Ma Lab Publications

Google Scholar Profile

NCBI/PubMed Collection

underline: lab members and mentees; * equal contribution; # co-corresponding

• S Wang*, Q Jia*, Y Cui*, H Qu, R Li, L Yu, X Wang, CS Teng, S Liu, C Xu, Y Zhang, S Wang, SK Yin, LL Ho, M Wang, W Chen, W Zhong, J Zhu, D Seymour, SW Ding, S Xu, W Ma#, Y Xu#, Z Jia#. ‘‘CHAP-GWAS: Leveraging chromosomal haplotypes to improve genome-wide association studies.’’ Submitted. 2026.

• J Zou, W Ma, S Xu. ‘‘Genomic Mating.’’ Submitted. 2026.

• GN Filippova, E Sanger, J MacDonald, H Fang, C Groneck, M Takasaki, A Meleshko, W Ma, Y Liu, G Li, R Zhang, CE Murry, D Van Dyke, A Skakkebaek, CH Gravholt, WS Noble, T Bammler, JE Young, X Deng, JB Berletch, CM Disteche. ‘‘Cell-type specific allelic dampening of sex-linked genes in sex chromosome aneuploidy.’’ Submitted. 2026.

• L Costantino*, T Ye*, K Boardman, S Xiang, J Luo, Y Mu, W Ma, D Koshland. ‘‘Cohesin acetylation and ATPase activity control cohesion and loop architecture through distinct mechanisms.’’ PNAS. 123(17):e2531218123, 2026.

• J Huang, R Ma, M Strobel, Y Hu, T Ye, T Jiang#, W Ma#. ‘‘SHICEDO: Single-cell Hi-C data enhancement with reduced over-smoothing.’’ Bioinformatics. 41(12):btaf575, 2025. [GitHub]

• J Lin*, J Zhang*, L Ma, H Fang, R Ma, C Groneck, GN Filippova, X Deng, C Kinoshita, JE Young, W Ma#, CM Disteche#, JB Berletch#. ‘‘KDM6A facilitates Xist upregulation at the onset of X inactivation.’’ Biology of Sex Differences. 16(1):1, 2025.

• R Ma, J Huang, T Jiang#, W Ma#. ‘‘A mini-review of single-cell Hi-C embedding methods.’’ Computational and Structural Biotechnology Journal. 23(2024):4027-4035, 2024.

• H Liu, W Ma. ‘‘DiffGR: Detecting differentially interacting genomic regions from Hi-C contact maps.’’ Genomics, Proteomics & Bioinformatics. qzae028, 2024 [GitHub]

• H Liu, W Ma. ‘‘scHiCDiff: Detecting differential chromatin interactions in single-cell Hi-C data.’’ Bioinformatics. 39(10):btad625, 2023. [GitHub]

• P Singh, S Lonardi, Q Liang, P Vydyam, E Khabirova, T Fang, S Gihaz, J Thekkiniath, M Munshi, S Abel, L Ciampossin, G Batugedara, M Gupta, XM Lu, T Lenz, S Chakravarty, E Cornillot, Y Hu, W Ma, LM Gonzalez, S Sanchez, K Estrada, A Sanchez-Flores, E Montero, OS Harb, KG Le Roch, CB Mamoun. ‘‘Babesia duncani multi-omics identifies virulence factors and drug targets.’’ Nature Microbiology. 8:845-859, 2023.

• T Ye#, Y Hu, S Pun, W Ma#. ‘‘HiCube: Interactive visualization of multiscale and multimodal Hi-C and 3D genome data.’’ Bioinformatics. 39(4):btad154, 2023. [GitHub]

• W Ma#, H Fang, N Pease, GN Filippova, CM Disteche, JB Berletch#. ‘‘Sex-biased and parental allele-specifc gene regulation by KDM6A.’’ Biology of Sex Differences. 13:40, 2022.

• Y Hu, W Ma. ‘‘EnHiC: Learning fine-resolution Hi-C contact maps using a generative adversarial framework.’’ Bioinformatics. 37(Suppl_1):i272-i279, 2021 (ISMB/ECCB 2021). [GitHub]

• M Salloum, D Jeske, W Ma, V Papalexakis, C Shelton, V Tsotras, S Zhou. ‘‘Developing an Interdisciplinary Data Science Program.’’ In Proceedings of the 52nd ACM Technical Symposium on Computer Science Education (SIGCSE ’21), Pages 509-5151, March 2021.

• J Zhou, P Li, W Zeng, W Ma, Z Lu, R Jiang, Q Zhang, T Jiang. “IRIS: A method for predicting in vivo RNA secondary structures using PARIS data.” Quantitative Biology. 8(4):369-381, 2020. [GitHub]

• T Ye, W Ma. ‘‘ASHIC: Hierarchical Bayesian modeling of diploid chromatin contacts and structures.’’ Nucleic Acids Research. 48(21):e123, 2020. [GitHub]

• AZ Virji, J Thekkiniath, W Ma, L Lawres, J Knight, A Swei, KG Le Roch, CB Mamoun. “Insights into the evolution and drug susceptibility of Babesia duncani from the sequence of its mitochondrial and apicoplast genomes.” International Journal for Parasitology. 49(2019):105-113, 2019.

• W Ma, G Bonora, JB Berletch, X Deng, WS Noble, CM Disteche. “X-chromosome inactivation and escape from X inactivation in mouse.” Methods in Molecular Biology. 1861:205-219, 2018.

• T Barr, S Sureshchandra, P Ruegger, J Zhang, W Ma, J Borneman, K Grant, I Messaoudi. “Concurrent gut transcriptome and microbiota profiling following chronic ethanol consumption in nonhuman primates.” Gut Microbes. 9(4):338-356, 2018.

• W Ma, F Ay, C Lee, G Gulsoy, X Deng, S Cook, J Hesson, C Cavanaugh, CB Ware, A Krumm, J Shendure, CA Blau, CM Disteche, WS Noble, Z Duan. “Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution.” Methods. 142(2018):59-73, 2018.

• Y Qiu, EK Pasoreck, AK Reddy, A Nagatani, W Ma, J Chory, M Chen. “Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B.” Nature Communications. 8(1):1905, 2017.

• W Ma, L Yang, R Rohs, WS Noble. “DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.” Bioinformatics, 33(19):3003-3010, 2017. [Bitbucket]

• V Ramani, DA Cusanovich, RJ Hause, W Ma, R Qiu, X Deng, CA Blau, CM Disteche, WS Noble, J Shendure, Z Duan. “Mapping three-dimensional genome architecture through in situ DNase Hi-C.” Nature Protocols. 11(11):2104-2121, 2016.

• JB Berletch*, W Ma*, F Yang, J Shendure, WS Noble, CM Disteche, X Deng. “Identification of genes escaping X inactivation by allelic expression analysis in a novel hybrid mouse model.” Data in Brief. 5:761-769, 2015.

• X Deng*, W Ma*, V Ramani, A Hill, F Yang, F Ay, JB Berletch, CA Blau, J Shendure, Z Duan, WS Noble, CM Disteche. “Bipartite structure of the inactive mouse X chromosome.” Genome Biology. 16:152, 2015.

• JB Berletch*, W Ma*, F Yang, J Shendure, WS Noble, CM Disteche, X Deng. “Escape from X inactivation varies in mouse tissues.” PLOS Genetics. 11(3):e1005079, 2015.

• F Yang, X Deng, W Ma, JB Berletch, N Rabaia, G Wei, JM Moore, GN Filippova, J Xu, Y Liu, WS Noble, J Shendure, CM Disteche. “The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation.” Genome Biology. 16:52, 2015.

• W Ma, F Ay, C Lee, G Gulsoy, X Deng, S Cook, J Hesson, C Cavanaugh, CB Ware, A Krumm, J Shendure, CA Blau, CM Disteche, WS Noble, Z Duan. “Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes.” Nature Methods. 12(1):71-78, 2015.

• W Ma, WS Noble and TL Bailey. “Motif-based analysis of large nucleotide datasets using MEME- ChIP.” Nature Protocols. 9(6):1428-1450, 2014.

• J Cao, J Ni, W Ma, V Shiu, LA Milla, S Park, ML Spletter, S Tang, J Zhang, X Wei, SK Kim, MP Scott. “Insight into insulin secretion from transcriptome and genetic analysis of insulin-producing cells of drosophila.” Genetics. 197:175-192, 2014.

• X Deng, JB Berletch, W Ma, DK Nguyen, JB Hiatt, WS Noble, J Shendure, CM Disteche. “Mammalian X upregulation is associated with enhanced transcription initiation, RNA half-life, and MOF-mediated H4K16 acetylation.” Developmental Cell. 25(1):55-68, 2013.

• KA Peterson, Y Nishi, W Ma, A Vedenko, L Shokri, X Zhang, M McFarlane, JM Baizabal, JP Junker, A van Oudenaarden, T Mikkelsen, BE Bernstein, TL Bailey, ML Bulyk, WH Wong, AP McMahon. “Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning.” Genes & Development. 26(24):2802-2816, 2012.

• JS Park, W Ma, LL O'Brien, E Chung, JJ Guo, JG Cheng, MT Valerius, JA McMahon, WH Wong, AP McMahon. “Six2 and Wnt regulate self-renewal and commitment of nephron progenitors through shared gene regulatory networks.” Developmental Cell. 23(3):637-651, 2012.

• W Ma, WH Wong. “The analysis of ChIP-seq data.” Methods in Enzymology. 497:51-73, 2011.

• H Ji, H Jiang, W Ma, WH Wong. “Using CisGenome to Analyze ChIP-chip and ChIP-seq Data.” Current Protocols in Bioinformatics. 2:2, 2011.

• EY Lee, H Ji, Z Ouyang, B Zhou, W Ma, SA Vokes, AP McMahon, WH Wong, MP Scott. “Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis.” Proceedings of the National Academy of Sciences. 107(21):9736-9741, 2010.

• H Ji, H Jiang, W Ma, DS Johnson, RM Myers, WH Wong. “An integrated software system for analyzing ChIP-chip and ChIP-seq data.” Nature Biotechnology. 26(11):1293-1300, 2008.

• J Choi, LK Southworth, KY Sarin, AS Venteicher, W Ma, W Chang, P Cheung, S Jun, MK Artandi, N Shah, SK Kim, SE Artandi. “TERT promotes epithelial proliferation through transcriptional control of a Myc-and Wnt-related developmental program.” PLOS Genetics. 4(1):e10, 2008.

Dissertation

• W Ma. “Computational Algorithms and Statistical Modeling of ChIP Sequencing Analysis.” Stanford University. 2012.