1) SETDB1 acts as a topological accessory to Cohesin via an
H3K9me3-independent, genomic shunt for regulating cell fates. Warrier T, Farran CE, Zeng Y, Ho BSQ, Bao Q, Zheng ZH, Bi X, Ng HH, Ong
DST, Chu JJH, Sanyal A, Fullwood MJ, Collins JJ, Li H, Xu J, Loh Y-H. Nucleic Acids Res. 2022 Jul
22;50(13):7326-7349.
2) Analysis of aneuploidy spectrum from whole-genome sequencing
provides rapid assessment of clonal variation within established cancer cell
lines. Khalil
AIS, Chattopadhyay A*, Sanyal A*. (*corresponding
author). Cancer
Inform. 2021; 20: 11769351211049236.
3)
Identification and utilization of copy number information for correcting Hi-C
contact map of cancer cell lines. Khalil
AIS, Muzaki SRBM, Chattopadhyay A*, Sanyal
A*. (*corresponding author). BMC
Bioinformatics. 2020 Nov 7;21(1):506.
4) Spatial
inter-centromeric interactions facilitated the emergence of evolutionary new
centromeres. Guin K,
Chen Y, Mishra R, Muzaki SRBM, Thimmappa BC, O'Brien CE, Butler G, Sanyal A*, Sanyal K*. (*corresponding author). Elife. 2020
May 29;9:e58556. Faculty Opinions
Recommendation https://facultyopinions.com/prime/738043801
5)
Hierarchical discovery of large-scale and focal copy number alterations in
low-coverage cancer genomes. Khalil AIS, Khyriem C, Chattopadhyay A*, Sanyal A*. (*corresponding
author). BMC Bioinformatics.
2020 Apr 16;21(1):147. - and Sreekumar L, Jaitly P, Chen Y, Thimmappa BC,
6)Cistrans-chromosomal interactions define pericentric
boundaries in the absence of conventional heterochromatin.Sanyal A, Sanyal K. Genetics. 2019 Aug;212(4):1121-1132.
7)
High-resolution RNA allelotyping along the inactive X chromosome: evidence of
RNA polymerase III in regulating chromatin configuration. Hong R,
Lin B, Lu X, Lai LT, Chen X, Sanyal A, Ng HH, Zhang K, Zhang LF. Sci
Rep. 2017 Apr 3;7:45460.
8) Genetics and Genomics of
Longitudinal Lung Function Patterns in Individuals with Asthma. McGeachie MJ, Yates KP,
Zhou X, Guo F, Sternberg AL, Van Natta ML, Wise RA, Szefler SJ, Sharma S, Kho
AT, Cho MH, Croteau-Chonka DC, Castaldi PJ, Jain G, Sanyal A, Zhan Y, Lajoie
BR, Dekker J, Stamatoyannopoulos J, Covar RA, Zeiger RS, Adkinson NF, Williams
PV, Kelly HW, Grasemann H, Vonk JM, Koppelman GH, Postma DS, Raby BA, Houston
I, Lu Q, Fuhlbrigge AL, Tantisira KG, Silverman EK, Tonascia J, Strunk RC,
Weiss ST; CAMP Research Group. Am J Respir Crit Care Med. 2016 Dec 15;194(12):1465-1474.
9) Patterns of Growth
and Decline in Lung Function in Persistent Childhood Asthma. McGeachie MJ, Yates KP, Zhou
X, Guo F, Sternberg AL, Van Natta ML, Wise RA, Szefler SJ, Sharma S, Kho AT,
Cho MH, Croteau-Chonka DC, Castaldi PJ, Jain G, Sanyal A, Zhan Y, Lajoie
BR, Dekker J, Stamatoyannopoulos J, Covar RA, Zeiger RS, Adkinson NF, Williams
PV, Kelly HW, Grasemann H, Vonk JM, Koppelman GH, Postma DS, Raby BA, Houston
I, Lu Q, Fuhlbrigge AL, Tantisira KG, Silverman EK, Tonascia J, Weiss ST,
Strunk RC; CAMP Research Group. N Engl J Med.
2016 May 12;374(19):1842-52.
10) Architectural protein
subclasses shape 3-D organization of genomes during lineage commitment. Phillips-Cremins JE, Sauria
MEG, Sanyal A, Gerasimova TI,
Lajoie BR, Bell JSK, Ong C-T, Hookway TA, Guo C, Sun Y, Bland MJ,
Wagstaff W, Dalton S, McDevitt TC, Sen R, Dekker J, Taylor J, Corces VG. Cell. 2013 Jun 6;153(6):1281-95.
11) From cells to
chromatin: Capturing snapshots of genome organization with 5C technology. Ferraiuolo MA, Sanyal A, Naumova N, Dekker J, Dostie
J. Methods. 2012 Nov;58(3):255-67.
12) The long-range
interaction landscape of gene promoters. Sanyal A1,
Lajoie BR1, Jain G, Dekker J. (1equal contributions). Nature. 2012 Sep 6;489(7414):109-13.
13) 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.
14) An integrated
encyclopedia of DNA elements in the human genome. ENCODE Project Consortium
et.al. (author list removed due to page limit). Nature. 2012 Sep 6;489(7414):57-74.
15) An encyclopedia of
mouse DNA elements (Mouse ENCODE). Mouse ENCODE Consortium,
Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM,
Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M,
Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman
RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold
BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T,
Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas
O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA,
Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A,
Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S,
Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba
T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent
WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. Genome Biol. 2012 Aug 13;13(8):418.
16) A user's guide to the
encyclopedia of DNA elements (ENCODE). ENCODE Project Consortium, Myers
RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE,
Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE, Bernstein BE, Epstein CB,
Shoresh N, Ernst J, Mikkelsen TS, Kheradpour P, Zhang X, Wang L, Issner R,
Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Lin MF, Kellis M,
Gingeras TR, Davis CA, Kapranov P, Dobin A, Zaleski C, Schlesinger F, Batut P,
Chakrabortty S, Jha S, Lin W, Drenkow J, Wang H, Bell K, Gao H, Bell I, Dumais
E, Dumais J, Antonarakis SE, Ucla C, Borel C, Guigo R, Djebali S, Lagarde J,
Kingswood C, Ribeca P, Sammeth M, Alioto T, Merkel A, Tilgner H, Carninci P,
Hayashizaki Y, Lassmann T, Takahashi H, Abdelhamid RF, Hannon G, Fejes-Toth K,
Preall J, Gordon A, Sotirova V, Reymond A, Howald C, Graison E, Chrast J, Ruan
Y, Ruan X, Shahab A, Ting Poh W, Wei CL, Crawford GE, Furey TS, Boyle AP,
Sheffield NC, Song L, Shibata Y, Vales T, Winter D, Zhang Z, London D, Wang T,
Birney E, Keefe D, Iyer VR, Lee BK, McDaniell RM, Liu Z, Battenhouse A, Bhinge
AA, Lieb JD, Grasfeder LL, Showers KA, Giresi PG, Kim SK, Shestak C, Myers RM,
Pauli F, Reddy TE, Gertz J, Partridge EC, Jain P, Sprouse RO, Bansal A, Pusey
B, Muratet MA, Varley KE, Bowling KM, Newberry KM, Nesmith AS, Dilocker JA,
Parker SL, Waite LL, Thibeault K, Roberts K, Absher DM, Wold B, Mortazavi A,
Williams B, Marinov G, Trout D, Pepke S, King B, McCue K, Kirilusha A, DeSalvo
G, Fisher-Aylor K, Amrhein H, Vielmetter J, Sherlock G, Sidow A, Batzoglou S,
Rauch R, Kundaje A, Libbrecht M, Margulies EH, Parker SC, Elnitski L, Green ED,
Hubbard T, Harrow J, Searle S, Kokocinski F, Aken B, Frankish A, Hunt T,
Despacio-Reyes G, Kay M, Mukherjee G, Bignell A, Saunders G, Boychenko V, Van
Baren M, Brown RH, Khurana E, Balasubramanian S, Zhang Z, Lam H, Cayting P,
Robilotto R, Lu Z, Guigo R, Derrien T, Tanzer A, Knowles DG, Mariotti M, James
Kent W, Haussler D, Harte R, Diekhans M, Kellis M, Lin M, Kheradpour P, Ernst
J, Reymond A, Howald C, Graison EA, Chrast J, Tress M, Rodriguez JM, Snyder M,
Landt SG, Raha D, Shi M, Euskirchen G, Grubert F, Kasowski M, Lian J, Cayting
P, Lacroute P, Xu Y, Monahan H, Patacsil D, Slifer T, Yang X, Charos A, Reed B,
Wu L, Auerbach RK, Habegger L, Hariharan M, Rozowsky J, Abyzov A, Weissman SM,
Gerstein M, Struhl K, Lamarre-Vincent N, Lindahl-Allen M, Miotto B, Moqtaderi
Z, Fleming JD, Newburger P, Farnham PJ, Frietze S, O'Geen H, Xu X, Blahnik KR,
Cao AR, Iyengar S, Stamatoyannopoulos JA, Kaul R, Thurman RE, Wang H, Navas PA,
Sandstrom R, Sabo PJ, Weaver M, Canfield T, Lee K, Neph S, Roach V, Reynolds A,
Johnson A, Rynes E, Giste E, Vong S, Neri J, Frum T, Johnson EM, Nguyen ED,
Ebersol AK, Sanchez ME, Sheffer HH, Lotakis D, Haugen E, Humbert R, Kutyavin T,
Shafer T, Dekker J, Lajoie BR, Sanyal A,
James Kent W, Rosenbloom KR, Dreszer TR, Raney BJ, Barber GP, Meyer LR, Sloan
CA, Malladi VS, Cline MS, Learned K, Swing VK, Zweig AS, Rhead B, Fujita PA,
Roskin K, Karolchik D, Kuhn RM, Haussler D, Birney E, Dunham I, Wilder SP,
Keefe D, Sobral D, Herrero J, Beal K, Lukk M, Brazma A, Vaquerizas JM, Luscombe
NM, Bickel PJ, Boley N, Brown JB, Li Q, Huang H, Gerstein M, Habegger L, Sboner
A, Rozowsky J, Auerbach RK, Yip KY, Cheng C, Yan KK, Bhardwaj N, Wang J,
Lochovsky L, Jee J, Gibson T, Leng J, Du J, Hardison RC, Harris RS, Song G,
Miller W, Haussler D, Roskin K, Suh B, Wang T, Paten B, Noble WS, Hoffman MM,
Buske OJ, Weng Z, Dong X, Wang J, Xi H, Tenenbaum SA, Doyle F, Penalva LO,
Chittur S, Tullius TD, Parker SC, White KP, Karmakar S, Victorsen A, Jameel N,
Bild N, Grossman RL, Snyder M, Landt SG, Yang X, Patacsil D, Slifer T, Dekker
J, Lajoie BR, Sanyal A, Weng Z, Whitfield TW, Wang J, Collins PJ, Trinklein
ND, Partridge EC, Myers RM, Giddings MC, Chen X, Khatun J, Maier C, Yu Y,
Gunawardena H, Risk B, Feingold EA, Lowdon RF, Dillon LA, Good PJ, Harrow J,
Searle S. PLoS Biol. 2011 Apr;9(4):e1001046 (1-21).
17) Chromatin globules: a
common motif of higher order chromosome structure? Sanyal A,
Baù D, Martí-Renom MA, Dekker J. Curr Opin Cell Biol. 2011 Jun;23(3):325-31.
18) A long noncoding RNA
maintains active chromatin to coordinate homeotic gene expression. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen
Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M,
Dekker J, Helms JA, Chang HY. Nature. 2011 Apr 7;472(7341):120-4.
19) The three-dimensional
folding of the α-globin gene domain reveals formation of chromatin globules. Baù D1, Sanyal A1, Lajoie BR1,
Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA. (1equal contributions). Nat Struct Mol Biol. 2011 Jan;18(1):107-14. 20) My5C: web tools for
chromosome conformation capture studies. Lajoie BR, van Berkum NL, Sanyal A, Dekker J. Nat Methods. 2009 Oct;6(10):690-1.
21) Insights into male germ
cell apoptosis due to depletion of gonadotropins caused by GnRH antagonists. Pareek TK, Joshi AR, Sanyal A, Dighe RR. Apoptosis. 2007 Jun;12(6):1085-100.
INNOVATION
Open-source bioinformatics tools (software) developed
1) CNAtra
3) AStra