2022 | 2021 | 2020 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013

2022

Lin X#, Liu Y#, Liu S#, Zhu X, Wu L, Zhu Y, Zhao D, Xu X, Chemparathy A, Wang H, Cao Y, Nakamura `M, Noordermeer JN, La Russa M, Wong WH, Zhao K, Qi LS. Science (2022). ­­­­­Nested Epistasis Enhancer Networks for Robust Genome Regulation. Commented by Nature "News & Views”. Two-layer design protects genes from mutations in their enhancers

Guo L#*, Bian J#, Davis AE, Liu P, Kempton HR, Zhang X, Chemparathy A, Gu B, Lin X, Rane DA, Xu X, Jamiolkowski RM, Hu Y, Wang S*, Qi LS*. Nature Cell Biology (2022). Multiplexed genome regulation in vivo with hyper-efficient Cas12a.

Gu T#, Hao D#, Woo J, Huang TW, Guo L, Lin X, Guzman AG, Tovy A, Rosas C, Jeong M, Zhou Y, Deneen B, Huang Y, Li W, Goodell MA. Nature Genetics (2022). The disordered N-terminal domain of DNMT3A recognizes H2AK119ub and is required for postnatal development.

Zeng L#, Liu Y#, Nguyenla XH, Abbott TR, Han M, Zhu Y, Chemparathy A, Lin X, Chen X, Wang H, Rane DA, Spatz JM, Jain S, Rustagi A, Pinsky B, Zepeda AE, Kadina AP, Walker JA, Holden K, Temperton N, Cochran JR, Barron AE, Connolly MD, Blish CA, Lewis DB, Stanley SA*, Russa ML*, Qi LS*. Nature Communications (2022). Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro.

2021

Lin X#, Liu Y#, Chemparathy A#, Pande T, Russia ML, Qi LS. Cell Reports Medicine (2021). A comprehensive analysis and resource to use CRISPR-Cas13 for broad-spectrum targeting of RNA viruses.

2020

Abbott TR#, Dhamdhere G#, Liu Y#, Lin X#, Goudy L#, Zeng L, Chemparathy A, Chmura S, Heaton NS, Debs R, Pande T, Endy d, Russa ML*, Lewis DB*, Qi LS*. Cell (2020). Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza. (PDF)

Lin X, Chemparathy A, Russa ML, Daley T, Qi LS. Annual Review of Biomedical Data Science (2020). Computational Methods for Analysis of Large-Scale CRISPR Screens.

Bodapati S, Daley TP, Lin X, Zou J*, Qi LS*. Genome Biology  (2020). A benchmark of algorithms for the analysis of pooled CRISPR screens.

2018

Gu T#, Lin X#, Cullen S, Luo M, Jeong M, Estecio M, Shen J, Hardikar S, Sun D, Su J, Rux D, Guzman A, Lee M, Qi L, Chen­ J,  Kyba M, Huang Y, Chen T, Li W*, Goodell MA*. Genome Biology (2018). DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells.

Wang H, Xu X, Nguyen CM, Liu Y, Gao Y, Lin X, Daley T, Kipniss NH, La Russa M, Qi LS. Cell (2018). CRISPR-mediated programmable 3D genome positioning and nuclear organization.

Liu Y#, Yu C#, Daley T#, Wang F, Cao WS, Bhate S, Lin X, Still II C, Liu H, Zhao D, Wang H, Xie X, Ding S, Wong WH, Wernig M, Qi LS. Cell Stem Cell (2018). CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming.

Daley T#*, Lin Z, Lin X,  Liu Y, Wong WH, Qi LS. Genome Biology (2018). CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens.

Su J#, Huang Y#, Cui X, Zhang X, Wang X, Xin Y, Lin X, Chen K, Lv J, Xu J, Goodell MA* and Li W*. Genome Biology (2018). Homeobox oncogene activation by pan-cancer DNA hypermethylation.

2017

Lin X, Su J, Chen K, Rodrigues B, Li W. Genome Biology (2017). Sparse conserved under-methylated CpGs are associated with high-order chromatin structure.

2016

Xu J, Zhang W, Yan X, Lin X, Li W, Mi J, Li J, Zhu J, Chen Z, Chen S. Journal of Hematology & Oncology (2016). DNMT3A mutation leads to leukemia extramedullary infiltration mediated by TWIST1.

Yang L#, Rodriguez B#, Mayle A, Park HJ, Lin X, Luo M, Jeong M, Curry CV, Kim S,  Ruau D, Zhang X, Zhou T, Zhou M, Rebel VI, Challen GA, Gottgens B, Lee JS, Rau R, Li W*, Goodell MA*. Cancer Cell (2016). DNMT3A loss drives enhancer hypomethylation in FLT3-ITD-associated leukemias.

2015

Chen K, Chen Z, Wu D, Zhang L, Lin X, Su J, Rodriguez B, Xi Y, Xia Z, Chen X, Shi X, Wang Q, Li W. Nature Genetics (2015). Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes.

2014

Ho JWK#, Jung YL#, Liu T#, Alver B. H, Lee S, Ikegami K, Sohn K, Minoda A, Tolstorukov MY, Appert A, Parker SCJ, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RAJ, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM*, Strome S*, Elgin SCR*, Liu XS*, Lieb JD*, Ahringer J*, Karpen GH*, Park PJ*. Nature (2014). Comparative analysis of metazoan chromatin organization.

Wang J, Lin X, Wang S, Wang C, Wang Q, Duan X, Lu P, Wang Q, Wang C, Liu XS, Huang J. Scientific Reports (2014). PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression.

2013

Lin X, Sun D, Rodriguez B, Zhao Q, Sun H, Zhang Y, Li W. Bioinformatics (2013). BSeQC: Quality Control of Bisulfite Sequencing Experiments.

Sun H, Qin B, Liu T, Wang Q, Liu J, Wang J, Lin X, Yang Y, Taing L, Rao PK, Brown M, Zhang Y, Long HW, Liu XS. Bioinformatics (2013). CistromeFinder for ChIP-seq and DNase-seq data reuse.