MGH Center for Systems Biology

Bernstein B, Meissner A, Lander E

The mammalian epigenome.

Cell. 2007;128(4):669-81 - PMID: 17320505 - DOI: 10.1016/j.cell.2007.01.033

Bernstein B, Mikkelsen T, Xie X, Kamal M, Huebert D, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber S, Lander E

A bivalent chromatin structure marks key developmental genes in embryonic stem cells.

Cell. 2006;125(2):315-26 - PMID: 16630819 - DOI: 10.1016/j.cell.2006.02.041

Bernstein B, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey D, Huebert D, McMahon S, Karlsson E, Kulbokas E, Gingeras T, Schreiber S, Lander E

Genomic maps and comparative analysis of histone modifications in human and mouse.

Cell. 2005;120(2):169-81 - PMID: 15680324 - DOI: 10.1016/j.cell.2005.01.001

Schreiber S, Bernstein B

Signaling network model of chromatin.

Cell. 2002;111(6):771-8 - PMID: 12526804 - DOI: 10.1016/s0092-8674(02)01196-0

Zhong L, D'Urso A, Toiber D, Sebastian C, Henry RE, Vadysirisack DD, Guimaraes A, Marinelli B, Wikstrom JD, Nir T, Clish CB, Vaitheesvaran B, Iliopoulos O, Kurland I, Dor Y, Weissleder R, Shirihai OS, Ellisen LW, Espinosa JM, Mostoslavsky R

The Histone Deacetylase Sirt6 Regulates Glucose Homeostasis via Hif1alpha.

Cell. 2010;140(2):280-293 - PMID: 20141841 - PMCID: PMC2821045 - DOI: 10.1016/j.cell.2009.12.041

Jiang H, Shukla A, Wang X, Chen WY, Bernstein BE, Roeder RG

Role for Dpy-30 in ES Cell-Fate Specification by Regulation of H3K4 Methylation within Bivalent Domains.

Cell. 2011;144(4):513-25 - PMID: 21335234 - PMCID: PMC3572774 - DOI: 10.1016/j.cell.2011.01.020

Walhout AJM, Aebersold R, Meyer T, Bork P, Kirschner MW

Systems Biology: What's the Next Challenge?

Cell. 2011;144:6

Pittet MJ, Weissleder R

Intravital imaging.

Cell. 2011;147(5):983-91 - PMID: 22118457 - PMCID: PMC3824153 - DOI: 10.1016/j.cell.2011.11.004

Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, Bernstein BE

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells.

Cell. 2011;147(7):1628-39 - PMID: 22196736 - PMCID: PMC3312319 - DOI: 10.1016/j.cell.2011.09.057

Ying H, Kimmelman AC, Lyssiotis CA, Hua S, Chu GC, Fletcher-Sananikone E, Locasale JW, Son J, Zhang H, Coloff JL, Yan H, Wang W, Chen S, Viale A, Zheng H, Paik JH, Lim C, Guimaraes AR, Martin ES, Chang J, Hezel AF, Perry SR, Hu J, Gan B, Xiao Y, Asara JM, Weissleder R, Wang YA, Chin L, Cantley LC, Depinho RA

Oncogenic Kras Maintains Pancreatic Tumors through Regulation of Anabolic Glucose Metabolism.

Cell. 2012;149(3):656-70 - PMID: 22541435 - PMCID: PMC3472002 - DOI: 10.1016/j.cell.2012.01.058

Zullo JM, Demarco IA, Piqué-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, Singh H

DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina.

Cell. 2012;149(7):1474-87 - PMID: 22726435 - DOI: 10.1016/j.cell.2012.04.035

Sebastián C, Zwaans BM, Silberman DM, Gymrek M, Goren A, Zhong L, Ram O, Truelove J, Guimaraes AR, Toiber D, Cosentino C, Greenson JK, Macdonald AI, McGlynn L, Maxwell F, Edwards J, Giacosa S, Guccione E, Weissleder R, Bernstein BE, Regev A, Shiels PG, Lombard DB, Mostoslavsky R

The Histone Deacetylase SIRT6 Is a Tumor Suppressor that Controls Cancer Metabolism.

Cell. 2012;151(6):1185-99 - PMID: 23217706 - PMCID: PMC3526953 - DOI: 10.1016/j.cell.2012.10.047

Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, Durham T, Miri M, Deshpande V, De Jager PL, Bennett DA, Houmard JA, Muoio DM, Onder TT, Camahort R, Cowan CA, Meissner A, Epstein CB, Shoresh N, Bernstein BE

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues.

Cell. 2013;152(3):642-54 - PMID: 23333102 - PMCID: PMC3563935 - DOI: 10.1016/j.cell.2012.12.033

Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells.

Cell. 2013;153(5):1149-1163 - PMID: 23664763 - PMCID: PMC3709577 - DOI: 10.1016/j.cell.2013.04.037

Suvà ML, Rheinbay E, Gillespie SM, Patel AP, Wakimoto H, Rabkin SD, Riggi N, Chi AS, Cahill DP, Nahed BV, Curry WT, Martuza RL, Rivera MN, Rossetti N, Kasif S, Beik S, Kadri S, Tirosh I, Wortman I, Shalek AK, Rozenblatt-Rosen O, Regev A, Louis DN, Bernstein BE

Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells.

Cell. 2014;157(3):580-94 - PMID: 24726434 - PMCID: PMC4004670 - DOI: 10.1016/j.cell.2014.02.030

Aceto N, Bardia A, Miyamoto DT, Donaldson MC, Wittner BS, Spencer JA, Yu M, Pely A, Engstrom A, Zhu H, Brannigan BW, Kapur R, Stott SL, Shioda T, Ramaswamy S, Ting DT, Lin CP, Toner M, Haber DA, Maheswaran S

Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis.

Cell. 2014;158(5):1110-22 - PMID: 25171411 - PMCID: PMC4149753 - DOI: 10.1016/j.cell.2014.07.013

Deindl S, Hwang WL, Hota SK, Blosser TR, Prasad P, Bartholomew B, Zhuang X

ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps.

Cell. 2013;152(3):442-52 - PMID: 23374341 - PMCID: PMC3647478 - DOI: 10.1016/j.cell.2012.12.040

Weissleder R

Scaling down imaging: molecular mapping of cancer in mice

Nat Rev Cancer. 2002;2:1-8 - PMID: 11902581 - DOI: 10.1038/nrc701

Weissleder R.

Molecular Imaging in Cancer

Science. 2006;312:1168-1171 - PMID: 16728630 - DOI: 10.1126/science.1125949

Shaw S, Wang J

Knotting of a DNA chain during ring closure.

Science. 1993;260(5107):533-6 - PMID: 8475384 - DOI: 10.1126/science.8475384

Sundrud MS, Koralov SB, Feuerer M, Calado DP, Kozhaya AE, Rhule-Smith A, Lefebvre RE, Unutmaz D, Mazitschek R, Waldner H, Whitman M, Keller T, Rao A

Halofuginone Inhibits TH17 Cell Differentiation by Activating the Amino Acid Starvation Response.

Science. 2009;324(5932):1334-1338 - PMID: 19498172 - PMCID: PMC2803727 - DOI: 10.1126/science.1172638

Swirski* FK, Nahrendorf* M, Etzrodt M, Wildgruber M, Cortez-Retamozo V, Panizzi P, Figueiredo JL, Kohler RH, Chudnovskiy A, Waterman P, Aikawa E, Mempel TR, Libby P, Weissleder R, Pittet MJ

Identification of Splenic Reservoir Monocytes and Their Deployment to Inflammatory Sites

Science. 2009;325 (5940):612-6 - PMID: 19644120 - PMCID: PMC2803111 - DOI: 10.1126/science.1175202

Chi A, Bernstein B

Developmental biology. Pluripotent chromatin state.

Science. 2009;323(5911):220-1 - PMID: 19131621 - PMCID: PMC4126799 - DOI: 10.1126/science.1166261

Huang D, Swanson E, Lin C, Schuman J, Stinson W, Chang W, Hee M, Flotte T, Gregory K, Puliafito C

Optical coherence tomography.

Science. 1991;254:1178-81 - PMID: 1957169 - PMCID: PMC4638169 - DOI: 10.1126/science.1957169

Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses.

Science. 2009;326(5950):257-63 - PMID: 19729616 - PMCID: PMC2879337 - DOI: 10.1126/science.1179050

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Science. 2009;326(5950):289-93 - PMID: 19815776 - PMCID: PMC2858594 - DOI: 10.1126/science.1181369

Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D

The structure of haplotype blocks in the human genome.

Science. 2002;296(5576):2225-9 - PMID: 12029063 - DOI: 10.1126/science.1069424

Rauch PJ*, Chudnovskiy A*, Robbins CS*, Weber GF, Etzrodt M, Hilgendorf I, Tiglao E, Figueiredo JL, Iwamoto Y, Theurl I, Gorbatov R, Waring MT, Chicoine AT, Mouded M, Pittet MJ, Nahrendorf M, Weissleder R, Swirski FK

Innate Response Activator B Cells Protect Against Microbial Sepsis

Science. 2012;335(6068):597-601 - PMID: 22245738 - PMCID: PMC3279743 - DOI: 10.1126/science.1215173

Ryan RJ, Bernstein BE

Molecular biology. Genetic events that shape the cancer epigenome.

Science. 2012;336(6088):1513-4 - PMID: 22723401 - DOI: 10.1126/science.1223730

Swirski FK, Nahrendorf M

Leukocyte behavior in atherosclerosis, myocardial infarction, and heart failure.

Science. 2013;339(6116):161-6 - PMID: 23307733 - PMCID: PMC3891792 - DOI: 10.1126/science.1230719

Suvà ML, Riggi N, Bernstein BE

Epigenetic reprogramming in cancer.

Science. 2013;339(6127):1567-70 - PMID: 23539597 - PMCID: PMC3821556 - DOI: 10.1126/science.1230184

Viaud S, Saccheri F, Mignot G, Yamazaki T, Daillère R, Hannani D, Enot DP, Pfirschke C, Engblom C, Pittet MJ, Schlitzer A, Ginhoux F, Apetoh L, Chachaty E, Woerther PL, Eberl G, Bérard M, Ecobichon C, Clermont D, Bizet C, Gaboriau-Routhiau V, Cerf-Bensussan N, Opolon P, Yessaad N, Vivier E, Ryffel B, Elson CO, Doré J, Kroemer G, Lepage P, Boneca IG, Ghiringhelli F, Zitvogel L

The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide.

Science. 2013;342(6161):971-6 - PMID: 24264990 - PMCID: PMC4048947 - DOI: 10.1126/science.1240537

Katsimpardi L, Litterman NK, Schein PA, Miller CM, Loffredo FS, Wojtkiewicz GR, Chen JW, Lee RT, Wagers AJ, Rubin LL

Vascular and Neurogenic Rejuvenation of the Aging Mouse Brain by Young Systemic Factors.

Science. 2014;344(6184):630-4 - PMID: 24797482 - PMCID: PMC4123747 - DOI: 10.1126/science.1251141

Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, Cahill DP, Nahed BV, Curry WT, Martuza RL, Louis DN, Rozenblatt-Rosen O, Suvà ML, Regev A, Bernstein BE

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.

Science. 2014;344(6190):1396-401 - PMID: 24925914 - PMCID: PMC4123637 - DOI: 10.1126/science.1254257

Perez JM, Josephson L, O'Loughlin T, Hogemann D, Weissleder R

Magnetic relaxation switches capable of sensing molecular interactions

Nat Biotechnol. 2002;20:816-20 - PMID: 12134166 - DOI: 10.1038/nbt720

Weissleder R

A clearer vision for in vivo imaging

Nat Biotechnol. 2001;19:316-7 - PMID: 11283581 - DOI: 10.1038/86684

Lewin M, Carlesso N, Tung CH, Tang XW, Cory D, Scadden DT, Weissleder R

Tat peptide-derivatized magnetic nanoparticles allow in vivo tracking and recovery of progenitor cells

Nat Biotechnol. 2000;18:410-4 - PMID: 10748521 - DOI: 10.1038/74464

Weissleder R, Tung CH, Mahmood U, Bogdanov A Jr

In vivo imaging of tumors with protease-activated near-infrared fluorescent probes

Nat Biotechnol. 1999;17:375-8 - PMID: 10207887 - DOI: 10.1038/7933

Ntziachristos V, Ripoll J, Wang L, Weissleder R

Looking and Listening to light: the evolution of whole-body photonic imaging

Nat Biotechnol. 2005;23:313-320 - PMID: 15765087 - DOI: 10.1038/nbt1074

Weissleder R, Kelly K, Sun E, Shtatland T, Josephson L.

Cell-specific targeting of nanoparticles by multivalent attachment of small molecules

Nat Biotechnol. 2005;23:1418-1423 - PMID: 16244656 - DOI: 10.1038/nbt1159

Peterson R, Shaw S, Peterson T, Milan D, Zhong T, Schreiber S, MacRae C, Fishman M

Chemical suppression of a genetic mutation in a zebrafish model of aortic coarctation.

Nat Biotechnol. 2004;22(5):595-9 - PMID: 15097998 - DOI: 10.1038/nbt963

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Nat Biotechnol. 2010;28(10):1097-105 - PMID: 20852635 - PMCID: PMC2955169 - DOI: 10.1038/nbt.1682

Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA

The NIH Roadmap Epigenomics Mapping Consortium.

Nat Biotechnol. 2010;28(10):1045-8 - PMID: 20944595 - PMCID: PMC3607281 - DOI: 10.1038/nbt1010-1045

Leuschner F, Dutta P, Gorbatov R, Novobrantseva TI, Donahoe JS, Courties G, Lee KM, Kim JI, Markmann JF, Marinelli B, Panizzi P, Lee WW, Iwamoto Y, Milstein S, Epstein-Barash H, Cantley W, Wong J, Cortez-Retamozo V, Newton A, Love K, Libby P, Pittet MJ, Swirski FK, Koteliansky V, Langer R, Weissleder R, Anderson DG, Nahrendorf M

Therapeutic siRNA silencing in inflammatory monocytes in mice

Nat Biotechnol. 2011;29(11):1005-10 - PMID: 21983520 - PMCID: PMC3212614 - DOI: 10.1038/nbt.1989

Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE

Locus-specific editing of histone modifications at endogenous enhancers.

Nat Biotechnol. 2013;31(12):1133-6 - PMID: 24013198 - PMCID: PMC3858395 - DOI: 10.1038/nbt.2701

Zangi L, Lui KO, von Gise A, Ma Q, Ebina W, Ptaszek LM, Später D, Xu H, Tabebordbar M, Gorbatov R, Sena B, Nahrendorf M, Briscoe DM, Li RA, Wagers AJ, Rossi DJ, Pu WT, Chien KR

Modified mRNA directs the fate of heart progenitor cells and induces vascular regeneration after myocardial infarction.

Nat Biotechnol. 2013;31(10):898-907 - PMID: 24013197 - PMCID: PMC4058317 - DOI: 10.1038/nbt.2682

Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello JF, Wilkinson MF, Joung JK

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins.

Nat Biotechnol. 2013;31(12):1137-42 - PMID: 24108092 - PMCID: PMC3858462 - DOI: 10.1038/nbt.2726

Im H*, Shao H*, Park YI, Peterson VM, Castro CM, Weissleder R*, Lee H*

Label-free detection and molecular profiling of exosomes with a nano-plasmonic sensor

Nat Biotechnol. 2014;32(5):490-5 - PMID: 24752081 - PMCID: PMC4356947 - DOI: 10.1038/nbt.2886

Tannous B*, Grimm J*, Perry K, Chen J, Weissleder R, Breakefield X.

Metabolic Biotinylation of Cell Surface Receptors for in vivo Imaging

Nat Methods. 2006;3(5):391-396 - PMID: 16628210 - DOI: 10.1038/nmeth875

Vinegoni C, Pitsouli C, Razansky D, Perrimon N, Ntziachristos V

In vivo imaging of Drosophila melanogaster pupae with mesoscopic fluorescence tomography.

Nat Methods. 2007;5(1):45-7 - PMID: 18066071 - DOI: 10.1038/nmeth1149