Publications

2026

1. Rivera M, Liu L, Enlund S, Lim CE, Zhang H, Yang K, Sasik R, Crews LA, Fisch KM, Eskander RN, Holm F, Jiang Q. APOBEC3B enhances the efficacy of PARP inhibitors in elimination of ovarian cancer stem cell. Sci Rep [Internet]. Springer Science and Business Media LLC; 2026 Jan 14; Available from: http://dx.doi.org/10.1038/s41598-026-35939-y PMID: 41535339

2. Rosenthal SB, Maihofer AX, Nievergelt CM, Dochtermann D, Gerstenberger A, Whisenant T, Pyarajan S, Allen-Brady K, Krieger JN, Million Veteran Program, Afari N, Gasperi M. A large-scale multi-ancestry genome-wide association study of chronic prostatitis/chronic pelvic pain syndrome in men. Nat Commun. Springer Science and Business Media LLC; 2026 Jan 9;17(1):343. PMCID: PMC12789528

3. Kim HY, Mizrahi O, Lee W, Rosenthal SB, Han C, Yee BA, Blue SM, Diaz J, Jonnalagadda JP, Street LA, Hokutan K, Jang H, Miciano C, Ma CT, Bobkov AA, Sergienko E, Jackson MR, Jovanovic M, Stefanovic B, Kisseleva T, Yeo GW, Brenner DA. RNA-binding protein LARP6 coordinates hepatic stellate cell activation and liver fibrosis. J Clin Invest [Internet]. American Society for Clinical Investigation; 2026 Apr 15;136(8). Available from: http://dx.doi.org/10.1172/JCI197923 PMCID: PMC13078889

4. Mehta-Doshi A, Tsu BL, Sauceda C, Kairs SN, Liu J, Rai J, Whisenant T, Sasik R, Barnes CA, Ban DK, Gonzalez DJ, Aran K. Age-dependent neuroinflammatory effects of red blood cells and their exosomes in a human brain-on-chip model. Blood Red Cells Iron. Elsevier BV; 2026 Mar;2(1):100044. PMCID: PMC13055018

5. Chen XL, Tharp KM, Ojalill M, Ozmadenci D, Boyer A, Haanen TJ 3rd, Lawson C, Lee HJ, Xia M, Tahon E, Zhang Y, Minor C, Khan SU, Anderson CC, Nemkov T, Rose M, Estrada MV, Molinolo AA, Warren E, Penalosa P, Eskander RN, McHale MT, Wang SE, Connolly DC, Fisch KM, Stupack DG, Schlaepfer DD. FAK inhibition in ovarian cancer releases omega-3 fatty acids to program CXCL13-producing anti-tumor resident peritoneal macrophages. Cell Rep. Elsevier BV; 2026 Mar 24;45(3):117009. PMCID: PMC13086164

6. Aisagbonhi O, Jacobs MB, Meads M, Stanley V, Lamale-Smith LM, Emeruwa UN, Laurent LC, Fisch KM, Horii M. Determinants of placental versus maternal preeclampsia. Hypertension. Ovid Technologies (Wolters Kluwer Health); 2026 Apr;83(4):e26236. PMCID: PMC13098728

7. Kalahasti NV, Donepudi G, Bauersfeld S, Jandu S, Tayal A, John DJ, Kacham S, Muruhathasan V, Ramsey C, Jang SS, Flagg M, Hogarth M, Califano J, Fisch KM. Clinicogenomic real-world data enable prediction of hospital readmissions at a comprehensive cancer center. JCO Clin Cancer Inform. American Society of Clinical Oncology (ASCO); 2026 Apr;10(2):e2500172. PMID: 42044461

2025

1. Lee W, Liu X, Rosenthal SB, Miciano C, Sakane S, Hokutan K, Dhar D, Kim HY, Brenner DA, Kisseleva T. ETS1 suppresses hepatic stellate cell activation and liver fibrosis. JCI Insight [Internet]. American Society for Clinical Investigation; 2025 Dec 22;10(24). Available from: http://dx.doi.org/10.1172/jci.insight.195242 PMID: 41196693

2. Gasperi M, Rosenthal SB, Maihofer AX, Gerstenberger A, Dochtermann D, Choquet H, Pressman A, Panizzon MS, Stein MB, Schuster NM, Pyarajan S, VA Million Veteran Program, Afari N, Nievergelt CM. A multi-ancestry meta genome-wide association study of migraine among veterans: associations with traumatic brain injury, depression, and post-traumatic stress disorder. Mol Psychiatry [Internet]. Springer Science and Business Media LLC; 2025 Dec 19; Available from: http://dx.doi.org/10.1038/s41380-025-03392-4 PMID: 41420111

3. Kumar AJ, Epler K, Wang J, Shen A, Samandari N, Rolfsen ML, Barnes LA, Shadel GS, Moyzis AG, Sainz AG, Ulubabyan K, Li K, Jepsen K, Li X, Fuster MM, Spragg RG, Sasik R, Vallon V, Goodluck H, Ix JH, Singh P, Hepokoski ML. Kidney mitochondrial DNA contributes to systemic IL-6 release in sepsis-associated acute kidney injury. JCI Insight [Internet]. American Society for Clinical Investigation; 2025 Dec 8;10(23). Available from: http://dx.doi.org/10.1172/jci.insight.177004 PMID: 41355794

4. Pham J, Nandi SP, Balaian L, Engstrom C, Chang P, Mack K, van der Werf I, Klacking E, Sneifer J, Katragadda N, Wirtjes K, Ruiz A, Chilin-Fuentes D, Molina E, Mesci P, Stoudemire J, Morris SR, Whisenant T, Alexandrov LB, Jamieson CHM. Space-associated stem cell hallmarks of aging and resilience in astronauts. Cell Stem Cell. Elsevier BV; 2025 Dec 4;32(12):1886-1903.e7. PMID: 41289992

5. Calderon RI, Sah N, Huang M, Kallol S, Kittle RH, Shaik WB, Abdelbaki A, Chousal JN, Morey R, Bui T, Mitre A, Fogarty NME, Gerri C, Manalo Z, Zheng C, De Hoff P, Home P, Niakan KK, Cook-Andersen H, Fisch KM, Paul S, Soncin F. VGLL1 contributes to both the transcriptome and epigenome of the developing trophoblast compartment. Proc Natl Acad Sci U S A. Proceedings of the National Academy of Sciences; 2025 Dec 2;122(48):e2508432122. PMCID: PMC12685074

6. Viebahn GK, Khurana A, Freund L, Chilin-Fuentes D, Jepsen K, Rosenthal SB, Chatterjee S, Ellenrieder V, Hsu CL, Schnabl B, Hartmann P. Retatrutide improves steatohepatitis in an accelerated mouse model of diet-induced steatohepatitis with a fructose binge. Am J Physiol Gastrointest Liver Physiol. American Physiological Society; 2025 Dec 1;329(6):G680–G695. PMCID: PMC12643026

7. Chang H, Zeng L, Malakoutikhah Z, Nasamran CA, Herdman S, Corr M, Fisch KM, Webster NJG, Raz E, Bertin S. Single-cell transcriptomics reveals immune remodeling of the murine lung microenvironment following chronic house dust mite exposure. Front Immunol. Frontiers Media SA; 2025 Nov 27;16(1652539):1652539. PMCID: PMC12723145

8. McCubbin RA, Auwal MA, Wang S, Alvarez Zepeda S, Sasik R, Zeller RW, Ross KG, Zayas RM. Smed-pou4-2 regulates mechanosensory neuron regeneration and function in planarians. Elife [Internet]. eLife Sciences Publications, Ltd; 2025 Nov 18;14(RP107718). Available from: http://dx.doi.org/10.7554/eLife.107718 PMCID: PMC12626421

9. Do VM, Simpson S, Fisch KM, Gabriel RA. Associations between social determinants of health and opioid-use disorder among chronic pain patients from a multi-institutional dataset. Anesth Analg. Ovid Technologies (Wolters Kluwer Health); 2025 Nov 1;141(5):1149–1158. PMCID: PMC12183315

10. Podvin S, Rosenthal B, Mosier C, Wei E, Fisch KM, Hook V. Dysregulation of huntingtin interacting protein networks in human juvenile Huntington’s disease brain. J Huntingtons Dis. SAGE Publications; 2025 Nov;14(4):354–368. PMCID: PMC12602727

11. Jeelani I, Franco da Cunha F, Rohm TV, Nasamran CA, Wang L, Moon JS, Prakash S, Oswari J, Isaac R, Murphy C, Glass CK, Olefsky JM, Lee YS. CCL26 and CXCL12 preserve insulin-sensitizing macrophages in subcutaneous adipose tissue in obesity. Cell Rep. Elsevier BV; 2025 Oct 28;44(10):116450. PMCID: PMC12587491

12. Yamazaki T, Yang Y, Schöler D, Yukawa-Muto Y, Kouno T, Harberts A, Sakane S, Freund L, Hsu CL, Whisenant TC, Rosenthal SB, Kisseleva T, Cable EE, Schnabl B. Single-nuclei RNA sequencing shows the engagement of PPAR-delta target genes primarily in hepatocytes and cholangiocytes by the selective PPAR-delta agonist seladelpar. PPAR Res. Wiley; 2025 Oct 23;2025(1):2935230. PMCID: PMC12575037

13. Pham J, Isquith J, Balaian L, Nandi SP, Engstrom C, Mack K, van der Werf I, Chang P, Stoudemire J, Ladel L, Klacking E, Ruiz A, Chilin-Fuentes D, Sneifer J, Mays D, Gamble P, Giza S, Janowitz J, Nienaber T, Mishra T, Khachatrian AA, Molina E, Snyder MP, Morris SR, Clements T, Muotri AR, Whisenant T, Alexandrov LB, Jamieson CHM. Nanobioreactor detection of space-associated hematopoietic stem and progenitor cell aging. Cell Stem Cell. Elsevier BV; 2025 Sept 4;32(9):1403-1420.e8. PMCID: PMC12764381

14. Parmar A, Srinivasan A, Krockenberger L, Augustine A, Gong O, Bullard AC, Kalra R, Ledvin L, Pilz D, Tawil J, Tea CE, Wang KC, Urso O, Kaube LM, Sun Y, Sasik R, Gaulton KJ, Fisch KM, Ferguson CJ. Polycomb repressive complexes 1 and 2 independently and dynamically regulate euchromatin during cerebellar neurodevelopment. PLoS One. Public Library of Science (PLoS); 2025 Sept;21(9):e1011843. PMCID: PMC12500107

15. Martellucci S, Heredia M, Wang Z, Whisenant T, Strickland DK, Sanchez R, Arai T, Zhang M, Wang H, Gong Z, Asam K, Aouizerat BE, Pekkurnaz G, Ye Y, Campana WM. The low-density lipoprotein receptor-related protein-1 (LRP1) in Schwann cells controls mitochondria homeostasis in peripheral nerves. Prog Neurobiol. Elsevier BV; 2025 Aug;251(102796):102796. PMID: 40541732

16. Saddawi-Konefka R, Msari RA, Tang S, Philips C, Sadat S, Clubb LM, Luna S, Fassardi S, Jones R, Pietryga IF, Faraji F, Schokrpur S, Yung BS, Allevato MM, Decker KE, Nasamran CA, Chilin-Fuentes D, Rosenthal SB, Jensen SM, Fox BA, Bell RB, Gutkind JS, Sharabi A, Califano JA. The tumor-sentinel lymph node immuno-migratome reveals CCR7+ dendritic cells drive response to sequenced immunoradiotherapy. Nat Commun. Springer Science and Business Media LLC; 2025 July 17;16(1):6578. PMCID: PMC12271439

17. Chumappumkal Joseph B, Whisenant TC, Cooke EJ, Zhou JY, Falah N, De-Pablo Moreno JA, von Drygalski A. Synovial Gene expression after Hemarthrosis differs between FVIII-deficient mice treated with recombinant FVIII or FVIII-Fc Fusion Protein. PLoS One. 2025 May 19;20(5):e0320322. PMCID: PMC12088034

18. Kim HY, Rosenthal SB, Liu X, Miciano C, Hou X, Miller M, Buchanan J, Poirion OB, Chilin-Fuentes D, Han C, Housseini M, Carvalho-Gontijo Weber R, Sakane S, Lee W, Zhao H, Diggle K, Preissl S, Glass CK, Ren B, Wang A, Brenner DA, Kisseleva T. Multi-modal analysis of human hepatic stellate cells identifies novel therapeutic targets for metabolic dysfunction-associated steatotic liver disease. J Hepatol. Elsevier BV; 2025 May;82(5):882–897. PMCID: PMC12306656

19. Nakagawa T, Luebeck J, Zhu K, Lange JT, Sasik R, Phillips C, Sadat S, Javadzadeh S, Yang Q, Monther A, Fassardi S, Wang A, Pestonjamasp K, Rosenthal B, Fisch KM, Mischel P, Bafna V, Califano JA. Inhibition of human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer. Nat Commun. Springer Science and Business Media LLC; 2025 Mar 26;16(1):2964. PMCID: PMC11947173

20. Barber AG, Quintero CM, Hamilton M, Rajbhandari N, Sasik R, Zhang Y, Kim C, Husain H, Sun X, Reya T. Regulation of lung cancer initiation and progression by the stem cell determinant Musashi. Elife [Internet]. eLife Sciences Publications, Ltd; 2025 Mar 6;13(RP97021). Available from: http://dx.doi.org/10.7554/eLife.97021 PMCID: PMC11884785

21. Park BH, Macias AA, Fisch KM, Simpson S, Chen J, Gabriel RA. The association of social determinants of health with reported daily pain scores among patients with a history of chronic pain using the “all of us” research program. Anesth Analg. 2025 Mar 1;140(3):732–735. PMCID: PMC11805467

22. Gabby LC, Jones CK, McIntyre BB, Manalo Z, Meads M, Pizzo DP, Diaz-Vigil J, Soncin F, Fisch KM, Ramos GA, Jacobs MB, Parast MM. Chronic villitis as a distinctive feature of placental injury in maternal SARS-CoV-2 infection. Am J Obstet Gynecol. Elsevier BV; 2025 Jan;232(1):123.e1-123.e12. PMID: 38580043

2024

1. Joshi V, Carter D, Chen AE, Murphy K, Higgins JW, Gurel M, Chilin Fuentes D, Rosenthal SB, Fisch KM, Kisseleva T, Brenner DA. Induction of MASH in three-dimensional bioprinted human liver tissue. PLoS One. Public Library of Science (PLoS); 2024 Dec 30;19(12):e0312615. PMCID: PMC11684678

2. Jeelani I, Moon JS, da Cunha FF, Nasamran CA, Jeon S, Zhang X, Bandyopadhyay GK, Dobaczewska K, Mikulski Z, Hosseini M, Liu X, Kisseleva T, Brenner DA, Singh S, Loomba R, Kim M, Lee YS. HIF-2α drives hepatic Kupffer cell death and proinflammatory recruited macrophage activation in nonalcoholic steatohepatitis. Sci Transl Med. American Association for the Advancement of Science (AAAS); 2024 Sept 11;16(764):eadi0284. PMCID: PMC11665927

3. Hernandez F, Chavez H, Goemans SL, Kirakosyan Y, Luevano CD, Canfield D, Laurent LC, Jacobs M, Woelkers D, Tarsa M, Gyamfi-Bannerman C, Fisch KM. Aspirin resistance in pregnancy is associated with reduced interleukin-2 (IL-2) concentrations in maternal serum: Implications for aspirin prophylaxis for preeclampsia. Pregnancy Hypertens. Elsevier BV; 2024 Sept;37(101131):101131. PMCID: PMC11610477

4. Ganguly S, Rosenthal SB, Ishizuka K, Troutman TD, Rohm TV, Khader N, Aleman-Muench G, Sano Y, Archilei S, Soroosh P, Olefsky JM, Feldstein AE, Kisseleva T, Loomba R, Glass CK, Brenner DA, Dhar D. Lipid-associated macrophages’ promotion of fibrosis resolution during MASH regression requires TREM2. Proc Natl Acad Sci U S A. Proceedings of the National Academy of Sciences; 2024 Aug 27;121(35):e2405746121. PMCID: PMC11363294

5. Huang M, Mark A, Pham J, Vera K, Saravia-Butler AM, Beheshti A, Jiang Q, Fisch KM. RNA editing regulates host immune response and T cell homeostasis in SARS-CoV-2 infection. PLoS One. Public Library of Science (PLoS); 2024 Aug 23;19(8):e0307450. PMCID: PMC11343423

6. Yu SB, Wang H, Sanchez RG, Carlson NM, Nguyen K, Zhang A, Papich ZD, Abushawish AA, Whiddon Z, Matysik W, Zhang J, Whisenant TC, Ghassemian M, Koberstein JN, Stewart ML, Myers SA, Pekkurnaz G. Neuronal activity-driven O-GlcNAcylation promotes mitochondrial plasticity. Dev Cell. Elsevier BV; 2024 Aug 19;59(16):2143-2157.e9. PMCID: PMC11338717

7. Aisagbonhi O, Ghlichloo I, Hong DS, Roma A, Fadare O, Eskander R, Saenz C, Fisch KM, Song W. Comprehensive next-generation sequencing identifies novel putative pathogenic or likely pathogenic germline variants in patients with concurrent tubo-ovarian and endometrial serous and endometrioid carcinomas or precursors. Gynecol Oncol. Elsevier BV; 2024 Aug;187:241–248. PMID: 38833993

8. Ruoss S, Nasamran CA, Ball ST, Chen JL, Halter KN, Bruno KA, Whisenant TC, Parekh JN, Dorn SN, Esparza MC, Bremner SN, Fisch KM, Engler AJ, Ward SR. Comparative single-cell transcriptional and proteomic atlas of clinical-grade injectable mesenchymal source tissues. Sci Adv. American Association for the Advancement of Science (AAAS); 2024 July 12;10(28):eadn2831. PMCID: PMC11244553

9. Shepard RM, Ghebremedhin A, Pratumchai I, Robinson SR, Betts C, Hu J, Sasik R, Fisch KM, Zak J, Chen H, Paradise M, Rivera J, Amjad M, Uchiyama S, Seo H, Campos AD, Dayao DA, Tzipori S, Piedra-Mora C, Das S, Hasteh F, Russo H, Sun X, Xu L, Crotty Alexander LE, Duran JM, Odish M, Pretorius V, Kirchberger NC, Chin SM, Von Schalscha T, Cheresh D, Morrey JD, Alargova R, O’Connell B, Martinot TA, Patel SP, Nizet V, Martinot AJ, Coussens LM, Teijaro JR, Varner JA. PI3Kγ inhibition circumvents inflammation and vascular leak in SARS-CoV-2 and other infections. Sci Transl Med. American Association for the Advancement of Science (AAAS); 2024 July 3;16(754):eadi6887. PMCID: PMC11272418

10. Fisch KM, Rosenthal SB, Mark A, Sasik R, Nasamran CA, Clifford R, Derebery MJ, Boussaty E, Jepsen K, Harris J, Friedman RA. The genomic landscape of Ménière’s disease: a path to endolymphatic hydrops. BMC Genomics. Springer Science and Business Media LLC; 2024 June 28;25(1):646. PMCID: PMC11212243

11. Martellucci S, Flütsch A, Carter M, Norimoto M, Pizzo D, Mantuano E, Sadri M, Wang Z, Chillin-Fuentes D, Rosenthal SB, Azmoon P, Gonias SL, Campana WM. Axon-derived PACSIN1 binds to the Schwann cell survival receptor, LRP1, and transactivates TrkC to promote gliatrophic activities. Glia. Wiley; 2024 May;72(5):916–937. PMID: 38372375

12. Lin ET, Bae Y, Birkett R, Sharma AM, Zhang R, Fisch KM, Funk W, Mestan KK. Cord blood adductomics reveals oxidative stress exposure pathways of bronchopulmonary dysplasia. Antioxidants (Basel). MDPI AG; 2024 Apr 20;13(4):494. PMCID: PMC11047351

13. Nakagawa T, Santos J, Nasamran CA, Sen P, Sadat S, Monther A, Bendik J, Ebisumoto K, Hu J, Preissl S, Guo T, Vavinskaya V, Fisch KM, Califano JA. Defining the relationship of salivary gland malignancies to novel cell subpopulations in human salivary glands using single nucleus RNA-sequencing. Int J Cancer. Wiley; 2024 Apr 15;154(8):1492–1503. PMID: 37971144

14. Patta I, Zand M, Lee L, Mishra S, Bortnick A, Lu H, Prusty A, McArdle S, Mikulski Z, Wang HY, Cheng CS, Fisch KM, Hu M, Murre C. Nuclear morphology is shaped by loop-extrusion programs. Nature. Springer Science and Business Media LLC; 2024 Mar;627(8002):196–203. PMCID: PMC11052650

15. Tan PK, Ostertag T, Rosenthal SB, Chilin-Fuentes D, Aidnik H, Linker S, Murphy K, Miner JN, Brenner DA. Role of hepatic stellate and liver sinusoidal endothelial cells in a human primary cell three-dimensional model of nonalcoholic steatohepatitis. Am J Pathol. Elsevier BV; 2024 Mar;194(3):353–368. PMCID: PMC10913759

16. Rivera M, Zhang H, Pham J, Isquith J, Zhou QJ, Balaian L, Sasik R, Enlund S, Mark A, Ma W, Holm F, Fisch KM, Kuo DJ, Jamieson C, Jiang Q. Malignant A-to-I RNA editing by ADAR1 drives T cell acute lymphoblastic leukemia relapse via attenuating dsRNA sensing. Cell Rep. Elsevier BV; 2024 Feb 27;43(2):113704. PMCID: PMC10962356

17. Ou AH, Rosenthal SB, Adli M, Akiyama K, Akula N, Alda M, Amare AT, Ardau R, Arias B, Aubry JM, Backlund L, Bauer M, Baune BT, Bellivier F, Benabarre A, Bengesser S, Bhattacharjee AK, Biernacka JM, Cervantes P, Chen GB, Chen HC, Chillotti C, Cichon S, Clark SR, Colom F, Cousins DA, Cruceanu C, Czerski PM, Dantas CR, Dayer A, Del Zompo M, Degenhardt F, DePaulo JR, Étain B, Falkai P, Fellendorf FT, Ferensztajn-Rochowiak E, Forstner AJ, Frisén L, Frye MA, Fullerton JM, Gard S, Garnham JS, Goes FS, Grigoroiu-Serbanescu M, Grof P, Gruber O, Hashimoto R, Hauser J, Heilbronner U, Herms S, Hoffmann P, Hofmann A, Hou L, Jamain S, Jiménez E, Kahn JP, Kassem L, Kato T, Kittel-Schneider S, König B, Kuo PH, Kusumi I, Lackner N, Laje G, Landén M, Lavebratt C, Leboyer M, Leckband SG, Jaramillo CAL, MacQueen G, Maj M, Manchia M, Marie-Claire C, Martinsson L, Mattheisen M, McCarthy MJ, McElroy SL, McMahon FJ, Mitchell PB, Mitjans M, Mondimore FM, Monteleone P, Nievergelt CM, Nöthen MM, Novák T, Ösby U, Ozaki N, Papiol S, Perlis RH, Pisanu C, Potash JB, Pfennig A, Reich-Erkelenz D, Reif A, Reininghaus EZ, Rietschel M, Rouleau GA, Rybakowski JK, Schalling M, Schofield PR, Schubert KO, Schulze TG, Schweizer BW, Seemüller F, Severino G, Shekhtman T, Shilling PD, Shimoda K, Simhandl C, Slaney CM, Squassina A, Stamm T, Stopkova P, Tighe SK, Tortorella A, Turecki G, Vieta E, Volkert J, Witt S, Wray NR, Wright A, Young LT, Zandi PP, Kelsoe JR. Lithium response in bipolar disorder is associated with focal adhesion and PI3K-Akt networks: a multi-omics replication study. Transl Psychiatry. Springer Science and Business Media LLC; 2024 Feb 23;14(1):109. PMCID: PMC10891068

18. Kim HY, Sakane S, Eguileor A, Carvalho Gontijo Weber R, Lee W, Liu X, Lam K, Ishizuka K, Rosenthal SB, Diggle K, Brenner DA, Kisseleva T. The origin and fate of liver myofibroblasts. Cell Mol Gastroenterol Hepatol. Elsevier BV; 2024;17(1):93–106. PMCID: PMC10665929

19. Niemsiri V, Rosenthal SB, Nievergelt CM, Maihofer AX, Marchetto MC, Santos R, Shekhtman T, Alliey-Rodriguez N, Anand A, Balaraman Y, Berrettini WH, Bertram H, Burdick KE, Calabrese JR, Calkin CV, Conroy C, Coryell WH, DeModena A, Eyler LT, Feeder S, Fisher C, Frazier N, Frye MA, Gao K, Garnham J, Gershon ES, Goes FS, Goto T, Harrington GJ, Jakobsen P, Kamali M, Kelly M, Leckband SG, Lohoff FW, McCarthy MJ, McInnis MG, Craig D, Millett CE, Mondimore F, Morken G, Nurnberger JI, Donovan CO, Øedegaard KJ, Ryan K, Schinagle M, Shilling PD, Slaney C, Stapp EK, Stautland A, Tarwater B, Zandi PP, Alda M, Fisch KM, Gage FH, Kelsoe JR. Focal adhesion is associated with lithium response in bipolar disorder: evidence from a network-based multi-omics analysis. Mol Psychiatry. Springer Science and Business Media LLC; 2024 Jan;29(1):6–19. PMCID: PMC11078741

2023

1. Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell. Elsevier BV; 2023 Dec 21;186(26):5690-5704.e20. PMCID: PMC10795731

2. Aisagbonhi O, Bui T, Nasamran CA, St Louis H, Pizzo D, Meads M, Mulholland M, Magallanes C, Lamale-Smith L, Laurent LC, Morey R, Jacobs MB, Fisch KM, Horii M. High placental expression of FLT1, LEP, PHYHIP and IL3RA – In persons of African ancestry with severe preeclampsia. Placenta. Elsevier BV; 2023 Dec;144:13–22. PMCID: PMC10843761

3. Agarwal K, Choudhury B, Robinson LS, Morrill SR, Bouchibiti Y, Chilin-Fuentes D, Rosenthal SB, Fisch KM, Peipert JF, Lebrilla CB, Allsworth JE, Lewis AL, Lewis WG. Resident microbes shape the vaginal epithelial glycan landscape. Sci Transl Med. American Association for the Advancement of Science (AAAS); 2023 Nov 29;15(724):eabp9599. PMCID: PMC11419735

4. Zapata RC, Zhang D, Yoon D, Nasamran CA, Chilin-Fuentes DR, Libster A, Chaudry BS, Lopez-Valencia M, Ponnalagu D, Singh H, Petrascheck M, Osborn O. Targeting Clic1 for the treatment of obesity: A novel therapeutic strategy to reduce food intake and body weight. Mol Metab. Elsevier BV; 2023 Oct;76(101794):101794. PMCID: PMC10480059

5. Morey R, Bui T, Fisch KM, Horii M. Modeling placental development and disease using human pluripotent stem cells. Placenta. Elsevier BV; 2023 Sept 26;141:18–25. PMCID: PMC10148925

6. Qualliotine JR, Nakagawa T, Rosenthal SB, Sadat S, Ballesteros-Merino C, Xu G, Mark A, Nasamran A, Gutkind JS, Fisch KM, Guo T, Fox BA, Khan Z, Molinolo AA, Califano JA. A network landscape of HPVOPC reveals methylation alterations as significant drivers of gene expression via an immune-mediated GPCR signal. Cancers (Basel). MDPI AG; 2023 Sept 1;15(17):4379. PMCID: PMC10486378

7. Cooke EJ, Joseph BC, Nasamran CA, Fisch KM, von Drygalski A. Maladaptive lymphangiogenesis is associated with synovial iron accumulation and delayed clearance in factor VIII-deficient mice after induced hemarthrosis. J Thromb Haemost. Elsevier BV; 2023 Sept;21(9):2390–2404. PMCID: PMC10792547

8. Sluka KA, Wager TD, Sutherland SP, Labosky PA, Balach T, Bayman EO, Berardi G, Brummett CM, Burns J, Buvanendran A, Caffo B, Calhoun VD, Clauw D, Chang A, Coffey CS, Dailey DL, Ecklund D, Fiehn O, Fisch KM, Frey Law LA, Harris RE, Harte SE, Howard TD, Jacobs J, Jacobs JM, Jepsen K, Johnston N, Langefeld CD, Laurent LC, Lenzi R, Lindquist MA, Lokshin A, Kahn A, McCarthy RJ, Olivier M, Porter L, Qian WJ, Sankar CA, Satterlee J, Swensen AC, Vance CGT, Waljee J, Wandner LD, Williams DA, Wixson RL, Zhou XJ, A2CPS Consortium. Predicting chronic postsurgical pain: current evidence and a novel program to develop predictive biomarker signatures. Pain. Ovid Technologies (Wolters Kluwer Health); 2023 Sept 1;164(9):1912–1926. PMCID: PMC10436361

9. Wright SN, Leger BS, Rosenthal SB, Liu SN, Jia T, Chitre AS, Polesskaya O, Holl K, Gao J, Cheng R, Garcia Martinez A, George A, Gileta AF, Han W, Netzley AH, King CP, Lamparelli A, Martin C, St Pierre CL, Wang T, Bimschleger H, Richards J, Ishiwari K, Chen H, Flagel SB, Meyer P, Robinson TE, Solberg Woods LC, Kreisberg JF, Ideker T, Palmer AA. Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks. Cell Rep. Elsevier BV; 2023 Aug 29;42(8):112873. PMCID: PMC10546330

10. Zapata RC, Nasamran CA, Chilin-Fuentes DR, Dulawa SC, Osborn O. Identification of adipose tissue transcriptomic memory of anorexia nervosa. Mol Med. Springer Science and Business Media LLC; 2023 Aug 15;29(1):109. PMCID: PMC10428576

11. Baghdassarian H, Blackstone SA, Clay OS, Philips R, Matthiasardottir B, Nehrebecky M, Hua VK, McVicar R, Liu Y, Tucker SM, Randazzo D, Deuitch N, Rosenzweig S, Mark A, Sasik R, Fisch KM, Pimpale Chavan P, Eren E, Watts NR, Ma CA, Gadina M, Schwartz DM, Sanyal A, Werner G, Murdock DR, Horita N, Chowdhury S, Dimmock D, Jepsen K, Remmers EF, Goldbach-Mansky R, Gahl WA, O’Shea JJ, Milner JD, Lewis NE, Chang J, Kastner DL, Torok K, Oda H, Putnam CD, Broderick L. Variant STAT4 and response to ruxolitinib in an autoinflammatory syndrome. N Engl J Med. Massachusetts Medical Society; 2023 June 15;388(24):2241–2252. PMCID: PMC10392571

12. Knorr J, Kaufmann B, Inzaugarat ME, Holtmann TM, Geisler L, Hundertmark J, Kohlhepp MS, Boosheri LM, Chilin-Fuentes DR, Birmingham A, Fisch KM, Schilling JD, Loosen SH, Trautwein C, Roderburg C, Demir M, Tacke F, Hoffman HM, Feldstein AE, Wree A. Interleukin-18 signaling promotes activation of hepatic stellate cells in mouse liver fibrosis. Hepatology. Ovid Technologies (Wolters Kluwer Health); 2023 June 1;77(6):1968–1982. PMCID: PMC9984672

13. Rosenthal SB, Wright SN, Liu S, Churas C, Chilin-Fuentes D, Chen CH, Fisch KM, Pratt D, Kreisberg JF, Ideker T. Mapping the common gene networks that underlie related diseases. Nat Protoc. Springer Science and Business Media LLC; 2023 June;18(6):1745–1759. PMCID: PMC10257754

14. Vasquez-Bolanos LS, Gibbons MC, Ruoss S, Wu IT, Esparza MC, Fithian DC, Lane JG, Singh A, Nasamran CA, Fisch KM, Ward SR. Transcriptional time course after rotator cuff repair in 6 month old female rabbits. Front Physiol. 2023 May 9;14:1164055. PMCID: PMC10203179

15. van der Werf I, Mondala PK, Steel SK, Balaian L, Ladel L, Mason CN, Diep RH, Pham J, Cloos J, Kaspers GJL, Chan WC, Mark A, La Clair JJ, Wentworth P, Fisch KM, Crews LA, Whisenant TC, Burkart MD, Donohoe ME, Jamieson CHM. Detection and targeting of splicing deregulation in pediatric acute myeloid leukemia stem cells. Cell Rep Med. Elsevier BV; 2023 Mar 21;4(3):100962. PMCID: PMC10040387

16. Crews LA, Ma W, Ladel L, Pham J, Balaian L, Steel SK, Mondala PK, Diep RH, Wu CN, Mason CN, van der Werf I, Oliver I, Reynoso E, Pineda G, Whisenant TC, Wentworth P, La Clair JJ, Jiang Q, Burkart MD, Jamieson CHM. Reversal of malignant ADAR1 splice isoform switching with Rebecsinib. Cell Stem Cell. Elsevier BV; 2023 Mar 2;30(3):250-263.e6. PMCID: PMC10134781

17. Fielding-Miller R, Karthikeyan S, Gaines T, Garfein RS, Salido RA, Cantu VJ, Kohn L, Martin NK, Wynn A, Wijaya C, Flores M, Omaleki V, Majnoonian A, Gonzalez-Zuniga P, Nguyen M, Vo AV, Le T, Duong D, Hassani A, Tweeten S, Jepsen K, Henson B, Hakim A, Birmingham A, De Hoff P, Mark AM, Nasamran CA, Rosenthal SB, Moshiri N, Fisch KM, Humphrey G, Farmer S, Tubb HM, Valles T, Morris J, Kang J, Khaleghi B, Young C, Akel AD, Eilert S, Eno J, Curewitz K, Laurent LC, Rosing T, Knight R, SEARCH. Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools. Lancet Reg Health Am. Elsevier BV; 2023 Mar;19(100449):100449. PMCID: PMC9939935

18. McCoy AM, Lakhdari O, Shome S, Caoili K, Hernandez GE, Aghaeepour N, Butcher LD, Fisch K, Prince LS. Sp3 is essential for normal lung morphogenesis and cell cycle progression during mouse embryonic development. Development [Internet]. The Company of Biologists; 2023 Mar 1;150(5). Available from: http://dx.doi.org/10.1242/dev.200839 PMCID: PMC10110423

19. Fielding-Miller R, Karthikeyan S, Gaines T, Garfein RS, Salido RA, Cantu VJ, Kohn L, Martin NK, Wynn A, Wijaya C, Flores M, Omaleki V, Majnoonian A, Gonzalez-Zuniga P, Nguyen M, Vo AV, Le T, Duong D, Hassani A, Tweeten S, Jepsen K, Henson B, Hakim A, Birmingham A, De Hoff P, Mark AM, Nasamran CA, Rosenthal SB, Moshiri N, Fisch KM, Humphrey G, Farmer S, Tubb HM, Valles T, Morris J, Kang J, Khaleghi B, Young C, Akel AD, Eilert S, Eno J, Curewitz K, Laurent LC, Rosing T, Knight R. Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project. medRxiv [Internet]. 2023 Jan 25; Available from: http://dx.doi.org/10.1101/2021.10.19.21265226 PMCID: PMC8547528

20. Granados JC, Watrous JD, Long T, Rosenthal SB, Cheng S, Jain M, Nigam SK. Regulation of human endogenous metabolites by drug transporters and drug metabolizing enzymes: An analysis of targeted SNP-metabolite associations. Metabolites. MDPI AG; 2023 Jan 24;13(2):171. PMCID: PMC9958903

21. Ferguson LP, Gatchalian J, McDermott ML, Nakamura M, Chambers K, Rajbhandari N, Lytle NK, Rosenthal SB, Hamilton M, Albini S, Wartenberg M, Zlobec I, Galván JA, Karamitopoulou E, Vavinskaya V, Wascher A, Lowy AM, Schürch CM, Puri PL, Bruneau BG, Hargreaves DC, Reya T. Smarcd3 is an epigenetic modulator of the metabolic landscape in pancreatic ductal adenocarcinoma. Nat Commun. Springer Science and Business Media LLC; 2023 Jan 18;14(1):292. PMCID: PMC9849267

22. Rios-Covian D, Butcher LD, Ablack AL, den Hartog G, Matsubara MT, Ly H, Oates AW, Xu G, Fisch KM, Ahrens ET, Toden S, Brown CC, Kim K, Le D, Eckmann L, Dhar B, Izumi T, Ernst PB, Crowe SE. A novel hypomorphic Apex1 mouse model implicates apurinic/apyrimidinic endonuclease 1 in oxidative DNA damage repair in gastric epithelial cells. Antioxid Redox Signal. SAGE Publications; 2023 Jan;38(1–3):183–197. PMCID: PMC10039277

23. Garcia C, Velez LM, Ujagar N, Del Mundo Z, Nguyen T, Fox C, Mark A, Fisch KM, Lawson MA, Duleba AJ, Seldin MM, Nicholas DA. Lipopolysaccharide-induced chronic inflammation increases female serum gonadotropins and shifts the pituitary transcriptomic landscape. Front Endocrinol (Lausanne). 2023;14:1279878. PMCID: PMC10801245

24. Goyal NP, Rosenthal SB, Nasamran C, Behling CA, Angeles JE, Fishbein MH, Harlow KE, Jain AK, Molleston JP, Newton KP, Ugalde-Nicalo P, Xanthankos SA, Yates K, Schork NJ, Fisch KM, Schwimmer JB, NASH Clinical Research Network. Nonalcoholic fatty liver disease risk and histologic severity are associated with genetic polymorphisms in children. Hepatology. Ovid Technologies (Wolters Kluwer Health); 2023 Jan 1;77(1):197–212. PMCID: PMC9653518

2022

1. Ruoss S, Nasamran CA, Singh A, Lane JG, Ward SR. Are there sex-dependent transcriptional differences in human subacromial bursa from traumatic versus degenerative rotator cuff tears? J Orthop Res. Wiley; 2022 Dec;40(12):2705–2707. PMID: 36250743

2. Jones MK, Agarwal D, Mazo KW, Chopra M, Jurlina SL, Dash N, Xu Q, Ogata AR, Chow M, Hill AD, Kambli NK, Xu G, Sasik R, Birmingham A, Fisch KM, Weinreb RN, Enke RA, Skowronska-Krawczyk D, Wahlin KJ. Chromatin accessibility and transcriptional differences in human stem cell-derived early-stage retinal organoids. Cells. MDPI AG; 2022 Oct 28;11(21):3412. PMCID: PMC9657268

3. Ruoss S, Esparza MC, Vasquez-Bolanos LS, Nasamran CA, Fisch KM, Engler AJ, Ward SR. Spatial transcriptomics tools allow for regional exploration of heterogeneous muscle pathology in the pre-clinical rabbit model of rotator cuff tear. J Orthop Surg Res. Springer Science and Business Media LLC; 2022 Oct 4;17(1):440. PMCID: PMC9531386

4. Su H, Yang F, Fu R, Trinh B, Sun N, Liu J, Kumar A, Baglieri J, Siruno J, Le M, Li Y, Dozier S, Nair A, Filliol A, Sinchai N, Rosenthal SB, Santini J, Metallo CM, Molina A, Schwabe RF, Lowy AM, Brenner DA, Sun B, Karin M. Collagenolysis-dependent DDR1 signalling dictates pancreatic cancer outcome. Nature. Springer Science and Business Media LLC; 2022 Oct;610(7931):366–372. PMCID: PMC9588640

5. Whisenant TC, Nigam SK. Organic anion transporters (OAT) and other SLC22 transporters in progression of renal cell carcinoma. Cancers (Basel). MDPI AG; 2022 Sept 29;14(19):4772. PMCID: PMC9563088

6. Kumari A, Ayala-Ramirez R, Zenteno JC, Huffman K, Sasik R, Ayyagari R, Borooah S. Single cell RNA sequencing confirms retinal microglia activation associated with early onset retinal degeneration. Sci Rep. Springer Science and Business Media LLC; 2022 Sept 10;12(1):15273. PMCID: PMC9464204

7. Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, McHardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature. Springer Science and Business Media LLC; 2022 Sept;609(7925):101–108. PMCID: PMC9433318

8. Zapata RC, Carretero M, Reis FCG, Chaudry BS, Ofrecio J, Zhang D, Sasik R, Ciaraldi T, Petrascheck M, Osborn O. Adipocytes control food intake and weight regain via Vacuolar-type H+ ATPase. Nat Commun. Springer Science and Business Media LLC; 2022 Aug 30;13(1):5092. PMCID: PMC9427743

9. Hepokoski ML, Odish M, Lam MT, Coufal NG, Rolfsen ML, Shadel GS, Moyzis AG, Sainz AG, Takiar PG, Patel S, Leonard AJ, Samandari N, Hansen E, Trescott S, Nguyen C, Jepsen K, Cutter G, Gillespie MN, Spragg RG, Sasik R, Ix JH. Absolute quantification of plasma mitochondrial DNA by droplet digital PCR marks COVID-19 severity over time during intensive care unit admissions. Am J Physiol Lung Cell Mol Physiol. American Physiological Society; 2022 July 1;323(1):L84–L92. PMCID: PMC9273271

10. Soncin F, Morey R, Bui T, Requena DF, Cheung VC, Kallol S, Kittle R, Jackson MG, Farah O, Chousal J, Meads M, Pizzo D, Horii M, Fisch KM, Parast MM. Derivation of functional trophoblast stem cells from primed human pluripotent stem cells. Stem Cell Reports. Elsevier BV; 2022 June 14;17(6):1303–1317. PMCID: PMC9214048

11. Levitsky J, Kandpal M, Guo K, Zhao L, Kurian S, Whisenant T, Abecassis M. Prediction of liver transplant rejection with a biologically relevant gene expression signature. Transplantation. Ovid Technologies (Wolters Kluwer Health); 2022 May 1;106(5):1004–1011. PMCID: PMC9301991

12. Gabriel RA, Harjai B, Prasad RS, Simpson S, Chu I, Fisch KM, Said ET. Machine learning approach to predicting persistent opioid use following lower extremity joint arthroplasty. Reg Anesth Pain Med. BMJ; 2022 May;47(5):313–319. PMCID: PMC8961772

13. Berardi G, Frey-Law L, Sluka KA, Bayman EO, Coffey CS, Ecklund D, Vance CGT, Dailey DL, Burns J, Buvanendran A, McCarthy RJ, Jacobs J, Zhou XJ, Wixson R, Balach T, Brummett CM, Clauw D, Colquhoun D, Harte SE, Harris RE, Williams DA, Chang AC, Waljee J, Fisch KM, Jepsen K, Laurent LC, Olivier M, Langefeld CD, Howard TD, Fiehn O, Jacobs JM, Dakup P, Qian WJ, Swensen AC, Lokshin A, Lindquist M, Caffo BS, Crainiceanu C, Zeger S, Kahn A, Wager T, Taub M, Ford J, Sutherland SP, Wandner LD. Multi-site observational study to assess biomarkers for susceptibility or resilience to chronic pain: The acute to Chronic Pain Signatures (A2CPS) study protocol. Front Med (Lausanne). 2022 Apr 25;9:849214. PMCID: PMC9082267

14. Honda A, Hoeksema MA, Sakai M, Lund SJ, Lakhdari O, Butcher LD, Rambaldo TC, Sekiya NM, Nasamran CA, Fisch KM, Sajti E, Glass CK, Prince LS. The lung microenvironment instructs gene transcription in neonatal and adult alveolar macrophages. J Immunol. The American Association of Immunologists; 2022 Apr 15;208(8):1947–1959. PMCID: PMC9012679

15. Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, McHardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv [Internet]. 2022 Apr 4; Available from: http://dx.doi.org/10.1101/2021.12.21.21268143 PMCID: PMC8996633

16. Gonzalez CG, Mills RH, Kordahi MC, Carrillo-Terrazas M, Secaira-Morocho H, Widjaja CE, Tsai MS, Mittal Y, Yee BA, Vargas F, Weldon K, Gauglitz JM, Delaroque C, Sauceda C, Rossitto LA, Ackermann G, Humphrey G, Swafford AD, Siegel CA, Buckey JC Jr, Raffals LE, Sadler C, Lindholm P, Fisch KM, Valaseck M, Suriawinata A, Yeo GW, Ghosh P, Chang JT, Chu H, Dorrestein P, Zhu Q, Chassaing B, Knight R, Gonzalez DJ, Dulai PS. The host-microbiome response to hyperbaric oxygen therapy in ulcerative colitis patients. Cell Mol Gastroenterol Hepatol. Elsevier BV; 2022 Apr 1;14(1):35–53. PMCID: PMC9117812

17. Moshiri N, Fisch KM, Birmingham A, DeHoff P, Yeo GW, Jepsen K, Laurent LC, Knight R. The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction. Sci Rep. Springer Science and Business Media LLC; 2022 Mar 24;12(1):5077. PMCID: PMC8943356

18. Makowski C, van der Meer D, Dong W, Wang H, Wu Y, Zou J, Liu C, Rosenthal SB, Hagler DJ Jr, Fan CC, Kremen WS, Andreassen OA, Jernigan TL, Dale AM, Zhang K, Visscher PM, Yang J, Chen CH. Discovery of genomic loci of the human cerebral cortex using genetically informed brain atlases. Science. 2022 Feb 4;375(6580):522–528. PMCID: PMC9469470

19. Rosenthal SB, Wang H, Shi D, Liu C, Abagyan R, McEvoy LK, Chen CH. Mapping the gene network landscape of Alzheimer’s disease through integrating genomics and transcriptomics. PLoS Comput Biol. Public Library of Science (PLoS); 2022 Feb;18(2):e1009903. PMCID: PMC8906581

20. Saxena A, Sharma V, Muthuirulan P, Neufeld SJ, Tran MP, Gutierrez HL, Chen KD, Erberich JM, Birmingham A, Capellini TD, Cobb J, Hiller M, Cooper KL. Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas. Curr Biol. Elsevier BV; 2022 Jan 24;32(2):289-303.e6. PMCID: PMC8792248

21. Podvin S, Rosenthal SB, Poon W, Wei E, Fisch KM, Hook V. Mutant huntingtin protein interaction map implicates dysregulation of multiple cellular pathways in neurodegeneration of Huntington’s disease. J Huntingtons Dis. SAGE Publications; 2022;11(3):243–267. PMCID: PMC9484122

2021

1. Wang H, Rosenthal BS, Makowski C, Lo MT, Andreassen OA, Salem RM, McEvoy LK, Fiecas M, Chen CH. Causal association of cognitive reserve on Alzheimer’s disease with putative sex difference. Alzheimers Dement (Amst). Wiley; 2021 Dec 31;13(1):e12270. PMCID: PMC8719428

2. Pang J, Nguyen N, Luebeck J, Ball L, Finegersh A, Ren S, Nakagawa T, Flagg M, Sadat S, Mischel PS, Xu G, Fisch K, Guo T, Cahill G, Panuganti B, Bafna V, Califano J. Extrachromosomal DNA in HPV-mediated oropharyngeal cancer drives diverse oncogene transcription. Clin Cancer Res. American Association for Cancer Research (AACR); 2021 Dec 15;27(24):6772–6786. PMCID: PMC8710294

3. Rosenthal SB, Willsey HR, Xu Y, Mei Y, Dea J, Wang S, Curtis C, Sempou E, Khokha MK, Chi NC, Willsey AJ, Fisch KM, Ideker T. A convergent molecular network underlying autism and congenital heart disease. Cell Syst. Elsevier BV; 2021 Nov 17;12(11):1094-1107.e6. PMCID: PMC8602730

4. Moon JS, da Cunha FF, Huh JY, Andreyev AY, Lee J, Mahata SK, Reis FC, Nasamran CA, Lee YS. ANT2 drives proinflammatory macrophage activation in obesity. JCI Insight [Internet]. American Society for Clinical Investigation; 2021 Oct 22;6(20). Available from: http://dx.doi.org/10.1172/jci.insight.147033 PMCID: PMC8564915

5. Karlsson Linnér R, Mallard TT, Barr PB, Sanchez-Roige S, Madole JW, Driver MN, Poore HE, de Vlaming R, Grotzinger AD, Tielbeek JJ, Johnson EC, Liu M, Rosenthal SB, Ideker T, Zhou H, Kember RL, Pasman JA, Verweij KJH, Liu DJ, Vrieze S, COGA Collaborators, Kranzler HR, Gelernter J, Harris KM, Tucker-Drob EM, Waldman ID, Palmer AA, Harden KP, Koellinger PD, Dick DM. Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction. Nat Neurosci. Springer Science and Business Media LLC; 2021 Oct;24(10):1367–1376. PMCID: PMC8484054

6. Martin-Sancho L, Tripathi S, Rodriguez-Frandsen A, Pache L, Sanchez-Aparicio M, McGregor MJ, Haas KM, Swaney DL, Nguyen TT, Mamede JI, Churas C, Pratt D, Rosenthal SB, Riva L, Nguyen C, Beltran-Raygoza N, Soonthornvacharin S, Wang G, Jimenez-Morales D, De Jesus PD, Moulton HM, Stein DA, Chang MW, Benner C, Ideker T, Albrecht RA, Hultquist JF, Krogan NJ, García-Sastre A, Chanda SK. Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy. Nat Microbiol. Springer Science and Business Media LLC; 2021 Oct;6(10):1319–1333. PMCID: PMC9683089

7. Keehner J, Horton LE, Binkin NJ, Laurent LC, SEARCH Alliance, Pride D, Longhurst CA, Abeles SR, Torriani FJ. Resurgence of SARS-CoV-2 infection in a highly vaccinated health system workforce. N Engl J Med. Massachusetts Medical Society; 2021 Sept 30;385(14):1330–1332. PMCID: PMC8451183

8. Baglieri J, Zhang C, Liang S, Liu X, Nishio T, Rosenthal SB, Dhar D, Su H, Cong M, Jia J, Hosseini M, Karin M, Kisseleva T, Brenner DA. Nondegradable collagen increases liver fibrosis but not hepatocellular carcinoma in mice. Am J Pathol. Elsevier BV; 2021 Sept;191(9):1564–1579. PMCID: PMC8406794

9. Vasquez-Bolanos LS, Gibbons MC, Ruoss S, Wu IT, Vargas-Vila M, Hyman SA, Esparza MC, Fithian DC, Lane JG, Singh A, Nasamran CA, Fisch KM, Ward SR. Transcriptional time course after rotator cuff tear. Front Physiol. Frontiers Media SA; 2021 Aug 6;12:707116. PMCID: PMC8378535

10. Shoshani O, Bakker B, de Haan L, Tijhuis AE, Wang Y, Kim DH, Maldonado M, Demarest MA, Artates J, Zhengyu O, Mark A, Wardenaar R, Sasik R, Spierings DCJ, Vitre B, Fisch K, Foijer F, Cleveland DW. Transient genomic instability drives tumorigenesis through accelerated clonal evolution. Genes Dev. Cold Spring Harbor Laboratory; 2021 Aug 1;35(15–16):1093–1108. PMCID: PMC8336898

11. Rosenthal SB, Liu X, Ganguly S, Dhar D, Pasillas MP, Ricciardelli E, Li RZ, Troutman TD, Kisseleva T, Glass CK, Brenner DA. Heterogeneity of HSCs in a mouse model of NASH. Hepatology. Ovid Technologies (Wolters Kluwer Health); 2021 Aug;74(2):667–685. PMCID: PMC8346581

12. Nishio T, Koyama Y, Liu X, Rosenthal SB, Yamamoto G, Fuji H, Baglieri J, Li N, Brenner LN, Iwaisako K, Taura K, Hagood JS, LaRusso NF, Bera TK, Pastan I, Brenner DA, Kisseleva T. Immunotherapy-based targeting of MSLN+ activated portal fibroblasts is a strategy for treatment of cholestatic liver fibrosis. Proc Natl Acad Sci U S A. Proceedings of the National Academy of Sciences; 2021 July 20;118(29):e2101270118. PMCID: PMC8307749

13. Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Becker ME, Pratt D, Churas C, Rosenthal SB, Liu S, Weston S, De Jesus PD, O’Neill AM, Gounder AP, Nguyen C, Pu Y, Curry HM, Oom AL, Miorin L, Rodriguez-Frandsen A, Zheng F, Wu C, Xiong Y, Urbanowski M, Shaw ML, Chang MW, Benner C, Hope TJ, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK. Functional landscape of SARS-CoV-2 cellular restriction. Mol Cell. Elsevier BV; 2021 June 17;81(12):2656-2668.e8. PMCID: PMC8043580

14. Ganguly S, Muench GA, Shang L, Rosenthal SB, Rahman G, Wang R, Wang Y, Kwon HC, Diomino AM, Kisseleva T, Soorosh P, Hosseini M, Knight R, Schnabl B, Brenner DA, Dhar D. Nonalcoholic steatohepatitis and HCC in a hyperphagic mouse accelerated by Western diet. Cell Mol Gastroenterol Hepatol. Elsevier BV; 2021 May 29;12(3):891–920. PMCID: PMC8342972

15. Wang H, Lo MT, Rosenthal SB, Makowski C, Andreassen OA, Salem RM, McEvoy LK, Fiecas M, Chen CH. Similar genetic architecture of Alzheimer’s disease and differential APOE effect between sexes. Front Aging Neurosci. Frontiers Media SA; 2021 May 28;13:674318. PMCID: PMC8194397

16. Overbey EG, Saravia-Butler AM, Zhang Z, Rathi KS, Fogle H, da Silveira WA, Barker RJ, Bass JJ, Beheshti A, Berrios DC, Blaber EA, Cekanaviciute E, Costa HA, Davin LB, Fisch KM, Gebre SG, Geniza M, Gilbert R, Gilroy S, Hardiman G, Herranz R, Kidane YH, Kruse CPS, Lee MD, Liefeld T, Lewis NG, McDonald JT, Meller R, Mishra T, Perera IY, Ray S, Reinsch SS, Rosenthal SB, Strong M, Szewczyk NJ, Tahimic CGT, Taylor DM, Vandenbrink JP, Villacampa A, Weging S, Wolverton C, Wyatt SE, Zea L, Costes SV, Galazka JM. NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data. iScience. Elsevier BV; 2021 Apr 23;24(4):102361. PMCID: PMC8044432

17. Ruoss S, Walker JT, Nasamran CA, Fisch KM, Paez CJ, Parekh JN, Ball ST, Chen JL, Ahmed SS, Ward SR. Strategies to identify mesenchymal stromal cells in minimally manipulated human bone marrow aspirate concentrate lack consensus. Am J Sports Med. SAGE Publications; 2021 Apr;49(5):1313–1322. PMCID: PMC8409176

18. Zhou Y, Bastian IN, Long MD, Dow M, Li W, Liu T, Ngu RK, Antonucci L, Huang JY, Phung QT, Zhao XH, Banerjee S, Lin XJ, Wang H, Dang B, Choi S, Karin D, Su H, Ellisman MH, Jamieson C, Bosenberg M, Cheng Z, Haybaeck J, Kenner L, Fisch KM, Bourgon R, Hernandez G, Lill JR, Liu S, Carter H, Mellman I, Karin M, Shalapour S. Activation of NF-κB and p300/CBP potentiates cancer chemoimmunotherapy through induction of MHC-I antigen presentation. Proc Natl Acad Sci U S A. Proceedings of the National Academy of Sciences; 2021 Feb 23;118(8):e2025840118. PMCID: PMC7923353

19. Nasamran CA, Sachan ANS, Mott J, Kuras YI, Scherzer CR, Study HB, Ricciardelli E, Jepsen K, Edland SD, Fisch KM, Desplats P. Differential blood DNA methylation across Lewy body dementias. Alzheimers Dement (Amst). Wiley; 2021 Feb 20;13(1):e12156. PMCID: PMC7896631

20. Jiang Q, Isquith J, Ladel L, Mark A, Holm F, Mason C, He Y, Mondala P, Oliver I, Pham J, Ma W, Reynoso E, Ali S, Morris IJ, Diep R, Nasamran C, Xu G, Sasik R, Rosenthal SB, Birmingham A, Coso S, Pineda G, Crews L, Donohoe ME, Venter JC, Whisenant T, Mesa RA, Alexandrov LB, Fisch KM, Jamieson C. Inflammation-driven deaminase deregulation fuels human pre-leukemia stem cell evolution. Cell Rep. Elsevier BV; 2021 Jan 26;34(4):108670. PMCID: PMC8477897

21. Kurian SM, Whisenant TC, Marsh CL. Toward improved and standardized diagnostic pipelines in transplantation. Transplantation. Ovid Technologies (Wolters Kluwer Health); 2021 Jan 1;105(1):12–13. PMID: 33350625

2020

1. Rutter L, Barker R, Bezdan D, Cope H, Costes SV, Degoricija L, Fisch KM, Gabitto MI, Gebre S, Giacomello S, Gilroy S, Green SJ, Mason CE, Reinsch SS, Szewczyk NJ, Taylor DM, Galazka JM, Herranz R, Muratani M. A New Era for space life science: International Standards for Space Omics Processing. Patterns (N Y). Elsevier BV; 2020 Dec 11;1(9):100148. PMCID: PMC7733874

2. Liu T, Zhu B, Liu Y, Zhang X, Yin J, Li X, Jiang L, Hodges AP, Rosenthal SB, Zhou L, Yancey J, McQuade A, Blurton-Jones M, Tanzi RE, Huang TY, Xu H. Multi-omic comparison of Alzheimer’s variants in human ESC-derived microglia reveals convergence at APOE. J Exp Med [Internet]. 2020 Dec 7;217(12). Available from: http://dx.doi.org/10.1084/jem.20200474 PMCID: PMC7953740

3. 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. Springer Science and Business Media LLC; 2020 Dec;22(12):1411–1422. PMCID: PMC8092813

4. da Silveira WA, Fazelinia H, Rosenthal SB, Laiakis EC, Kim MS, Meydan C, Kidane Y, Rathi KS, Smith SM, Stear B, Ying Y, Zhang Y, Foox J, Zanello S, Crucian B, Wang D, Nugent A, Costa HA, Zwart SR, Schrepfer S, Elworth RAL, Sapoval N, Treangen T, MacKay M, Gokhale NS, Horner SM, Singh LN, Wallace DC, Willey JS, Schisler JC, Meller R, McDonald JT, Fisch KM, Hardiman G, Taylor D, Mason CE, Costes SV, Beheshti A. Comprehensive multi-omics analysis reveals mitochondrial stress as a central biological hub for spaceflight impact. Cell. Elsevier BV; 2020 Nov 25;183(5):1185-1201.e20. PMCID: PMC7870178

5. Brifault C, Romero H, Van-Enoo A, Pizzo D, Azmoon P, Kwon H, Nasamran C, Gonias SL, Campana WM. Deletion of the gene encoding the NMDA receptor GluN1 subunit in Schwann cells causes ultrastructural changes in Remak bundles and hypersensitivity in pain processing. J Neurosci. Society for Neuroscience; 2020 Nov 18;40(47):9121–9136. PMCID: PMC7672997

6. Bickler SW, Prieto JM, Cauvi DM, De Cos V, Nasamran C, Ameh E, Amin S, Nicholson S, Din H, Mocumbi AO, Noormahomed EV, Tellez-Isaias G, Fisch KM, De Maio A. Differential expression of nuclear genes encoding mitochondrial proteins from urban and rural populations in Morocco. Cell Stress Chaperones. Elsevier BV; 2020 Nov;25(6):847–856. PMCID: PMC7591688

7. Zapata RC, Rosenthal SB, Fisch K, Dao K, Jain M, Osborn O. Metabolomic profiles associated with a mouse model of antipsychotic-induced food intake and weight gain. Sci Rep. Springer Science and Business Media LLC; 2020 Oct 29;10(1):18581. PMCID: PMC7596057

8. Ren S, Gaykalova DA, Guo T, Favorov AV, Fertig EJ, Tamayo P, Callejas-Valera JL, Allevato M, Gilardi M, Santos J, Fukusumi T, Sakai A, Ando M, Sadat S, Liu C, Xu G, Fisch KM, Wang Z, Molinolo AA, Gutkind JS, Ideker T, Koch WM, Califano JA. HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers. Oncogene. Springer Science and Business Media LLC; 2020 Oct;39(40):6327–6339. PMCID: PMC7529583

9. Koch E, Rosenthal B, Lundquist A, Chen CH, Kauppi K. Interactome overlap between schizophrenia and cognition. Schizophr Res. Elsevier BV; 2020 Aug;222:167–174. PMID: 32546371

10. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O’Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O’Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d’Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. Springer Science and Business Media LLC; 2020 July;583(7816):459–468. PMCID: PMC7431030

11. Estaki M, Jiang L, Bokulich NA, McDonald D, González A, Kosciolek T, Martino C, Zhu Q, Birmingham A, Vázquez-Baeza Y, Dillon MR, Bolyen E, Caporaso JG, Knight R. QIIME 2 enables comprehensive end-to-end analysis of diverse microbiome data and comparative studies with publicly available data. Curr Protoc Bioinformatics. Wiley; 2020 June;70(1):e100. PMCID: PMC9285460

12. Shires SE, Quiles JM, Najor RH, Leon LJ, Cortez MQ, Lampert MA, Mark A, Gustafsson ÅB. Nuclear Parkin activates the ERRα transcriptional program and drives widespread changes in gene expression following hypoxia. Sci Rep. Springer Science and Business Media LLC; 2020 May 22;10(1):8499. PMCID: PMC7244578

13. Sakai A, Ando M, Fukusumi T, Ren S, Liu C, Qualliotine J, Haft S, Sadat S, Saito Y, Guo TW, Xu G, Sasik R, Fisch KM, Gutkind JS, Fertig EJ, Molinolo AA, Califano JA. Aberrant expression of CPSF1 promotes head and neck squamous cell carcinoma via regulating alternative splicing. PLoS One. Public Library of Science (PLoS); 2020 May 21;15(5):e0233380. PMCID: PMC7241804

14. Liu X, Xu J, Rosenthal S, Zhang LJ, McCubbin R, Meshgin N, Shang L, Koyama Y, Ma HY, Sharma S, Heinz S, Glass CK, Benner C, Brenner DA, Kisseleva T. Identification of lineage-specific transcription factors that prevent activation of hepatic stellate cells and promote fibrosis resolution. Gastroenterology. Elsevier BV; 2020 May;158(6):1728-1744.e14. PMCID: PMC7252905

15. Ma HY, Yamamoto G, Xu J, Liu X, Karin D, Kim JY, Alexandrov LB, Koyama Y, Nishio T, Benner C, Heinz S, Rosenthal SB, Liang S, Sun M, Karin G, Zhao P, Brodt P, Mckillop IH, Quehenberger O, Dennis E, Saltiel A, Tsukamoto H, Gao B, Karin M, Brenner DA, Kisseleva T. IL-17 signaling in steatotic hepatocytes and macrophages promotes hepatocellular carcinoma in alcohol-related liver disease. J Hepatol. Elsevier BV; 2020 May;72(5):946–959. PMCID: PMC7167339

16. Ryan AF, Nasamran CA, Pak K, Draf C, Fisch KM, Webster N, Kurabi A. Single-cell transcriptomes reveal a complex cellular landscape in the middle ear and differential capacities for acute response to infection. Front Genet. Frontiers Media SA; 2020 Apr 15;11:358. PMCID: PMC7174727

17. Bajaj J, Hamilton M, Shima Y, Chambers K, Spinler K, Van Nostrand EL, Yee BA, Blue SM, Chen M, Rizzeri D, Chuah C, Oehler VG, Broome HE, Sasik R, Scott-Browne J, Rao A, Yeo GW, Reya T. An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia. Nat Cancer. Springer Science and Business Media LLC; 2020 Apr;1(4):410–422. PMCID: PMC8186448

18. Saito Y, Favorov AV, Forman M, Ren S, Sakai A, Fukusumi T, Liu C, Sadat S, Ando M, Xu G, Khan Z, Pang J, Valsamakis A, Fisch KM, Califano JA. Rational genomic optimization of DNA detection for human papillomavirus type 16 in head and neck squamous cell carcinoma. Head Neck. Wiley; 2020 Apr;42(4):688–697. PMCID: PMC7699136

19. Liu X, Rosenthal SB, Meshgin N, Baglieri J, Musallam SG, Diggle K, Lam K, Wu R, Pan SQ, Chen Y, Dorko K, Presnell S, Benner C, Hosseini M, Tsukamoto H, Brenner D, Kisseleva T. Primary alcohol-activated human and mouse hepatic stellate cells share similarities in gene-expression profiles. Hepatol Commun. Ovid Technologies (Wolters Kluwer Health); 2020 Apr;4(4):606–626. PMCID: PMC7109347

20. Svensson K, LaBarge SA, Sathe A, Martins VF, Tahvilian S, Cunliffe JM, Sasik R, Mahata SK, Meyer GA, Philp A, David LL, Ward SR, McCurdy CE, Aslan JE, Schenk S. p300 and cAMP response element-binding protein-binding protein in skeletal muscle homeostasis, contractile function, and survival. J Cachexia Sarcopenia Muscle. Wiley; 2020 Apr;11(2):464–477. PMCID: PMC7113519

21. Shahidi B, Fisch KM, Gibbons MC, Ward SR. Increased fibrogenic gene expression in multifidus muscles of patients with chronic versus acute lumbar spine pathology. Spine (Phila Pa 1976). Ovid Technologies (Wolters Kluwer Health); 2020 Feb 15;45(4):E189–E195. PMCID: PMC6994378

22. Xu J, Ma HY, Liu X, Rosenthal S, Baglieri J, McCubbin R, Sun M, Koyama Y, Geoffroy CG, Saijo K, Shang L, Nishio T, Maricic I, Kreifeldt M, Kusumanchi P, Roberts A, Zheng B, Kumar V, Zengler K, Pizzo DP, Hosseini M, Contet C, Glass CK, Liangpunsakul S, Tsukamoto H, Gao B, Karin M, Brenner DA, Koob GF, Kisseleva T. Blockade of IL-17 signaling reverses alcohol-induced liver injury and excessive alcohol drinking in mice. JCI Insight [Internet]. American Society for Clinical Investigation; 2020 Feb 13;5(3). Available from: http://dx.doi.org/10.1172/jci.insight.131277 PMCID: PMC7098802

23. Sowa JN, Jiang H, Somasundaram L, Tecle E, Xu G, Wang D, Troemel ER. The Caenorhabditis elegans RIG-I homolog DRH-1 mediates the intracellular pathogen response upon viral infection. J Virol [Internet]. American Society for Microbiology; 2020 Jan 6;94(2). Available from: http://dx.doi.org/10.1128/JVI.01173-19 PMCID: PMC6955277

2019

1. Shiga Y, Shiga A, Mesci P, Kwon H, Brifault C, Kim JH, Jeziorski JJ, Nasamran C, Ohtori S, Muotri AR, Gonias SL, Campana WM. Tissue-type plasminogen activator-primed human iPSC-derived neural progenitor cells promote motor recovery after severe spinal cord injury. Sci Rep. Springer Science and Business Media LLC; 2019 Dec 17;9(1):19291. PMCID: PMC6917728

2. Ventura CG, Whisenant T, Gelbart T, David DSR, Agena F, Salomon DR, David-Neto E, Kurian SM. Discovery and cross-validation of peripheral blood and renal biopsy gene expression signatures from ethnically diverse kidney transplant populations. Am J Transplant. Elsevier BV; 2019 Dec;19(12):3356–3366. PMCID: PMC6883121

3. Narayanan JSS, Ray P, Hayashi T, Whisenant TC, Vicente D, Carson DA, Miller AM, Schoenberger SP, White RR. Irreversible electroporation combined with checkpoint blockade and TLR7 stimulation induces antitumor immunity in a Murine pancreatic cancer model. Cancer Immunol Res. American Association for Cancer Research (AACR); 2019 Oct;7(10):1714–1726. PMCID: PMC6774877

4. Weathington N, O’Brien ME, Radder J, Whisenant TC, Bleecker ER, Busse WW, Erzurum SC, Gaston B, Hastie AT, Jarjour NN, Meyers DA, Milosevic J, Moore WC, Tedrow JR, Trudeau JB, Wong HP, Wu W, Kaminski N, Wenzel SE, Modena BD. BAL cell gene expression in severe asthma reveals mechanisms of severe disease and influences of medications. Am J Respir Crit Care Med. Oxford University Press (OUP); 2019 Oct 1;200(7):837–856. PMCID: PMC6812436

5. Diaz Osterman CJ, Ozmadenci D, Kleinschmidt EG, Taylor KN, Barrie AM, Jiang S, Bean LM, Sulzmaier FJ, Jean C, Tancioni I, Anderson K, Uryu S, Cordasco EA, Li J, Chen XL, Fu G, Ojalill M, Rappu P, Heino J, Mark AM, Xu G, Fisch KM, Kolev VN, Weaver DT, Pachter JA, Győrffy B, McHale MT, Connolly DC, Molinolo A, Stupack DG, Schlaepfer DD. FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy. Elife [Internet]. eLife Sciences Publications, Ltd; 2019 Sept 3;8(e47327). Available from: http://dx.doi.org/10.7554/eLife.47327 PMCID: PMC6721800

6. Nishio T, Hu R, Koyama Y, Liang S, Rosenthal SB, Yamamoto G, Karin D, Baglieri J, Ma HY, Xu J, Liu X, Dhar D, Iwaisako K, Taura K, Brenner DA, Kisseleva T. Activated hepatic stellate cells and portal fibroblasts contribute to cholestatic liver fibrosis in MDR2 knockout mice. J Hepatol. Elsevier BV; 2019 Sept;71(3):573–585. PMID: 31071368

7. Rosenthal SB, Bush KT, Nigam SK. A network of SLC and ABC transporter and DME genes involved in Remote Sensing and signaling in the gut-liver-kidney axis. Sci Rep. Springer Science and Business Media LLC; 2019 Aug 15;9(1):11879. PMCID: PMC6695406

8. Canchi S, Raao B, Masliah D, Rosenthal SB, Sasik R, Fisch KM, De Jager PL, Bennett DA, Rissman RA. Integrating gene and protein expression reveals perturbed functional networks in Alzheimer’s disease. Cell Rep. Elsevier BV; 2019 July 23;28(4):1103-1116.e4. PMCID: PMC7503200

9. Haft S, Ren S, Xu G, Mark A, Fisch K, Guo TW, Khan Z, Pang J, Ando M, Liu C, Sakai A, Fukusumi T, Califano JA. Mutation of chromatin regulators and focal hotspot alterations characterize human papillomavirus-positive oropharyngeal squamous cell carcinoma. Cancer. Wiley; 2019 July 15;125(14):2423–2434. PMCID: PMC6602825

10. Rule A, Birmingham A, Zuniga C, Altintas I, Huang SC, Knight R, Moshiri N, Nguyen MH, Rosenthal SB, Pérez F, Rose PW. Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. PLoS Comput Biol. Public Library of Science (PLoS); 2019 July;15(7):e1007007. PMCID: PMC6657818

11. Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA. Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun. Springer Science and Business Media LLC; 2019 May 29;10(1):2415. PMCID: PMC6541594

12. Coras R, Kavanaugh A, Boyd T, Huynh D, Lagerborg KA, Xu YJ, Rosenthal SB, Jain M, Guma M. Choline metabolite, trimethylamine N-oxide (TMAO), is associated with inflammation in psoriatic arthritis. Clin Exp Rheumatol. 2019 May;37(3):481–484. PMCID: PMC6529247

13. Lytle NK, Ferguson LP, Rajbhandari N, Gilroy K, Fox RG, Deshpande A, Schürch CM, Hamilton M, Robertson N, Lin W, Noel P, Wartenberg M, Zlobec I, Eichmann M, Galván JA, Karamitopoulou E, Gilderman T, Esparza LA, Shima Y, Spahn P, French R, Lewis NE, Fisch KM, Sasik R, Rosenthal SB, Kritzik M, Von Hoff D, Han H, Ideker T, Deshpande AJ, Lowy AM, Adams PD, Reya T. A multiscale map of the stem cell state in pancreatic adenocarcinoma. Cell. Elsevier BV; 2019 Apr 18;177(3):572-586.e22. PMCID: PMC6711371

14. Henderson-Smith A, Fisch KM, Hua J, Liu G, Ricciardelli E, Jepsen K, Huentelman M, Stalberg G, Edland SD, Scherzer CR, Dunckley T, Desplats P. DNA methylation changes associated with Parkinson’s disease progression: outcomes from the first longitudinal genome-wide methylation analysis in blood. Epigenetics. Informa UK Limited; 2019 Apr;14(4):365–382. PMCID: PMC6557551

15. Wallace ZS, Rosenthal SB, Fisch KM, Ideker T, Sasik R. On entropy and information in gene interaction networks. Bioinformatics. Oxford University Press (OUP); 2019 Mar 1;35(5):815–822. PMCID: PMC7245360

16. Gleber-Netto FO, Rao X, Guo T, Xi Y, Gao M, Shen L, Erikson K, Kalu NN, Ren S, Xu G, Fisch KM, Akagi K, Seiwert T, Gillison M, Frederick MJ, Johnson FM, Wang J, Myers JN, Califano J, Skinner HD, Pickering CR. Variations in HPV function are associated with survival in squamous cell carcinoma. JCI Insight. American Society for Clinical Investigation; 2019 Jan 10;4(1):e124762. PMCID: PMC6485353

17. Fisch KM. Biological interpretation of complex genomic data. Methods Mol Biol. 2019;1908:61–71. PMCID: PMC7269365

18. Friedewald JJ, Kurian SM, Heilman RL, Whisenant TC, Poggio ED, Marsh C, Baliga P, Odim J, Brown MM, Ikle DN, Armstrong BD, Charette JI, Brietigam SS, Sustento-Reodica N, Zhao L, Kandpal M, Salomon DR, Abecassis MM, Clinical Trials in Organ Transplantation 08 (CTOT-08). Development and clinical validity of a novel blood-based molecular biomarker for subclinical acute rejection following kidney transplant. Am J Transplant. 2019 Jan;19(1):98–109. PMCID: PMC6387870

2018

1. Fisch KM, Gamini R, Alvarez-Garcia O, Akagi R, Saito M, Muramatsu Y, Sasho T, Koziol JA, Su AI, Lotz MK. Identification of transcription factors responsible for dysregulated networks in human osteoarthritis cartilage by global gene expression analysis. Osteoarthritis Cartilage. Elsevier BV; 2018 Nov;26(11):1531–1538. PMCID: PMC6245598

2. Meyer AN, Gallo LH, Ko J, Cardenas G, Nelson KN, Siari A, Campos AR, Whisenant TC, Donoghue DJ. Oncogenic mutations in IKKβ function through global changes induced by K63-linked ubiquitination and result in autocrine stimulation. PLoS One. Public Library of Science (PLoS); 2018 Oct 18;13(10):e0206014. PMCID: PMC6193727

3. Liu C, Guo T, Xu G, Sakai A, Ren S, Fukusumi T, Ando M, Sadat S, Saito Y, Khan Z, Fisch KM, Califano J. Characterization of alternative splicing events in HPV-negative head and neck squamous cell carcinoma identifies an oncogenic DOCK5 variant. Clin Cancer Res. 2018 Oct 15;24(20):5123–5132. PMCID: PMC6440699

4. Garcia-Carbonell R, Wong J, Kim JY, Close LA, Boland BS, Wong TL, Harris PA, Ho SB, Das S, Ernst PB, Sasik R, Sandborn WJ, Bertin J, Gough PJ, Chang JT, Kelliher M, Boone D, Guma M, Karin M. Elevated A20 promotes TNF-induced and RIPK1-dependent intestinal epithelial cell death. Proc Natl Acad Sci U S A. Proceedings of the National Academy of Sciences; 2018 Sept 25;115(39):E9192–E9200. PMCID: PMC6166836

5. Finger AJ, Mahardja B, Fisch KM, Benjamin A, Lindberg J, Ellison L, Ghebremariam T, Hung TC, May B. A conservation hatchery population of delta smelt shows evidence of genetic adaptation to captivity after 9 generations. J Hered. 2018 Aug 24;109(6):689–699. PMID: 30016452

6. Birmingham A, Mark AM, Mazzaferro C, Xu G, Fisch KM. Efficient population-scale variant analysis and prioritization with VAPr. Bioinformatics. 2018 Aug 15;34(16):2843–2845. PMCID: PMC6084604

7. Narasimhan R, Coras R, Rosenthal SB, Sweeney SR, Lodi A, Tiziani S, Boyle D, Kavanaugh A, Guma M. Serum metabolomic profiling predicts synovial gene expression in rheumatoid arthritis. Arthritis Res Ther. 2018 Aug 3;20(1):164. PMCID: PMC6091066

8. Kauppi K, Rosenthal SB, Lo MT, Sanyal N, Jiang M, Abagyan R, McEvoy LK, Andreassen OA, Chen CH. Revisiting antipsychotic drug actions through gene networks associated with schizophrenia. Am J Psychiatry. American Psychiatric Association Publishing; 2018 July 1;175(7):674–682. PMCID: PMC6028303

9. Velimezi G, Robinson-Garcia L, Muñoz-Martínez F, Wiegant WW, Ferreira da Silva J, Owusu M, Moder M, Wiedner M, Rosenthal SB, Fisch KM, Moffat J, Menche J, van Attikum H, Jackson SP, Loizou JI. Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48. Nat Commun. Springer Science and Business Media LLC; 2018 June 11;9(1):2280. PMCID: PMC5996029

10. Scully KM, Lahmy R, Signaevskaia L, Sasik R, Medal R, Kim H, French R, James B, Wu Y, Lowy AM, Itkin-Ansari P. E47 governs the MYC-CDKN1B/p27KIP1-RB network to growth arrest PDA cells independent of CDKN2A/p16INK4A and wild-type p53. Cell Mol Gastroenterol Hepatol. 2018 May 16;6(2):181–198. PMCID: PMC6039985

11. Bloss CS, Stoler J, Schairer CE, Rosenthal SB, Cheung C, Rus HM, Block JL, Yang JAJ, Morton D, Bixenman H, Wellis D. Characteristics of likely precision medicine initiative participants drawn from A large blood donor population. Health Aff (Millwood). 2018 May;37(5):786–792. PMID: 29733733

12. Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet. 2018 Apr;50(4):613–620. PMCID: PMC5893414

13. Chen K, Jih A, Osborn O, Kavaler ST, Fu W, Sasik R, Saito R, Kim JJ. Distinct gene signatures predict insulin resistance in young mice with high fat diet-induced obesity. Physiol Genomics. 2018 Mar 1;50(3):144–157. PMCID: PMC5899230

14. Zhao D, Badur MG, Luebeck J, Magaña JH, Birmingham A, Sasik R, Ahn CS, Ideker T, Metallo CM, Mali P. Combinatorial CRISPR-Cas9 metabolic screens reveal critical redox control points dependent on the KEAP1-NRF2 regulatory axis. Mol Cell. Elsevier BV; 2018 Feb 15;69(4):699-708.e7. PMCID: PMC5819357

15. Gibbons MC, Fisch KM, Pichika R, Cheng T, Engler AJ, Schenk S, Lane JG, Singh A, Ward SR. Heterogeneous muscle gene expression patterns in patients with massive rotator cuff tears. PLoS One. 2018 Jan 2;13(1):e0190439. PMCID: PMC5749784

16. Rosenthal SB, Len J, Webster M, Gary A, Birmingham A, Fisch KM. Interactive network visualization in Jupyter notebooks: visJS2jupyter. Bioinformatics. 2018 Jan 1;34(1):126–128. PMCID: PMC6075087

2017

1. Balakrishnan A, Gloude N, Sasik R, Ball ED, Morris GP. Proinflammatory dual receptor T cells in chronic graft-versus-host disease. Biol Blood Marrow Transplant. 2017 Nov;23(11):1852–1860. PMCID: PMC5682197

2. Ying W, Riopel M, Bandyopadhyay G, Dong Y, Birmingham A, Seo JB, Ofrecio JM, Wollam J, Hernandez-Carretero A, Fu W, Li P, Olefsky JM. Adipose tissue macrophage-derived exosomal miRNAs can modulate in vivo and in vitro insulin sensitivity. Cell. Elsevier BV; 2017 Oct 5;171(2):372-384.e12. PMID: 28942920

3. Widjaja CE, Olvera JG, Metz PJ, Phan AT, Savas JN, de Bruin G, Leestemaker Y, Berkers CR, de Jong A, Florea BI, Fisch K, Lopez J, Kim SH, Garcia DA, Searles S, Bui JD, Chang AN, Yates JR 3rd, Goldrath AW, Overkleeft HS, Ovaa H, Chang JT. Proteasome activity regulates CD8+ T lymphocyte metabolism and fate specification. J Clin Invest. 2017 Oct 2;127(10):3609–3623. PMCID: PMC5617668

4. Kesby JP, Najera JA, Romoli B, Fang Y, Basova L, Birmingham A, Marcondes MCG, Dulcis D, Semenova S. HIV-1 TAT protein enhances sensitization to methamphetamine by affecting dopaminergic function. Brain Behav Immun. 2017 Oct;65:210–221. PMCID: PMC5537017

5. Isoda T, Moore AJ, He Z, Chandra V, Aida M, Denholtz M, Piet van Hamburg J, Fisch KM, Chang AN, Fahl SP, Wiest DL, Murre C. Non-coding transcription instructs chromatin folding and compartmentalization to dictate enhancer-promoter communication and T cell fate. Cell. 2017 Sept 21;171(1):103-119.e18. PMCID: PMC5621651

6. Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. Springer Science and Business Media LLC; 2017 June;14(6):573–576. PMCID: PMC5449203

7. Akagi R, Akatsu Y, Fisch KM, Alvarez-Garcia O, Teramura T, Muramatsu Y, Saito M, Sasho T, Su AI, Lotz MK. Dysregulated circadian rhythm pathway in human osteoarthritis: NR1D1 and BMAL1 suppression alters TGF-β signaling in chondrocytes. Osteoarthritis Cartilage. Elsevier BV; 2017 June;25(6):943–951. PMCID: PMC5438901

8. Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo GW, Gutkind JS, Ideker T. Interaction landscape of inherited polymorphisms with somatic events in cancer. Cancer Discov. 2017 Apr;7(4):410–423. PMCID: PMC5460679

9. Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, Lozupone C, Zaneveld JR, Vázquez-Baeza Y, Birmingham A, Hyde ER, Knight R. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. Springer Science and Business Media LLC; 2017 Mar 3;5(1):27. PMCID: PMC5335496

10. Cowell AN, Loy DE, Sundararaman SA, Valdivia H, Fisch K, Lescano AG, Baldeviano GC, Durand S, Gerbasi V, Sutherland CJ, Nolder D, Vinetz JM, Hahn BH, Winzeler EA. Selective whole-genome amplification is a robust method that enables scalable whole-genome sequencing of Plasmodium vivax from unprocessed clinical samples. MBio [Internet]. American Society for Microbiology; 2017 Feb 7;8(1). Available from: http://dx.doi.org/10.1128/mBio.02257-16 PMCID: PMC5296604

2016

1. Kaneda MM, Messer KS, Ralainirina N, Li H, Leem CJ, Gorjestani S, Woo G, Nguyen AV, Figueiredo CC, Foubert P, Schmid MC, Pink M, Winkler DG, Rausch M, Palombella VJ, Kutok J, McGovern K, Frazer KA, Wu X, Karin M, Sasik R, Cohen EEW, Varner JA. PI3Kγ is a molecular switch that controls immune suppression. Nature. Springer Science and Business Media LLC; 2016 Nov 17;539(7629):437–442. PMCID: PMC5479689

2. Chen S, Miyazaki M, Chandra V, Fisch KM, Chang AN, Murre C. Id3 orchestrates germinal center B cell development. Mol Cell Biol. Informa UK Limited; 2016 Oct 15;36(20):2543–2552. PMCID: PMC5038142

3. Alvarez-Garcia O, Olmer M, Akagi R, Akasaki Y, Fisch KM, Shen T, Su AI, Lotz MK. Suppression of REDD1 in osteoarthritis cartilage, a novel mechanism for dysregulated mTOR signaling and defective autophagy. Osteoarthritis Cartilage. 2016 Sept;24(9):1639–1647. PMCID: PMC4992644

4. Kaneda MM, Cappello P, Nguyen AV, Ralainirina N, Hardamon CR, Foubert P, Schmid MC, Sun P, Mose E, Bouvet M, Lowy AM, Valasek MA, Sasik R, Novelli F, Hirsch E, Varner JA. Macrophage PI3Kγ drives pancreatic ductal adenocarcinoma progression. Cancer Discov. 2016 Aug;6(8):870–885. PMCID: PMC5091937

5. Alvarez-Garcia O, Fisch KM, Wineinger NE, Akagi R, Saito M, Sasho T, Su AI, Lotz MK. Increased DNA methylation and reduced expression of transcription factors in human osteoarthritis cartilage. Arthritis Rheumatol. 2016 Aug;68(8):1876–1886. PMCID: PMC4963260

6. Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, Zhou J, Knight R. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. Oxford University Press (OUP); 2016 July;10(7):1669–1681. PMCID: PMC4918442

7. Fox RG, Lytle NK, Jaquish DV, Park FD, Ito T, Bajaj J, Koechlein CS, Zimdahl B, Yano M, Kopp J, Kritzik M, Sicklick J, Sander M, Grandgenett PM, Hollingsworth MA, Shibata S, Pizzo D, Valasek M, Sasik R, Scadeng M, Okano H, Kim Y, MacLeod AR, Lowy AM, Reya T. Image-based detection and targeting of therapy resistance in pancreatic adenocarcinoma. Nature. 2016 June 16;534(7607):407–411. PMCID: PMC4998062

8. Banno A, Garcia DA, van Baarsel ED, Metz PJ, Fisch K, Widjaja CE, Kim SH, Lopez J, Chang AN, Geurink PP, Florea BI, Overkleeft HS, Ovaa H, Bui JD, Yang J, Chang JT. Downregulation of 26S proteasome catalytic activity promotes epithelial-mesenchymal transition. Oncotarget. 2016 Apr 19;7(16):21527–21541. PMCID: PMC5008303

2015

1. McDonald D, Birmingham A, Knight R. Context and the human microbiome. Microbiome. Springer Science and Business Media LLC; 2015 Nov 4;3(1):52. PMCID: PMC4632476

2. Kwon HY, Bajaj J, Ito T, Blevins A, Konuma T, Weeks J, Lytle NK, Koechlein CS, Rizzieri D, Chuah C, Oehler VG, Sasik R, Hardiman G, Reya T. Tetraspanin 3 is required for the development and propagation of acute Myelogenous Leukemia. Cell Stem Cell. Elsevier BV; 2015 Aug 6;17(2):152–164. PMCID: PMC4664079

3. Bossen C, Murre CS, Chang AN, Mansson R, Rodewald HR, Murre C. The chromatin remodeler Brg1 activates enhancer repertoires to establish B cell identity and modulate cell growth. Nat Immunol. Springer Science and Business Media LLC; 2015 July;16(7):775–784. PMCID: PMC4474778

4. Kashyap MK, Kumar D, Villa R, La Clair JJ, Benner C, Sasik R, Jones H, Ghia EM, Rassenti LZ, Kipps TJ, Burkart MD, Castro JE. Targeting the spliceosome in chronic lymphocytic leukemia with the macrolides FD-895 and pladienolide-B. Haematologica. Ferrata Storti Foundation (Haematologica); 2015 July;100(7):945–954. PMCID: PMC4486229

5. Fisch KM, Meißner T, Gioia L, Ducom JC, Carland TM, Loguercio S, Su AI. Omics Pipe: a community-based framework for reproducible multi-omics data analysis. Bioinformatics. Oxford University Press (OUP); 2015 June 1;31(11):1724–1728. PMCID: PMC4443682

6. Meißner T, Fisch KM, Gioia L, Su AI. OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing. BMC Med Genomics. Springer Science and Business Media LLC; 2015 May 21;8(1):24. PMCID: PMC4494802

7. Patel V, Carrion K, Hollands A, Hinton A, Gallegos T, Dyo J, Sasik R, Leire E, Hardiman G, Mohamed SA, Nigam S, King CC, Nizet V, Nigam V. The stretch responsive microRNA miR-148a-3p is a novel repressor of IKBKB, NF-κB signaling, and inflammatory gene expression in human aortic valve cells. FASEB J. Wiley; 2015 May;29(5):1859–1868. PMCID: PMC4771066

8. Miyazaki M, Miyazaki K, Chen S, Chandra V, Wagatsuma K, Agata Y, Rodewald HR, Saito R, Chang AN, Varki N, Kawamoto H, Murre C. The E-Id protein axis modulates the activities of the PI3K-AKT-mTORC1-Hif1a and c-myc/p19Arf pathways to suppress innate variant TFH cell development, thymocyte expansion, and lymphomagenesis. Genes Dev. Cold Spring Harbor Laboratory; 2015 Feb 15;29(4):409–425. PMCID: PMC4335296

9. Banerjee I, Carrion K, Serrano R, Dyo J, Sasik R, Lund S, Willems E, Aceves S, Meili R, Mercola M, Chen J, Zambon A, Hardiman G, Doherty TA, Lange S, del Álamo JC, Nigam V. Cyclic stretch of embryonic cardiomyocytes increases proliferation, growth, and expression while repressing Tgf-β signaling. J Mol Cell Cardiol. Elsevier BV; 2015 Feb;79:133–144. PMCID: PMC4302020