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Publications

Preprints
  • Chidester B, Do M, and Ma J.
    Rotation equivariance and invariance in convolutional neural networks.
    arXiv:1805.12301 [stat.ML]
  • Chen Y, Zhang Y, Wang Y, Zhang L, Brinkman EK, Adam SA, Goldman R, van Steensel B, Ma J, and Belmont AS.
    TSA-Seq mapping of nuclear genome organization.
    bioRxiv, doi: https://doi.org/10.1101/307892
2018
  • Yang Y, Gu Q, Sasaki T, Crivello J, O'Neill R, Gilbert DM, and Ma J.
    Continuous-trait probabilistic model for comparing multi-species functional genomic data.
    Cell Systems, doi: https://doi.org/10.1016/j.cels.2018.05.022, 2018.
    • Early version appeared in Proceedings of the 22nd Annual Conference on Research in Computational Molecular Biology (RECOMB), 2018.
  • Chen J, Xu P, Wang L, Ma J, and Gu Q.
    Covariate adjusted precision matrix estimation via nonconvex optimization.
    ICML, in Proceedings of the 35th International Conference on Machine Learning, to appear, 2018.
  • Zhang R, Wang Y, Yang Y, Zhang Y, and Ma J.
    Predicting CTCF-mediated chromatin loops using CTCF-MP.
    ISMB, in Proceedings of the 26th Conference on Intelligent Systems for Molecular Biology
    Bioinformatics, 34(13):i133–i141, 2018.
  • Singh S, Poczos B, and Ma J.
    Minimax reconstruction risk of convolutional sparse dictionary learning.
    AISTATS, in Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, PMLR 84:1327-1336, 2018.
  • Singh S, Yang Y, Poczos B, and Ma J.
    Predicting enhancer-promoter interaction from genomic sequence with deep neural networks.
    Quantitative Biology, in press; bioRxiv, doi: http://dx.doi.org/10.1101/085241, 2018.
  • Subramanian V, Tang W, Chidester B, Ma J, and Do M.
    Integration of spatial distribution in imaging-genetics.
    MICCAI, in Proceedings of the 21st International Conference on Medical Image Computing and Computer Assisted Intervention, to appear, 2018.
  • Subramanian V, Chidester B, Ma J, and Do M.
    Correlating cellular features with gene expression using CCA.
    ISBI, in Proceedings of the IEEE 15th International Symposium on Biomedical Imaging, pp. 805-808, 2018; arXiv:1802.08910 [eess.SP]
  • Chidester B, Do M, and Ma J.
    Discriminative bag-of-cells for imaging-genomics.
    PSB, in Proceedings of the Pacific Symposium on Biocomputing, 23:319-330, 2018.
  • Rajaraman A and Ma J.
    Toward recovering allele-specific cancer genome graphs.
    Journal of Computational Biology, doi: 10.1089/cmb.2018.0022, 2018 (journal version of the RECOMB 2017 paper).
  • Tasan I, Sustackova G, Zhang L, Kim J, Sivaguru M, HamediRad M, Wang Y, Genova J, Ma J, Belmont AS, and Zhao H.
    CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci.
    Nucleic Acids Research, doi: 10.1093/nar/gky501, 2018.
  • Kim Y-C, Seok S, Byun S, Kong B, Zhang Y, Guo G, Xie W, Ma J, Kemper B, and Kemper JK.
    AhR and SHP regulate phosphatidylcholine and S-adenosylmethionine levels in the one-carbon cycle.
    Nature Communications, 9(1):540, 2018.
  • Ma S, Hseih Y-P, Ma J, and Lu C.
    Low-input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex.
    Science Advances, 4(4):eaar8187, 2018.
  • Seok S, Kim Y-C, Byun S, Choi S, Xiao Z, Iwamori N, Zhang Y, Wang C, Ma J, Ge K, Kemper B, and Kemper JK.
    Fasting-induced JMJD3 histone demethylase epigenetically activates mitochondrial fatty acid β-oxidation.
    Journal of Clinical Investigation, doi: 10.1172/JCI97736, 2018.
2017
  • Xu P, Ma J, and Gu Q.
    Speeding up latent variable Gaussian graphical model estimation via nonconvex optimizations.
    NIPS, in Proceedings of the 31st Annual Conference on Neural Information Processing Systems, 2017.
  • Kim J, Farre MB, Auvil L, Capitanu B, Larkin D*, Ma J*, and Lewin HA*.
    Reconstruction and evolutionary history of eutherian chromosomes.
    Proceedings of the National Academy of Sciences (PNAS), 114(27) E5379-E5388, 2017.
    [News in Science] [ScienceDaily]
  • Yang Y, Zhang R, Singh S, and Ma J.
    Exploiting sequence-based features for predicting enhancer-promoter interactions.
    ISMB, in Proceedings of the 25th Conference on Intelligent Systems for Molecular Biology
    Bioinformatics, 33(14): i252-i260, 2017.
    [F1000Prime Recommended]
  • Rajaraman A and Ma J.
    Towards recovering allele-specific cancer genome graphs.
    RECOMB, in Proceedings of the 21th Annual International Conference on Research in Computational Molecular Biology, LNCS, vol 10229, 2017.
  • Anantharaman A, Tripathi V, Khan A, Yoon JH, Singh DK, Gholmalamdari O, Guang S, Ohlson J, Wahlstedt H, Ohmann M, Jantsch MF, Conrad NK, Ma J, Gorospe M, Prasanth SG, and Prasanth KV.
    ADAR2 regulates RNA stability by modifying access of decay-promoting RNA-binding proteins.
    Nucleic Acids Research, 45(7):4189-4201, 2017.
  • Singh DK, Gholamalamdari O, Jadaliha M, Li XL , Lin Y-C, Zhang Y, Guang S, Hashemikhabir S, Tiwari S, Khan A, Thomas A, Chakraborty A, Macias V, Balla AK, Bhargava R, Janga SC, Ma J, Prasanth SG, Lal A, and Prasanth KV.
    PSIP1/p75 promotes tumorigenicity in breast cancer cells by promoting the transcription of cell cycle genes.
    Carcinogenesis, 38(10):966-975, 2017.
  • Byun S, Kim Y-C, Zhang Y, Kong B, Guo G, Sadoshima J, Ma J, Kemper B, and Kemper JK.
    A postprandial FGF19-SHP-LSD1 regulatory axis mediates epigenetic repression of hepatic autophagy.
    The EMBO Journal, 36(12):1755-1769, 2017.
  • Dekker J et al. (as part of the 4D Nucleome Network).
    The 4D nucleome project.
    Nature, 549(7671):219-226, 2017.
2016
  • Li Y, Zhou S, Schwartz DC, and Ma J.
    Allele-specific quantification of structural variations in cancer genomes.
    Cell Systems, 3(1):21-34, 2016.
    [CMU News] [GenomeWeb Story]
    • Early version appeared in Proceedings of the 20th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2016.
  • Tian D, Gu Q*, and Ma J*.
    Identifying gene regulatory network rewiring using latent differential graphical models.
    Nucleic Acids Research, 44(17):e140, 2016.
  • Hou JP, Emad A, Puleo GJ, Ma J*, and Milenkovic O*.
    A new correlation clustering method for cancer mutation analysis.
    Bioinformatics, 32(24):3717-28, 2016.
  • Rajaraman A and Ma J.
    Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction.
    BMC Bioinformatics, 17:414, 2016.
  • Heo Y, Ramachandran A, Hwu W-M, Ma J, and Chen D.
    BLESS 2: Accurate, memory-efficient, and fast error correction method.
    Bioinformatics, 32(15):2369-71, 2016.
  • He F, Li Y, Tang Y-H, Ma J*, and Zhu H*
    Identifying micro-inversions using high-throughput sequencing reads.
    BMC Genomics, 17 Suppl 1:4, 2016.
  • Bryan C, Guterman G, Ma KL, Lewin H, Larkin D, Kim J, Ma J, and Farre M.
    Synteny Explorer: An interactive visualization application for teaching genome evolution.
    IEEE Trans Vis Comput Graph, 23(1):711-720, 2016.
2015
  • Ma J and Milenkovic O.
    Expanding the biology toolkit - Computing power for genomics.
    Cell, 163:1306, 2015. (Invited)
  • Kim Y-C, Byun S, Zhang Y, Seok S, Kemper BW, Ma J*, and Kemper JK*.
    Liver ChIP-seq analysis in FGF19-treated mice reveals SHP as a global transcriptional partner of SREBP-2.
    Genome Biology, 16:268, 2015.
  • Gupta A, Place M, Goldstein S, Sarkar D, Zhou S, Potamousis K, Kim J, Flanagan C, Li Y, Newton MA, Callander NS, Hematti P, Bresnick EH, Ma J, Asimakopoulos F, and Schwartz DC.
    Single molecule analysis reveals widespread structural variation in multiple myeloma.
    Proceedings of the National Academy of Sciences (PNAS), 112(25):7689-94, 2015.
  • Yazdi SMHT, Yuan Y, Ma J, Zhao H, and Milenkovic O.
    A rewritable, random-access DNA-based storage system.
    Scientific Reports, 5, 14138; doi: 10.1038/srep14138, 2015.
    [New York Times]
  • Silva GO, He X, Parker JS, Gatza ML, Carey LA, Hou JP, Moulder SL, Marcom PK, Ma J, Rosen JM, and Perou CM.
    Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer.
    Breast Cancer Res Treat, 152(2):347-56, 2015.
  • Yazdi SMHT, Kiah HM, Garcia-Ruiz E, Ma J, Zhao H, and Milenkovic O.
    DNA-based storage: Trends and methods.
    IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, 1(3):230-48, 2015. (Invited)
  • Ramachandran A, Heo Y, Hwu W-M, Ma J, and Chen D.
    FPGA accelerated DNA error correction.
    DATE, in Proceedings of IEEE/ACM Design, Automation & Test in Europe, 2015.
  • Koepfli KP, Paten B, the Genome 10K Community of Scientists (including Ma J), O'Brien SJ.
    The Genome 10K Project: A way forward.
    Annu Rev Anim Biosci, 3:57-111, 2015.
2014
  • Seok S, Fu T, Choi SE, Li Y, Zhu R, Kumar S, Sun X, Yoon G, Kang Y, Zhong W, Ma J, Kemper B, and Kemper JK.
    Transcriptional regulation of autophagy by an FXR-CREB axis.
    Nature, 516(7529):108-11, 2014.
    [News & Views, Nature] [Research Highlight, Nat Rev Endocrinol] [F1000Prime Recommended]
  • Yokoyama KD, Zhang Y, and Ma J.
    Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework.
    PLOS Computational Biology, 10(8): e1003771, 2014.
  • Hou JP and Ma J.
    DawnRank: Discovering personalized driver genes in cancer.
    Genome Medicine, 6:56, 2014.
  • Kim J and Ma J.
    PSAR-Align: improving multiple sequence alignment using probabilistic sampling.
    Bioinformatics, 30(7):1010-2, 2014.
  • Heo Y, Wu X-L, Chen D, Ma J, and Hwu W-M.
    BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads.
    Bioinformatics, 30(10):1354-62, 2014.
  • Liu Y, Gu Q, Hou JP, Han J, and Ma J.
    A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression.
    BMC Bioinformatics, 15:37, 2014.
  • Burns PD, Li Y, Ma J, and Borodovsky M.
    UnSplicer: Mapping spliced RNA-seq reads in compact genomes and filtering noisy splicing.
    Nucleic Acids Research, 42(4):e25, 2014.
  • Rittschof CC, Bukhari SA, Sloofman L, Troy JM, Caetano-Anolles D, Cash-Ahmed A, Kent M, Lu X, Sanogo O, Weisner PA, Zhang H, Bell AM, Ma J, Sinha S, Robinson GE, and Stubbs L.
    Neuromolecular responses to social challenge: common mechanisms across mice, fish and bees.
    Proceedings of the National Academy of Sciences (PNAS), 111(50):17929-34, 2014.
  • Earl D, Nguyen NK, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney B, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, Hou M, Herrero J, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, and Paten B.
    Alignathon: A competitive assessment of whole genome alignment methods.
    Genome Research, 24(12):2077-89, 2014.
  • Martignetti JA, Camacho-Vanegas O, Priedigkeit N, Camacho C, Pereira E, Lin L, Losic B, Shah H, Ma J, Lahiri P, Chee M, Schadt EE, and Dottino P.
    Personalized ovarian cancer disease surveillance and detection of candidate therapeutic drug targets in circulating tumor DNA.
    Neoplasia, 16(1):97-103, 2014.
  • Honey Bee Genome Sequencing Consortium.
    Finding the missing honey bee genes: lessons learned from a genome upgrade.
    BMC Genomics, 15:86, 2014.
  • Fang et al. (including Ma J)
    Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax.
    Nature Communications, 5:3966, 2014.
  • Costello et al. (including Hou JP and Ma J as part of NCI-DREAM Community)
    A community effort to assess and improve drug sensitivity prediction algorithms
    Nature Biotechnology, 32(12):1202-12, 2014.
2013
  • Kim J, Larkin DM, Cai Q, Asan, Zhang Y, Ge RL, Auvil L, Capitanu B, Zhang G, Lewin HA*, and Ma J*.
    Reference-assisted chromosome assembly.
    Proceedings of the National Academy of Sciences (PNAS), 110(5):1785-90, 2013.
  • Li-Byarlay H, Li Y, Stroud H, Feng S, Newman TC, Kaneda M, Hou KK, Worley KA, Elsik C, Wickline SA, Jacobsen SE, Ma J, and Robinson GE.
    RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee.
    Proceedings of the National Academy of Sciences (PNAS), 110(31):12750-5, 2013.
    [Cover Story] [F1000Prime Recommended]
  • Li Y, Li-Byarlay H, Burns P, Borodovsky M, Robinson GE, and Ma J.
    TrueSight: a new algorithm for splice junction detection using RNA-seq.
    Nucleic Acids Research, 41(4):e51, 2013.
    • Early version "TrueSight: self-training algorithm for splice junction detection using RNA-seq" appeared in Proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2012.
  • Hou JP and Ma J.
    Identifying driver mutations in cancer
    In "Bioinformatics for Diagnosis, Prognosis and Treatment of Complex Diseases", Springer, 2013.
  • Ge et al. (including Kim J and Ma J)
    Draft genome sequence of the Tibetan antelope.
    Nature Communications, 4:1858, 2013.
  • Cui Y, Lindo J, Hughes CE, Johnson J, Hernandez AG, Kemp BM, Ma J, Cunningham R, Petzelt B, Mitchell J, Archer D, Cybulski JS, and Malhi RS.
    Ancient DNA analysis of mid-Holocene individuals from the Northwest Coast of North America reveals different evolutionary paths for mitogenomes.
    PLoS ONE, 8(7):e66948, 2013.
  • Wang VW, Laborde RR, Asmann YW, Li Y, Ma J, Eckloff BW, Tombers NM, Olsen SM, Moore EJ, Olsen KD, and Smith DI.
    Search for chromosome rearrangements: New approaches toward discovery of novel translocations in head and neck squamous cell carcinoma.
    Head Neck, 35(6):831-5, 2013.
2012
  • Wu X-L, Heo Y, El Hajj I, Hwu W-M, Chen D, and Ma J.
    TIGER: tiled iterative genome assembler.
    BMC Bioinformatics, 13(Suppl 19):S18, 2012.
  • Groenen et al. (including Kim J and Ma J).
    Analyses of pig genomes provide insight into porcine demography and evolution.
    Nature, 491(7424):393-8, 2012.
  • Qiu et al. (including Kim J and Ma J)
    The yak genome and adaptation to life at high-altitude.
    Nature Genetics, 44(8):946-9, 2012.
2011
  • Kim J and Ma J.
    PSAR: Measuring multiple sequence alignment reliability by probabilistic sampling.
    Nucleic Acids Research, 39(15):6359-68, 2011.
    • Early version appeared in Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2011.
  • Li Y, Chien J, Smith DI, and Ma J.
    FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.
    Bioinformatics, 27(12):1708-10, 2011.
  • Orangutan Genome Sequencing and Analysis Consortium.
    Comparative and demographic analysis of orangutan genomes.
    Nature, 469(7331):529-33, 2011.
  • Ma J.
    Reconstructing the history of large-scale genomic changes: Biological questions and computational challenges.
    Journal of Computational Biology, 18(7):879-93, 2011.
  • Paten B, Diekhans M, Earl D, St John J, Ma J, Suh B, and Haussler D.
    Cactus graphs for genome comparisons.
    Journal of Computational Biology, 18(3):469-81, 2011.
    • Early version appeared in Proceedings of the 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2010.
2010
  • Ma J.
    A probabilistic framework for inferring ancestral genomic orders.
    BIBM, in Proceedings of IEEE International Conference on Bioinformatics & Biomedicine, 179-184, 2010.
  • Li G, Ma J, and Zhang L.
    Greedy selection of species for ancestral state reconstruction on phylogenies: elimination is better than insertion.
    PLoS ONE, 5(2):e8985, 2010.
  • Ma J and Zhang L.
    Modern BLAST programs.
    The Problem Solving Handbook for Computational Biology and Bioinformatics. Springer, 2010.
Prior to moving to Illinois in 2009
  • Ma J, Ratan A, Raney BJ, Suh BB, Miller W, and Haussler D.
    The infinite sites model of genome evolution.
    Proceedings of the National Academy of Sciences (PNAS), 105(38):14254-14261, 2008.
  • Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, and Haussler D.
    DUPCAR: Reconstructing contiguous ancestral regions with duplications.
    Journal of Computational Biology, 15(8):1007-1027, Oct 2008.
  • Ma J.
    Reconstructing ancient DNA sequences in silico.
    In Handbook of Human Molecular Evolution. John Wiley & Sons, Inc, 2008.
  • Rhesus Macaque Genome Sequencing and Analysis Consortium.
    Evolutionary and biomedical insights from the rhesus macaque genome.
    Science, 13(316):222-234, Apr 2007.
  • Ma J, Ratan A, Zhang L, Miller W, and Haussler D.
    A heuristic algorithm for reconstructing ancestral gene orders with duplications.
    In Proceedings of the 5th RECOMB Comparative Genomics Satellite Workshop.
    Lecture Notes in Computer Science, 4751:122-35, 2007.
  • Li G, Ma J, and Zhang L.
    Selecting genomes of reconstruction of ancestral genomes.
    In Proceedings of the 5th RECOMB Comparative Genomics Satellite Workshop.
    Lecture Notes in Computer Science, 4751:110-21, 2007.
  • Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, and Miller W.
    Reconstructing contiguous regions of an ancestral genome.
    Genome Research, 16(12):1557-1565, Dec 2006.
    • Commented on by Genome Research, 16(12):1441-4;
    • Early stage of the project reported on Science, 308(5727):1401-2.
  • Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, and Miller W.
    Mulan: Multiple-sequence local alignment and visualization for studying function and evolution.
    Genome Research, 15(1):184-194, Jan 2005.

† = co-first author; * = co-corresponding author