP, Koromani F, Prince RL, Lewis JR, Langdahl BL, Hermann AP, Jensen JE, Kaptoge S, Khaw KT, Reeve J, Formosa MM, Xuereb-Anastasi A, Åkesson K, McGuigan FE, Garg G, Olmos JM, Zarrabeitia MT, Riancho JA, Ralston SH, Alonso N, Jiang X, Goltzman D, Pastinen T, Grundberg E, Gauguier D, Orwoll ES, Karasik D, Davey-Smith G; AOGC Consortium, Smith AV, Siggeirsdottir K, Harris TB, Zillikens MC, van Meurs JB, Thorsteinsdottir U, Maurano MT, Timpson NJ, Soranzo N, Durbin R, Wilson SG, Ntzani EE, Brown MA, Stefansson K, Hinds DA, Spector T, Cupples LA, Ohlsson C, Greenwood CM; UK10K Consortium, Jackson RD, Rowe DW, Loomis CA, Evans DM, Ackert-Bicknell CL, Joyner AL, Duncan EL, Kiel DP, Rivadeneira F, Richards JB. Nature. 2015 Oct 1;526(7571):112-7. PMCID: PMC4755714

    6. Role of DNA Methylation in Modulating Transcription Factor Occupancy.
    ​Maurano MT, Wang H, John S, Shafer A, Canfield T, Lee K, Stamatoyannopoulos JA. Cell Rep. 2015 Aug 18;12(7):1184-95. PMID: 26257180
     

    7. Genomic discovery of potent chromatin insulators for human gene therapy.
    Liu M, Maurano MT, Wang H, Qi H, Song CZ, Navas PA, Emery DW, Stamatoyannopoulos JA, Stamatoyannopoulos G. Nat Biotechnol. 2015 Feb;33(2):198-203. PMID: 25580597
     

    8. Personal and population genomics of human regulatory variation.
    ​Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA, Akey JM. Genome Res. 2012 Sep;22(9):1689-97. PMCID: PMC3431486

    9. Widespread plasticity in CTCF occupancy linked to DNA methylation.
    Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, Thurman RE, Kaul R, Myers RM, Stamatoyannopoulos JA. Genome Res. 2012 Sep;22(9):1680-8. PMCID: PMC3431485

    10. Systematic localization of common disease-associated variation in regulatory DNA.
    ​Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA. Science. 2012 Sep 7;337(6099):1190-5. PMCID: PMC3771521

    11. An expansive human regulatory lexicon encoded in transcription factor footprints.
    ​Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA. Nature. 2012 Sep 6;489(7414):83-90. PMCID: PMC3736582

    12. The accessible chromatin landscape of the human genome.
    Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. Nature. 2012 Sep 6;489(7414):75-82. PMCID: PMC3721348

    13. BEDOPS: high-performance genomic feature operations.
    ​Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, Sandstrom R, Humbert R, Stamatoyannopoulos JA. Bioinformatics. 2012 Jul 15;28(14):1919-20. PMCID: PMC3389768

    14. Widespread site-dependent buffering of human regulatory polymorphism.
    ​Maurano MT, Wang H, Kutyavin T, Stamatoyannopoulos JA. PLoS Genet. 2012;8(3):e1002599. PMCID: PMC3310774


    Dr. Marcus Noyes - Assistant Professor - All Publications

    1. Multi-reporter selection for the design of active and more specific zinc-finger nucleases for genome editing.
    Oakes BL, Xia DF, Rowland EF, Xu DJ, Ankoudinova I, Borchardt JS, Zhang L, Li P, Miller JC, Rebar EJ, Noyes MB. Nat Commun. 2016 Jan 7;7:10194. PMCID: PMC4729830

    2. A systematic survey of the Cys2His2 zinc finger DNA-binding landscape.
    ​Persikov AV, Wetzel JL, Rowland EF, Oakes BL, Xu DJ, Singh M, Noyes MB. Nucleic Acids Res. 2015 Feb 18;43(3):1965-84. PMCID: PMC4330361

    3. Understanding DNA-binding specificity by bacteria hybrid selection.
    Xu DJ, Noyes MB. Brief Funct Genomics. 2015 Jan;14(1):3-16. PMID: 25539837
     

    4. Rapid synthesis and screening of chemically activated transcription factors with GFP-based reporters.
    ​McIsaac RS, Oakes BL, Botstein D, Noyes MB. J Vis Exp. 2013 Nov 26;(81):e51153. PMCID: PMC3992113

    5. Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.
    ​Persikov AV, Rowland EF, Oakes BL, Singh M, Noyes MB. Nucleic Acids Res. 2014 Feb;42(3):1497-508. PMCID: PMC3919609

    6. Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.
    ​McIsaac RS, Oakes BL, Wang X, Dummit KA, Botstein D, Noyes MB. Nucleic Acids Res. 2013 Feb 1;41(4):e57. PMCID: PMC3575806

    7. Characterization of the DNA-binding properties of the Mohawk homeobox transcription factor.
    Anderson DM, George R, Noyes MB, Rowton M, Liu W, Jiang R, Wolfe SA, Wilson-Rawls J, Rawls A. J Biol Chem. 2012 Oct 12;287(42):35351-9. PMCID: PMC3471766

    8. Recognition models to predict DNA-binding specificities of homeodomain proteins.
    Christensen RG, Enuameh MS, Noyes MB, Brodsky MH, Wolfe SA, Stormo GD. Bioinformatics. 2012 Jun 15;28(12):i84-9. PMCID: PMC3371834 
     

    9. Exploring the DNA-recognition potential of homeodomains.
    Chu SW, Noyes MB, Christensen RG, Pierce BG, Zhu LJ, Weng Z, Stormo GD, Wolfe SA. Genome Res. 2012 Oct;22(10):1889-98. PMCID: PMC3460184

    10. Analysis of specific protein-DNA interactions by bacterial one-hybrid assay.
    ​Noyes MB. Methods Mol Biol. 2012;786:79-95. PMID: 21938621
     

    11. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites.
    ​Noyes MB, Christensen RG, Wakabayashi A, Stormo GD, Brodsky MH, Wolfe SA. Cell. 2008 Jun 27;133(7):1277-89. PMCID: PMC2478728

    12. Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases.
    ​Meng X, Noyes MB, Zhu LJ, Lawson ND, Wolfe SA. Nat Biotechnol. 2008 Jun;26(6):695-701. PMCID: PMC2502069

    13. A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system.
    ​Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA. Nucleic Acids Res. 2008 May;36(8):2547-60. PMCID: PMC2377422