Publications

Refereed Journal Papers

1. Tindle C, Katkar GD, Fonseca AG, Taheri S, Lee J, Maity P, Sayed IM, Ibeawuchi SR, Vidales E, Pranadinata RF, Fuller M, Stec DL, Anandachar MS, Perry K, Le HN, Ear J, Boland BS, Sandborn WJ, Sahoo D, Das S, Ghosh P. A Living Organoid Biobank of Crohn's Disease Patients Reveals Molecular Subtypes for Personalized Therapeutics. bioRxiv. 2023 Mar 13:2023.03.11.532245. doi: 10.1101/2023.03.11.532245. Preprint. PMID: 36993763

2. Vo D, Ghosh P, Sahoo D. Artificial intelligence-guided discovery of gastric cancer continuum. Gastric Cancer. 2023 Mar;26(2):286-297. doi: 10.1007/s10120-022-01360-3. Epub 2023 Jan 24. PMID: 36692601

3. Zage PE, Huo Y, Subramonian D, Le Clorennec C, Ghosh P, Sahoo D. Identification of a novel gene signature for neuroblastoma differentiation using a Boolean implication network. Genes Chromosomes Cancer. 2023 Jan 21. doi: 10.1002/gcc.23124. Online ahead of print. PMID: 36680522

4. Ghosh P, Campos VJ, Vo DT, Guccione C, Goheen-Holland V, Tindle C, Mazzini GS, He Y, Alexandrov LB, Lippman SM, Gurski RR, Das S, Yadlapati R, Curtius K, Sahoo D. AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas. JCI Insight. 2022 Sep 22;7(18):e161334. doi: 10.1172/jci.insight.161334. PMID: 36134663

5. Subramanian R, Sahoo D. Boolean implication analysis of single-cell data predicts retinal cell type markers. BMC Bioinformatics. 2022 Sep 16;23(1):378. doi: 10.1186/s12859-022-04915-4. PMID: 36114457 

6. Stobdan T, Sahoo D, Haddad GG. A Boolean approach for novel hypoxia-related gene discovery. PLoS One. 2022 Aug 25;17(8):e0273524. doi: 10.1371/journal.pone.0273524. eCollection 2022. PMID: 36006949 

7. Sinha S, Castillo V, Espinoza CR, Tindle C, Fonseca AG, Dan JM, Katkar GD, Das S, Sahoo D, Ghosh P.  COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.  EBioMedicine. 2022 Aug;82:104185. doi: 10.1016/j.ebiom.2022.104185. Epub 2022 Jul 20. PMID: 35870428 PMCID: PMC9297827.

8. Buschhaus JM, Rajendran S, Humphries BA, Cutter AC, Muñiz AJ, Ciavattone NG, Buschhaus AM, Cañeque T, Nwosu ZC, Sahoo D, Bevoor AS, Shah YM, Lyssiotis CA, Ghosh P, Wicha MS, Rodriguez R, Luker GD. Effects of iron modulation on mesenchymal stem cell-induced drug resistance in estrogen receptor-positive breast cancer. Oncogene. 2022 Jul;41(29):3705-3718. doi: 10.1038/s41388-022-02385-9. Epub 2022 Jun 22. PMID: 35732800; PMCID: PMC9288981.

9. Rotz SJ, Worley S, Hu B, Bazeley P, Baedke JL, Hudson MM, Kuo DJ, Oeffinger KC, Robison LL, Sahoo D, Wang F, Yasui Y, Armstrong GT, Bhatia S. Genome Wide Association Study of Pregnancy in Childhood Cancer Survivors: A Report from the Childhood Cancer Survivor Study. Cancer Epidemiol Biomarkers Prev. 2022 Jun 14:cebp.0314.2022-3-18 10:35:08.940. doi: 10.1158/1055-9965.EPI-22-0314. Epub ahead of print. PMID: 35700038.

10. Hazra T, Tapryal N, Chakraborty A, Rayavara K, Wakamiya M, Islam A, Pan L, Hsu J, Tat V, Maruyama J, Hosoki K, Sayed I, Alcantara J, Castillo V, Tindle C, Sarker A, Cardenas V, Sharma G, Alexander LC, Sur S, Ghosh G, Paessler S, Sahoo D, Ghosh P, Das S, Boldogh I, Tseng CT. The DNA glycosylase NEIL2 plays a vital role in combating SARS-CoV-2 infection. Res Sq [Preprint]. 2022 May 27:rs.3.rs-1690354. doi: 10.21203/rs.3.rs-1690354/v1. PMID: 35665009; PMCID: PMC9164514.

11. Kumar D, Das M, Oberg A, Sahoo D, Wu P, Sauceda C, Jih L, Ellies LG, Langiewicz MT, Sen S, Webster NJG. Hepatocyte Deletion of IGF2 Prevents DNA Damage and Tumor Formation in Hepatocellular Carcinoma. Adv Sci (Weinh). 2022 Jul;9(21):e2105120. doi: 10.1002/advs.202105120. Epub 2022 May 26. PMID: 35615981; PMCID: PMC9313545.

12. Ghosh P, Katkar GD, Shimizu C, Kim J, Khandelwal S, Tremoulet AH, Kanegaye JT; Pediatric Emergency Medicine Kawasaki Disease Research Group, Bocchini J, Das S, Burns JC, Sahoo D. An Artificial Intelligence-guided signature reveals the shared host immune response in MIS-C and Kawasaki disease. Nat Commun. 2022 May 16;13(1):2687. doi: 10.1038/s41467-022-30357-w. PMID: 35577777; PMCID: PMC9110726.

13. Katkar GD, Sayed IM, Anandachar MS, Castillo V, Vidales E, Toobian D, Usmani F, Sawires JR, Leriche G, Yang J, Sandborn WJ, Das S, Sahoo D, Ghosh P. Artificial intelligence-rationalized balanced PPARα/γ dual agonism resets dysregulated macrophage processes in inflammatory bowel disease. Commun Biol. 2022 Mar 14;5(1):231. doi: 10.1038/s42003-022-03168-4. PMID: 35288651; PMCID: PMC8921270.

14. Hisamori S, Mukohyama J, Koul S, Hayashi T, Rothenberg ME, Maeda M, Isobe T, Valencia Salazar LE, Qian X, Johnston DM, Qian D, Lao K, Asai N, Kakeji Y, Gennarino VA, Sahoo D, Dalerba P, Shimono Y. Upregulation of BMI1-suppressor miRNAs (miR-200c, miR-203) during terminal differentiation of colon epithelial cells. J Gastroenterol. 2022 Jun;57(6):407-422. doi: 10.1007/s00535-022-01865-9. Epub 2022 Mar 4. PMID: 35244768.

15. Sinha S, Castillo V, Espinoza CR, Tindle C, Fonseca AG, Dan JM, Katkar GD, Das S, Sahoo D, Ghosh P. COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis. bioRxiv [Preprint]. 2022 Jul 18:2021.11.28.470269. doi: 10.1101/2021.11.28.470269. Update in: EBioMedicine. 2022 Jul 20;82:104185. PMID: 34873597; PMCID: PMC8647648.

16. Raab WJ, Mazzocchi A, Radice P, Sahoo D, Castelli C, Dalerba P; Colon Cancer Immunology and Immunotherapy (CCII) study group. A Microsatellite in the Coding Sequence of HLA-A/B Is a Mutation Hotspot in Colon Cancer With Microsatellite Instability. Gastroenterology. 2022 Mar;162(3):960-963.e3. doi: 10.1053/j.gastro.2021.10.006. Epub 2021 Oct 12. PMID: 34653421; PMCID: PMC8881331.

17. Vo DT, Fuller MR, Tindle C, Anandachar MS, Das S, Sahoo D, Ghosh P. SPT6 loss permits the transdifferentiation of keratinocytes into an intestinal fate that resembles Barrett's metaplasia. iScience. 2021 Sep 11;24(10):103121. doi: 10.1016/j.isci.2021.103121. PMID: 34622168; PMCID: PMC8481972.

18. Tindle C, Fuller M, Fonseca A, Taheri S, Ibeawuchi SR, Beutler N, Katkar GD, Claire A, Castillo V, Hernandez M, Russo H, Duran J, Crotty Alexander LE, Tipps A, Lin G, Thistlethwaite PA, Chattopadhyay R, Rogers TF, Sahoo D, Ghosh P, Das S. Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19. Elife. 2021 Aug 13;10:e66417. doi: 10.7554/eLife.66417. PMID: 34463615; PMCID: PMC8463074.

19. Sahu D, Huan J, Wang H, Sahoo D, Casteel DE, Klemke RL, Boss GR, Hansel DE. Bladder Cancer Invasion Is Mediated by Mammalian Target of Rapamycin Complex 2-Driven Regulation of Nitric Oxide and Invadopodia Formation. Am J Pathol. 2021 Dec;191(12):2203-2218. doi: 10.1016/j.ajpath.2021.08.002. Epub 2021 Aug 21. PMID: 34428425.

20. Reynoso S, Castillo V, Katkar GD, Lopez-Sanchez I, Taheri S, Espinoza C, Rohena C, Sahoo D, Gagneux P, Ghosh P. GIV/Girdin, a non-receptor modulator for Gαi/s, regulates spatiotemporal signaling during sperm capacitation and is required for male fertility. Elife. 2021 Aug 19;10:e69160. doi: 10.7554/eLife.69160. PMID: 34409938; PMCID: PMC8376251.

21. Ambrosi TH, Marecic O, McArdle A, Sinha R, Gulati GS, Tong X, Wang Y, Steininger HM, Hoover MY, Koepke LS, Murphy MP, Sokol J, Seo EY, Tevlin R, Lopez M, Brewer RE, Mascharak S, Lu L, Ajanaku O, Conley SD, Seita J, Morri M, Neff NF, Sahoo D, Yang F, Weissman IL, Longaker MT, Chan CKF. Aged skeletal stem cells generate an inflammatory degenerative niche. Nature. 2021 Sep;597(7875):256-262. doi: 10.1038/s41586-021-03795-7. Epub 2021 Aug 11. PMID: 34381212; PMCID: PMC8721524.

22. Sahoo D, Swanson L, Sayed IM, Katkar GD, Ibeawuchi SR, Mittal Y, Pranadinata RF, Tindle C, Fuller M, Stec DL, Chang JT, Sandborn WJ, Das S, Ghosh P. Artificial intelligence guided discovery of a barrier-protective therapy in inflammatory bowel disease. Nat Commun. 2021 Jul 12;12(1):4246. doi: 10.1038/s41467-021-24470-5. PMID: 34253728; PMCID: PMC8275683.

23. Sahoo D, Katkar GD, Khandelwal S, Behroozikhah M, Claire A, Castillo V, Tindle C, Fuller M, Taheri S, Rogers TF, Beutler N, Ramirez SI, Rawlings SA, Pretorius V, Smith DM, Burton DR, Alexander LEC, Duran J, Crotty S, Dan JM, Das S, Ghosh P. AI-guided discovery of the invariant host response to viral pandemics. EBioMedicine. 2021 Jun;68:103390. doi: 10.1016/j.ebiom.2021.103390. Epub 2021 Jun 11. PMID: 34127431; PMCID: PMC8193764.

24. Bakowski MA, Beutler N, Wolff KC, Kirkpatrick MG, Chen E, Nguyen TH, Riva L, Shaabani N, Parren M, Ricketts J, Gupta AK, Pan K, Kuo P, Fuller M, Garcia E, Teijaro JR, Yang L, Sahoo D, Chi V, Huang E, Vargas N, Roberts AJ, Das S, Ghosh P, Woods AK, Joseph SB, Hull MV, Schultz PG, Burton DR, Chatterjee AK, McNamara CW, Rogers TF. Drug repurposing screens identify chemical entities for the development of COVID-19 interventions. Nat Commun. 2021 Jun 3;12(1):3309. doi: 10.1038/s41467-021-23328-0. PMID: 34083527; PMCID: PMC8175350.

25. Sahoo D, Katkar GD, Shimizu C, Kim J, Khandelwal S, Tremoulet AH, Kanegaye J; Pediatric Emergency Medicine Kawasaki Disease Research Group, Bocchini J, Das S, Burns JC, Ghosh P. An AI-guided signature reveals the nature of the shared proximal pathways of host immune response in MIS-C and Kawasaki disease. bioRxiv [Preprint]. 2021 Aug 9:2021.04.11.439347. doi: 10.1101/2021.04.11.439347. PMID: 33880476; PMCID: PMC8057241.

26. Ying W, Tang K, Avolio E, Schilling JM, Pasqua T, Liu MA, Cheng H, Gao H, Zhang J, Mahata S, Ko MS, Bandyopadhyay G, Das S, Roth DM, Sahoo D, Webster NJG, Sheikh F, Ghosh G, Patel HH, Ghosh P, van den Bogaart G, Mahata SK. Immunosuppression of Macrophages Underlies the Cardioprotective Effects of CST (Catestatin). Hypertension. 2021 May 5;77(5):1670-1682. doi: 10.1161/HYPERTENSIONAHA.120.16809. Epub 2021 Apr 7. PMID: 33826401; PMCID: PMC8116433.

27. Pezhouman A, Engel JL, Nguyen NB, Skelton RJP, Gilmore WB, Qiao R, Sahoo D, Zhao P, Elliott DA, Ardehali R. Isolation and characterization of human embryonic stem cell-derived heart field-specific cardiomyocytes unravels new insights into their transcriptional and electrophysiological profiles. Cardiovasc Res. 2022 Feb 21;118(3):828-843. doi: 10.1093/cvr/cvab102. PMID: 33744937; PMCID: PMC9020202.

28. Ear J, Abd El-Hafeez AA, Roy S, Ngo T, Rajapakse N, Choi J, Khandelwal S, Ghassemian M, McCaffrey L, Kufareva I, Sahoo D, Ghosh P. A long isoform of GIV/Girdin contains a PDZ-binding module that regulates localization and G-protein binding. J Biol Chem. 2021 Jan-Jun;296:100493. doi: 10.1016/j.jbc.2021.100493. Epub 2021 Mar 3. PMID: 33675748; PMCID: PMC8042451.

29. Campbell CA, Fursova O, Cheng X, Snella E, McCune A, Li L, Solchenberger B, Schmid B, Sahoo D, Morton M, Traver D, Espín-Palazón R. A zebrafish model of granulin deficiency reveals essential roles in myeloid cell differentiation. Blood Adv. 2021 Feb 9;5(3):796-811. doi: 10.1182/bloodadvances.2020003096. PMID: 33560393; PMCID: PMC7876888.

30. Vo D, Singh SC, Safa S, Sahoo D. Boolean implication analysis unveils candidate universal relationships in microbiome data. BMC Bioinformatics. 2021 Feb 5;22(1):49. doi: 10.1186/s12859-020-03941-4. PMID: 33546590; PMCID: PMC7863539.

31. Sharma A, Lee J, Fonseca AG, Moshensky A, Kothari T, Sayed IM, Ibeawuchi SR, Pranadinata RF, Ear J, Sahoo D, Crotty-Alexander LE, Ghosh P, Das S. E-cigarettes compromise the gut barrier and trigger inflammation. iScience. 2021 Jan 6;24(2):102035. doi: 10.1016/j.isci.2021.102035. PMID: 33537654; PMCID: PMC7841355.

32. Espanola SG, Song H, Ryu E, Saxena A, Kim ES, Manegold JE, Nasamran CA, Sahoo D, Oh CK, Bickers C, Shin U, Grainger S, Park YH, Pandolfo L, Kang MS, Kang S, Myung K, Cooper KL, Yelon D, Traver D, Lee Y. Haematopoietic stem cell-dependent Notch transcription is mediated by p53 through the Histone chaperone Supt16h. Nat Cell Biol. 2020 Dec;22(12):1411-1422. doi: 10.1038/s41556-020-00604-7. Epub 2020 Nov 23. PMID: 33230303; PMCID: PMC8092813.

33. Shigeyasu K, Toden S, Ozawa T, Matsuyama T, Nagasaka T, Ishikawa T, Sahoo D, Ghosh P, Uetake H, Fujiwara T, Goel A. The PVT1 lncRNA is a novel epigenetic enhancer of MYC, and a promising risk-stratification biomarker in colorectal cancer. Mol Cancer. 2020 Nov 5;19(1):155. doi: 10.1186/s12943-020-01277-4. PMID: 33148262; PMCID: PMC7643275.

34. Sayed IM, Chakraborty A, Abd El-Hafeez AA, Sharma A, Sahan AZ, Huang WJM, Sahoo D, Ghosh P, Hazra TK, Das S. The DNA Glycosylase NEIL2 Suppresses Fusobacterium-Infection-Induced Inflammation and DNA Damage in Colonic Epithelial Cells. Cells. 2020 Aug 28;9(9):1980. doi: 10.3390/cells9091980. PMID: 32872214; PMCID: PMC7565382.

35. Aron M, Park S, Lowenthal BM, Gupta S, Sahoo D, Cheville JC, Hansel DE. Primary Female Urethral Carcinoma: Proposed Staging Modifications Based on Assessment of Female Urethral Histology and Analysis of a Large Series of Female Urethral Carcinomas. Am J Surg Pathol. 2020 Dec;44(12):1591-1601. doi: 10.1097/PAS.0000000000001569. PMID: 32868524; PMCID: PMC8315296.

36. Abbasi N, Long T, Li Y, Yee BA, Cho BS, Hernandez JE, Ma E, Patel PR, Sahoo D, Sayed IM, Varki N, Das S, Ghosh P, Yeo GW, Huang WJM. DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis. Life Sci Alliance. 2020 Aug 18;3(10):e202000772. doi: 10.26508/lsa.202000772. PMID: 32817263; PMCID: PMC7441524.

37. Rohena C, Rajapakse N, Lo IC, Novick P, Sahoo D, Ghosh P. GIV/Girdin and Exo70 Collaboratively Regulate the Mammalian Polarized Exocytic Machinery. iScience. 2020 Jul 24;23(7):101246. doi: 10.1016/j.isci.2020.101246. Epub 2020 Jun 7. PMID: 32590327; PMCID: PMC7322189.

38. Tal MC, Torrez Dulgeroff LB, Myers L, Cham LB, Mayer-Barber KD, Bohrer AC, Castro E, Yiu YY, Lopez Angel C, Pham E, Carmody AB, Messer RJ, Gars E, Kortmann J, Markovic M, Hasenkrug M, Peterson KE, Winkler CW, Woods TA, Hansen P, Galloway S, Wagh D, Fram BJ, Nguyen T, Corey D, Kalluru RS, Banaei N, Rajadas J, Monack DM, Ahmed A, Sahoo D, Davis MM, Glenn JS, Adomati T, Lang KS, Weissman IL, Hasenkrug KJ. Upregulation of CD47 Is a Host Checkpoint Response to Pathogen Recognition. mBio. 2020 Jun 23;11(3):e01293-20. doi: 10.1128/mBio.01293-20. PMID: 32576678; PMCID: PMC7315125.

39. Rohena C, Kalogriopoulos N, Rajapakse N, Roy S, Lopez-Sanchez I, Ablack J, Sahoo D, Ghosh P. GIV•Kindlin Interaction Is Required for Kindlin-Mediated Integrin Recognition and Activation. iScience. 2020 Jun 26;23(6):101209. doi: 10.1016/j.isci.2020.101209. Epub 2020 May 28. PMID: 32535026; PMCID: PMC7300163.

40. Sayed IM, Sahan AZ, Venkova T, Chakraborty A, Mukhopadhyay D, Bimczok D, Beswick EJ, Reyes VE, Pinchuk I, Sahoo D, Ghosh P, Hazra TK, Das S. Helicobacter pylori infection downregulates the DNA glycosylase NEIL2, resulting in increased genome damage and inflammation in gastric epithelial cells. J Biol Chem. 2020 Aug 7;295(32):11082-11098. doi: 10.1074/jbc.RA119.009981. Epub 2020 Jun 9. PMID: 32518160; PMCID: PMC7415988.

41. Humphries BA, Cutter AC, Buschhaus JM, Chen YC, Qyli T, Palagama DSW, Eckley S, Robison TH, Bevoor A, Chiang B, Haley HR, Sahoo S, Spinosa PC, Neale DB, Boppisetti J, Sahoo D, Ghosh P, Lahann J, Ross BD, Yoon E, Luker KE, Luker GD. Enhanced mitochondrial fission suppresses signaling and metastasis in triple-negative breast cancer. Breast Cancer Res. 2020 Jun 5;22(1):60. doi: 10.1186/s13058-020-01301-x. PMID: 32503622; PMCID: PMC7275541.

42. Sahoo D, Zaramela LS, Hernandez GE, Mai U, Taheri S, Dang D, Stouch AN, Medal RM, McCoy AM, Aschner JL, Blackwell TS, Zengler K, Prince LS. Transcriptional profiling of lung macrophages identifies a predictive signature for inflammatory lung disease in preterm infants. Commun Biol. 2020 May 22;3(1):259. doi: 10.1038/s42003-020-0985-2. PMID: 32444859; PMCID: PMC7244484.

43. Dang D, Taheri S, Das S, Ghosh P, Prince LS, Sahoo D. Computational Approach to Identifying Universal Macrophage Biomarkers. Front Physiol. 2020 Apr 8;11:275. doi: 10.3389/fphys.2020.00275. PMID: 32322218; PMCID: PMC7156600.

44. Ghosh P, Swanson L, Sayed IM, Mittal Y, Lim BB, Ibeawuchi SR, Foretz M, Viollet B, Sahoo D, Das S. The stress polarity signaling (SPS) pathway serves as a marker and a target in the leaky gut barrier: implications in aging and cancer. Life Sci Alliance. 2020 Feb 10;3(3):e201900481. doi: 10.26508/lsa.201900481. PMID: 32041849; PMCID: PMC7012149.

45. Lowenthal BM, Sahoo D, Amin MB, Hansel DE. Urothelial Proliferation of Unknown Malignant Potential Involving the Bladder: Histopathologic Features and Risk of Progression in De Novo Cases and Cases With Prior Neoplasia. Arch Pathol Lab Med. 2020 Jul 1;144(7):853-862. doi: 10.5858/arpa.2019-0005-OA. PMID: 31825667; PMCID: PMC8312373.

46. Limso C, Ngo JM, Nguyen P, Leal S, Husain A, Sahoo D, Ghosh P, Bhandari D. The Gα-interacting vesicle-associated protein interacts with and promotes cell surface localization of GRP78 during endoplasmic reticulum stress. FEBS Lett. 2020 Mar;594(6):1088-1100. doi: 10.1002/1873-3468.13685. Epub 2019 Nov 30. PMID: 31736058; PMCID: PMC7093220.

47. Mukohyama J, Isobe T, Hu Q, Hayashi T, Watanabe T, Maeda M, Yanagi H, Qian X, Yamashita K, Minami H, Mimori K, Sahoo D, Kakeji Y, Suzuki A, Dalerba P, Shimono Y. miR-221 Targets QKI to Enhance the Tumorigenic Capacity of Human Colorectal Cancer Stem Cells. Cancer Res. 2019 Oct 15;79(20):5151-5158. doi: 10.1158/0008-5472.CAN-18-3544. Epub 2019 Aug 15. PMID: 31416845; PMCID: PMC6801097.

48. Pandey S, Sahoo D. Identification of gene expression logical invariants in Arabidopsis. Plant Direct. 2019 Mar 20;3(3):e00123. doi: 10.1002/pld3.123. PMID: 31245766; PMCID: PMC6508763.

49. Dabydeen SA, Desai A, Sahoo D. Unbiased Boolean analysis of public gene expression data for cell cycle gene identification. Mol Biol Cell. 2019 Jul 1;30(14):1770-1779. doi: 10.1091/mbc.E19-01-0013. Epub 2019 May 15. PMID: 31091168; PMCID: PMC6727750.

50. Rajasekaran S, Nagarajha Selvan LD, Dotts K, Kumar R, Rishi P, Khetan V, Bisht M, Sivaraman K, Krishnakumar S, Sahoo D, Campbell MJ, Elchuri SV, Miles WO. Non-coding and Coding Transcriptional Profiles Are Significantly Altered in Pediatric Retinoblastoma Tumors. Front Oncol. 2019 Apr 16;9:221. doi: 10.3389/fonc.2019.00221. PMID: 31058073; PMCID: PMC6477087.

51. Ghosh P, Garg S, Mohanty I, Sahoo D, Pradhan RC. Comparison and storage study of ultra-filtered clarified jamun (Syzygium cumini) juice. J Food Sci Technol. 2019 Apr;56(4):1877-1889. doi: 10.1007/s13197-019-03648-2. Epub 2019 Feb 19. PMID: 30996423; PMCID: PMC6443697.

52. Stobdan T, Sahoo D, Azad P, Hartley I, Heinrichsen E, Zhou D, Haddad GG. High fat diet induces sex-specific differential gene expression in Drosophila melanogaster. PLoS One. 2019 Mar 12;14(3):e0213474. doi: 10.1371/journal.pone.0213474. PMID: 30861021; PMCID: PMC6413938.

53. Rubinstein MR, Baik JE, Lagana SM, Han RP, Raab WJ, Sahoo D, Dalerba P, Wang TC, Han YW. Fusobacterium nucleatum promotes colorectal cancer by inducing Wnt/β-catenin modulator Annexin A1. EMBO Rep. 2019 Apr;20(4):e47638. doi: 10.15252/embr.201847638. Epub 2019 Mar 4. PMID: 30833345; PMCID: PMC6446206.

54. Kahn SA, Wang X, Nitta RT, Gholamin S, Theruvath J, Hutter G, Azad TD, Wadi L, Bolin S, Ramaswamy V, Esparza R, Liu KW, Edwards M, Swartling FJ, Sahoo D, Li G, Wechsler-Reya RJ, Reimand J, Cho YJ, Taylor MD, Weissman IL, Mitra SS, Cheshier SH. Publisher Correction: Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma. Nat Commun. 2018 Nov 2;9(1):4651. doi: 10.1038/s41467-018-07182-1. Erratum for: Nat Commun. 2018 Oct 8;9(1):4121. PMID: 30389946; PMCID: PMC6214967.

55. Chan CKF, Gulati GS, Sinha R, Tompkins JV, Lopez M, Carter AC, Ransom RC, Reinisch A, Wearda T, Murphy M, Brewer RE, Koepke LS, Marecic O, Manjunath A, Seo EY, Leavitt T, Lu WJ, Nguyen A, Conley SD, Salhotra A, Ambrosi TH, Borrelli MR, Siebel T, Chan K, Schallmoser K, Seita J, Sahoo D, Goodnough H, Bishop J, Gardner M, Majeti R, Wan DC, Goodman S, Weissman IL, Chang HY, Longaker MT. Identification of the Human Skeletal Stem Cell. Cell. 2018 Sep 20;175(1):43-56.e21. doi: 10.1016/j.cell.2018.07.029. PMID: 30241615; PMCID: PMC6400492.

56. Aznar N, Ear J, Dunkel Y, Sun N, Satterfield K, He F, Kalogriopoulos NA, Lopez-Sanchez I, Ghassemian M, Sahoo D, Kufareva I, Ghosh P. Convergence of Wnt, growth factor, and heterotrimeric G protein signals on the guanine nucleotide exchange factor Daple. Sci Signal. 2018 Feb 27;11(519):eaao4220. doi: 10.1126/scisignal.aao4220. PMID: 29487190; PMCID: PMC5862031.

57. Sereti KI, Nguyen NB, Kamran P, Zhao P, Ranjbarvaziri S, Park S, Sabri S, Engel JL, Sung K, Kulkarni RP, Ding Y, Hsiai TK, Plath K, Ernst J, Sahoo D, Mikkola HKA, Iruela-Arispe ML, Ardehali R. Analysis of cardiomyocyte clonal expansion during mouse heart development and injury. Nat Commun. 2018 Feb 21;9(1):754. doi: 10.1038/s41467-018-02891-z. PMID: 29467410; PMCID: PMC5821855.

58. Sahoo D, Wei W, Auman H, Hurtado-Coll A, Carroll PR, Fazli L, Gleave ME, Lin DW, Nelson PS, Simko J, Thompson IM, Leach RJ, Troyer DA, True LD, McKenney JK, Feng Z, Brooks JD. Boolean analysis identifies CD38 as a biomarker of aggressive localized prostate cancer. Oncotarget. 2018 Jan 5;9(5):6550-6561. doi: 10.18632/oncotarget.23973. PMID: 29464091; PMCID: PMC5814231.

59. Leivo MZ, Sahoo D, Hamilton Z, Mirsadraei L, Shabaik A, Parsons JK, Kader AK, Derweesh I, Kane C, Hansel DE. Analysis of T1 Bladder Cancer on Biopsy and Transurethral Resection Specimens: Comparison and Ranking of T1 Quantification Approaches to Predict Progression to Muscularis Propria Invasion. Am J Surg Pathol. 2018 Jan;42(1):e1-e10. doi: 10.1097/PAS.0000000000000964. PMID: 29076872.

60. Medal RM, Im AM, Yamamoto Y, Lakhdari O, Blackwell TS, Hoffman HM, Sahoo D, Prince LS. The innate immune response in fetal lung mesenchymal cells targets VEGFR2 expression and activity. Am J Physiol Lung Cell Mol Physiol. 2017 Jun 1;312(6):L861-L872. doi: 10.1152/ajplung.00554.2016. Epub 2017 Mar 23. PMID: 28336813; PMCID: PMC5495951.

61. Sin MLY, Mach KE, Sinha R, Wu F, Trivedi DR, Altobelli E, Jensen KC, Sahoo D, Lu Y, Liao JC. Deep Sequencing of Urinary RNAs for Bladder Cancer Molecular Diagnostics. Clin Cancer Res. 2017 Jul 15;23(14):3700-3710. doi: 10.1158/1078-0432.CCR-16-2610. Epub 2017 Feb 13. PMID: 28193625; PMCID: PMC5873297.

62. Cai S, Kalisky T, Sahoo D, Dalerba P, Feng W, Lin Y, Qian D, Kong A, Yu J, Wang F, Chen EY, Scheeren FA, Kuo AH, Sikandar SS, Hisamori S, van Weele LJ, Heiser D, Sim S, Lam J, Quake S, Clarke MF. A Quiescent Bcl11b High Stem Cell Population Is Required for Maintenance of the Mammary Gland. Cell Stem Cell. 2017 Feb 2;20(2):247-260.e5. doi: 10.1016/j.stem.2016.11.007. Epub 2016 Dec 29. PMID: 28041896; PMCID: PMC5341693.

63. Ngo M, Han A, Lakatos A, Sahoo D, Hachey SJ, Weiskopf K, Beck AH, Weissman IL, Boiko AD. Antibody Therapy Targeting CD47 and CD271 Effectively Suppresses Melanoma Metastasis in Patient-Derived Xenografts. Cell Rep. 2016 Aug 9;16(6):1701-1716. doi: 10.1016/j.celrep.2016.07.004. Epub 2016 Jul 28. PMID: 27477289.

64. Dalerba P, Sahoo D, Clarke MF. CDX2 as a Prognostic Biomarker in Colon Cancer. N Engl J Med. 2016 Jun 2;374(22):2184. doi: 10.1056/NEJMc1602584. PMID: 27248627; PMCID: PMC4955394.

65. Krampitz GW, George BM, Willingham SB, Volkmer JP, Weiskopf K, Jahchan N, Newman AM, Sahoo D, Zemek AJ, Yanovsky RL, Nguyen JK, Schnorr PJ, Mazur PK, Sage J, Longacre TA, Visser BC, Poultsides GA, Norton JA, Weissman IL. Identification of tumorigenic cells and therapeutic targets in pancreatic neuroendocrine tumors. Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):4464-9. doi: 10.1073/pnas.1600007113. Epub 2016 Mar 31. Erratum in: Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):E5538. PMID: 27035983; PMCID: PMC4843455.

66. Rennert RC, Achrol AS, Januszyk M, Kahn SA, Liu TT, Liu Y, Sahoo D, Rodrigues M, Maan ZN, Wong VW, Cheshier SH, Chang SD, Steinberg GK, Harsh GR, Gurtner GC. Multiple Subsets of Brain Tumor Initiating Cells Coexist in Glioblastoma. Stem Cells. 2016 Jun;34(6):1702-7. doi: 10.1002/stem.2359. Epub 2016 Mar 28. PMID: 26991945.

67. Chen JY, Miyanishi M, Wang SK, Yamazaki S, Sinha R, Kao KS, Seita J, Sahoo D, Nakauchi H, Weissman IL. Hoxb5 marks long-term haematopoietic stem cells and reveals a homogenous perivascular niche. Nature. 2016 Feb 11;530(7589):223-7. doi: 10.1038/nature16943. PMID: 26863982; PMCID: PMC4854608.

68. Dalerba P, Sahoo D, Paik S, Guo X, Yothers G, Song N, Wilcox-Fogel N, Forgó E, Rajendran PS, Miranda SP, Hisamori S, Hutchison J, Kalisky T, Qian D, Wolmark N, Fisher GA, van de Rijn M, Clarke MF. CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer. N Engl J Med. 2016 Jan 21;374(3):211-22. doi: 10.1056/NEJMoa1506597. PMID: 26789870; PMCID: PMC4784450.

69. Skelton RJ, Brady B, Khoja S, Sahoo D, Engel J, Arasaratnam D, Saleh KK, Abilez OJ, Zhao P, Stanley EG, Elefanty AG, Kwon M, Elliott DA, Ardehali R. CD13 and ROR2 Permit Isolation of Highly Enriched Cardiac Mesoderm from Differentiating Human Embryonic Stem Cells. Stem Cell Reports. 2016 Jan 12;6(1):95-108. doi: 10.1016/j.stemcr.2015.11.006. PMID: 26771355; PMCID: PMC4720015.

70. Cheah MT, Chen JY, Sahoo D, Contreras-Trujillo H, Volkmer AK, Scheeren FA, Volkmer JP, Weissman IL. CD14-expressing cancer cells establish the inflammatory and proliferative tumor microenvironment in bladder cancer. Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):4725-30. doi: 10.1073/pnas.1424795112. Epub 2015 Mar 30. PMID: 25825750; PMCID: PMC4403197.

71. Chan CK, Seo EY, Chen JY, Lo D, McArdle A, Sinha R, Tevlin R, Seita J, Vincent-Tompkins J, Wearda T, Lu WJ, Senarath-Yapa K, Chung MT, Marecic O, Tran M, Yan KS, Upton R, Walmsley GG, Lee AS, Sahoo D, Kuo CJ, Weissman IL, Longaker MT. Identification and specification of the mouse skeletal stem cell. Cell. 2015 Jan 15;160(1-2):285-98. doi: 10.1016/j.cell.2014.12.002. PMID: 25594184; PMCID: PMC4297645.

72. Scheeren FA, Kuo AH, van Weele LJ, Cai S, Glykofridis I, Sikandar SS, Zabala M, Qian D, Lam JS, Johnston D, Volkmer JP, Sahoo D, van de Rijn M, Dirbas FM, Somlo G, Kalisky T, Rothenberg ME, Quake SR, Clarke MF. A cell-intrinsic role for TLR2-MYD88 in intestinal and breast epithelia and oncogenesis. Nat Cell Biol. 2014 Dec;16(12):1238-48. doi: 10.1038/ncb3058. Epub 2014 Nov 2. PMID: 25362351.

73. Pan Y, Volkmer JP, Mach KE, Rouse RV, Liu JJ, Sahoo D, Chang TC, Metzner TJ, Kang L, van de Rijn M, Skinner EC, Gambhir SS, Weissman IL, Liao JC. Endoscopic molecular imaging of human bladder cancer using a CD47 antibody. Sci Transl Med. 2014 Oct 29;6(260):260ra148. doi: 10.1126/scitranslmed.3009457. Epub 2014 Oct 29. PMID: 25355698.

74. Shin K, Lim A, Zhao C, Sahoo D, Pan Y, Spiekerkoetter E, Liao JC, Beachy PA. Hedgehog signaling restrains bladder cancer progression by eliciting stromal production of urothelial differentiation factors. Cancer Cell. 2014 Oct 13;26(4):521-33. doi: 10.1016/j.ccell.2014.09.001. PMID: 25314078; PMCID: PMC4326077.

75. Mohapatra PC, Sarangi A, Sarangi AK, Dalai RK, Sahoo D. Sequential Serum Cytokine Levels of TNF-Alpha, IL-4 and IL-12 are Associated with Prognosis in Plasmodium falciparum Malaria. Indian J Clin Biochem. 2014 Jul;29(3):321-6. doi: 10.1007/s12291-013-0359-3. Epub 2013 Jul 14. PMID: 24966480; PMCID: PMC4062674.

76. Dimov IK, Lu R, Lee EP, Seita J, Sahoo D, Park SM, Weissman IL, Lee LP. Discriminating cellular heterogeneity using microwell-based RNA cytometry. Nat Commun. 2014 Mar 25;5:3451. doi: 10.1038/ncomms4451. PMID: 24667995; PMCID: PMC4075946.

77. Voskoboynik A, Newman AM, Corey DM, Sahoo D, Pushkarev D, Neff NF, Passarelli B, Koh W, Ishizuka KJ, Palmeri KJ, Dimov IK, Keasar C, Fan HC, Mantalas GL, Sinha R, Penland L, Quake SR, Weissman IL. Identification of a colonial chordate histocompatibility gene. Science. 2013 Jul 26;341(6144):384-7. doi: 10.1126/science.1238036. PMID: 23888037; PMCID: PMC3810301.

78. Chan CK, Lindau P, Jiang W, Chen JY, Zhang LF, Chen CC, Seita J, Sahoo D, Kim JB, Lee A, Park S, Nag D, Gong Y, Kulkarni S, Luppen CA, Theologis AA, Wan DC, DeBoer A, Seo EY, Vincent-Tompkins JD, Loh K, Walmsley GG, Kraft DL, Wu JC, Longaker MT, Weissman IL. Clonal precursor of bone, cartilage, and hematopoietic niche stromal cells. Proc Natl Acad Sci U S A. 2013 Jul 30;110(31):12643-8. doi: 10.1073/pnas.1310212110. Epub 2013 Jul 15. PMID: 23858471; PMCID: PMC3732968.

79. Voskoboynik A, Neff NF, Sahoo D, Newman AM, Pushkarev D, Koh W, Passarelli B, Fan HC, Mantalas GL, Palmeri KJ, Ishizuka KJ, Gissi C, Griggio F, Ben-Shlomo R, Corey DM, Penland L, White RA 3rd, Weissman IL, Quake SR. The genome sequence of the colonial chordate, Botryllus schlosseri. Elife. 2013 Jul 2;2:e00569. doi: 10.7554/eLife.00569. PMID: 23840927; PMCID: PMC3699833.

80. Wu B, Sahoo D, Brooks JD. Comprehensive gene expression changes associated with mouse postnatal kidney development. J Urol. 2013 Jun;189(6):2385-90. doi: 10.1016/j.juro.2012.12.002. Epub 2012 Dec 5. PMID: 23220383.

81. Rinkevich Y, Mori T, Sahoo D, Xu PX, Bermingham JR Jr, Weissman IL. Identification and prospective isolation of a mesothelial precursor lineage giving rise to smooth muscle cells and fibroblasts for mammalian internal organs, and their vasculature. Nat Cell Biol. 2012 Dec;14(12):1251-60. doi: 10.1038/ncb2610. Epub 2012 Nov 11. PMID: 23143399; PMCID: PMC3685475.

82. Sahoo D. The power of boolean implication networks. Front Physiol. 2012 Jul 23;3:276. doi: 10.3389/fphys.2012.00276. PMID: 22934030; PMCID: PMC3429050.

83. Seita J, Sahoo D, Rossi DJ, Bhattacharya D, Serwold T, Inlay MA, Ehrlich LI, Fathman JW, Dill DL, Weissman IL. Gene Expression Commons: an open platform for absolute gene expression profiling. PLoS One. 2012;7(7):e40321. doi: 10.1371/journal.pone.0040321. Epub 2012 Jul 18. PMID: 22815738; PMCID: PMC3399844.

84. Lewis PW, Sahoo D, Geng C, Bell M, Lipsick JS, Botchan MR. Drosophila lin-52 acts in opposition to repressive components of the Myb-MuvB/dREAM complex. Mol Cell Biol. 2012 Aug;32(16):3218-27. doi: 10.1128/MCB.00432-12. Epub 2012 Jun 11. PMID: 22688510; PMCID: PMC3434544.

85. Willingham SB, Volkmer JP, Gentles AJ, Sahoo D, Dalerba P, Mitra SS, Wang J, Contreras-Trujillo H, Martin R, Cohen JD, Lovelace P, Scheeren FA, Chao MP, Weiskopf K, Tang C, Volkmer AK, Naik TJ, Storm TA, Mosley AR, Edris B, Schmid SM, Sun CK, Chua MS, Murillo O, Rajendran P, Cha AC, Chin RK, Kim D, Adorno M, Raveh T, Tseng D, Jaiswal S, Enger PØ, Steinberg GK, Li G, So SK, Majeti R, Harsh GR, van de Rijn M, Teng NN, Sunwoo JB, Alizadeh AA, Clarke MF, Weissman IL. The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors. Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6662-7. doi: 10.1073/pnas.1121623109. Epub 2012 Mar 26. PMID: 22451913; PMCID: PMC3340046.

86. Volkmer JP, Sahoo D, Chin RK, Ho PL, Tang C, Kurtova AV, Willingham SB, Pazhanisamy SK, Contreras-Trujillo H, Storm TA, Lotan Y, Beck AH, Chung BI, Alizadeh AA, Godoy G, Lerner SP, van de Rijn M, Shortliffe LD, Weissman IL, Chan KS. Three differentiation states risk-stratify bladder cancer into distinct subtypes. Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2078-83. doi: 10.1073/pnas.1120605109. Epub 2012 Jan 19. Erratum in: Proc Natl Acad Sci U S A. 2012 Feb 28;109(9):3600. PMID: 22308455; PMCID: PMC3277552.

87. Pang WW, Price EA, Sahoo D, Beerman I, Maloney WJ, Rossi DJ, Schrier SL, Weissman IL. Human bone marrow hematopoietic stem cells are increased in frequency and myeloid-biased with age. Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20012-7. doi: 10.1073/pnas.1116110108. Epub 2011 Nov 28. PMID: 22123971; PMCID: PMC3250139.

88. Dalerba P, Kalisky T, Sahoo D, Rajendran PS, Rothenberg ME, Leyrat AA, Sim S, Okamoto J, Johnston DM, Qian D, Zabala M, Bueno J, Neff NF, Wang J, Shelton AA, Visser B, Hisamori S, Shimono Y, van de Wetering M, Clevers H, Clarke MF, Quake SR. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol. 2011 Nov 13;29(12):1120-7. doi: 10.1038/nbt.2038. PMID: 22081019; PMCID: PMC3237928.

89. Tang C, Lee AS, Volkmer JP, Sahoo D, Nag D, Mosley AR, Inlay MA, Ardehali R, Chavez SL, Pera RR, Behr B, Wu JC, Weissman IL, Drukker M. An antibody against SSEA-5 glycan on human pluripotent stem cells enables removal of teratoma-forming cells. Nat Biotechnol. 2011 Aug 14;29(9):829-34. doi: 10.1038/nbt.1947. PMID: 21841799; PMCID: PMC3537836.

90. Ooi AG, Sahoo D, Adorno M, Wang Y, Weissman IL, Park CY. MicroRNA-125b expands hematopoietic stem cells and enriches for the lymphoid-balanced and lymphoid-biased subsets. Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21505-10. doi: 10.1073/pnas.1016218107. Epub 2010 Nov 30. PMID: 21118986; PMCID: PMC3003003.

91. Sahoo D, Seita J, Bhattacharya D, Inlay MA, Weissman IL, Plevritis SK, Dill DL. MiDReG: a method of mining developmentally regulated genes using Boolean implications. Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):5732-7. doi: 10.1073/pnas.0913635107. Epub 2010 Mar 15. PMID: 20231483; PMCID: PMC2851930.

92. Inlay MA, Bhattacharya D, Sahoo D, Serwold T, Seita J, Karsunky H, Plevritis SK, Dill DL, Weissman IL. Ly6d marks the earliest stage of B-cell specification and identifies the branchpoint between B-cell and T-cell development. Genes Dev. 2009 Oct 15;23(20):2376-81. doi: 10.1101/gad.1836009. Erratum in: Genes Dev. 2013 Sep 15;27(18):2063. PMID: 19833765; PMCID: PMC2764492.

93. Sahoo D, Dill DL, Gentles AJ, Tibshirani R, Plevritis SK. Boolean implication networks derived from large scale, whole genome microarray datasets. Genome Biol. 2008 Oct 30;9(10):R157. doi: 10.1186/gb-2008-9-10-r157. PMID: 18973690; PMCID: PMC2760884.

94. Bhamre S, Sahoo D, Tibshirani R, Dill DL, Brooks JD. Temporal changes in gene expression induced by sulforaphane in human prostate cancer cells. Prostate. 2009 Feb 1;69(2):181-90. doi: 10.1002/pros.20869. PMID: 18973173; PMCID: PMC2612096.

95. Shachaf CM, Gentles AJ, Elchuri S, Sahoo D, Soen Y, Sharpe O, Perez OD, Chang M, Mitchel D, Robinson WH, Dill D, Nolan GP, Plevritis SK, Felsher DW. Genomic and proteomic analysis reveals a threshold level of MYC required for tumor maintenance. Cancer Res. 2008 Jul 1;68(13):5132-42. doi: 10.1158/0008-5472.CAN-07-6192. PMID: 18593912; PMCID: PMC4191850.

96. Wu CH, Sahoo D, Arvanitis C, Bradon N, Dill DL, Felsher DW. Combined analysis of murine and human microarrays and ChIP analysis reveals genes associated with the ability of MYC to maintain tumorigenesis. PLoS Genet. 2008 Jun 6;4(6):e1000090. doi: 10.1371/journal.pgen.1000090. Erratum in: PLoS Genet. 2013 Oct;9(10). doi:10.1371/annotation/a0e06cef-a7e4-4ec9-9f35-9df5e50bf7a2. PMID: 18535662; PMCID: PMC2390767.

97. Sahoo D, Dill DL, Tibshirani R, Plevritis SK. Extracting binary signals from microarray time-course data. Nucleic Acids Res. 2007;35(11):3705-12. doi: 10.1093/nar/gkm284. Epub 2007 May 21. PMID: 17517782; PMCID: PMC1920252.

Refereed Conference Papers

1. [DOC] [PDF] [PPT] Debashis Sahoo, David L. Dill, Andrew J. Gentles, Rob Tibshirani, Sylvia K. Plevritis. Implication networks from large gene-expression datasets. RECOMB satellite conference on Systems Biology. San Diego, CA, USA, Nov 30-Dec 1, 2007.

2. [PDF] Debashis Sahoo, Jawahar Jain, Subramanian Iyer, David L. Dill, E. Allen Emerson. Predictive reachability using a sample-based approach. In Proceedings of the 13th IFIP WG 10.5 Advanced Research Working Conference on Correct Hardware Design and Verification Methods, CHARME 2005, LNCS 3725, pp. 388-392, Saarbrücken, Germany, October 3-6, 2005.

3. [PDF] Subramanian Iyer, Debashis Sahoo, Jawahar Jain, Mukul Prasad, Tom Sidle. Error detection using BMC in a parallel environment. In Proceedings of the 13th IFIP WG 10.5 Advanced Research Working Conference on Correct Hardware Design and Verification Methods, CHARME 2005, LNCS 3725, pp. 354-358, Saarbrücken, Germany, October 3-6, 2005

4. [PDF] Debashis Sahoo, Jawahar Jain, Subramanian Iyer, David L. Dill. A New Reachability Algorithm for Symmetric Multi-processor Architecture. In Proceedings of the Third International Symposium on Automated Technology for Verification and Analysis, ATVA 2005, LNCS 3707, pp. 26-38, Taipei, Taiwan, October 4-7, 2005

5. [WWW] [PDF] [PPT] Subramanian Iyer, Jawahar Jain, Debashis Sahoo , E. Allen Emerson. Under-approximation heuristics for Grid-based BMC. In Proceedings of the 4th International Workshop on Parallel and Distributed Methods in Verification, PDMC 2005, ENTCS, Vol. 135, Issue 2, pp. 1-80, Lisbon, Portugal 10 July 2005

6. [PDF] [PPT] Subramanian Iyer, Debashis Sahoo, E. Allen Emerson, Jawahar Jain. On Partitioning and Symbolic Model Checking. In Proceedings of Formal Methods, International Symposium of Formal Methods Europe, LNCS 3582 pp. 497-511, Newcastle, UK, July 18-22, 2005

7. [PDF] [PPT] Debashis Sahoo, Jawahar Jain, Subramanian Iyer, David L. Dill, E. Allen Emerson. Multi-threaded Reachability. In Proceedings of the 42nd Design Automation Conference, DAC 2005, pp. 467-470, San Diego, CA, USA, June 13-17, 2005

8. [PDF] Debashis Sahoo, Subramanian Iyer, Jawahar Jain, Christian Stangier, Amit Narayan, David L. Dill, E. Allen Emerson. A Partitioning Methodology for BDD-based Verification. In Proceedings of the 5th International Conference on Formal Methods in Computer-Aided Design, FMCAD 2004, LNCS 3312, pp. 399-413, Austin, USA, November 14-17, 2004

9. [PDF] Subramanian Iyer, Debashis Sahoo, Christian Stangier, Amit Narayan, Jawahar Jain. Improved Symbolic Verification using Partitioning Techniques. In Proceedings of the 12th IFIP Advanced Research Working Conference on Correct Hardware Design and Verification Methods, CHARME 2003, LNCS 2860, pp. 410-424, L'Aquila, Italy, October 21-24, 2003

Invited Talks

1. High-throughput Automatic Annotation of Normal and Cancer Cells. School of Biomedical Informatics, Faculty Candidate Seminar, Sept 6-8, 2012, UTHealth, The University of Texas, Health Science Center at Houston, TX

2. Boolean analysis reboots systems immunology. ITI Computational and Systems Immunology Faculty Candidate Seminar, Aug 10, 2012, Stanford, CA

3. High-throughput Automatic Annotation of Normal and Cancer Cells. Peggy and Charles Stephenson Cancer Center, Faculty Candidate Seminar, July 26-27, 2012, Biomedical Research Center, Oklahoma City, OK

4. High-throughput Automatic Annotation of Normal and Cancer Cells. BMIR Faculty Candidate Seminar, June 25, 2012, Stanford, CA

5. Application of Boolean networks to discover stem and progenitor cells in normal and cancer tissues. Bioinformatics and Integrative Biology Faculty Seminar at U Mass Medical School, Feb 13-14, 2012, Worcester, MA

6. Systematic identification of novel markers of differentiation in human bladder cancer . CCSB Annual Symposium, May 2-3, 2011, Stanford, CA

7. Scholar-in-Training Award. Systematic identification of novel markers of differentiation in human bladder cancer that predict survival. AACR-NCI Conference on Systems Biology: Confronting the Complexity of Cancer. February 27-March 2, 2011, Hyatt Regency, La Jolla, San Diego, California

8. MiDReG: A Method of Mining Developmental Regulated Genes Using Boolean Implications. Computational Systems Bioinformatics, Aug 16-18 2010, Stanford, California, USA

9. MiDReG: A Method of Mining Developmental Regulated Genes Using Boolean Implications. UC, Irvine - Systems Biology of Stem Cells Symposium, May 24, 2010, Hyatt Regency, Newport Beach, California, USA

10. Computational prediction of developmentally regulated genes. Harvard Stem Cell Institute, Harvard Medical School, Boston MA, USA, October 29, 2008

11. Computational prediction of developmentally regulated genes. Stem Cell Inc. Palo Alto, CA, USA, September 9, 2008

12. Novel BDD-based applications. Palo Alto Venture. Palo Alto, CA, USA, July 17, 2006

13. POBDD-based applications. Artiman Ventures. Palo Alto, CA, USA, April 3, 2006

14. A new Reachability Algorithm for Symmetric Multi-processor Architecture. In Formal Equivalence and Assertion-based Verification Workshop. Madonna Di Campiglio, Italy, July 26-Aug 1, 2005

Workshops and Posters

1. M Behroozikhah, D Dang, Debashis Sahoo, "Deep-learning approaches to validate formal models of biological systems", accepted to be presented in IEEE/ACM FMCAD 2019 

2. S Taheri, D Dang, Debashis Sahoo, " A Novel Formal Method to Discover Cancer biomarkers ", accepted to be presented in IEEE/ACM FMCAD 2019.

3. [Poster_PPT] [Talk_PPT] Debashis Sahoo, Jun Seita, Deepta Bhattacharya, Irving L. Weissman, Sylvia K. Plevritis, David L. Dill. MiDReG: Mining developmentally regulated genes using Boolean implications. Biomedical Computation at Stanford. Stanford, CA, October 25, 2008

4. Matthew A. Inlay, Deepta Bhattacharya, Debashis Sahoo, Holger Karsunky, Tom Serwold, Sylvia K. Plevritis, David L. Dill, and Irving L. Weissman.Identification of the branchpoint between B and T cell development through MiDReG. Biomedical Computation at Stanford. Stanford, CA, October 25, 2008

5. [Poster_PPT] Debashis Sahoo, David L. Dill, Andrew J. Gentles, Rob Tibshirani, Sylvia K. Plevritis. Boolean analysis of large gene-expression datasets. Biomedical Computation at Stanford. Stanford, CA, October 27, 2007

6. [Poster_PDF] Debashis Sahoo, David L. Dill, Rob Tibshirani, Sylvia K. Plevritis. Extracting binary signals from microarray time-course data. Biomedical Computation at Stanford. Stanford, CA, October 21, 2006

7. [Poster_PDF] Debashis Sahoo, David L. Dill, Rob Tibshirani, Sylvia K. Plevritis. Extracting binary signals from microarray time-course data. National Cancer Institute's Integrative Cancer Biology Program. Nashville, TN, April 30-May 2, 2006

8. [PDF] Subramanian Iyer, Jawahar Jain, Debashis Sahoo, Takeshi Shimuzu. Verification of Industrial Designs Using a Computing Grid with More than 100 Nodes. In Industry Session at Asian Test Symposium 2005.

9. [PPT] Debashis Sahoo, Jawahar Jain, Subramanian Iyer, David L. Dill. A new Reachability Algorithm for Symmetric Multi-processor Architecture . In Formal Equivalence and Assertion-based Verification Workshop. Madonna Di Campiglio, Italy, July 26-Aug 1, 2005

10. Subramanian Iyer, Debashis Sahoo, E. Allen Emerson, Jawahar Jain. A new algorithm for partitioned model checking. In Proceedings of the 14th IEEE/ACM International Workshop on Logic & Synthesis, IWLS 2005, Lake Arrowhead, USA, June 8-10, 2005.

11. Debashis Sahoo, Subramanian Iyer, Jawahar Jain, Christian Stangier, Amit Narayan David L. Dill, E. Allen Emerson. A Partitioning Methodology for BDD-based Verification. In Proceedings of the 13th IEEE/ACM International Workshop on Logic & Synthesis, pp. 192-199, Temecula, USA, June 2-4, 2004.

12. Subramanian Iyer, Christian Stangier, Debashis Sahoo, Amit Narayan, Jawahar Jain. Using Partitioned-OBDDs for Efficient Symbolic Model Checking. In Proceedings of the 12th IEEE/ACM International Workshop on Logic & Synthesis, pp. 236-243, Laguna Beach, USA, May 28-30, 2003

Issued Patents

1. 7,281,225 - Circuit verification using multiple engines

2. 7,216,312 - Determining one or more reachable states in a circuit using distributed computing and one or more partitioned data structures

3. 7,032,197 - System and method for executing image computation associated with a target circuit

4. 7,028,279 - Circuit verification

5. 6,904,578 - System and method for verifying a plurality of states associated with a target circuit

Other Patents

1. 20070124711 - Multithreaded Reachability

2. 20060173666 - Circuit Verification

3. 20050138474 - Circuit verification using multiple engines

4. 20040199887 - Determining one or more reachable states in a circuit using distributed computing and one or more partitioned data structures

5. 20040093572 - System and method for executing image computation associated with a target circuit

6. 20040093571 - Circuit verification

7. 20040093570 - System and method for verifying a plurality of states associated with a target circuit

8. 20040093541 - System and method for evaluating an erroneous state associated with a target circuit