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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9303280/

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.
https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC8521761/

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7648276/

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7292649/
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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7160937/

6) Cis- and trans-chromosomal interactions define pericentric boundaries in the absence of conventional heterochromatin.
Sreekumar L, Jaitly P, Chen Y, Thimmappa BC, Sanyal A, Sanyal K.
Genetics. 2019 Aug;212(4):1121-1132. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6707466/

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5377358/

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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215031/

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032024/

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712340

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874844/

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3555147/

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3721348/

14) An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium et.al. (Sanyal A was a member of the consortium)
Nature. 2012 Sep 6;489(7414):57-74. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439153/

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491367/

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). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079585/

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109114/

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670758/

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056208/

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. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859197/

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.