Research

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Recent Alt Lab Publications

2016

Long neural genes harbor recurrent DNA break clusters in neural stem/progenitor cells.
Wei P-C, Chang AN, Kao J, Du Z, Meyers RM, Alt FW, Schwer B. Cell (2016) Feb 11;164(4):644-55.
(PDF)

Sequential activation and distinct functions for distal and proximal modules within the IgH 3' regulatory region.
Garot A, Marquet M, Saintamand A, Bender S, Le Noir S, Rouaud P, Carrion C, Oruc Z, Bébin A-G, Moreau J, Lebrigand K, Denizot Y, Alt FW, Cogné M, Pinaud E. Proc Natl Acad Sci U S A. (2016) 113(6):1618-23. (PDF)

Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells. 
Schwer B, Wei P-C, Chang AN, Kao J, Du Z, Meyers RM, Alt FW. Proc. Natl. Acad. Sci. USA  (2016) 113(8):2258-63. (PDF)

Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing.
Hu J, Meyers RM, Dong J, Panchakshari RA, Alt FW, Frock RL. Nat Protoc. (2016) 11(5):853-71. (PDF)

NEHJ and other repair factors in V(D)J recombination.
Kumar V, Alt FW. In: Ratcliffe MJH. Editor in Chief, Encyclopedia of Immunobiology, Vol. 2, Oxford: Academic Press, pp. 107–14. (PDF)

An Ectopic CTCF Binding Element Inhibits Tcrd Rearrangement by Limiting Contact between Vδ and Dδ Gene Segments.
Chen L, Zhao L, Alt FW, Krangel MS.
J Immunol (2016), Volume: 197, Issue: 8, Pages: 3188-3197

Induction of HIV Neutralizing Antibody Lineages in Mice with Diverse Precursor Repertoires
Tian M, Cheng C, Chen X, Duan H, Cheng HL, Dao M, Sheng Z, Kimble M, Wang L, Lin S, Schmidt SD, Du Z, Joyce MG, Chen Y, DeKosky BJ, Chen Y, Normandin E, Cantor E, Chen RE, Doria-Rose NA, Zhang Y, Shi W, Kong WP, Choe M, Henry AR, Laboune F, Georgiev IS, Huang PY, Jain S, McGuire AT, Georgeson E, Menis S, Douek DC, Schief WR, Stamatatos L, Kwong PD, Shapiro L, Haynes BF, Mascola JR, Alt FW
Cell (2016), Volume: 166, Issue: 6, Pages: 1471-1484

PAXX and XLF DNA repair factors are functionally redundant in joining DNA breaks in a G1-arrested progenitor B-cell line.
Kumar V, Alt FW, Frock RL.
Proc Natl Acad Sci U S A (2016), Volume: 113, Issue: 38, Pages: 10619-24

Orientation-specific RAG activity in chromosomal loop domains contributes to Tcrd V(D)J recombination during T cell development.
Zhao L, Frock RL, Du Z, Hu J, Chen L, Krangel MS, Alt FW.
J Exp Med (2016), Volume: 213, Issue: 9, Pages: 1921-36

Highly sensitive and unbiased approach for elucidating antibody repertoires.
Lin SG, Ba Z, Du Z, Zhang Y, Hu J, Alt FW.
Proc Natl Acad Sci U S A (2016), Volume: 113, Issue: 28, Pages: 7846-51

Pillars Article: A Functional T3 Molecule Associated with a Novel Heterodimer on the Surface of Immature Human Thymocytes. Nature. 1986. 322: 179-181.
Bank I, DePinho RA, Brenner MB, Cassimeris J, Alt FW, Chess L.
J Immunol (2016), Volume: 196, Issue: 9, Pages: 3514-6



2015


The Mechanism of IgH Class Switch Recombination. 
Meng F-L, Alt FW and Tian M , In: Alt FW, Honjo T, Radbruch A, Reth M editors.  San Diego: Academic Press: Molecular Biology of B Cells, (2015), Pages 345-356  (PDF)

Frock R L, Hu J, Meyers RM, HoY-J, Kii E Alt, FW.  Nature Biotechnology, (2015), Volume: 33, Pages: 179-186 (PDF)

Lin S G, Guo C, Su A, Zhang Y,  Alt FW.  PNAS (2015), Volume: 112, Pages: 1815-1820 (PDF)

Jiang W, Lee BJ, Chen L, Dubois RL, Gostissa M, Alt FW, Zha S.  Blood (2015), Volume: 125, Pages: 2665-2668 (PDF)

Zhang B, Calado D P, Wang Z, Fröhler S, Köchert K, Qian Y, Koralov SB, Schmidt-Supprian M, Sasaki Y, Unitt C, Rodig S, Chen W, Dalla-Favera R, Alt FW, Pasqualucci L, Rajewsky K. Cell Reports, (2015), Volume: 11, Pages: 715-726 (PDF)

Ba Z, Meng F-L, Gostissa M, Huang P-Y, Ke Q, Wang Z, Dao MN, Fuiwara Y, Rajewsky K, Zhang B,  Alt  FW.  Cancer Immunol. Res.(2015), Volume: 3, Pages: 641-649 (PDF)

Hwang J, Alt FW, Yeap, L-S.  Microbiology Spectrum, (2015), Volume: 3 (PDF)

Dong J, Panchakshari RA, Zhang T, Zhang Y, Hu J, Volpi SA, Meyers RM, Ho Y-J, Du Z, Robbiani DF, Meng F, Gostissa M, Nussenzweig  M C, Manis J P, Alt FW.  Nature, (2015), Volume: 525, Pages: 134-139  (PDF)

Sequence-intrinsic mechanisms that target AID mutational outcomes on antibody genes 

Yeap LS, Hwang JK, Du Z, Meyers RM, Meng F-L, Jakubauskaite A, Liu M, Mani V, Neuberg D, Kepler TB, Wang JH, Alt FW.  Cell, (2015), Volume: 163 Pages: 1124-1137 (PDF)

Chromosomal loop domains direct the recombination of antigen receptor genes 
Hu J, Zhang Y, Zhao L, Frock R L, Du Z, Meyers RM, Meng F-L, Schatz DG, Alt FW.  Cell, (2015), Volume: 163, Pages: 947-959.  

Mechanisms of recurrent chromosomal translocations 
Frock RL, Hu J, Alt F W, In: Rowley, J.D., Le Beau  M M, Rabbitts T H editors.  Chromosomal Translocations and Genome Rearrangements in Cancer, (2015) Pages: 27-51  (PDF)


2014

A systematic analysis of recombination activity and genotype-phenotype correlation in human recombination-activating gene 1 deficiency.     
Lee YN, Frugoni F, Dobbs K, Walter JE, Giliani S, Gennery AR, Al-Herz W, Haddad E, LeDeist F, Bleesing JH, Henderson LA, Pai S-Y, Nelson RP, El-Ghoneimy DH, El-Feky RA, Reda SM, Hossny E, Soler-Palacin P, Fuleihan RL, Patel NC, Massaad MJ, Geha RS, Puck JM, Palma P, Cancrini C, Chen K, Vihinen M, Alt FW, Notarangelo LD   J. Allergy & Clinical Immunology (2014), Volume: 133,  Pages: 1099-1108 (PDF)

Precise and in situ genetic humanization of 6 Mb of mouse immunoglobulin genes.
Macdonald LE, Karow M, Stevens S, Auerbach W, Poueymirou WT, Yasenchak J, Frendewey D, Valenzuela DM, Giallourakis CC, Alt FW, Yancopoulos G D, Murphy AJ Proc. Natl. Acad. Sci. USA (2014), Volume 111, Pages: 5147-52  (PDF)

Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability.   
Meng F-L, Du Z, Federation A, Hu J, Wang Q, Kieffer-Kwon KR, Meyers RM, Amor C, Wasserman CR, Neuberg D, Casellas R, Nussenzweig MC, Bradner JE, Liu XS,  Alt FW  Cell (2014), Volume: 159, PagesL 1538-48 (PDF)

IgH class switching exploits a general property of two DNA breaks to be joined in cis over long chromosomal distances
Gostissa M, Schwer B, Chang A, Dong J, Meyers RM, Marecki GT, Choi VW, Chiarle R, Zarrin AA, Alt FW.
Proc Natl Acad Sci U S A. (2014), Volume: 111, Issue: 7, Pages: 2644-9 (PDF)

Kumar Vipul, Alt Frederick W, Oksenych Valentyn.
DNA Repair (2014), Volume: 16, Pages: 11-22 (PDF)

Hu J, Tepsuporn S, Meyers RM, Gostissa M, Alt FW.
PNAS (2014), Volume: 111, Issue: 28, Pages: 10269-74 (PDF)

Tepsuporn S, Hu J, Gostissa M, Alt FW

Cancer Immunol Res. (2014), Volume: 2, Issue: 9, Pages: 857-66 (PDF)


2013

Oksenych V, Kumar V, Liu X, Guo C, Schwer B, Zha S, Alt FW.
Proc Natl Acad Sci U S A. (2013), Volume: 110, Issue: 6, Pages: 2234-9 (PDF)

Alt FW, Zhang Y, Meng FL, Guo C, Schwer B
Cell (2013), Volume: 152, Issue: 3, Pages: 417-29 (PDF)

Gostissa M, Bianco JM, Malkin DJ, Kutok JL, Rodig SJ, Morse HC 3rd, Bassing CH, Alt FW
Proc Natl Acad Sci U S A. (2013), Volume: 110, Issue: 8, Pages: 2934-9 (PDF)

Wesemann DR, Portuguese AJ, Meyers RM, Gallagher MP, Cluff-Jones K, Magee JM, Panchakshari RA, Rodig SJ, Kepler TB, Alt FW
Nature (2013), Volume: 501, Issue: 7465, Pages: 112-5 (PDF)

Rass E, Chandramouly G, Zha S, Alt FW, Xie A
J Biol Chem (2013), Volume: 288, Issue: 10, Pages: 7086-95

Selimyan R, Gerstein RM, Ivanova I, Precht P, Subrahmanyam R, Perlot T, Alt FW, Sen R. 
PLoS Biol (2013), Volume: 11, Issue: 1, Pages: :e1001475

Shi W, Bain AL, Schwer B, Al-Ejeh F, Smith C, Wong L, Chai H, Miranda MS, Ho U, Kawaguchi M, Miura Y, Finnie JW, Wall M, Heierhorst J, Wicking C, Spring KJ, Alt FW, Khanna KK. 
PLoS Genet (2013), Volume: 9, Issue: 2, Pages: e1003298

Callen E, Di Virgilio M, Kruhlak MJ, Nieto-Soler M, Wong N, Chen HT, Faryabi RB, Polato F, Santos M, Starnes LM, Wesemann DR, Lee JE, Tubbs A, Sleckman BP, Daniel JA, Ge K, Alt FW, Fernandez-Capetillo O, Nussenzweig MC, Nussenzweig A
Cell (2013), Volume: 153, Issue: 6, Pages: 1266--80

Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire.
Medvedovic J, Ebert A, Tagoh H, Tamir IM, Schwickert TA, Novatchkova M, Sun Q, Huis In 't Veld PJ, Guo C, Yoon HS, Denizot Y, Holwerda SJ, de Laat W, Cogné M, Shi Y, Alt FW, Busslinger M
Immunity (2013), Volume: 39, Issue: 2, Pages: 229-44

Dougan SK, Ashour J, Karssemeijer RA, Popp MW, Avalos AM, Barisa M, Altenburg AF, Ingram JR, Cragnolini JJ, Guo C, Alt FW, Jaenisch R, Ploegh HL
Nature (2013), Volume: 503, Issue: 7476, Pages: 406-9

SIRT7 represses Myc activity to suppress ER stress and prevent fatty liver disease.
Shin J, He M, Liu Y, Paredes S, Villanova L, Brown K, Qiu X, Nabavi N, Mohrin M, Wojnoonski K, Li P, Cheng HL, Murphy AJ, Valenzuela DM, Luo H, Kapahi P, Krauss R, Mostoslavsky R, Yancopoulos GD, Alt FW, Chua KF, Chen D
Cell Rep (2013), Volume: 5, Issue: 3, Pages: 654-65
 
Lee YN, Frugoni F, Dobbs K, Walter JE, Giliani S, Gennery AR, Al-Herz W, Haddad E, Ledeist F, Bleesing JH, Henderson LA, Pai SY, Nelson RP, El-Ghoneimy DH, El-Feky RA, Reda SM, Hossny E, Soler-Palacin P, Fuleihan RL, Patel NC, Massaad MJ, Geha RS, Puck JM, Palma P, Cancrini C, Chen K, Vihinen M, Alt FW, Notarangelo LD
J Allergy Clin Immunol (2013), Volume: S0091-6749, Issue: 13, Pages: 01558-3

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