Publications – The Singh Laboratory

Link to Dr. Singh’s Google Scholar Page

Featured Publications

17. Widespread intronic polyadenylation diversifies immune cell transcriptomes
Singh I, Lee S, Sperling A, Samur MK, Tai Y, Fulciniti M, Munshi N, Mayr C, Leslie C
Nature Communications 9: 1716 (2018)

16. Widespread intronic polyadenylation inactivates tumor suppressor genes in leukemia
[Lee S*, Singh I*], Lee S, Tisdale S, Abdel-Wahab O, Leslie C, Mayr C [*Co-first authors]
Nature 561, 127–131 (2018)

15. Chromatin landscapes reveal developmentally encoded transcriptional states that define glioblastoma
[Mack SC*,Singh I*, Wang X*], Hirsch R, Wu Q, Bernatchez JA, Zhu Z, Gimple RC, Kim LJY, Morton A, Lai S, Qiu Z, Villagomez R, Prager BC, Bertrand KC, Mah C, Zhou W, Lee C, Barnett GH, Vogelbaum MA, Sloan AE, Chavez L, Bao S, Scacheri PC, Siqueira-Neto JL, Lin CY, Rich JN [*Co-first authors]
Journal of Experimental Medicine, 216 (5), 1071 (2019)

14. Learning the recognition code for transcription factor and RNA-binding protein families from high-throughput binding assays
Pelossof R, Singh I, Yang J, Weirauch M, Hughes T, Leslie C
Nature Biotechnology 33, 1242–1249(2015)

13. Global profiling of stimulus-induced polyadenylation in cells using a poly (A) trap
Curanovic D, Cohen M, Singh I, Slagle CE, Leslie CS, Jaffrey SR
Nature Chemical Biology 9, 671–673(2013)

Other Publications

12. Dissociation of nanosilicates induces downstream endochondral differentiation gene expression program.
Brokesh AM, Cross LM, Kersey AL, Murali A, Richter C, Gregory CA, Singh I*, Gaharwar AK*. [*Co-corresponding authors]
Science advances 8 (17), eabl9404 1 (2022)

11. ZFTA-RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma.
Arabzade A, Zhao Y, Varadharajan S, Chen HS, Jessa S, Rivas B, Stuckert AJ, Solis M, Kardian A, Tlais D, Golbourn BJ, Stanton ACJ, Chan YS, Olson C, Karlin KL, Kong K, Kupp R, Hu B, Injac SJ, Ngo M, Wang PR, Leon LAD, Sahm F, Kawauchi D, Pfister SM, Lin CY, Hodges HC, Singh I, Westbrook TF, Chintagumpala MM, Blaney SM, Parsons DW, Pajtler KW, Agnihotri S, Gilbertson RJ, Yi J, Jabado N, Kleinman CL, Bertrand KC, Deneen B, Mack SC.
Cancer Discovery,11 (9): 2200–2215 (2021)

10. Engineered Biomaterials for In situ Tissue Regeneration.
Gaharwar AK, Singh I, Khademhosseini A,
Nature Review Materials 5, 686–705 (2020)

9. Photothermal Modulation of Human Stem Cells Using Light-responsive 2D Nanomaterials.
Carrow J., Singh KA, Jaiswal MK, Ramirez A, Lokhande A, Yeh A, Sarkar TA, Singh I*, Gaharwar AK*. [*Co-corresponding authors]
Proceedings of the National Academy of Sciences, 117 (24), 13329-13338 (2020)

8. Nanoengineered Osteoinductive Bioink for 3D Bioprinting Bone Tissue.
Chimene D, Miller L, Cross L, Jaiswal MK, Singh I, Gaharwar AK.
ACS Applied Materials & Interfaces, 12 (14), 15976-15988 (2020)

7. A C19MC-MYCN-LIN28A oncogenic circuit driven by hijacked super-enhancers represents a distinct therapeutic vulnerability in ETMRs
Sin-Chan P*, Mumal I*, Suwal T, Ho B, Xiaolian F, Singh I, Lu M, Torchia J, Lovejoy DB, Guilhamon P, Fouladi M, Lassaletta A, Afzal S, Philips J, Solano-Paez P, Lindsey M. Hoffman, Van Meter T, Leary S, Nakamura H, Massimi L, Grundry R, Fangusaro J, Johnston D, Hwang E, Wang Y, Scharnhorst D, Camelo-Piragua S, Reddy A, Gillespie Y, Catchpoole D, Hansford J, Gil da Costa MJ, Michaud J, Levy JM, Ellezam B, Ramanujachar R, Lindsay HB, Singh SK, Jabado N, Kleinman CL, Taylor MD, Hawkins CE, Bouffet E, Arrowsmith CH, Dirks PB, Li XN, Lin CY, Rich JN, Mack SC, Huang A.,
Cancer Cell 36 (1), 51-67. e7 (2019)

6. Non-overlapping control of transcriptome by Promoter and Super-Enhancer-Associated Dependencies
Fulciniti M*, Lin CY*, Samur MK, Lopez MA, Singh I, Lawlor MA, Szalat RE, Ott CJ, Avet-Loiseau H, Anderson KC, Young RA, Bradner JE, Munshi NC
Cell Reports 25: 3693-3705.e6 (2018)

5. Widespread changes in transcriptome profile of human mesenchymal stem cells induced by two-dimensional nanosilicates
Carrow J, Cross L, Reese R, Jaiswal M, Gregory C, Kaunas R, Singh I*, Gaharwar A* [*Co-corresponding authors]
Proceedings of the National Academy of Sciences 115,E3905-E3913(2018)

4. An allelic series of miR-17~92 mutant mice uncovers functional specialization and cooperation among members of a miRNA polycistron
Han Y, Vidigal J, Mu P, Yao E, Singh I, Gonzalez A, Concepcion C, Bonetti C, Ogrodowski P, Carver B, Selleri L, Betel D, Leslie C, Ventura A
Nature Genetics 47, 766–775(2015)

3. Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provides insights into adoption of a parasitic lifestyle and prospects for disease control
Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Kumar U, Saier M, Wang Y, Cai H, Gu J, Mather MW, Vaidya AB, Wilkes DE, Rajagopalan V, Asai DJ, Pearson CG, Findly RC, Dickerson HW, Badger JH, Wu M, Martens C, Van de Peer Y, Roos DS, Cassidy-Hanley DM, Clark TG
Genome Biology 12(10): R100 (2011)

2. Virus interactions with human signal transduction pathways
Zhao Z, Xia J, Tastan O, Singh I, Kshirsagar M, Carbonell J and Klein-Seetharaman J
International Journal of Computational Biology and Drug Design, 4(1): 83–105 (2011)

1. Comparison of virus interactions with human signal transduction pathways
Singh I, Tastan O and Klein-Seetharaman J
Proceedings of the First Association of Computing Machinery (ACM) International Conference on Bioinformatics and Computational Biology, 17-24 (2010)