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2022​​​

  1. Su K, Katebi A, Kohar V, Clauss B, Gordin D, Qin ZS, Karuturi RKM, Li S, Lu M. NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity. Genome Biology. 2022 Dec 27;23(1):270. PMID: 36575445 
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  2. Antel M, Raj R, Masoud MYG, Pan Z, Li S, Mellone BG, Inaba M. Interchromosomal interaction of homologous Stat92E alleles regulates transcriptional switch during stem-cell differentiation. Nature Communications. 2022 Jul 9;13(1):3981. PMID: 35810185               

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2021

  1. Liu Y*, Rosikiewicz W*, Pan Z*, Jillette N, Wang P, Taghbalout A, Foox J, Mason CE, Carroll M, Cheng A, Li S. DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation. Genome Biology. 2021 Oct 18;22(1):295. PMID: 34663425 *Co-first author                                                                                                                    Homepage art of the Long Read Sequencing Collection of Genome Biology.                      (www.biomedcentral.com/collections/long-read).
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  2. Landay A, Bartley J, Banerjee D, Hargis G, Haynes L, Keshavarzian A, Kuo CL, Kwon OS, Li S, Li S, Oh J, Ozbolat IT, Ucar D, Xu M, Yao X, Unutmaz D, Kuchel GA. Network Topology of Biological Aging and Geroscience-Guided Approaches to COVID-19. Frontiers in Aging. 2021 Jul;2:695218. PMID: 35128530                                                  

  3. Chen X, Ashoor H, Musich R, Wang J, Zhang M, Zhang C, Lu M, Li S. epihet for intra-tumoral epigenetic heterogeneity analysis and visualization. Scientific Reports. 2021 Jan 11;11(1):376. PMID: 33432081​ ​

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​2020​​

  1. Malkani S, Chin CR, Cekanaviciute E, Mortreux M, Okinula H, Tarbier M, Schreurs AS, Shirazi-Fard Y, Tahimic CGT, Rodriguez DN, Sexton BS, Butler D, Verma A, Bezdan D, Durmaz C, MacKay M, Melnick A, Meydan C, Li S, Garrett-Bakelman F, Fromm B, Afshinnekoo E, Langhorst BW, Dimalanta ET, Cheng-Campbell M, Blaber E, Schisler JC, Vanderburg C, Friedländer MR, McDonald JT, Costes SV, Rutkove S, Grabham P, Mason CE, Beheshti A. Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development. Cell Reports. 2020 Nov 21:108448. PMID: 33242410​​​​​
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  2. Zhao Y, Pan Z, Namburi S, Pattison A, Posner A, Balachander S, Paisie C.A., Reddi H.V., Rueter J, Gill AJ, Fox S, Raghav KPS., Flynn WF, Tothill RW, Li S**, Karuturi RKM**, George J**. CUP-AI-Dx: a tool for inferring cancer tissue of origin and molecular subtype using RNA gene-expression data and artificial intelligence. EBioMedicine. 2020 Nov;61:103030. PMID: 33039710 **Co-corresponding author.                                                                                     Highlighted as the best paper of oncology in Commentary 2020: A year to remember at EBioMedicine (doi: 10.1016/j.ebiom.2020.103185)                                               

  3. Li P, Lu M, Shi J, Gong Z, Hua L, Li Q, Lim B, Zhang XH, Chen X, Li S, Shultz LD, Ren G. Lung mesenchymal cells elicit lipid storage in neutrophils that fuel breast cancer lung metastasis. Nature Immunology. 2020 Nov;21(11):1444-1455. PMID: 32958928
     

  4. Tong L, Wu PY, Phan JH, Hassazadeh HR, Jones WD, Shi L, Fischer M, Mason CE, Li S, Xu J, Shi W, Wang J, Thierry-Mieg J, Thierry-Mieg D, Hertwig F, Berthold F, Hero B, Liao Y, Smyth GK, Kreil D, Łabaj PP, Megherbi D, Schroth G, Fang H, Tong W, Wang MD. Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction. Scientific Reports. 2020 Oct 21;10(1):17925. PMID: 33087762
     

  5. Li S**, Chen X*, Wang J, Meydan C, Glass JL, Shih AH, Delwel R, Levine RL, Mason CE, Melnick AM**. Somatic mutations drive specific, but reversible epigenetic heterogeneity states in AML. Cancer Discovery. 2020 Dec;10(12):1934-1949. PMID: 32938585 *Co-first author, **Co-corresponding author
     

  6. Lee B, Wang J, Cai L, Kim M, Namburi S, Tjong H, Feng Y, Wang P, Tang Z, Abbas A, Wei C, Ruan Y, Li S. ChIA-PIPE: a fully automated pipeline for comprehensive ChIA-PET data analysis and visualization. Science Advances. 2020 Jul 10;6(28):eaay2078. PMID: 32832596
     

  7. Karlebach G, Hansen P, Veiga DF, Steinhaus R, Danis D, Li S, Anczukow O, Robinson PN. HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis. Genome Biology. 2020 Jul 13;21(1):171. PMID: 32660516
     

  8. Rosikiewicz W*, Chen X*, Dominguez PM*, Ghamlouch H, Aoufouchi S, Bernard OA, Melnick A**, Li S**. TET2 deficiency reprograms the germinal center B-cell epigenome and silences genes linked to lymphomagenesis. Science Advances. 2020 Jun 17;6(25):eaay5872. PMID: 32596441 *Co-first author, **Co-corresponding author
     

  9. Du M, Jillette N, Zhu JJ, Li S, Cheng A.W. CRISPR artificial splicing factors. Nature Communications. 2020 Jun 12;11(1):2973. PMID: 32532987
     

  10. Zhang Z, Zhou C, Li X, Barnes SD, Deng S, Hoover E, Chen CC, Lee YS, Zhang Y, Wang C, Metang LA, Wu C, Tirado CR, Johnson NA, Wongvipat J, Navrazhina K, Cao Z, Choi D, Huang CH, Linton E, Chen X, Liang Y, Mason CE, de Stanchina E, Abida W, Lujambio A, Li S, Lowe SW, Mendell JT, Malladi VS, Sawyers CL, Mu P. Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation. Cancer Cell. 2020 Apr 13;37(4):584-598.e11. PMID: 32220301
     

  11. Ashoor H, Chen X, Rosikiewicz W, Wang J, Ruan Y, Li S. Graph embedding resolves genomic sub-compartments and powers deep neural network predictive model. Nature Communications. 2020 Mar 3;11(1):1173. PMID: 32127534
     

  12. Parsa S, Ortega-Molina A, Ying HY, Jiang M, Teater M, Wang J, Zhao C, Reznik E, Pasion JP, Kuo D, Mohan P, Wang S, Camarillo JM, Thomas PM, Jain N, Garcia-Bermudez J, Cho BK, Tam W, Kelleher NL, Socci N, Dogan A, De Stanchina E, Ciriello G, Green M.R., Li S, Birsoy K, Melnick AM, Wendel HG. 2020. The serine hydroxymethyltransferase-2 (SHMT2) initiates lymphoma development through epigenetic tumor suppressor silencing. Nature Cancer. 2020 Jun 22;1, 653–664. 
     

  13. Somarelli JA, Gardner H, CannataroVL, Gunady EF, Boddy AM, Johnson NA, Fisk JN, Gaffney SG, Chuang JH, Li S, Ciccarelli FD, Panchenko AR, Megquier K, Kumar S, Dornburg A, DeGregori J, Townsend JP. Molecular biology and evolution of cancer: from discovery to action. Molecular Biology and Evolution. 2020 Feb 1;37(2):320-326. PMID: 31642480

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2019

  1. Taghbalout A, Du M, Jillette N, Rosikiewicz W, Rath A, Heinen CD, Li S, Cheng AW. Enhanced CRISPR-based DNA demethylation by RNA-guided coupling methylcytosine oxidation and DNA repair pathways. Nature Communications. 2019 Sep 20;10(1):4296. PMID: 31541098

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2018

  1. Dominguez PM*, Ghamlouch H*,  Rosikiewicz W*, Kumar P, Béguelin W, Fontán L, Rivas MA, Pawlikowska P, Armand M, Mouly E, Torres-Martin M, Doane AS, Calvo Fernandez  MT, Durant M, Della-Valle V, Teater M, Cimmino L, Droin N, Tadros S, Motanagh S,  Shih AH, Rubin MA, Tam W, Aifantis I, Levine RL, Elemento O, Inghirami G, Green MR, Figueroa ME, Bernard OA**, Aoufouchi S**, Li S**, Shaknovich R**,  Melnick AM**.  TET2 deficiency causes germinal center hyperplasia, impairs plasma cell differentiation and promotes B-cell lymphomagenesis. Cancer Discovery. 2018 Dec;8(12):1632-1653. PMID: 30274971 *Co-first author, **Co-corresponding author
     

  2. Zuo WL, Shenoy SA, Li S, O’Beirne SL, Strulovici-Barel Y, Leopold PL, Wang G, Staudt MR, Walters MS, Mason C, Kaner RJ, Mezey JG, Crystal RG. Ontology and biology of human small airway epithelial club cells. American Journal of Respiratory and Critical Care Medicine. 2018 Dec 1;198(11):1375-1388. PMID: 29874100
     

  3. Rutherford SC, Fachel AA, Li S, Sawh S, Muley A, Ishii J, Saxena A, Dominguez PM, Caldas LE, Agirre X, Chambwe N, Correa F, Jiang Y, Richard KL, Betel D, Shaknovich R. Extracellular vesicles in DLBCL provide abundant clues to aberrant transcriptional programming and genomic alterations.  Blood. 2018 Aug 16;132(7):e13-e23. PMID: 29967128

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2017

  1. Kleppe M, Spitzer MH, Li S, Hill CE, Dong L, Papelexi E, De Groote S, Bowman RL, Keller M, Koppikar P, Rapaport FT, Teruya-Feldstein J, Gandara J, Mason CE, Nolan GP, Levine RL. Jak1 integrates cytokine sensing to regulate hematopoietic stem cell function and stress hematopoiesis.  Cell Stem Cell. 2017 Oct 5;21(4):489-501.e7. PMID: 28965767
     

  2. Hassan C., Afshinnekoo E, Li S, Wu S, Mason CE. Genetic and epigenetic heterogeneity and the impact on cancer relapse.  Experimental Hematology. 2017 Oct;54:26-30. PMID: 28705639
     

  3. Alexa BR, McIntyre A, Alexander N, Burton AS, Castro-Wallace S, Chiu CY, John KK, Stahl SE, Li S, Mason CE. Nanopore detection of bacterial DNA base modifications. bioRxiv. 2017 Apr 13;127100. doi: https://doi.org/10.1101/127100

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2016

  1. Vijay P, McIntyre AB, Mason CE, Greenfield JP, Li S. Clinical Genomics:  Challenges and Opportunities. Critical Reviews of Eukaryotic Gene Expression. 2016;26(2):97-113. PMID: 27480773
     

  2. Li S, Garrett-Bakelman FE, Chung SS, Sanders MA, Hricik T, Rapaport F, Patel J, Dillon R, Vijay P, Brown AL, Perl AE, Cannon J, Bullinger L, Luger S, Becker M, Lewis ID, To LB, Delwel R, Löwenberg B, Döhner H, Döhner K, Guzman ML, Hassane DC, Roboz GJ, Grimwade D, Valk PJ, D'Andrea RJ, Carroll M, Park CY, Neuberg D, Levine R, Melnick AM, Mason CE. Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. Nature Medicine. 2016 Jul;22(7):792-9. PMID: 27322744                        Highlighted by commentary articles from the editors at Nature Review Genetics (doi:10.1038/nrg.2016.89) and Nature Medicine (doi: 10.1038/nm.4136)                                  

  3. Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. A benchmark for RNA-seq quantification pipelines. Genome Biology. 2016 Apr 23;17:74. PMID: 27107712
     

  4. Li S, Mason CE, Melnick AM. Genetic and Epigenetic Heterogeneity in Acute Myeloid Leukemia. Current Opinion in Genetics & Development. 2016 Feb;36:100-6. PMID: 27162099

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2014

  1. Li S, Garrett-Bakelman F, Perl AE, Luger SM, Zhang C, To BL, Lewis ID, Brown AL, D'Andrea RJ, Ross ME, Levine R, Carroll M, Melnick A, Mason CE. Dynamic evolution of clonal epialleles revealed by methclone. Genome Biology. 2014 Sep 27;15(9):472. PMID: 25260792
     

  2. Munro SA, Lund SP, Pine PS, Binder H, Clevert DA, Conesa A, Dopazo J, Fasold M, Hochreiter S, Hong H, Jafari N, Kreil DP, Łabaj PP, Li S, Liao Y, Lin SM, Meehan J, Mason CE, Santoyo-Lopez J, Setterquist RA, Shi L, Shi W, Smyth GK, Stralis-Pavese N, Su Z, Tong W, Wang C, Wang J, Xu J, Ye Z, Yang Y, Yu Y, Salit M. Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. Nature Communications. 2014 Sep 25;5:5125. PMID: 25254650
     

  3. Su Z*, Łabaj P*, Li S*, et al., SEQC/MAQC-III Consortium. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature Biotechnology. 2014 Sep;32(9):903-14. PMID: 25150838 *Co-first author
     

  4. Li S, Łabaj PP, Zumbo P, Sykacek P, Shi W, Shi L, Phan J, Wu PY, Wang M, Wang C, Thierry-Mieg D, Thierry-Mieg J, Kreil DP, Mason CE. Detecting and correcting systematic variation in large-scale RNA sequencing data. Nature Biotechnology. 2014 Sep;32(9):888-95. PMID: 25150837
     

  5. Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, Kim D, Boland J, Hicks B, Kim R, Chhangawala S, Jafari N, Raghavachari N, Gandara J, Garcia-Reyero N, Hendrickson C, Roberson D, Rosenfeld J, Smith T, Underwood JG, Wang M, Zumbo P, Baldwin DA, Grills GS, Mason CE. Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. Nature Biotechnology. 2014 Sep;32(9):915-925. PMID: 25150835.                   Publication 3-5 were highlighted as the cover of Nature Biotechnology 2014 September issue.                                                                                                                                          

  6. Li S and Mason CE. 2014. The pivotal regulatory landscape of RNA modifications. Annual Review of Genomics and Human Genetics. 2014;15:127-50. PMID: 24898039

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2013

  1. Abdel-Wahab O, Gao J, Adli M, Dey A, Trimarchi T, Chung YR, Kuscu C, Hricik T, Ndiaye-Lobry D, Lafave LM, Koche R, Shih AH, Guryanova OA, Kim E, Li S, Pandey S, Shin JY, Telis L, Liu J, Bhatt PK, Monette S, Zhao X, Mason CE, Park CY, Bernstein BE, Aifantis I, Levine RL. Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo. Journal of Experimental Medicine. 2013 Nov 18;210(12):2641-59. PMID: 24218140
     

  2. Engström PG, Steijger T, Sipos B, Grant GR, Kahles A; RGASP Consortium, Alioto T, Behr J, Bertone P, Bohnert R, Campagna D, Davis CA, Dobin A, Engström PG, Gingeras TR, Goldman N, Grant GR, Guigó R, Harrow J, Hubbard TJ, Jean G, Kahles A, Kosarev P, Li S, et al., RGASP Consortium. Systematic evaluation of spliced alignment programs for RNA-seq data.  Nature Methods. 2013 Dec;10(12):1185-91. PMID: 24185836
     

  3. Ricarte-Filho JC*, Li S*, Garcia-Rendueles ME, Montero-Conde C, Voza F, Knauf JA, Heguy A, Viale A, Bogdanova T, Thomas GA, Mason CE, Fagin JA. Identification of kinase fusion oncogenes in post-Chernobyl radiation-induced thyroid cancers. Journal of Clinical Investigation. 2013 Nov;123(11):4935-44. PubMed PMID: 24135138 *Co-first author
     

  4. Li S, Garrett-Bakelman FE, Akalin A, Zumbo P, Levine R, To BL, Lewis ID, Brown AL, D'Andrea RJ, Melnick A, Mason CE. An optimized algorithm for detecting and annotating regional differential methylation. BMC Bioinformatics. 2013;14 Suppl 5(Suppl 5):S10. PMID: 23735126
     

  5. Meyer JA, Wang J, Hogan LE, Yang JJ, Dandekar S, Patel JP, Tang Z, Zumbo P, Li S, Zavadil J, Levine RL, Cardozo T, Hunger SP, Raetz EA, Evans WE, Morrison DJ, Mason CE, Carroll WL. Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia. Nature Genetics. 2013 Mar;45(3):290-4. PMID: 23377183
     

  6. Pipes L*, Li S*, Bozinoski M*, Palermo R, Peng X, Blood P, Kelly S, Weiss JM, Thierry-Mieg J, Thierry-Mieg D, Zumbo P, Chen R, Schroth GP, Mason CE, Katze MG. The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. Nucleic Acids Research. 2013 Jan;41(Database issue):D906-14. PMID: 23203872 *Co-first author

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2012

  1. Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biology. 2012 Oct 3;13(10):R87. PMID: 23034086

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2011

  1. Zuo WL*, Li S*, Huang JH, Yang DL, Zhang G, Chen SL, Ruan YC, Ye KN, Cheng CH, Zhou WL. 2011. Sodium coupled bicarbonate influx regulates intracellular and apical pH in cultured rat caput epididymal epithelium. PLoS One. 2011;6(8):e22283. PMID: 21887217 *Co-first author
     

  2. Zuo WL, Du JY, Huang JH, Li S, Zhang G, Chen SL, Ruan YC, Cheng CH, Zhou WL. Tyrosine phosphorylation modulates store-operated calcium entry in cultured rat epididymal basal cells. Journal of Cellular Physiology. 2011 Apr;226(4):1069-73. PMID: 20857412

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2010

  1. Zuo WL, Huang JH, Shan JJ, Li S, Wong PY, Zhou WL. Functional studies of acid transporter in cultured rat epididymal cell. Fertility Sterility. 2010 May 15;93(8):2744-9. PMID: 20362281

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2009

  1. Du JY, Zuo WL, Ruan YC, Yang ZH, Chen MH, Chen SL, Li S, Wu ZL, Xiang H, Zhou WL. Stimulating effects of dopamine on chloride transport across the rat caudal epididymal epithelium in culture. Biology of Reproduction. 2009 Jan;80(1):13-23. PMID: 18784353

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