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# Co-first authors; * Co-corresponding authors
2024
- Paczkowska J#, Tang M#, Wright KT#, Song L, Luu K, Shanmugam V, Welsh EL, Weirather JL, Besson N, Olszewski H, Porter BA, Pfaff KL, Redd RA, Cader FZ, Mandato E, Ouyang J, Calabretta E, Bai G, Lawton LN, Armand P, Rodig SJ, Liu XS, Shipp MA. Cancer-specific innate and adaptive immune rewiring drives resistance to PD-1 blockade in classic Hodgkin lymphoma. Nat Commun. 2024 Dec 30;15(1):10740.
[Abstract] - Nicol PB, Paulson D, Qian G, Liu XS, Irizarry R, Sahu AD. Robust identification of perturbed cell types in single-cell RNA-seq data. Nat Commun. 2024 Sep 1;15(1):7610. doi: 10.1038/s41467-024-51649-3.
[Abstract] - Deshpande D#*, Chhugani K#, Ramesh T, Pellegrini M, Shiffman S, Abedalthagafi MS, Alqahtani S, Ye J, Liu XS, Leek JT, Brazma A, Ophoff RA, Rao G, Butte AJ, Moore JH, Katritch V, Mangul S*. The evolution of computational research in a data-centric world. Cell. 2024 Aug 22;187(17):4449-4457.
[Abstract]
2023
- Yang L#, Wang J#, Altreuter J#, Jhaveri A#, Wong CJ, Song L, Fu J, Taing
L, Bodapati S, Sahu A, Tokheim C, Zhang Y, Zeng Z, Bai G, Tang M,
Qiu X, Long HW, Michor F, Liu Y, Liu XS. 2023. Tutorial:
integrative computational analysis of bulk RNA-sequencing data to
characterize tumor immunity using RIMA. Nat Protoc.
18(8):2404-2414.
[Abstract] - Zhang Y#, Xiang G, Jiang AY, Lynch A, Zeng Z, Wang C, Zhang W, Fan
J, Kang J, Gu SS, Wan C, Zhang B, Liu XS*, Brown M*, Meyer
CA*.2023. MetaTiME integrates single-cell gene expression to
characterize the meta-components of the tumor immune
microenvironment. Nat Commun. 2023 May 6;14(1):2634.
[Abstract] - Soto-Feliciano YM#, Sánchez-Rivera FJ#, Perner F#, Barrows DW,
Kastenhuber ER, Ho YJ, Carroll T, Xiong Y, Anand D, Soshnev AA,
Gates L, Beytagh MC, Cheon D, Gu S, Liu XS, Krivtsov AV, Meneses
M, de Stanchina E, Stone RM, Armstrong SA*, Lowe SW*, Allis
CD*. 2023. A Molecular Switch between Mammalian MLL Complexes
Dictates Response to Menin-MLL Inhibition. Cancer Discov.
13(1):146-169.
[Abstract] - Theodoris CV, Xiao L, Chopra A, Chaffin MD, Al Sayed ZR, Hill MC,
Mantineo H, Brydon EM, Zeng Z, Liu XS, Ellinor PT. 2023.
Transfer learning enables predictions in network biology. Nature.
618(7965):616-624.
[Abstract] - Ito Y, Pan D, Zhang W, Zhang X, Juan TY, Pyrdol JW, Kyrysyuk O,
Doench JG, Liu XS, Wucherpfennig KW. 2023. Addressing Tumor
Heterogeneity by Sensitizing Resistant Cancer Cells to T
cell-Secreted Cytokines. Cancer Discov. 13(5):1186-1209.
[Abstract] - Song L, Bai G, Liu XS, Li B, Li H. 2023. Efficient and accurate
KIR and HLA genotyping with massively parallel sequencing data.
Genome Res. 33(6):923-931.
[Abstract] - Sahu A, Wang X, Munson P, Klomp JPG, Wang X, Gu SS, Han Y, Qian G,
Nicol P, Zeng Z, Wang C, Tokheim C, Zhang W, Fu J, Wang J, Nair NU,
Rens JAP, Bourajjaj M, Jansen B, Leenders I, Lemmers J, Musters M,
van Zanten S, van Zelst L, Worthington J, Liu JS, Juric D, Meyer CA,
Oubrie A, Liu XS, Fisher DE, Flaherty KT. 2023. Discovery of
Targets for Immune-Metabolic Antitumor Drugs Identifies
Estrogen-Related Receptor Alpha. Cancer Discov. 13(3):672-701.
[Abstract]
2022
- Zeng Z#, Gu SS#, Ouardaoui N, Tymm C, Yang L, Wong CJ, Li D, Zhang
W, Wang X, Weirather JL, Rodig SJ, Hodi FS*, Brown M*, Liu
XS*. 2022. Hippo signaling pathway regulates cancer
cell-intrinsic MHC-II expression. Cancer Immunol Res. CIR-22-0227.
[Abstract] - Zeng Z#, Gu SS#, Wong CJ, Yang L, Ouardaoui N, Li D, Zhang W, Brown
M, Liu XS*. 2022. Machine learning on syngeneic mouse tumor
profiles to model clinical immunotherapy response. Sci Adv.
8(41):eabm8564
[Abstract] - Lynch AW#, Theodoris CV#, Long HW, Brown M, Liu XS*, Meyer
CA*. 2022. MIRA: joint regulatory modeling of multimodal expression
and chromatin accessibility in single cells. Nat Methods.
19(9):1097-1108.
[Abstract] - Song L, Ouyang Z, Cohen D, Cao Y, Altreuter J, Bai G, Hu X, Livak
KJ, Li H, Tang M, Li B, Liu XS*. 2022. Comprehensive
Characterizations of Immune Receptor Repertoire in Tumors and Cancer
Immunotherapy Studies. Cancer Immunol Res. 10(7):788-799.
[Abstract] - Hu X*, Liu XS*. 2022. A high-resolution view of intra-tumoral
B cell immunity. Immunity. 55(3):387-389.
[Abstract] - Liao Y#, Chen CH#, Xiao T, Peña Avalos B, Dray EV, Cai C, Gao S,
Shah N, Zhang Z, Feit A, Xue P, Liu Z, Yang M, Ji HL, Xu H, Li W,
Mei X, Pierre RS, Shu S, Fei T, Duarte M, Xhao J, Badner JE, Polyak
K, Kantoff PW, Long H, Balk SP, Liu XS*, Brown M*, Xu
K*. 2022. Inhibition of EZH2 transactivation function sensitizes
solid tumors to genotoxic stress. Proc Natl Acad Sci USA.
119(3):e2105898119
[Abstract] [Full Paper] - Choi YS, Erlich TH, von Franque M, Rachmin I, Flesher JL, Schiferle
EB, Zhang Y, Pereira da Silva M, Jiang A, Dobry AS, Su M, Germana S,
Lacher S, Freund O, Feder E, Cortez JL, Ryu S, Babila Propp T,
Samuels YL, Zakka LR, Azin M, Burd CE, Sharpless NE, Liu XS,
Meyer C, Austen WG Jr, Bojovic B, Cetrulo CL Jr, Mihm MC, Hoon DS,
Demehri S, Hawryluk EB, Fisher DE. 2022. Topical therapy for
regression and melanoma prevention of congenital giant nevi. Cell.
185(12):2071-2085.e12.
[Abstract] - Aubrey BJ, Cutler JA, Bourgeois W, Donovan KA, Gu S, Hatton C,
Perlee S, Perner F, Rahnamoun H, Theall ACP, Henrich JA, Zhu Q,
Nowak RP, Kim YJ, Parvin S, Cremer A, Olsen SN, Eleuteri NA, Pikman
Y, McGeehan GM, Stegmaier K, Letai A, Fischer ES, Liu XS,
Armstrong SA. 2022. IKAROS and MENIN coordinate therapeutically
actionable leukemogenic gene expression in MLL-r acute myeloid
leukemia. Nat Cancer. 3(5):595-613.
[Abstract] - Obradovic A, Graves D, Korrer M, Wang Y, Roy S, Naveed A, Xu Y,
Luginbuhl A, Curry J, Gibson M, Idrees K, Hurley P, Jiang P, Liu
XS, Uppaluri R, Drake CG, Califano A, Kim YJ. 2022.
Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can
Predict Immunotherapy Response in Head and Neck Cancer. Clin Cancer
Res. 28(10):2094-2109.
[Abstract] - Zhou L#, Zeng Z#, Egloff AM, Guo F, Campbell KM, Du P, Fu J, Zolkind
P, Ma X, Zhang Z, Zhang Y, Wang X, Gu S, Riley R, Nakahori Y, Keegan
J, Haddad R, Schoenfeld JD, Griffith O, Manguso RT, Lederer JA,
Liu XS, Uppaluri R*. 2022. Checkpoint blockade-induced CD+
Tcell differentiation in head and neck cancer responders. J
Immunother Cancer. 10(1):e004034.
[Abstract] [Full Paper]
2021
- Zhang Y#, Liu Y, Liu XS*. 2021. Neural network architecture
search with AMBER. Nat Machine Intell 3:372-373.
[Full Paper] - Liu J#, Tokheim C#, Lee JD#, Gan W, North BJ, Liu XS*, Pandolfi
PP*, Wei W*. 2021. Genetic fusions favor tumorigenesis through
degron loss in oncogenes. Nat Commun 12(1):6704.
[Abstract] [Full Paper] - Zhang H#, Song L#, Wang X, Cheng H, Wang C, Meyer CA, Liu T, Tang M,
Aluru S, Yur F, Liu XS*, Li H*. 2021. Fast alignment and
preprocessing of chromatin profiles with Chromap. Nat Commun
12(1):1-6.
[Abstract] [Full Paper] - Wang X#, Tokheim C, Gu SS, Wang B, Tang Q, Li Y, Traugh N, Zeng Z,
Zhang Y, Li Z, Shang B, Fu J, Xiao T, Li W, Meyer CA, Chu J, Jiang
P, Cejas P, Lim K, Long H, Brown M*, Liu XS*. 2021. In vivo
CRISPR screens identify the E3 ligase Cop1 as a modulator of
macrophage infiltration and cancer immunotherapy target. Cell
184(21):5357-5374.
[Abstract] [Full Paper] - Zeng Z#, Wong C#, Yang L#, Ouardaoui N, Li D, Zhang W, Gu SS, Zhang
Y, Liu Y, Wang Z, Fu J, Zhou L, Zhang B, Kim S, Yates KB, Brown M,
Freeman GJ, Uppaluri R, Manguso, Liu XS. 2021. TISMO: syngeneic
mouse tumor database to model tumor immunity and immunotherapy
response. Nuc Acids Res.
[Abstract] [Full Paper] - Song L#, Cohen D, Ouyang Z, Cao Y, Hu X, Liu XS. 2021. TRUST4:
immune repertoire reconstruction from bulk and single-cell RNA-seq
data. Nat Methods 18:627-630.
[Abstract] [Full Paper] [Code] - Gu S#, Zhang W, Wang X, Jiang P, Traugh N, Li Z, Meyer C, Stewig B,
Xie Y, Bu X, Manos MP, Font-Tello A, Gjini E, Lako A, Lim K, Conway
J, Tewari AK, Zeng Z, Das Sahu A, Tokheim C, Weirather JL, Fu J,
Zhang Y, Kroger B, Liang JH, Cejas P, Freeman GJ, Rodig S, Long HW,
Gewurz BE, Hodi FS, Brown M*, Liu XS*. 2021. Therapeutically
increasing MHC-I expression potentiates immune checkpoint blockade.
Cancer Discov 11:1-18.
[Abstract] [Full Paper] [Data and Code] - Tokheim C#, Wang X, Timms RT, Zhang B, Mena EL, Wang B, Chen C, Ge
J, Zhang W, Elledge SJ*, Brown M*, Liu XS*. 2021. Systematic
characterization of mutations altering protein degradation in human
cancers. Mol Cell 81:1-17.
[Abstract] [Full Paper] [Code and Documentation] - Qiu X, Feit AS, Feiglin A, Xie Y, Taing L, Perkins J, Gu S, Li Y,
Cejas P, Zhou N, Jeselsohn R, Brown M, Liu XS, Long HW. 2021.
COBRA: Containerized bioinformatics workflow for reproducible
ChIP/ATAC-seq analysis. Genomics Proteomics Bioinformatics.
[Abstract] [Full Paper] - Taing L#, Bai G#, Cousins C#, Cejas P, Oiu X, Herbert ZT, Brown M,
Meyer CA, Liu XS, Long HW*, Tang M*. 2021. CHIPS: A snakemake
pipeline for quality control and reproducible processing of
chromatin profiling data (version 1; peer review: awaiting peer
review). F1000 Rsch 10:517.
[Abstract] [Full Paper] [Code] - Wu SZ, Al-Eryani G, Roden DL, Junakar S, Harvey K, Andersson A et
al. 2021. A single-cell and spatially resolved atlas of human breast
cancers. Nat Genet 53(9):1334-1337.
[Abstract] [Full Paper] - Penter L, Zhang Y, Saveli A Huang T, Cieri N, thrash EM, Kim-Schulze
S, Jhaveri A, Fu J, Ranasinghe S, Li S, Zhang W, Hathaway ES,
Nazzaro M, Kim HT, Chen H, Thurin M, Rodig SJ, Severgnini M,
Cibulskis C, Gabriel S, Livak KJ, Cutler C, Antin JH, Nikiforow S,
Koreth J, Ho VT, Armand P, Ritz J, Streicher H, Neuberg D, Hodi FS,
Gnjatic S, Soiffer RJ, Liu XS, Davids MS*, Bachireddy P*, Wu
CJ*. 2021. Molecular and cellular features of CTLA-4 blockade for
relapsed myeloid malignancies after transplantation. Blood
137(23):3212-17.
[Abstract] [Full Paper] - Kumar S#, Zeng Z#, Bagati A, Tay RE, Sanz LA, Hartono SR, Ito Y,
Abderazzaq F, Hatchi E, Jiang P, Cartwright ANR, Olawoyin O,
Mathewson ND, Pyrdol JW, Li MZ, Doench JG, Booker MA, Tolstorukov
MY, Elledge SJ, Chedin F, Liu XS*, Wucherpfennig KW*. 2021.
CARM1 inhibition enables immunotherapy of resistant tumors by dual
action on tumor cells and T cells. Cancer Discov 11:2051-71.
[Abstract] [Full Paper] - Chen HX, Song M, Maecker HT, Gnjatic S, Patton D, Lee JJ, Adam SJ,
Moravec R, Liu XS, Cerami E, Lindsay J, Hodi FS, Wu C, Wistuba
II, Al-Atrash G, Bernatchez C, Bendall SC, Hewitt SM, Sharon E,
Streicher H, Enos RA, Bowman MD, Tatard-Leitman VM,
Sanchez-Espiridion B, Ranasinghe S, Pichavent M, Del Valle DM, Yu J,
Janssens S, Peterson-Klaus J, Rowe C, Bongers G, Jenq RR, Chang CC,
Abrams JS, Mooney M, Doroshow JH, Harris LN, Thurin M. 2021. Network
for biomarker immunoprofiling for cancer immunotherapy: cancer
immune monitoring and analysis centers and cancer immunologic Data
Commons (CIMAC-CIDC). Clin Cancer Res 27(18):5038-5048.
[Abstract] [Full Paper] - Mathewson ND, Ashenberg O, Tirosh I, Gritsch S, Perez EM, Marx S,
Jerby-Aron L, Chanoch-Myers R, Hara T, Richman AR, Ito Y, Pyrdol J,
Friedrich M, Schumann K, Poitras MJ, Gokhale PC, Gonzales Castro LN,
Shore ME, Hebert CM, Shaw B, Cahil HL, Drummond M, Zhang W, Olawoyin
O, Wakimoto H, Rozenblatt-Rosen O, Brastianos PK, Liu XS, Jones
PS, Cahill DP, Frosch MP, Louis DN, Freeman GJ, Ligon KL, Marson A,
Chiocca EA, Reardon DA*, Regev A*, Suvà ML*, Wucherpfennig
KW*. 2021. Inhibitory CD-161 receptor identified in
glioma-infiltrating T cells by single-cell analysis. Cell 184:1-18.
[Abstract] [Full Paper] - Cejas P, Xie Y, Font-Tello A, Lim K, Syamala S, Qiu X, Tewari AK,
Shah N, Nguyen HM, Patel RA, Brown L, Coleman I, Hackeng WM, Brosens
L, Dreijerink KMA, Ellis L, Abou Alaiwi S, Seo J, Baca S, Beltran H,
Khani F, Pomerantz M, Dall'Agnese A, Crowdis J, Van Allen EM,
Bellmunt J, Morrisey C, Nelson PS, DeCaprio J, Farago A, Dyson N,
Drapkin B, Liu XS, Freedman M, Haffner M, Corey E, Brown M*,
Long HW*. 2021. Subtype heterogeneity and epigenetic convergence in
neuroendocrine prostate cancer. Nat Commun 12:5775.
[Abstract] [Full Paper]
2020
- Meyer CA, Liu XS. 2020. Computaional approaches to modeling
transcription factor activity and gene regulation. Trends Biochem
Sci 45(12):1094-5.
[Abstract] [Full Paper] - Gu S#, Wang X#, Hu X#, Jiang P, Li Z, Traugh N, Bu X, Tang Q, Wang
C, Zeng Z, Fu J, Meyer CA, Zhang Y, Cejas P, Lim K, Wang J, Zhang W,
Tokheim C, Sahu A,, Xing X, Kroger B, Ouyang Z, Long H, Freeman G*,
Brown M*, Liu XS*. 2020. Clonal tracing reveals diverse
patters of response to immune checkpoint blockade. Genome Biol
21(1):263.
[Abstract] [Full Paper] - Li B, Li T, Liu JS, Liu XS. 2020. Computational deconvolution of
tumor-infiltrating immune components with bulk tumor gene expression
data. Methods Mol Biol 2120:249-262.
[Abstract] [Full Paper] - Cader FZ#, Hu F#, Goh W, Wienand K, Ouyang J, Mandato E, Redd R,
Lawton L, Chen PH, Weirather J, Schackman RC, Li B, Ma W, Armand P,
Rodig SJ, Neuberg D, Liu XS*, Shipp M*. 2020. A peripheral
immune signature of responsiveness to PD-1 blockade in patients with
classical Hodgkin lymphoma. NatMed 26(9):1468-1479.
[Abstract] [Full Paper] - Wang C#, Sun D#, Huang X, Wan C, Li Z, Han Y, Qin Q, Fan J, Qiu X,
Xie Y, Meyer C, Brown M, Tang M, Long H, Liu T*, Liu
XS*. 2020. Integrative analyses of single-cell transcriptome and
regulome using MAESTRO. Genome Biol 21:198.
[Abstract] [Full Paper] [Code] - Zhang J#, Lee D#, Dhiman V#, Jiang P#, Xu J#, McGillivray P#, Yang
H#, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky
L, Ung M, Ma L, Yu S, Cao Q, Harmanci A, Yan KK, Sethi A, Gürsoy G,
Schoenberg MR, Rozowsky J, Warrell J, Emani P, Yang YT, Galeev T,
Kong X, Liu S, Li X, Krishnan J, Feng Y, Rivera-Mulia JC, Adrian J,
Broach JR, Bolt M, Moran J, Fitzgerald D, Dileep V, Liu T, Mei S,
Sasaki T, Trevilla-Garcia C, Wang S, Wang Y, Zang C, Wang D, Klein
RJ, Snyder M, Gilbert DM, Yip K, Cheng C, Yue F*, Liu XS*,
White KP*, Gerstein M*. 2020. An integrative ENCODE resource for
cancer genomics. Nat Commun 11:3696.
[Abstract] [Full Paper] - Li Z#, Wang B#, Gu S, Peng J, Sahu A, Chen C, Han T, Shi S, Wang X,
Traugh N, Liu H, Liu Y, Wu Q, Brown M, Xiao T*, Boland G*, Liu
XS*. 2020. CRISPR screens identify essential cell growth
mediators in BRAF inhibitor-resistant melanoma. Genomics Proteomics
Bioinformatics 18(1):26-40.
[Abstract] [Full Paper] - Chen C#, Zheng R, Tokheim C, Dong X, Fan J, Wan C, Tang Q, Brown M,
Liu JS, Meyer C*, Liu XS*. 2020. Determinants of transcription
factor regulatory range. Nat Commun 11:2472.
[Abstract] [Full Paper] - Shi S#, Gu S#, Han T, Zhang W, Huang L, LiZ, Pan D, Fu J, Ge J,
Brown M, Zhang P, Jiang P*, Wucherpfennig KW*, Liu XS*. 2020.
Inhibition of MAN2A1 enhances tumor response to anti-PD-L1. Clin
Cancer Res 28:OF1-OF13
[Abstract] [Full Paper] - Fu J, Li K, Zhang W, Wan C, Zhang J*, Jiang P*, Liu
XS*. 2020. Large-scale public data reuse to model immunotherapy
response and resistance. Genome Med 12(1):21.
[Abstract] [Full Paper] - Qin Q#, Fan J#, Zheng R, Wan C, Mei S, Wu Q, Sun H, Brown M, Zhang
J*, Meyer CA*, Liu XS*. 2020. Lisa: inferring transcriptional
regulators through integrative modeling of public chromatin
accessibiltiy and ChIP-seq data. Genome Biol 21(1):32.
[Abstract] [Full Paper] [Website] [Code for LISA2] - Li, T#, Fu J#, Zeng Z, Cohen D, Li J, Chen Q, Li B, Liu,
XS*. 2020. TIMER2.0 for analysis of tumor-infiltrating immune
cells. Nucleic Acids Res 48(W1):W509-W514.
[Abstract] [Full Paper] - Zeng Z#, Fu J#, Cibulskis C, Jhivari A, Gumbs C, Das B,
Sanchez-Espiridion B, Janssens S, Taing L#, Wang J, Lindsay J,
Vilimas T, Zhang J, Tokheim C, Sahu AD, Jiang P, Yan C, Y. Duose D,
Cerami E, Chen L, Cohen D, Chen QR, Enos RA, Huang X, Lee JJ, Liu Y,
Neuberg DS, Nguyen C, Patterson C, Sarkar S, Shukla SA, Tang M,
Tsuji J, Uduman M, Wang X, Jason L Weirather, Jijun Yu, Joyce Yu,
Zhang J, Zhang J, Meerzaman D, Thurin M, Futreal PA, Karlovich C,
Gabriel SB, Wistuba II, Liu XS*, Wu C. 2020. Cross-site
concordance evaluation of tumor DNA and RNA sequencing platforms for
the CIMAC-CIDC network. Clin Cancer Res. 27(18):5049-5061.
[Abstract] [Full Paper] - Bagati A, Kumar A, Jiang P, Pyrdol J, Zou AE, Godicelj A, Mathewson
ND, Cartwright ANR, Cejas P, Brown M, Giobbie-Hurder A, Dillon D,
Agudo J, Mittendorf E, Liu XS, Wucherpfennig KW. 2020. Integrin
αvβ6-TGFβ-SOX4 pathway drives immune evasion in triple-negative
breast cancer. Cancer Cell 39:1-14.
[Abstract] [Full Paper] - Abou Alaiwi S, Nassar AH, Zie W, Bakouny Z, Berchuck JE, Braun DA,
Baca SC, Nuzzo PV, Flippot R, Mouhieddine TH, Spurr LF, Li YY, Li T,
Flaifel A, Steinharter JA, Margolis CA, Vokes NI, Du H, Shukla SA,
Cherniack AD, Sonpavde G, Haddad RI, Awad MM, Giannakis M, Hodi FS,
Liu XS, Signoretti S, Kadoch C, Freedman ML, KWiatkowski DJ, Van
Allen EM, Choueiri TK. 2020. Mammalian SWI/SNF complex genomic
alterations and immune checkpoint blockade in solid tumors. 2020
Cancer Immunol Res 8(8):1075-1084.
[Abstract] [Full Paper] - The ENCODE Project Consortium (List of authors provided in Supp.
Info. section). 2020. Expanded encyclopaedias of DNA elements in the
human and mouse genomes. Nature 583:699-710.
[Abstract] [Full Paper] - The ENCODE Project Consortium (List of authors provided in Supp.
Info. section). 2020. Perspectives on ENCODE. Nature 583:693-698.
[Abstract] [Full Paper] - Li X et al. (Complete list of authors available online). 2020.
Dynamic incorporation of multiple in silico functional annotations
empowers rare variant association analysis of large whole-genome
sequencing studies at scale. Nat Genet 52(9):969-983.
[Abstract] [Full Paper] - Gao Y, Nihira NT, Bu X, Chu C, Zhang J, Kolodziejczyk A, Fan Y, Chan
NT, Ma L, Liu J, Wang D, Dai X, Liu H, Ono M, Nakanishi A, Inuzuka
H, North BJ, Huang YH, Sharma S, Geng Y, Xu W, Liu XS, Li L,
Miki Y, Sicinski P, Freeman GJ, Wei W. Acetylation-dependent
regulation of PD-L1 nuclear translocation dictates the efficacy of
anti-PD-1 immunotherapy. Nat Cell Biol 22(9):1064-1075.
[Abstract] [Full Paper] - Wu SZ, Roden DL, Wang C, Holliday H, Harvey K, Cazet AS, Murphy KJ,
Pereira B, Al-Eryani G, Bartoniecek N, Hou R, Torpy JR, Junakar S,
Chan C, Lan CE, Hui MN, Gluch L, Beith J, Parker A, Robbins E,
Segara D, Mak C, Cooper C, Warrier S, Forrest A, Powell J, O'Toole
S, Cox T, Timpson P, Lim E, Liu XS, Swarbrick A. 2020. Stromal
cell diversity associated with immune evasion in human
triple-negative breast cancer. EMBO Jrnl 13:1-20.
[Abstract] [Full Paper] - Liu X, Liu T, Shang Y, Dai P, Zhang W, Lee BJ, Huang M, Yang D, Wu
Q, Liu DL, Zheng X, Zhou BO, Dong J, Yeap L, Hu J, Xiao T, Zha S,
Casellas R, Liu XS, Meng F. 2020. ERCC6L2 promotes DNA
orientation-specific recombination in mammalian cells. Cell Res
30(9):732-744.
[Abstract] [Full Paper] - Shu S, Wu HJ, Ge JY, Seid R, Harris IS, Jovanovic B, Murphy K, Wang
B, Qui X, Endress JE, Reyes J, Lim K, Font-Tello A, Syamala S, Ziao
T, Reddy Chilamakuri CS, Papachristou EK, D'Santos C, Anand J,
Hinohara K, Li W, McDonald TO, Luoma A, Modiste RJ, Nguyen QD,
Michel B, Cejas P, Kadoch C, Jaffe JD, Wucherpfennig KW, Qi J, Liu
XS, Long H, Brown M, Carroll JS, Brugge JS, Bradner J, Michor F,
Polyak K. 2020. Synthetic lethal and resistance interaction with BET
Bromodomain inhibitors in triple-negative breast cancer. Mol Cell
78(6):1096-1113.
[Abstract] [Full Paper] - Wan C, Keany M, Dong H, Al-Alem L, Pandya U, Saso S, Boehnke K,
Lynch K, Xu R, Zarrella D, Gu S, Cejas P, Lim K, Long H, Elias K,
Horowitz N, Reitmate C, Muto M, Worley M, Berkowitz R, Matulonis U,
Nucci M, Crum C, Rueda B, Brown M, Liu XS, Hill S. 2020.
Enhanced efficacy of simultaneous PD-1 and PD-L1 immune checkpoint
blockade in high grade serous ovarian cancer. Cancer Res
81(1):158-73.
[Abstract] [Full Paper] - Chu SH, Chabon JR, Matovina CN, Chen BR, Zhang J, Kuman V, Xiong Y,
Callen E, Hung PJ, Feng Z, Koche RP, Liu XS, Chaudhuri J,
Nussenzweig Z, Sleckman BP, Armstrong SA*. 2020. Loss of H3K36
Methyltransferase SETD2 impairs V(E)J recombination during lymphoid
development. iScience 23(3):100941.
[Abstract] [Full Paper]
2019
- Fei T#, Li W#, Peng J#, Xiao T, Chen CH, Wu A, Huang J, Zang C,
Liu XS*, Brown M*. 2019. Deciphering essential cistromes using
genome-wide CRISPR screens. Proc Natl Acad Sci U S A
115(50):25186-25195.
[Abstract] [Full Paper] - Zhang J, Hu X, Wang J, Sahu AD, Cohen D, Song L, Ouyang Z, Fan J,
Wang B, Fu J, Gu S, Sade-Feldman M, Hacohen N, Li W, Ying X*, Li
B*, Liu XS*. 2019. Immune receptor repertoires in pediatric
and adult acute myeloid leukemia. Genome Med 11(1)73.
[Abstract] [Full Paper] - Li S#, Wan C#, Zheng R, Fan J, Dong X, Meyer CA*, Liu
XS*. 2019. Cistrome-GO: a web server for functional enrichment
analysis of transcription factor ChIP-seq peaks. Nucleic Acids Res
47(W1):W206-W211
[Abstract] [Full Paper] - Köster J, Brown M, Liu, XS. 2019. A Bayesian model for single
cell transcript expression analysis on MERFISH data. Bioinformatics
35(6):995–1001.
[Abstract] [Full Paper] - Wang B#, Wang M#, Zhang W#, Xiao T, Chen CH, Wu A, Wu F, Traugh N,
Wang X, Li Z, Mei S, Cui Y, Shi S, Lipp JJ, Hinterndorfer M, Zuber
J, Brown M, Li W*, Liu XS*. 2019. Integrative analysis of
pooled CRISPR genetic screens using MAGeCKFlute. Nat Protoc
14(3):756-780.
[Abstract] [Full Paper] - Hu X#, Zhang J#, Wang J, Fu J, Li T, Zheng X, Wang B, Gu S, Jiang P,
Fan J, Ying X, Zhang J, Carroll MC, Wucherpfennig KW, Hacohen N,
Zhang F, Zhang P, Liu JS*, Li B*, Liu XS*. 2019. Landscape of
B cell immunity and related immune evasion in human cancers. Nat
Genet 51(3):560-567.
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Chinnaiyan AM, Pienta KJ and Brown M. 2007. A hierarchical network
of transcription factors governs androgen receptor dependent
prostate cancer growth. Mol Cell 27(3):380-92.
[Abstract] [Full Paper]
2006
- Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J,
Brodsky AS,KeetonEK, Fertuck KC,Hall GF, Wang Q, Bekiranov S,
Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS*, Brown
M*. 2006. Genome-wide analysis of estrogen receptor binding sites.
Nat Genet 38(11):1289-97.
[Abstract] [Full Paper] - Ji X*, Li W*, Song J, Wei L, Liu XS. 2006. CEAS:
cis-regulatory element annotation system. Nucleic Acids Res 34(Web
Server Issue):W551-4.
[Abstract] [Full Paper] - Johnson WE*, Li W*, Meyer CA*, Gottardo R, Carroll JS, Brown M,
Liu XS. 2006. MAT: Model-based analysis of tiling-arrays for
ChIP-chip. Proc Natl Acad Sci USA 103(33)12457-62.
[Abstract] [Full Paper] - Lieb JD, Beck S, Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu
XS, Okumura K, Shiota K, Ushijima T, Greally JM. 2006. Applying
whole-genome studies of epigenetic regulation to study human
disease. Cytogenet. Genome Res 114(1):1-15.
[Abstract] [Full Paper] - Nelson EA, Walker SR, Li W, Liu XS, Frank DA. 2006.
Identification of human STAT5-dependent gene regulatory elements
based on interspecies homology. J Biol Chem 281(36):26216-24.
[Abstract] [Full Paper] - Palomero T, Odom DT, O'Neil J, Ferrando AA, Margolin A, Neuberg DS,
Winter SS, Larson RS,Li W, Liu XS, Young RA, Look AT. 2006.
Transcriptional regulatory networks downstream of TAL1/SCL in T-cell
acute lymphoblastic leukemia. Blood 108(3):986-92.
[Abstract] [Full Paper] - Swinburn IA, Meyer CA, Liu XS, Silver PA, Brodsky AS. 2006.
Genomic localization of RNA-binding proteins reveals links between
pre-mRNA processing and transcription. Genome Res 16(7):912-21.
[Abstract] [Full Paper] - Zhang Y, Liu XS, Liu Q, Wei L. 2006. Genome-wide in silico
identification and analysis of cis Natural Antisense Transcripts
(cis-NATs) in Ten Species. Nucleic Acids Res 34(12):3465-75.
[Abstract] [Full Paper]
2005
- Brodsky AS, Meyer CA, Hall G, Swinburne IA, Keenan BJ, Liu
XS. 2005. Fox EA, Silver PA. Genomic mapping of RNA polymerase II
reveals sites of co-transcriptional regulation in human cells.
Genome Biol 6(8):R64.
[Abstract] - Liu XS. 2005. Gibbs sampling and bioinformatics. Encyclopedia of
Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons
Ltd, UK ISBN: 0-470-84974-6.
[Full Paper] - Li W, Meyer CA, Liu XS. 2005. A hidden Markov model for
analyzing ChIP-chip experiments on genome tiling arrays and its
application to p53 binding sequences. Bioinformatics 21
Suppl.1:i274-i282.
[Abstract] [Full Paper] - Ben-Yehuda S, Jujita M, Liu XS, Gorbatyuk B, Skoko D, Yan J,
Eichenberger P, Rudner DZ, Marko JF, Liu JS, Losick R. 2005.
Defining a centromere-like element in Bacillus subtilis by
identifying the binding sites for the chromosome-anchoring protein
RacA. Mol Cell 17(6):773-82.
[Abstract] [Full Paper] [Full Paper] - Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Shao
W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA, Brown M. 2005.
Chromosome-wide mapping of estrogen receptor binding reveals
long-range regulation requiring the forkhead protein FoxA1. Cell
122(1):33-43.
[Abstract] [Full Paper] - Hong P, Liu XS, Zhou Q, Lu X, Liu JS, Wong WH. 2005. A boosting
approach for motif modeling using ChIP-chip data. Bioinformatics
21(11):2636-43.
[Abstract] [Full Paper]
2004
- Liu Y*, Liu XS*, Wei L, Altman RB, Batzoglou S. 2004.
Eukaryotic regulatory element conservation analysis and
identification using comparative genomics. Genome Res 14(3):451-8.
[Abstract] [Full Paper] - Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS. 2004. A
suite of web-based programs to search for transcriptional regulatory
motifs. Nucleic Acids Res 32(Web Server Issue):W204-7.
[Abstract] [Full Paper] - Jensen ST, Liu XS, Zhou Q, Liu JS. 2004. Computational discovery
of gene regulatory binding motifs: a Bayesian perspective. Stat Sci
19(1):188-204.
[Full Paper] - Yildiz FH, Liu XS , Heydorn A, Schoolnik GK. 2004. Molecular
Analysis of Rugosity in a Vibrio cholerae O1 El Tor phase variant.
Mol Microbiol 53(2):497-515.
[Abstract] [Full Paper]
2003
- Conlon EM*, Liu XS*, Lieb JD, Liu JS. 2003. Integrating
regulatory motif discovery and genome-wide expression analysis. Proc
Nat Acad Sci USA 100(6):3339-44.
[Abstract] [Full Paper]
2002
- Liu XS*, Brutlag DL, Liu JS. 2002. An algorithm for finding
protein-DNA binding sites with applications to chromatin
immunoprecipitation microarray experiments. Nat Biotech 20(8):835-9.
*Liu X added middle name Shirley.
[Abstract] [Full Paper] - Liu JS, Gupta M, Liu X, Mayerhofere L, Lawrence CE. 2002.
Statistical models for biological sequence motif discovery. Case
Studies in Bayesian Statistics, IV, 2002, Springer-Verlag, New
York.
[Full Paper]
2001
- Lieb JD, Liu X, Botstein D, Brown PO. 2001. Promoter-specific
binding of Rap1 revealed by genome-wide maps of protein-DNA
association. Nat Genet 28(4):327-34.
[Abstract] [Full Paper] - Liu X, Brutlag DL, Liu JS. 2001. BioProspector: discovering
conserved DNA motifs in upstream regulatory regions of co-expressed
genes. Proc Pac Symp Biocomput 127-38.
[Abstract] [Full Paper]
1999
- Dugan JM, Berrios DC, Liu X, Kim DK, Kaizer H, Fagan LM. 1999.
Automation and integration of components for generalized semantic
markup of electronic medical texts. Proc AMIA Symp 736-40.
[Abstract] [Full Paper] - Fischer P, Liu X, Lizotte-Waniewski M, Kamal IH, Ramzy RM,
Williams SA. 1999. Development of a quantitative, competitive
polymerase chain reaction-enzyme-linked immunosorbent assay for the
detection of Wuchereria bancrofti DNA. XParasitol Res 85(3):176-83.
[Abstract] [Full Paper]
1998
- Liu X, Altman RB. 1998. Updating a bibliography using the
related articles function within PubMed. Proc AMIA Symp 750-4.
[Abstract] [Full Paper]