Center Publications (2023-Present)

1. Ager CR, Obradovic A, McCann P, Chaimowitz M, Wang ALE, Shaikh N, Shah P, Pan S, Laplaca CJ, Virk RK, Hill JC, Jugler C, DeFranco G, Bhattacharya N, Scher HI, DeCastro GJ, Anderson CB, McKiernan JM, Spina CS, Stein MN, Runcie K, Drake CG, Califano A, Dallos MC. Neoadjuvant androgen deprivation therapy with or without Fc-enhanced non-fucosylated anti-CTLA-4 (BMS-986218) in high risk localized prostate cancer: a randomized phase 1 trial. medRxiv.　2024. Epub 2024/09/24. doi: 10.1101/2024.09.09.24313308. PubMed PMID: 39314954; PMCID: PMC11419205.

2. Altorki NK, Walsh ZH, Melms JC, Port JL, Lee BE, Nasar A, Spinelli C, Caprio L, Rogava M, Ho P, Christos PJ, Saxena A, Elemento O, Bhinder B, Ager C, Amin AD, Sanfilippo NJ, Mittal V, Borczuk AC, Formenti SC, Izar B, McGraw TE. Neoadjuvant durvalumab plus radiation versus durvalumab alone in stages I-III non-small cell lung cancer: survival outcomes and molecular correlates of a randomized phase II trial. Nat Commun. 2023;14(1):8435. Epub 2023/12/20. doi: 10.1038/s41467-023-44195-x. PubMed PMID: 38114518; PMCID: PMC10730562.

3. Arriaga JM, Ronaldson-Bouchard K, Picech F, Nunes de Almeida F, Afari S, Chhouri H, Vunjak-Novakovic G, Abate-Shen C. In vivo genome-wide CRISPR screening identifies CITED2 as a driver of prostate cancer bone metastasis. Oncogene. 2024;43(17):1303-15. Epub 2024/03/08. doi: 10.1038/s41388-024-02995-5. PubMed PMID: 38454137; PMCID: PMC11101692.

4. Baldassarri I, Tavakol DN, Graney PL, Chramiec AG, Hibshoosh H, Vunjak-Novakovic G. An engineered model of metastatic colonization of human bone marrow reveals breast cancer cell remodeling of the hematopoietic niche. Proc Natl Acad Sci U S A. 2024;121(42):e2405257121. Epub 2024/10/07. doi: 10.1073/pnas.2405257121. PubMed PMID: 39374382; PMCID: PMC11494322.

5. Hasselluhn MC, Decker-Farrell AR, Vlahos L, Thomas DH, Curiel-Garcia A, Maurer HC, Wasko UN, Tomassoni L, Sastra SA, Palermo CF, Dalton TC, Ma A, Li F, Tolosa EJ, Hibshoosh H, Fernandez-Zapico ME, Muir A, Califano A, Olive KP. Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression. Cancer Discov. 2024;14(2):348-61. Epub 2023/11/15. doi: 10.1158/2159-8290.CD-23-0240. PubMed PMID: 37966260; PMCID: PMC10922937.

6. Hawley JE, Obradovic AZ, Dallos MC, Lim EA, Runcie K, Ager CR, McKiernan J, Anderson CB, Decastro GJ, Weintraub J, Virk R, Lowy I, Hu J, Chaimowitz MG, Guo XV, Zhang Y, Haffner MC, Worley J, Stein MN, Califano A, Drake CG. Anti-PD-1 immunotherapy with androgen deprivation therapy induces robust immune infiltration in metastatic castration-sensitive prostate cancer. Cancer Cell. 2023;41(11):1972-88 e5. Epub 2023/11/06. doi: 10.1016/j.ccell.2023.10.006. PubMed PMID: 37922910; PMCID: PMC11184948.

7. Hu LZ, Douglass E, Turunen M, Pampou S, Grunn A, Realubit R, Antolin AA, Wang ALE, Li H, Subramaniam P, Mundi PS, Karan C, Alvarez M, Califano A. Elucidating Compound Mechanism of Action and Polypharmacology with a Large-scale Perturbational Profile Compendium. bioRxiv. 2024. Epub 2023/10/24. doi: 10.1101/2023.10.08.561457. PubMed PMID: 37873470; PMCID: PMC10592689.

8. Jamison JK, Zhou M, Gelmann EP, Luk L, Bates SE, Califano A, Fojo T. Entinostat in patients with relapsed or refractory abdominal neuroendocrine tumors. Oncologist. 2024;29(9):817-e1213. Epub 2024/06/18. doi: 10.1093/oncolo/oyae118. PubMed PMID: 38886159; PMCID: PMC11379646.

9. Petrey D, Zhao H, Trudeau SJ, Murray D, Honig B. PrePPI: A Structure Informed Proteome-wide Database of Protein-Protein Interactions. J Mol Biol. 2023;435(14):168052. Epub 2023/03/19. doi: 10.1016/j.jmb.2023.168052. PubMed PMID: 36933822; PMCID: PMC10293085.

10. Rogava M, Aprati TJ, Chi WY, Melms JC, Hug C, Davis SH, Earlie EM, Chung C, Deshmukh SK, Wu S, Sledge G, Tang S, Ho P, Amin AD, Caprio L, Gurjao C, Tagore S, Ngo B, Lee MJ, Zanetti G, Wang Y, Chen S, Ge W, Melo LMN, Allies G, Rosler J, Gibney GT, Schmitz OJ, Sykes M, Creusot RJ, Tuting T, Schadendorf D, Rocken M, Eigentler TK, Molotkov A, Mintz A, Bakhoum SF, Beyaz S, Cantley LC, Sorger PK, Meckelmann SW, Tasdogan A, Liu D, Laughney AM, Izar B. Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation. Nat Cancer. 2024;5(3):433-47. Epub 2024/01/30. doi: 10.1038/s43018-023-00704-x. PubMed PMID: 38286827; PMCID: PMC11175596.

11. Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A. Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis. Nat Commun. 2024;15(1):3909. Epub 2024/05/10. doi: 10.1038/s41467-024-47957-3. PubMed PMID: 38724493; PMCID: PMC11082183.

12. Su J, Reynier JB, Fu X, Zhong G, Jiang J, Escalante RS, Wang Y, Aparicio L, Izar B, Knowles DA, Rabadan R. Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data. Genome Biol. 2023;24(1):291. Epub 2023/12/19. doi: 10.1186/s13059-023-03138-x. PubMed PMID: 38110959; PMCID: PMC10726548.

13. Wasko UN, Jiang J, Dalton TC, Curiel-Garcia A, Edwards AC, Wang Y, Lee B, Orlen M, Tian S, Stalnecker CA, Drizyte-Miller K, Menard M, Dilly J, Sastra SA, Palermo CF, Hasselluhn MC, Decker-Farrell AR, Chang S, Jiang L, Wei X, Yang YC, Helland C, Courtney H, Gindin Y, Muonio K, Zhao R, Kemp SB, Clendenin C, Sor R, Vostrejs WP, Hibshman PS, Amparo AM, Hennessey C, Rees MG, Ronan MM, Roth JA, Brodbeck J, Tomassoni L, Bakir B, Socci ND, Herring LE, Barker NK, Wang J, Cleary JM, Wolpin BM, Chabot JA, Kluger MD, Manji GA, Tsai KY, Sekulic M, Lagana SM, Califano A, Quintana E, Wang Z, Smith JAM, Holderfield M, Wildes D, Lowe SW, Badgley MA, Aguirre AJ, Vonderheide RH, Stanger BZ, Baslan T, Der CJ, Singh M, Olive KP. Tumour-selective activity of RAS-GTP inhibition in pancreatic cancer. Nature. 2024;629(8013):927-36. Epub 2024/04/09. doi: 10.1038/s41586-024-07379-z. PubMed PMID: 38588697; PMCID: PMC11111406.

14. Wu LW, Tao JJ, McDonnell D, Izar B. Pseudoprogression in a patient with metastatic melanoma treated with PD-1 and LAG-3 inhibition. Melanoma Res. 2024;34(4):382-5. Epub 2024/04/19. doi: 10.1097/CMR.0000000000000974. PubMed PMID: 38640504.

Center Publications (First Funding Cycle, 2016 – 2023)

1. Alvarez MJ, Subramaniam PS, Tang LH, Grunn A, Aburi M, Rieckhof G, Komissarova EV, Hagan EA, Bodei L, Clemons PA, Dela Cruz FS, Dhall D, Diolaiti D, Fraker DA, Ghavami A, Kaemmerer D, Karan C,　Kidd M, Kim KM, Kim HC, Kunju LP, Langel U, Li Z, Lee J, Li H, LiVolsi V, Pfragner R, Rainey AR, Realubit RB, Remotti H, Regberg J, Roses R, Rustgi A, Sepulveda AR, Serra S, Shi C, Yuan X, Barberis M, Bergamaschi R, Chinnaiyan AM, Detre T, Ezzat S, Frilling A, Hommann M, Jaeger D, Kim MK, Knudsen BS, Kung AL, Leahy E, Metz DC, Milsom JW, Park YS, Reidy-Lagunes D, Schreiber S, Washington K, Wiedenmann B, Modlin I, Califano A. A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors. Nat Genet. 2018;50(7):979-89. Epub 2018/06/20. doi: 10.1038/s41588-018-0138-4. PubMed PMID: 29915428; PMCID: PMC6421579.

2. Aparicio L, Bordyuh M, Blumberg AJ, Rabadan R. A Random Matrix Theory Approach to Denoise Single-Cell Data. Patterns (N Y). 2020;1(3):100035. Epub 2020/11/19. doi: 10.1016/j.patter.2020.100035. PubMed PMID: 33205104; PMCID: PMC7660363.

3. Arnes L, Liu Z, Wang J, Maurer C, Sagalovskiy I, Sanchez-Martin M, Bommakanti N, Garofalo DC, Balderes DA, Sussel L, Olive KP, Rabadan R. Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma. Gut. 2019;68(3):499-511. Epub 2018/02/15. doi: 10.1136/gutjnl-2017-314353. PubMed PMID: 29440233; PMCID: PMC6086768.

4. Arriaga JM, Panja S, Alshalalfa M, Zhao J, Zou M, Giacobbe A, Madubata CJ, Kim JY, Rodriguez A, Coleman I, Virk RK, Hibshoosh H, Ertunc O, Ozbek B, Fountain J, Jeffrey Karnes R, Luo J, Antonarakis ES, Nelson PS, Feng FY, Rubin MA, De Marzo AM, Rabadan R, Sims PA, Mitrofanova A, Abate-Shen C. A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance. Nat Cancer. 2020;1(11):1082-96. Epub 2021/06/05. doi: 10.1038/s43018-020-00125-0. PubMed PMID: 34085047; PMCID: PMC8171279.

5. Arrieta VA, Chen AX, Kane JR, Kang SJ, Kassab C, Dmello C, Zhao J, Burdett KB, Upadhyayula PS, Lee-Chang C, Shilati J, Jaishankar D, Chen L, Gould A, Zhang D, Yuan J, Zhao W, Ling X, Burks JK, Laffleur B, Amidei C, Bruce JN, Lukas RV, Yamaguchi JT, Cieremans D, Rothschild G, Basu U, McCord M, Brat DJ, Zhang H, Cooper LAD, Zhang B, Sims P, Cloughesy TF, Prins R, Canoll P, Stupp R, Heimberger AB, Horbinski C, Iwamoto FM, Rabadan R, Sonabend AM. ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma. Nat Cancer. 2021;2(12):1372-86. Epub 2022/02/06. doi: 10.1038/s43018-021-00260-2. PubMed PMID: 35121903; PMCID: PMC8818262.

6. Aytes A, Giacobbe A, Mitrofanova A, Ruggero K, Cyrta J, Arriaga J, Palomero L, Farran-Matas S, Rubin MA, Shen MM, Califano A, Abate-Shen C. NSD2 is a conserved driver of metastatic prostate cancer progression. Nat Commun. 2018;9(1):5201. Epub 2018/12/07. doi: 10.1038/s41467-018-07511-4. PubMed PMID: 30518758; PMCID: PMC6281610.

7. Banda JM, Evans L, Vanguri RS, Tatonetti NP, Ryan PB, Shah NH. A curated and standardized adverse drug event resource to accelerate drug safety research. Sci Data. 2016;3:160026. Epub 2016/05/20. doi: 10.1038/sdata.2016.26. PubMed PMID: 27193236; PMCID: PMC4872271.

8. Bansal M, He J, Peyton M, Kustagi M, Iyer A, Comb M, White M, Minna JD, Califano A. Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis. PLoS One. 2019;14(1):e0208646. Epub 2019/01/08. doi: 10.1371/journal.pone.0208646. PubMed PMID: 30615629; PMCID: PMC6322741.

9. Bell LC, Meydan C, Kim J, Foox J, Butler D, Mason CE, Shapira SD, Noursadeghi M, Pollara G. Transcriptional response modules characterise IL-1beta and IL-6 activity in COVID-19. bioRxiv. 2020. Epub 2020/12/11. doi: 10.1101/2020.07.22.202275. PubMed PMID: 33299992; PMCID: PMC7724660.

10. Bell LCK, Meydan C, Kim J, Foox J, Butler D, Mason CE, Shapira SD, Noursadeghi M, Pollara G. Transcriptional response modules characterize IL-1beta and IL-6 activity in COVID-19. iScience. 2021;24(1):101896. Epub 2020/12/16. doi: 10.1016/j.isci.2020.101896. PubMed PMID: 33319166; PMCID: PMC7721347.

11. Belver L, Yang AY, Albero R, Herranz D, Brundu FG, Quinn SA, Perez-Duran P, Alvarez S, Gianni F, Rashkovan M, Gurung D, Rocha PP, Raviram R, Reglero C, Cortes JR, Cooke AJ, Wendorff AA, Cordo V, Meijerink JP, Rabadan R, Ferrando AA. GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia. Cancer Discov. 2019;9(12):1774-91. Epub 2019/09/15. doi: 10.1158/2159-8290.CD-19-0471. PubMed PMID: 31519704; PMCID: PMC6891196.

12. Blasco MT, Navas C, Martin-Serrano G, Grana-Castro O, Lechuga CG, Martin-Diaz L, Djurec M, Li J, Morales-Cacho L, Esteban-Burgos L, Perales-Paton J, Bousquet-Mur E, Castellano E, Jacob HKC, Cabras L, Musteanu M, Drosten M, Ortega S, Mulero F, Sainz B, Jr., Dusetti N, Iovanna J, Sanchez-Bueno F, Hidalgo M, Khiabanian H, Rabadan R, Al-Shahrour F, Guerra C, Barbacid M. Complete Regression of Advanced Pancreatic Ductal Adenocarcinomas upon Combined Inhibition of EGFR and C-RAF. Cancer Cell. 2019;35(4):573-87 e6. Epub 2019/04/13. doi: 10.1016/j.ccell.2019.03.002. PubMed PMID: 30975481; PMCID: PMC10132447.

13. Boland MR, Jacunski A, Lorberbaum T, Romano JD, Moskovitch R, Tatonetti NP. Systems biology approaches for identifying adverse drug reactions and elucidating their underlying biological mechanisms. Wiley Interdiscip Rev Syst Biol Med. 2016;8(2):104-22. Epub 2015/11/13. doi: 10.1002/wsbm.1323. PubMed PMID: 26559926; PMCID: PMC4760887.

14. Boland MR, Polubriaginof F, Tatonetti NP. Development of A Machine Learning Algorithm to Classify Drugs Of Unknown Fetal Effect. Sci Rep. 2017;7(1):12839. Epub 2017/10/11. doi: 10.1038/s41598-017-12943-x. PubMed PMID: 28993650; PMCID: PMC5634437.

15. Boland MR, Tatonetti NP. Investigation of 7-dehydrocholesterol reductase pathway to elucidate off-target prenatal effects of pharmaceuticals: a systematic review. Pharmacogenomics J. 2016;16(5):411-29. Epub 2016/07/13. doi: 10.1038/tpj.2016.48. PubMed PMID: 27401223; PMCID: PMC5028238.

16. Broyde J, Simpson DR, Murray D, Paull EO, Chu BW, Tagore S, Jones SJ, Griffin AT, Giorgi FM, Lachmann A, Jackson P, Sweet-Cordero EA, Honig B, Califano A. Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses. Nat Biotechnol. 2021;39(2):215-24. Epub 2020/09/16. doi: 10.1038/s41587-020-0652-7. PubMed PMID: 32929263; PMCID: PMC7878435.

17. Bryant EE, Sunjevaric I, Berchowitz L, Rothstein R, Reid RJD. Rad5 dysregulation drives hyperactive recombination at replication forks resulting in cisplatin sensitivity and genome instability. Nucleic Acids Res. 2019;47(17):9144-59. Epub 2019/07/28. doi: 10.1093/nar/gkz631. PubMed PMID: 31350889; PMCID: PMC6753471.

18. Bush EC, Ray F, Alvarez MJ, Realubit R, Li H, Karan C, Califano A, Sims PA. PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens. Nat Commun. 2017;8(1):105. Epub 2017/07/26. doi: 10.1038/s41467-017-00136-z. PubMed PMID: 28740083; PMCID: PMC5524642.

19. Califano A, Alvarez MJ. The recurrent architecture of tumour initiation, progression and drug sensitivity. Nat Rev Cancer. 2017;17(2):116-30. Epub 2016/12/16. doi: 10.1038/nrc.2016.124. PubMed PMID: 27977008; PMCID: PMC5541669.

20. Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ. A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cell Stem Cell. 2018;22(4):575-88 e7. Epub 2018/04/07. doi: 10.1016/j.stem.2018.03.012. PubMed PMID: 29625070; PMCID: PMC5957284.

21. Chang JB, Quinnies KM, Realubit R, Karan C, Rand JH, Tatonetti NP. A novel, rapid method to compare the therapeutic windows of oral anticoagulants using the Hill coefficient. Sci Rep. 2016;6:29387. Epub 2016/07/22. doi: 10.1038/srep29387. PubMed PMID: 27439480; PMCID: PMC4954953.

22. Chen AX, Gartrell RD, Zhao J, Upadhyayula PS, Zhao W, Yuan J, Minns HE, Dovas A, Bruce JN, Lasorella A, Iavarone A, Canoll P, Sims PA, Rabadan R. Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker. Genome Med. 2021;13(1):88. Epub 2021/05/21. doi: 10.1186/s13073-021-00906-x. PubMed PMID: 34011400; PMCID: PMC8136167.

23. Chiu HS, Martinez MR, Bansal M, Subramanian A, Golub TR, Yang X, Sumazin P, Califano A. High-throughput validation of ceRNA regulatory networks. BMC Genomics. 2017;18(1):418. Epub 2017/06/01. doi: 10.1186/s12864-017-3790-7. PubMed PMID: 28558729; PMCID: PMC5450082.

24. Chiu HS, Martinez MR, Komissarova EV, Llobet-Navas D, Bansal M, Paull EO, Silva J, Yang X, Sumazin P, Califano A. The number of titrated microRNA species dictates ceRNA regulation. Nucleic Acids Res. 2018;46(9):4354-69. Epub 2018/04/24. doi: 10.1093/nar/gky286. PubMed PMID: 29684207; PMCID: PMC5961349.

25. Chiu TP, Rao S, Mann RS, Honig B, Rohs R. Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding. Nucleic Acids Res. 2017;45(21):12565-76. Epub 2017/10/19. doi: 10.1093/nar/gkx915. PubMed PMID: 29040720; PMCID: PMC5716191.

26. DelGiorno KE, Chung CY, Vavinskaya V, Maurer HC, Novak SW, Lytle NK, Ma Z, Giraddi RR, Wang D, Fang L, Naeem RF, Andrade LR, Ali WH, Tseng H, Tsui C, Gubbala VB, Ridinger-Saison M, Ohmoto M, Erikson GA, O'Connor C, Shokhirev MN, Hah N, Urade Y, Matsumoto I, Kaech SM, Singh PK, Manor U, Olive KP, Wahl GM. Tuft Cells Inhibit Pancreatic Tumorigenesis in Mice by Producing Prostaglandin D(2). Gastroenterology. 2020;159(5):1866-81 e8. Epub 2020/07/28. doi: 10.1053/j.gastro.2020.07.037. PubMed PMID: 32717220; PMCID: PMC7680354.

27. Diaz JE, Ahsen ME, Schaffter T, Chen X, Realubit RB, Karan C, Califano A, Losic B, Stolovitzky G. The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies. Elife. 2020;9. Epub 2020/09/19. doi: 10.7554/eLife.52707. PubMed PMID: 32945258; PMCID: PMC7546737.

28. Ding H, Douglass EF, Jr., Sonabend AM, Mela A, Bose S, Gonzalez C, Canoll PD, Sims PA, Alvarez MJ, Califano A. Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm. Nat Commun. 2018;9(1):1471. Epub 2018/04/18. doi: 10.1038/s41467-018-03843-3. PubMed PMID: 29662057; PMCID: PMC5902599.

29. Ding H, Wang W, Califano A. iterClust: a statistical framework for iterative clustering analysis. Bioinformatics. 2018;34(16):2865-6. Epub 2018/03/27. doi: 10.1093/bioinformatics/bty176. PubMed PMID: 29579153; PMCID: PMC6084607.

30. Dixit PD, Lyashenko E, Niepel M, Vitkup D. Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks. Cell Syst. 2020;10(2):204-12 e8. Epub 2019/12/23. doi: 10.1016/j.cels.2019.11.010. PubMed PMID: 31864963; PMCID: PMC7047530.

31. Elyada E, Bolisetty M, Laise P, Flynn WF, Courtois ET, Burkhart RA, Teinor JA, Belleau P, Biffi G, Lucito MS, Sivajothi S, Armstrong TD, Engle DD, Yu KH, Hao Y, Wolfgang CL, Park Y, Preall J, Jaffee EM, Califano A, Robson P, Tuveson DA. Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts. Cancer Discov. 2019;9(8):1102-23. Epub 2019/06/15. doi: 10.1158/2159-8290.CD-19-0094. PubMed PMID: 31197017; PMCID: PMC6727976.

32. Gayvert KM, Dardenne E, Cheung C, Boland MR, Lorberbaum T, Wanjala J, Chen Y, Rubin MA, Tatonetti NP, Rickman DS, Elemento O. A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors. Cell Rep. 2016;15(11):2348-56. Epub 2016/06/07. doi: 10.1016/j.celrep.2016.05.037. PubMed PMID: 27264179; PMCID: PMC4912004.

33. Giangreco NP, Tatonetti NP. A database of pediatric drug effects to evaluate ontogenic mechanisms from child growth and development. Med. 2022;3(8):579-95 e7. Epub 2022/06/26. doi: 10.1016/j.medj.2022.06.001. PubMed PMID: 35752163; PMCID: PMC9378670.

34. Giudice ID, Rigolin GM, Raponi S, Cafforio L, Ilari C, Wang J, Bordyuh M, Piciocchi A, Marinelli M, Nanni M, Tavolaro S, Filetti M, Bardi A, Tammiso E, Volta E, Negrini M, Saccenti E, Mauro FR, Rossi D, Gaidano G, Guarini A, Rabadan R, Cuneo A, Foa R. Refined karyotype-based prognostic stratification of chronic lymphocytic leukemia with a low- and very-low-risk genetic profile. Leukemia. 2018;32(2):543-6. Epub 2017/09/20. doi: 10.1038/leu.2017.292. PubMed PMID: 28924243; PMCID: PMC5898432.

35. Hao Y, Quinnies K, Realubit R, Karan C, Tatonetti NP. Tissue-Specific Analysis of Pharmacological Pathways. CPT Pharmacometrics Syst Pharmacol. 2018;7(7):453-63. Epub 2018/06/20. doi: 10.1002/psp4.12305. PubMed PMID: 29920991; PMCID: PMC6063738.

36. Hao Y, Tatonetti NP. Predicting G protein-coupled receptor downstream signaling by tissue expression. Bioinformatics. 2016;32(22):3435-43. Epub 2016/08/04. doi: 10.1093/bioinformatics/btw510. PubMed PMID: 27485444; PMCID: PMC5181570.

37. He J, Zhou Z, Reed M, Califano A. Accelerated parallel algorithm for gene network reverse engineering. BMC Syst Biol. 2017;11(Suppl 4):83. Epub 2017/09/28. doi: 10.1186/s12918-017-0458-5. PubMed PMID: 28950860; PMCID: PMC5615246.

38. Hwang H, Petrey D, Honig B. A hybrid method for protein-protein interface prediction. Protein Sci. 2016;25(1):159-65. Epub 2015/07/17. doi: 10.1002/pro.2744. PubMed PMID: 26178156; PMCID: PMC4815308.

39. Joseph TA, Chlenski P, Litman A, Korem T, Pe'er I. Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates. Genome Res. 2022;32(3):558-68. Epub 2022/01/07. doi: 10.1101/gr.275533.121. PubMed PMID: 34987055; PMCID: PMC8896461.

40. Joseph TA, Pe'er I. Inference of Population Structure from Time-Series Genotype Data. Am J Hum Genet. 2019;105(2):317-33. Epub 2019/07/02. doi: 10.1016/j.ajhg.2019.06.002. PubMed PMID: 31256878; PMCID: PMC6698887.

41. Khatamian A, Paull EO, Califano A, Yu J. SJARACNe: a scalable software tool for gene network reverse engineering from big data. Bioinformatics. 2019;35(12):2165-6. Epub 2018/11/06. doi: 10.1093/bioinformatics/bty907. PubMed PMID: 30388204; PMCID: PMC6581437.

42. Knowledge Base workgroup of the Observational Health Data S, Informatics c. Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data. J Biomed Semantics. 2017;8(1):11. Epub 2017/03/09. doi: 10.1186/s13326-017-0115-3. PubMed PMID: 28270198; PMCID: PMC5341176.

43. Kosaloglu Z, Zornig I, Halama N, Kaiser I, Buchhalter I, Grabe N, Eils R, Schlesner M, Califano A, Jager D. Identification of immunotherapeutic targets by genomic profiling of rectal NET metastases. Oncoimmunology. 2016;5(11):e1213931. Epub 2016/12/22. doi: 10.1080/2162402X.2016.1213931. PubMed PMID: 27999735; PMCID: PMC5139646.

44. Lasso G, Honig B, Shapira SD. A Sweep of Earth's Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease. Cell Syst. 2021;12(1):82-91 e3. Epub 2020/10/15. doi: 10.1016/j.cels.2020.09.006. PubMed PMID: 33053371; PMCID: PMC7552982.

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