Publications

2024:

  1. Multi-Modal Analysis of human Hepatic Stellate Cells identifies novel therapeutic targets for Metabolic Dysfunction-Associated Steatotic Liver Disease. J Hepatol. 2024 Nov 08. 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. PMID: 39522884.
  2. Lipid-associated macrophages’ promotion of fibrosis resolution during MASH regression requires TREM2. Proc Natl Acad Sci U S A. 2024 Aug 27; 121(35):e2405746121. 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. PMID: 39172787; PMCID: PMC11363294.
  3. The genomic landscape of Ménière’s disease: a path to endolymphatic hydrops. BMC Genomics. 2024 Jun 28; 25(1):646. Fisch KM, Rosenthal SB, Mark A, Sasik R, Nasamran CA, Clifford R, Derebery MJ, Boussaty E, Jepsen K, Harris J, Friedman RA. PMID: 38943082; PMCID: PMC11212243.
  4. Lithium response in bipolar disorder is associated with focal adhesion and PI3K-Akt networks: a multi-omics replication study. Transl Psychiatry. 2024 Feb 23; 14(1):109. 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. PMID: 38395906; PMCID: PMC10891068.
  5. Axon-derived PACSIN1 binds to the Schwann cell survival receptor, LRP1, and transactivates TrkC to promote gliatrophic activities. Glia. 2024 05; 72(5):916-937. 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. PMID: 38372375.
  6. Comparative single-cell transcriptional and proteomic atlas of clinical-grade injectable mesenchymal source tissues. Sci Adv. 2024 Jul 12; 10(28):eadn2831. 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. PMID: 38996032; PMCID: PMC11244553.
  7. Neuronal activity-driven O-GlcNAcylation promotes mitochondrial plasticity. Dev Cell. 2024 Aug 19; 59(16):2143-2157.e9. 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. PMID: 38843836; PMCID: PMC11338717.
  8. PI3Kγ inhibition circumvents inflammation and vascular leak in SARS-CoV-2 and other infections. Sci Transl Med. 2024 Jul 03; 16(754):eadi6887. 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, E Alexander LC, 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. PMID: 38959328; PMCID: PMC11272418.
  9. RNA editing regulates host immune response and T cell homeostasis in SARS-CoV-2 infection. PLoS One. 2024; 19(8):e0307450. Huang M, Mark A, Pham J, Vera K, Saravia-Butler AM, Beheshti A, Jiang Q, Fisch KM. PMID: 39178184; PMCID: PMC11343423.
  10. Aspirin resistance in pregnancy is associated with reduced interleukin-2 (IL-2) concentrations in maternal serum: Implications for aspirin prophylaxis for preeclampsia. Pregnancy Hypertens. 2024 Jun 07; 37:101131. 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. PMID: 38851168.
  11. 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. 2024 08; 187:241-248. Aisagbonhi O, Ghlichloo I, Hong DS, Roma A, Fadare O, Eskander R, Saenz C, Fisch KM, Song W. PMID: 38833993.
  12. Cord Blood Adductomics Reveals Oxidative Stress Exposure Pathways of Bronchopulmonary Dysplasia. Antioxidants (Basel). 2024 Apr 20; 13(4). Lin ET, Bae Y, Birkett R, Sharma AM, Zhang R, Fisch KM, Funk W, Mestan KK. PMID: 38671941; PMCID: PMC11047351.
  13. Chronic villitis as a distinctive feature of placental injury in maternal SARS-CoV-2 infection. Am J Obstet Gynecol. 2024 Apr 03. 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. PMID: 38580043.
  14. Nuclear morphology is shaped by loop-extrusion programs. Nature. 2024 Mar; 627(8002):196-203. 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. PMID: 38355805; PMCID: PMC11052650.
  15. Lipopolysaccharide-induced chronic inflammation increases female serum gonadotropins and shifts the pituitary transcriptomic landscape. Front Endocrinol (Lausanne). 2023; 14:1279878. 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. PMID: 38260148; PMCID: PMC10801245.
  16. 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. 2024;17(1):93–106

2023:

  1. 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 [Internet]. 2023 Dec 28; Available from: http://dx.doi.org/10.1016/j.ajpath.2023.12.005
  2. 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. 2023 Nov 29;15(724):eabp9599.
  3. 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. 2023 Oct;76:101794.
  4. 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. 2023 Dec;144:13–22.
  5. 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. 2023 Dec 21;186(26):5690–704.e20.
  6. 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 [Internet]. 2023 Nov 16
  7. 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 [Internet]. 2023 Sep 1;15(17). Available from: http://dx.doi.org/10.3390/cancers15174379
  8. Rivera M, Zhang H, Pham J, Isquith J, Zhou QJ, Sasik R, 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. Res Sq [Internet]. 2023 Jun 16; Available from: http://dx.doi.org/10.21203/rs.3.rs-2444524/v2
  9. 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. 2023 Sep 1;164(9):1912–26.
  10. 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. 2023 Aug 29;42(8):112873.
  11. Maladaptive lymphangiogenesis is associated with synovial iron accumulation and delayed Clearance in FVIII-/- mice after induced hemarthrosis. J Thromb Haemost. 2023 Apr 26. Cooke EJ, Joseph BC, Nasamran CA, Fisch KM, von Drygalski A. PMID: 37116753.
  12. Transcriptional time course after rotator cuff repair in 6 month old female rabbits. Front Physiol. 2023; 14:1164055. Vasquez-Bolanos LS, Gibbons MC, Ruoss S, Wu IT, Esparza MC, Fithian DC, Lane JG, Singh A, Nasamran CA, Fisch KM, Ward SR. PMID: 37228812; PMCID: PMC10203179.
  13. Variant STAT4 and Response to Ruxolitinib in an Autoinflammatory Syndrome. N Engl J Med. 2023 May 31. 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. PMID: 37256972.
  14. 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. 2023 Mar 29. doi: 10.1038/s41380-022-01909-9. Epub ahead of print. PMID: 36991131.
  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. 2023 Mar 21;4(3):100962. doi: 10.1016/j.xcrm.2023.100962. Epub 2023 Mar 7. PMID: 36889320; 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. 2023 Mar 2;30(3):250-263.e6. doi: 10.1016/j.stem.2023.01.008. Epub 2023 Feb 16. PMID: 36803553; PMCID: PMC10134781.
  17. 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. 2023 Mar 1;150(5):dev200839. doi: 10.1242/dev.200839. Epub 2023 Mar 3. PMID: 36762637; PMCID: PMC10110423.
  18. 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. 2023 Feb 20;19:100449. doi: 10.1016/j.lana.2023.100449. PMID: 36844610; PMCID: PMC9939935.
  19. 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. 2023 Jan;38(1-3):183-197. doi: 10.1089/ars.2021.0119. Epub 2022 Aug 29. PMID: 35754343; PMCID: PMC10039277.
  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. 2023 Jan 24;13(2):171. doi: 10.3390/metabo13020171. PMID: 36837791; 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. 2023 Jan 18;14(1):292. doi: 10.1038/s41467-023-35796-7. PMID: 36653361; PMCID: PMC9849267.
  22. 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. 2023 Jan 18. doi: 10.1038/s41596-022-00797-1. Epub ahead of print. PMID: 36653526.

2022:

  1. 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. 2022 Jul 1;323(1):L84-L92. doi: 10.1152/ajplung.00128.2022. Epub 2022 Jun 14. PMID: 35699291; PMCID: PMC9273271.
  2. Morey R, Bui T, Fisch KM, Horii M. Modeling placental development and disease using human pluripotent stem cells. Placenta. 2022 Oct 31:S0143-4004(22)00436-2. doi: 10.1016/j.placenta.2022.10.011. Epub ahead of print. PMID: 36333266.
  3. 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. 2022 Oct 28;11(21):3412. doi: 10.3390/cells11213412. PMID: 36359808; PMCID: PMC9657268.
  4. 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. 2022 Dec;40(12):2705-2707. doi: 10.1002/jor.25450. Epub 2022 Oct 17. PMID: 36250743.
  5. 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. 2022 Oct 4;17(1):440. doi: 10.1186/s13018-022-03326-8. PMID: 36195913; PMCID: PMC9531386.
  6. 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. 2022 Sep 4:10.1002/hep.32776. doi: 10.1002/hep.32776. Epub ahead of print. PMID: 36059147; PMCID: PMC9984672.
  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. 2022 Sep;609(7925):101-108. doi: 10.1038/s41586-022-05049-6. Epub 2022 Jul 7. PMID: 35798029; PMCID: PMC9433318.
  8. Whisenant TC, Nigam SK. Organic Anion Transporters (OAT) and Other SLC22 Transporters in Progression of Renal Cell Carcinoma. Cancers (Basel). 2022 Sep 29;14(19):4772. doi: 10.3390/cancers14194772. PMID: 36230695; PMCID: PMC9563088.
  9. 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. 2022 Sep 10;12(1):15273. doi: 10.1038/s41598-022-19351-w. PMID: 36088481; PMCID: PMC9464204.
  10. 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. 2022 Aug 30;13(1):5092. doi: 10.1038/s41467-022-32764-5. PMID: 36042358; PMCID: PMC9427743.
  11. ‘Mutant Huntingtin Protein Interaction Map Implicates Dysregulation of Multiple Cellular Pathways in Neurodegeneration of Huntington’s Disease. J Huntingtons Dis. 2022 Jul 15. Podvin S, Rosenthal SB, Poon W, Wei E, Fisch KM, Hook V. PMID: 35871359.’
  12. 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. 2022 Apr 15;208(8):1947-1959. doi: 10.4049/jimmunol.2101192. Epub 2022 Mar 30. PMID: 35354612; PMCID: PMC9012679.
  13. Goyal NP, Rosenthal SB, Nasamran C, Behling CA, Angeles JE, Fishbein MH, Harlow KE, Jain AK, Molleston JP, Newton KP, Ugalde-Nicalo P, Xanthankos A, Yates K, Schork NJ, Fisch KM, Schwimmer JB; N. A. S. H. Clinical Research Network. Nonalcoholic Fatty Liver Disease Risk and Histologic Severity are Associated with Genetic Polymorphisms in Children. Hepatology. 2022 May 13. doi: 10.1002/hep.32570. Epub ahead of print. PMID: 35560106.
  14. Derivation of functional trophoblast stem cells from primed human pluripotent stem cells. Stem Cell Reports. 2022 May 02. Soncin F, Morey R, Bui T, Requena DF, Cheung VC, Kallol S, Kittle R, Jackson MG, Farah O, Dumdie J, Meads M, Pizzo D, Horii M, Fisch KM, Parast MM. PMID: 35594858.
  15. 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; 9:849214. 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. PMID: 35547202; PMCID: PMC9082267.
  16. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv. 2022 Apr 04. 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. PMID: 35411350; PMCID: PMC8996633.
  17. The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients. Cell Mol Gastroenterol Hepatol. 2022 Apr 01. 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, 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. PMID: 35378331.
  18. The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction. Sci Rep. 2022 03 24; 12(1):5077. Moshiri N, Fisch KM, Birmingham A, DeHoff P, Yeo GW, Jepsen K, Laurent LC, Knight R. PMID: 35332213; PMCID: PMC8943356.
  19. Machine learning approach to predicting persistent opioid use following lower extremity joint arthroplasty. Reg Anesth Pain Med. 2022 May; 47(5):313-319. Gabriel RA, Harjai B, Prasad RS, Simpson S, Chu I, Fisch KM, Said ET. PMID: 35115414; PMCID: PMC8961772.
  20. Mapping the gene network landscape of Alzheimer’s disease through integrating genomics and transcriptomics. PLoS Comput Biol. 2022 02; 18(2):e1009903. Rosenthal SB, Wang H, Shi D, Liu C, Abagyan R, McEvoy LK, Chen CH. PMID: 35213535; PMCID: PMC8906581.
  21. Discovery of genomic loci of the human cerebral cortex using genetically informed brain atlases. Science. 2022 02 04; 375(6580):522-528. Makowski C, van der Meer D, Dong W, Wang H, Wu Y, Zou J, Liu C, Rosenthal SB, Hagler DJ, Fan CC, Kremen WS, Andreassen OA, Jernigan TL, Dale AM, Zhang K, Visscher PM, Yang J, Chen CH. PMID: 35113692.

 

2021:

  1. Kurian SM, Whisenant TC, Marsh CL. Toward Improved and Standardized Diagnostic Pipelines in Transplantation. Transplantation. 2021 Jan 1;105(1):12-13. doi: 10.1097/TP.0000000000003438. PMID: 33350625.
  2. 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. 2021 Oct 22;6(20):e147033. doi: 10.1172/jci.insight.147033. PMID: 34676827; PMCID: PMC8564915. https://pubmed.ncbi.nlm.nih.gov/34676827/
  3. 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. 2021 Aug 6;12:707116. doi: 10.3389/fphys.2021.707116. Erratum in: Front Physiol. 2021 Oct 29;12:775297. PMID: 34421646; PMCID: PMC8378535. https://pubmed.ncbi.nlm.nih.gov/34421646/
  4. 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. 2021 Jan 26;34(4):108670. doi: 10.1016/j.celrep.2020.108670. PMID: 33503434; PMCID: PMC8477897.
  5. 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. 2021 Nov 12:S0960-9822(21)01507-4. doi: 10.1016/j.cub.2021.10.063. Epub ahead of print. PMID: 34793695.
  6. Keehner J, Horton LE, Binkin NJ, Laurent LC, 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. 2021 Sep 30;385(14):1330-1332. doi: 10.1056/NEJMc2112981. Epub 2021 Sep 1. PMID: 34469645; PMCID: PMC8451183.
  7. Transient genomic instability drives tumorigenesis through accelerated clonal evolution. Genes Dev. 2021 Aug 01; 35(15-16):1093-1108.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. PMID: 34266887.
  8. An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia. Nat Cancer. 2020 Apr; 1(4):410-422.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. PMID: 34109316.
  9. 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. 2021 Jul 22. doi: 10.1097/TP.0000000000003895. Epub ahead of print. PMID: 34342962.
  10. Extrachromosomal DNA in HPV mediated oropharyngeal cancer drives diverse oncogene transcription. Clin Cancer Res. 2021 Sep 21. Pang J, Nguyen NP, 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. PMID: 34548317.
  11. Strategies to Identify Mesenchymal Stromal Cells in Minimally Manipulated Human Bone Marrow Aspirate Concentrate Lack Consensus. Severin Ruoss, J.Todd Walker, Chanond A. Nasamran,
    Kathleen M. Fisch, Conner J. Paez, Jesal N. Parekh, Scott T. Ball,
    Jeffrey L. Chen, Sonya S. Ahmed, and Samuel R. Ward. The American Journal of Sports Medicine. 1–10. DOI: 10.1177/0363546521993788
  12. Activation of NF-κB and p300/CBP potentiates cancer chemoimmunotherapy through induction of MHC-I antigen presentation. Yixuan Zhou, Ingmar Niels Bastian, Mark D. Long, Michelle Dow, Weihua Li, Tao Liu, Rachael Katie Ngu, Laura Antonucci, Jian Yu Huang, Qui T. Phung, Xi-he Zhao, Sourav Banerjee, Xue-Jia Lin, Hongxia Wang, Brian Dang, Sylvia Choi, Daniel Karin, Hua Su, Mark H. Ellisman, Christina Jamieson, Marcus Bosenberg, Zhang Cheng, Johannes Haybaeck, Lukas Kenner, Kathleen M. Fisch, Richard Bourgon, Genevive Hernandez, Jennie R. Lill, Song Liu, Hannah Carter, Ira Mellman, Michael Karin, Shabnam Shalapour. PNAS. 2021 Feb 23;118(8):e2025840118. doi: 10.1073/pnas.2025840118. PMID: 33602823
  13. Nasamran, CA, Sachan, ANS, Mott, J, et al. Differential blood DNA methylation across Lewy body dementias. Alzheimer’s Dement. 2021; 13:e12156. https://doi.org/10.1002/dad2.12156
  14. Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction. Nat Neurosci. 2021 Aug 26. 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. PMID: 34446935.
  15. Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy. Nat Microbiol. 2021 10; 6(10):1319-1333. 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. PMID: 34556855; PMCID: PMC9683089.
  16. A convergent molecular network underlying autism and congenital heart disease. Cell Syst. 2021 Aug 13. 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. PMID: 34411509
  17. Immunotherapy-based targeting of MSLN+ activated portal fibroblasts is a strategy for treatment of cholestatic liver fibrosis. Proc Natl Acad Sci U S A. 2021 Jul 20; 118(29). 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. PMID: 34253615
  18. Nondegradable Collagen Increases Liver Fibrosis but Not Hepatocellular Carcinoma in Mice. Am J Pathol. 2021 Jun 11. 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. PMID: 34119473
  19. Nonalcoholic Steatohepatitis and HCC in a Hyperphagic Mouse Accelerated by Western Diet. Cell Mol Gastroenterol Hepatol. 2021 May 29; 12(3):891-920. 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. PMID: 34062281
  20. Similar Genetic Architecture of Alzheimer’s Disease and Differential APOE Effect Between Sexes. Front Aging Neurosci. 2021; 13:674318. Wang H, Lo MT, Rosenthal SB, Makowski C, Andreassen OA, Salem RM, McEvoy LK, Fiecas M, Chen CH. PMID: 34122051
  21. Functional landscape of SARS-CoV-2 cellular restriction. Mol Cell. 2021 06 17; 81(12):2656-2668.e8. 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. PMID: 33930332
  22. NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data. iScience. 2021 Apr 23; 24(4):102361. 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. PMID: 33870146
  23. Heterogeneity of HSCs in a Mouse Model of NASH. Hepatology. 2021 Feb 07. Rosenthal SB, Liu X, Ganguly S, Dhar D, Pasillas MP, Ricciardelli E, Li RZ, Troutman TD, Kisseleva T, Glass CK, Brenner DA. PMID: 33550587

 

2020:

  1. A New Era for Space Life Science: International Standards for Space Omics Processing. Patterns (N Y). 2020 Dec 11; 1(9):100148. 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. PMID: 33336201.
  2. Espanola SG, Song H, Ryu E, Saxena A, Kim ES, Manegold JE, Nasamran CA, Sahoo D, Oh CK, Bickers C, Shin U, Grainger S, Park YH, Pandolfo L, Kang MS, Kang S, Myung K, Cooper KL, Yelon D, Traver D, Lee Y. Haematopoietic stem cell-dependent Notch transcription is mediated by p53 through the Histone chaperone Supt16h. Nat Cell Biol. 2020 Dec;22(12):1411-1422. doi: 10.1038/s41556-020-00604-7. Epub 2020 Nov 23. PMID: 33230303.
  3. Deletion of the gene encoding the N-Methyl-D-Aspartate Receptor GluN1 subunit in Schwann cells causes ultrastructural changes in Remak bundles and hypersensitivity in pain processing. J Neurosci. 2020 Oct 13. Brifault C, Romero H, Van-Enoo A, Pizzo D, Azmoon P, Kwon H, Nasamran C, Gonias SL, Campana WM. PMID: 33051351.
  4. Multi-omic comparison of Alzheimer’s variants in human ESC-derived microglia reveals convergence at APOE. J Exp Med. 2020 Dec 07; 217(12). 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. PMID: 32941599
  5. Comprehensive Multi-omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact. Cell. 2020 Nov 25; 183(5):1185-1201.e20. 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. PMID: 33242417
  6. Metabolomic profiles associated with a mouse model of antipsychotic-induced food intake and weight gain. Sci Rep. 2020 Oct 29; 10(1):18581. Zapata RC, Rosenthal SB, Fisch K, Dao K, Jain M, Osborn O. PMID: 33122657.
  7. HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers. Oncogene. 2020 Aug 26. 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. PMID: 32848210.
  8. Interactome overlap between schizophrenia and cognition. Schizophr Res. 2020 Jun 13. Koch E, Rosenthal B, Lundquist A, Chen CH, Kauppi K. PMID: 32546371.
  9. Aberrant expression of CPSF1 promotes head and neck squamous cell carcinoma via regulating alternative splicing. PLoS One. 2020; 15(5):e0233380. 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. PMID: 32437477.
  10. Nuclear Parkin Activates the ERRα Transcriptional Program and Drives Widespread Changes in Gene Expression Following Hypoxia. Sarah E Shires, Justin M Quiles, Rita H Najor, Leonardo J Leon, Melissa Q Cortez, Mark A Lampert, Adam Mark, Åsa B Gustafsson. Sci Rep. 2020 May 22;10(1):8499. PMID: 32444656.
  11. QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data.  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. Curr Protoc Bioinformatics. 2020 Jun. PMID: 32343490.
  12. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O’Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain 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 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. Nature. 2020 Apr 30. PMID: 32353859.
  13. Differential expression of nuclear genes encoding mitochondrial proteins from urban and rural populations in Morocco. 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. Cell Stress Chaperones. 2020 Apr 21. PMID: 32319023.
  14. Single-Cell Transcriptomes Reveal a Complex Cellular Landscape in the Middle Ear and Differential Capacities for Acute Response to Infection. Ryan AF, Nasamran CA, Pak K, Draf C, Fisch KM, Webster N, Kurabi A. Front Genet. 2020 April 15. PMID: 32351546.
  15. Primary Alcohol-Activated Human and Mouse Hepatic Stellate Cells Share Similarities in Gene-Expression Profiles. 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. Hepatol Commun. 2020 Apr; 4(4):606-626. PMID: 32258954.
  16. Rational Genomic Optimization of DNA Detection for Human Papillomavirus Type 16 in Head and Neck Squamous Cell Carcinoma. Yuki Saito, Alexander V Favorov, Michael Forman, Shuling Ren, Akihiro Sakai, Takahito Fukusumi, Chao Liu,  Sayed Sadat, Mizuo Ando, Guorong Xu, Zubair Khan, John Pang, Alex Valsamakis, Kathleen M Fisch,  Joseph A Califano. Head Neck. 2020 Apr;42(4):688-697. PMID: 3185059
  17. Blockade of IL-17 signaling reverses alcohol-induced liver injury and excessive alcohol drinking in mice. 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. JCI Insight. 2020 Feb 13; 5(3). PMID: 32051339.
  18. Identification of Lineage-specific Transcription Factors That Prevent Activation of Hepatic Stellate Cells and Promote Fibrosis Resolution. 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. Gastroenterology. 2020 Jan 20. PMID: 31982409.
  19. The Caenorhabditis Elegans RIG-I Homolog DRH-1 Mediates the Intracellular Pathogen Response Upon Viral Infection. Jessica N Sowa, Hongbing Jiang, Lakshmi Somasundaram, Eillen Tecle, Guorong Xu, David Wang , Emily R Troemel. J Virol. 2020 Jan 6; 94(2):e01173-19. PMID: 31619561
  20. p300 and cAMP response element-binding protein-binding protein in skeletal muscle homeostasis, contractile function, and survival. 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.  J Cachexia Sarcopenia Muscle. 2020 Jan 3. PMID: 31898871.

2019:

  1. IL-17 signaling in steatotic hepatocytes and macrophages promotes hepatocellular carcinoma in alcohol-related liver disease. Hsiao-Yen Ma, Gen Yamamoto, Jun Xu, Xiao Liu, Daniel Karin, Ju Youn Kim, Ludmil B. Alexandrov, Yukinori Koyama,  Takahiro Nishio, Chris Benner, Sven Heinz, Sara B. Rosenthal, Shuang Liang, Mengxi Sun, Gabriel Karin, Peng Zhao, Pnina Brodt, Iain H. Mckillop, Oswald Quehenberger, Ed Dennis, Alan Saltiel, Hidekazu Tsukamoto, Bin Gao, Michael Karin, David A. Brenner, Tatiana Kisseleva. Journal of Hepatology. 2019 Dec 31. PMID:31899206
  2. Rational genomic optimization of DNA detection for human papillomavirus type 16 in head and neck squamous cell carcinoma. 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. Head Neck. 2019 Dec 18. PMID: 31850594
  3. Tissue-type plasminogen activator-primed human iPSC-derived neural progenitor cells promote motor recovery after severe spinal cord injury. Shiga Y, Shiga A, Mesci P, Kwon H, Brifault C, Kim JH, Jeziorski JJ, Nasamran C, Ohtori S, Muotri AR, Gonias SL, Campana WM.  Scientific Reports. 2019 Dec 17. PMID: 31848365 
  4. BAL Cell Gene Expression in Severe Asthma Reveals Mechanisms of Severe Disease and Influences of Medications. 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. Am J Respir Crit Care Med. 2019 Oct 01; 200(7):837-856. PMID: 31161938.
  5. Irreversible Electroporation Combined with Checkpoint Blockade and TLR7 Stimulation Induces Antitumor Immunity in a Murine Pancreatic Cancer Model. Narayanan JSS, Ray P, Hayashi T, Whisenant TC, Vicente D, Carson DA, Miller AM, Schoenberger SP, White RR.  Cancer Immunol Res. 2019 Oct; 7(10):1714-1726. PMID: 31409607.
  6. Increased Fibrogenic Gene Expression in Multifidus Muscles of Patients with Chronic Versus Acute Lumbar Spine Pathology. Shahidi B, Fisch KM, Gibbons MC, Ward SR.  Spine (Phila Pa 1976). 2019 Sep 10. PMID: 31513095.
  7. Activated hepatic stellate cells and portal fibroblasts contribute to cholestatic liver fibrosis in MDR2 knockout mice. 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.  J Hepatol. 2019 Sep; 71(3):573-585. PMID: 31071368.
  8. FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy. 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, Gyorffy B, McHale MT, Connolly DC, Molinolo A, Stupack DG, Schlaepfer DD.  Elife. 2019 09 03; 8. PMID: 31478830.
  9. A Network of SLC and ABC Transporter and DME Genes Involved in Remote Sensing and Signaling in the Gut-Liver-Kidney Axis. Rosenthal SB, Bush KT, Nigam SK. Sci Rep. 2019 Aug 15; 9(1):11879. PMID: 31417100.
  10. Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. Rule A, Birmingham A, Zuniga C, Altintas I, Huang SC, Knight R, Moshiri N, Nguyen MH, Rosenthal SB, Pérez F, Rose PW.  PLoS Comput Biol. 2019 Jul; 15(7):e1007007. PMID: 31344036.
  11. Integrating Gene and Protein Expression Reveals Perturbed Functional Networks in Alzheimer’s Disease. Canchi S, Raao B, Masliah D, Rosenthal SB, Sasik R, Fisch KM, De Jager PL, Bennett DA, Rissman RA. Cell Rep. 2019 Jul 23; 28(4):1103-1116.e4. PMID: 31340147.
  12. Mutation of chromatin regulators and focal hotspot alterations characterize human papillomavirus-positive oropharyngeal squamous cell carcinoma. 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. Cancer. 2019 Jul 15; 125(14):2423-2434. PMID: 30933315.
  13. Mechanisms of vascular permeability and remodeling associated with hemarthrosis in factor VIII-deficient mice. Cooke EJ, Wyseure T, Zhou JY, Gopal S, Nasamran CA, Fisch KM, Manon-Jensen T, Karsdal MA, Mosnier LO, von Drygalski A.  J Thromb Haemost. 2019 Jul 13. PMID: 31301687.
  14. Discovery and cross-validation of peripheral blood and renal biopsy gene expression signatures from ethnically diverse kidney transplant populations. Ventura CG, Whisenant T, Gelbart T, David DSR, Agena F, Salomon DR, David-Neto E, Kurian SM.  Am J Transplant. 2019 Jun 01. PMID: 31152474.
  15. Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. 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.  Nat Commun. 2019 May 29; 10(1):2415. PMID: 31142745.
  16. Choline metabolite, trimethylamine N-oxide (TMAO), is associated with inflammation in psoriatic arthritis. Coras R, Kavanaugh A, Boyd T, Huynh D, Lagerborg KA, Xu YJ, Rosenthal SB, Jain M, Guma M.  Clin Exp Rheumatol. 2019 May-Jun; 37(3):481-484. PMID: 30620278.
  17. A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma. 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.  Cell. 2019 Apr 18; 177(3):572-586.e22. PMID: 30955884.
  18. DNA methylation changes associated with Parkinson’s disease progression: outcomes from the first longitudinal genome-wide methylation analysis in blood. 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.  Epigenetics. 2019 Apr; 14(4):365-382. PMID: 30871403.
  19. On entropy and information in gene interaction networks. Bioinformatics. Wallace ZS, Rosenthal SB, Fisch KM, Ideker T, Sasik R.  2019 Mar 01; 35(5):815-822. PMID: 30102349.
  20. Variations in HPV function are associated with survival in squamous cell carcinoma. 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.  JCI Insight. 2019 Jan 10; 4(1). PMID: 30626753.
  21. Biological Interpretation of Complex Genomic Data. Fisch KM.  Methods Mol Biol. 2019; 1908:61-71. PMID: 30649721.
  22. Development and clinical validity of a novel blood-based molecular biomarker for subclinical acute rejection following kidney transplant.  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. N, Zhao L, Kandpal M1, Salomon DR, Abecassis MM. Am J Transplant. 2019 Jan;19(1):98-109. PMID: 29985559

2018:

  1. Meyer AN, Gallo LH, Ko J, Cardenas G, Nelson KN, Siari A, Campos AR, Whisenant TC, Donoghue DJ. Oncogenic mutations in IKKß function through global changes induced by K63-linked ubiquitination and result in autocrine stimulation. PLoS One. 2018; 13(10):e0206014. PMID: 30335863.
  2. 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. 2018 Sep 25;115(39):E9192-E9200. PMID:30209212
  3. 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 08 24; 109(6):689-699. PMID: 30016452.
  4. 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 08 03; 20(1):164. PMID: 30075744.
  5. Bloss CS, Stoler J, Schairer CE, Rosenthal SB, Cheung C, Rus HM, Block JL, Yang JJ, Morton D, Bixenman H, Wellis D. Characteristics Of Likely Precision Medicine Initiative Participants Drawn From A Large Blood Donor Population. Health Aff (Millwood). 2018 05; 37(5):786-792. PMID: 29733733.
  6. 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. 2018 11; 26(11):1531-1538. PMID: 30081074.
  7. 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 10 15; 24(20):5123-5132. PMID: 29945995.
  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. 2018 07 01; 175(7):674-682. PMID: 29495895.
  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. 2018 06 11; 9(1):2280. PMID: 29891926.
  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. PMID:30003124.
  11. Amanda Birmingham, Adam M Mark, Carlo Mazzaferro, Guorong Xu, Kathleen M Fisch. Efficient population-scale variant analysis and prioritization with VAPr. Bioinformatics. 2018 Aug 15;34(16): 2843-2845. PMID:29659724.
  12. Wei Zhang, Ana Bojorquez-Gomez, Daniel Ortiz Velez, Guorong Xu, Kyle S. Sanchez, John Paul Shen, Kevin Chen, Katherine Licon, Collin Melton, Katrina M. Olson, Michael Ku Yu, Justin K. Huang, Hannah Carter, Emma K. Farley, Michael Snyder, Stephanie I. Fraley, Jason F. Kreisberg & Trey Ideker. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet. 2018 Apr;50(4):613-620. PMID:29610481.
  13. Zhao D, Badur M1, 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. 2018 Feb 15;69(4): 699-708.e7. PMID:29452643.
  14. 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. PMID:29341863.
  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; 13(1):e0190439. PMID: 29293645.
  16. Rosenthal SB, Len J, Webster M, Gary A, Birmingham A, Fisch KM. Interactive network visualization in Jupyter notebooks: visJS2jupyter. Bioinformatics. 2018 01 01; 34(1):126-128. PMID: 28968701.

2017:

  1. 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, Goldrath AW, Overkleeft HS, Ovaa H, Chang JT. Proteasome activity regulates CD8+ T lymphocyte metabolism and fate specification. J Clin Invest. 2017 Oct 02; 127(10):3609-3623. PMID: 28846070.
  2. 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 Sep 21; 171(1):103-119.e18. PMID: 28938112.
  3. Wei Ying, Matthew Riopel, Gautam Bandyopadhyay, Yi Dong, Amanda Birmingham, Jong Bae Seo, Jachelle M. Ofrecio, Joshua Wollam, Angelina Hernandez-Carretero, Wenxian Fu, Pingping Li, Jerrold M. Olefsky. Adipose Tissue Macrophage-Derived Exosomal miRNAs Can Modulate In Vivo and In Vitro Insulin Sensitivity. Cell. 2017 Oct 5;171(2):372-384.e12. PMID:28942920
  4. Balakrishnan A, Gloude N, Sasik R, Ball ED, Morris G. Pro-Inflammatory Dual Receptor T Cells in Chronic Graft Versus Host Disease. Biol Blood Marrow Transplant. 2017 Nov;23(11):1852-1860. PMID:28750779
  5. 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-ß signaling in chondrocytes. Osteoarthritis Cartilage. 2017 06; 25(6):943-951. PMID: 27884645.
  6. 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. PMID:28495611 
  7. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Jun; 14(6):573-576. 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. PMID: 28319113.
  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 04; 7(4):410-423. PMID: 28188128.
  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. 2017 Mar 3;5(1):27. PMID:28253908
  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. 2017 02 07; 8(1). PMID: 28174312.

2016:

  1. Chen S, Miyazaki M, Chandra V, Fisch KM, Chang AN, Murre C. Id3 Orchestrates Germinal Center B Cell Development. Mol Cell Biol. 2016 10 15; 36(20):2543-52. PMID: 27457619.
  2. Kaneda MM, Messer KS, Ralainirina N, Li H, Leem C, 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 EE, Varner JA. PI3Kγ is a molecular switch that controls immune suppression. Nature. 2016 Nov 17;539(7629): 437-442. PMID:27642729 
  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 09; 24(9):1639-47. PMID: 27118398.
  4. 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 08; 68(8):1876-86. PMID: 26881698.
  5. Sophie Weiss, Will Van Treuren, Catherine Lozupone, Karoline Faust, Jonathan Friedman, Ye Deng, Li Charlie Via, Zhenjiang Zech Xu, Luke Urseil, Eric J Alm, Amanda Birmingham, Jacob A Cram, Jed A Fuhrman, Jeroen Raes, Fengzhu Sun, Jizhong Zhou and Rob Knight. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. 2016 Jul;10(7):1669-81. PMID:26905627
  6. Fox RG, Lytle NK, Jaquish DV, Park FD, Ito T, Bajaj J, Koechlein CS, Zimdahl B, Yano M, Kopp JL, Kritzik M, Sicklick JK, Sander M, Grandgenett PM, Hollingsworth MA, Shibata S, Pizzo D, Valasek MA, Sasik R, Scadeng M, Okano H7, Kim Y, MacLeod AR, Lowy AM, Reya T.  Image-based detection and targeting of therapy resistance in pancreatic adenocarcinoma. Nature. 2016 Jun 16;534(7607):407-411. PMID:27281208
  7. 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):870-85. PMID: 27179037
  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):21527-41. PMID: 26930717.

2015:

  1. McDonald D, Birmingham A, Knight R. Context and the Human Microbiome. Microbiome. 2015; 3: 52. PMID: 26530830.
  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. 2015 Aug 6;17(2):152-164.PMID:26212080.
  3. 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. 2015 May 21; 8:24. PMID: 25989980.
  4. 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. 2015 Jul;16(7):775-84. PMID:25985234
  5. B. 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. Haematologica. 2015 Jul;100(7):945-54. PMID:25862704
  6. 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 lymphoma genesis. Genes Dev. 2015 Feb 15;29(4):409-25. PMID:25691468
  7. 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. 2015 Feb;79:133-44. PMID:25446186
  8. 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. 2015 Jun 01; 31(11):1724-8. PMID: 25637560.

2014:

  1. 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. 2015 May;29(5):1859-68. PMID:25630970 
  2. Gaffney PM, Imai DM, Clifford DL, Ghassemian M, Sasik R, Chang AN, O’Brien TD, Coppinger J, Trejo M, Masliah E, Munson L, Sigurdson C. Proteomic analysis of highly prevalent amyloid a amyloidosis endemic to endangered island foxes. PLoS One. 2014 Nov 26;9(11):e113765. PMID:25429466.
  3. Strong MJ, Xu G, Morici L, Splinter Bon-Durant S, Baddoo M, Lin Z, Fewell C, Taylor CM, Flemington EK. Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples. PLoS Pathog. 2014 Nov 20;10(11):e1004437. PMID:25412476
  4. Miyazaki M, Miyazaki K, Chen S, Itoi M, Miller M, Lu LF, Varki N, Chang AN, Broide DH, Murre C. Id2 and Id3 maintain the regulatory T cell pool to suppress inflammatory disease. Nat Immunol. 2014 Aug;15(8):767-76. PMID:24973820 
  5. Oh da Y, Walenta E, Akiyama TE, Lagakos WS, Lackey D, Pessentheiner AR, Sasik R, Hah N, Chi TJ, Cox JM, Powels MA, Di Salvo J, Sinz C, Watkins SM, Armando AM, Chung H, Evans RM, Quehenberger O, McNelis J, Bogner-Strauss JG, Olefsky JM. A Gpr120-selective agonist improves insulin resistance and chronic inflammation in obese mice. Nat Med. 2014 Aug;20(8):942-7.PMID:24997608
  6. Barnhill LM, Williams RT, Cohen O, Kim Y, Batova A, Mielke JA, Messer K, Pu M, Bao L, Yu AL, Diccianni MB. High expression of CAI2, a 9p21-embedded long noncoding RNA, contributes to advanced-stage neuroblastoma. Cancer Res. 2014 Jul 15;74(14):3753-63. PMID: 25028366 
  7. Lee YS, Kim JW, Osborne O, Oh da Y, Sasik R, Schenk S, Chen A, Chung H, Murphy A, Watkins SM, Quehenberger O, Johnson RS, Olefsky JM. Increased adipocyte O2 consumption triggers HIF-1α, causing inflammation and insulin resistance in obesity. Cell. 2014 Jun 5;157(6):1339-52. PMID:24906151.
  8. Carrion K, Dyo J, Patel V, Sasik R, Mohamed SA, Hardiman G, Nigam V. The long non-coding HOTAIR is modulated by cyclic stretch and WNT/β-CATENIN in human aortic valve cells and is a novel repressor of calcification genes. PLoS One. 2014 May 1;9(5):e96577. PMID: 24788418.
  9. Joshi S, Singh AR, Zulcic M, Bao L, Messer K, Ideker T, Dutkowski J, Durden DL. Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo. PLoS One. 2014 Apr 25;9(4):e95893. PMID:24770346.

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