2021:

  1. 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
  2. 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
  3. 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.
  4. 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
  5. 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.
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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. 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). 2020 Feb 15; 45(4):E189-E195. PMID: 31513095.
  18. 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.
  19. 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.
  20. 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
  21. 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. The C. elegans RIG-I homolog DRH-1 mediates the Intracellular Pathogen Response upon viral infection. Sowa JN, Jiang H, Somasundaram L, Tecle E, Xu G, Wang D, Troemel ER. . J Virol. 2019 Oct 16. PMID: 31619561
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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 July 15;125(14):2423-2434. PMID: 30933315.
  21. 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.
  22. 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.
  23. Biological Interpretation of Complex Genomic Data. Fisch KM.  Methods Mol Biol. 2019; 1908:61-71. PMID: 30649721.
  24. 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. Birmingham A, Mark AM, Mazzaferro C, Xu G, Fisch KM. Efficient population-scale variant analysis and prioritization with VAPr. Bioinformatics. 2018 08 15; 34(16):2843-2845. PMID: 29659724.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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.
  2. 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 
  3. 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.
  4. 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
  5. 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 
  6. 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
  7. 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 
  8. 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.
  9. Increased adipocyte O2 consumption triggers HIF-1α, causing inflammation and insulin resistance in obesity. Cell. 2014 Jun 5;157(6):1339-52. PMID:24906151.
  10. 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.
  11. 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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