Publications

Mar 1, 2019 J Clin Invest

Reduced expression of phosphatase PTPN2 promotes pathogenic conversion of Tregs in autoimmunity

Svensson MN, Doody KM, Schmiedel BJ, Bhattacharyya S, Panwar B, Wiede F, Yang S, Santelli E, Wu DJ, Sacchetti C, Gujar R, Seumois G, Kiosses WB, Aubry I, Kim G, Mydel P, Sakaguchi S, Kronenberg M, Tiganis T, Tremblay ML, Ay F, Vijayanand P, Bottini N

Feb 19, 2019 Proc Natl Acad Sci U S A

Comparative 3D genome organization in apicomplexan parasites

Bunnik EM, Venkat A, Shao J, McGovern KE, Batugedara G, Worth D, Prudhomme J, Lapp SA, Andolina C, Ross LS, Lawres L, Brady D, Sinnis P, Nosten F, Fidock DA, Wilson EH, Tewari R, Galinski MR, Ben Mamoun C, Ay F, Le Roch KG

Feb 7, 2019 Cell

Identifying cis elements for spatiotemporal control of mammalian DNA replication

Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM

Jan 31, 2019 Elife

Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies

Zheng Y, Ay F, Keles S

Nov 20, 2018 Sci Data

Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming

Du Z, Jia L, Wang Y, Wang C, Wen X, Chen J, Zhu Y, Yu D, Zhou L, Chen N, Zhang S, Celik I, Ay F, Gao S, Zhang S, Li W, Hoffman AR, Cui J, Hu JF

Oct 1, 2018 Nat Genet

Integrative detection and analysis of structural variation in cancer genomes

Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F

Sep 20, 2018 Mol Cell

The Evf2 ultraconserved enhancer lncRNA functionally and spatially organizes megabase distant genes in the developing forebrain

Cajigas I, Chakraborty A, Swyter KR, Luo H, Bastidas M, Nigro M, Morris ER, Chen S, VanGompel MJW, Leib D, Kohtz SJ, Martina M, Koh S, Ay F, Kohtz JD

May 15, 2018 Nat Commun

Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages

Bunnik EM, Cook KB, Varoquaux N, Batugedara G, Prudhomme J, Cort A, Shi L, Andolina C, Ross LS, Brady D, Fidock DA, Nosten F, Tewari R, Sinnis P, Ay F, Vert JP, Noble WS, Le Roch KG

Jan 1, 2018 Parasitology

Plasmodium knowlesi: a superb in vivo nonhuman primate model of antigenic variation in malaria

Galinski MR, Lapp SA, Peterson MS, Ay F, Joyner CJ, LE Roch KG, Fonseca LL, Voit EO; MAHPIC CONSORTIUM

Jan 1, 2018 Parasitology

PacBio assembly of a plasmodium knowlesi genome sequence with Hi-C correction and manual annotation of the SICAvar gene family

Lapp SA, Geraldo JA, Chien JT, Ay F, Pakala SB, Batugedara G, Humphrey J; MaHPIC consortium, DeBARRY JD, Le Roch KG, Galinski MR, Kissinger JCLapp SA, Geraldo JA, Chien JT, Ay F, Pakala SB, Batugedara G, Humphrey J; MaHPIC consortium, DeBARRY JD, Le Roch KG, Galinski MR, Kissinger JC

Oct 18, 2017 Bioinformatics

Identification of copy number variations and translocations in cancer cells from Hi-C data

Chakraborty A, Ay F

Apr 11, 2017 Proc Natl Acad Sci USA

Form and function of topologically associating genomic domains in budding yeast

Eser U, Chandler-Brown D, Ay F, Straight AF, Duan Z, Noble WS, Skotheim JM