• Yoo et al. (including Zhang Y, Yang M, and Ma J)
  Complete sequencing of ape genomes.
  bioRxiv, doi: https://doi.org/10.1101/2024.07.31.605654
• Gholamalamdari O^†, van Schaik T^†, Wang Y^†, Kumar P^†, Zhang L^†, Zhang Y^†, Gonzalez GAH, Vouzas AE, Zhao PA, Gilbert DM*, Ma J*, van Steensel B*, and Belmont AS*.
  Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function.
  bioRxiv, doi: https://doi.org/10.1101/2024.04.23.590809
• Kumar P, Gholamalamdari O, Zhang Y, Zhang L, Vertii A, van Schaik T, Peric-Hupkes D, Sasaki T, Gilbert DM, van Steensel B, Ma J, Kaufman PD, and Belmont AS.
  Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin in different cell types.
  bioRxiv, doi: https://doi.org/10.1101/2023.10.29.564613
• Bialy N, Alber F, Andrews B, Angelo M, Beliveau B, Bintu L, Boettiger A, Boehm U, Brown CM, Maina MB, Chambers JJ, Cimini B, Eliceiri K, Errington R, Faklaris O, Gaudreault N, Germain RN, Goscinski W, Grunwald D, Halter M, Hanein D, Hickey JW, Lacoste J, Laude A, Lundberg E, Ma J, Malacrida L, Moore J, Nelson G, Neumann EK, Nitschke R, Onami S, Pimentel JA, Plant AL, Radtke AJ, Sabata B, Schapiro D, Schöneberg K, Spraggins JM, Sudar D, Vierdag W-MAM, Volkmann N, Wählby C, Wang S, Yaniv Z, and Strambio-De-Castillia C.
  Harmonizing the generation and pre-publication stewardship of FAIR image data.
  arXiv, arXiv:2401.13022
• Yang Y, Wang Y, Zhang Y, and Ma J.
  CONCERT: Genome-wide prediction of sequence elements that modulate DNA replication timing.
  bioRxiv, doi: https://doi.org/10.1101/2022.04.21.488684
• Zhang R, Ma JZ*, and Ma J*.
  DANGO: Predicting higher-order genetic interactions.
  bioRxiv, doi: https://doi.org/10.1101/2020.11.26.400739

• Xiong K^†, Zhang R^†, and Ma J.
  scGHOST: Identifying single-cell 3D genome subcompartments.
  Nature Methods, 21(5):814-822, 2024.
• Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z*, and Ma J*.
  GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells.
  Nature Genetics, 56(8):1701-1711, 2024.
  [News & Views]
• Deng Y^†, Zhang R^†, Xu P, Ma J*, and Gu Q*.
  Pre-trained hypergraph convolutional neural networks with self-supervised learning.
  Transactions on Machine Learning Research, 2835-8856, 2024.
• Ma J (as part of a Voices piece "How has the AI boom impacted algorithmic biology?").
  A two-way street.
  Cell Systems, 15(6):483-487, 2024.
• Zitnik M, Li MM, Wells A, Glass K, Gysi DM, Krishnan A, Murali TM, Radivojac P, Roy S, Baudot A, Bozdag S, Chen DZ, Cowen L, Devkota K, Gitter A, Gosline S, Gu P, Guzzi PH, Huang H, Jiang M, Kesimoglu ZN, Koyuturk M, Ma J, Pico AR, Przulj N, Przytycka TM, Raphael BJ, Ritz A, Sharan R, Shen Y, Singh M, Slonim DK, Tong H, Yang XH, Yoon BJ, Yu H, and Milenkovic T.
  Current and future directions in network biology.
  Bioinformatics Advances, 4(1):vbae099, 2024.
• IGVF Consortium.
  Deciphering the impact of genomic variation on function.
  Nature, 633, 47–57, 2024.
• Chen V^†, Yang M^†, Cui W, Kim JS, Talwalkar A*, and Ma J*.
  Applying interpretable machine learning in computational biology - pitfalls, recommendations and opportunities for new developments.
  Nature Methods, 21(8):1454-1461, 2024.
  [CMU News]

• Chidester B^†, Zhou T^†, Alam S, and Ma J.
  SPICEMIX enables integrative single-cell spatial modeling of cell identity.
  Nature Genetics, 55(1):78-88, 2023.
  [Cover Article] [CMU News]
  • RECOMB, early version appeared in Proceedings of the 25th Annual Conference on Research in Computational Molecular Biology, 2021.
• Zhang Y, Boninsegna L, Yang M, Misteli T*, Alber F*, and Ma J*.
  Computational methods for analysing multiscale 3D genome organization.
  Nature Reviews Genetics, 25(2):123-141, 2024.
• Yang M and Ma J.
  UNADON: Transformer-based model to predict genome-wide chromosome spatial position.
  ISMB, in Proceedings of the 31st Conference on Intelligent Systems for Molecular Biology.
  Bioinformatics, 39(39 Suppl 1):i553-i562, 2023.
• Kamat K, Lao Z, Qi Y, Wang Y, Ma J, and Zhang B.
  Compartmentalization with nuclear landmarks yields random yet precise genome organization
  Biophysics Journal, 122(7):1376-1389, 2023.
• Calandrelli R, Wen X, Charles Richard JL, Luo Z, Nguyen TC, Chen CJ, Qi Z, Xue S, Chen W, Yan Z, Wu W, Zaleta-Rivera K, Hu R, Yu M, Wang Y, Li W, Ma J, Ren B, and Zhong S.
  Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.
  Nature Communications, 14(1):6519, 2023.
• Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S.
  Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.
  Molecular Cell, S1097-2765(23)00465-3, 2023.
  
• Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M; HuBMAP Consortium (including Ma J); Börner K, Snyder MP.
  Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP).
  Nature Cell Biology, doi: 10.1038/s41556-023-01194-w, 2023.
  

• Zhang R^†,*, Zhou T^†, and Ma J*.
  Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi.
  Cell Systems, 13(10):P798-807.E6, 2022.
  [Cover Article]
  • RECOMB, early version appeared in Proceedings of the 26th Annual Conference on Research in Computational Molecular Biology, 2022.
• Zhu X^†, Zhang Y^†, Wang Y, Tian D, Belmont AS, Swedlow JR, and Ma J.
  Nucleome Browser: An integrative and multimodal data navigation platform for 4D Nucleome.
  Nature Methods, 19(8):911-913, 2022.
• Yang Y, Wang Y, Zhang Y, and Ma J.
  CONCERT: Genome-wide prediction of sequence elements that modulate DNA replication timing.
  RECOMB, 2022.
• Reilly A, Creamer JP, Stewart S, Stolla MC, Wang Y, Du J, Wellington R, Busch S, Estey EH, Becker PS, Fang M, Keel SB, Abkowitz JL, Soma LA, Ma J, Duan Z, and Doulatov S.
  Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function.
  Cell Stem Cell, 29(4):577-592.e8, 2022.
• Melamed A, Fitzgerald TW, Wang Y, Ma J, Birney E, and Bangham CRM.
  Selective clonal persistence of human retroviruses in vivo: radial chromatin organization, integration site and host transcription.
  Science Advances, 8(17):eabm6210, 2022.
• Seok S, Kim YC, Zhang Y, Kong B, Guo G, Ma J, Kemper B, and Kemper JK.
  Feeding activates FGF15-SHP-TFEB-mediated lipophagy in the gut.
  EMBO J, 41(17):e109997, 2022.
• Yang M and Ma J.
  Machine learning methods for exploring sequence determinants of 3D genome organization.
  Journal of Molecular Biology, doi: 10.1016/j.jmb.2022.167666, 2022.
• SenNet Consortium.
  NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health.
  Nature Aging, https://doi.org/10.1038/s43587-022-00326-5, 2022.

• Zhang R, Zhou T, and Ma J.
  Multiscale and integrative single-cell Hi-C analysis with Higashi.
  Nature Biotechnology, 40:254–261, 2022. [Author Correction]
• Wang Y, Zhang Y, Zhang R, van Schaik T, Zhang L, Sasaki T, Peric-Hupkes D, Chen Y, Gilbert DM, van Steensel B, Belmont AS, and Ma J.
  SPIN reveals genome-wide landscape of nuclear compartmentalization.
  Genome Biology, 22:36, 2021.
• Chidester B^†, Zhou T^†, and Ma J.
  SPICEMIX: Integrative single-cell spatial modeling for inferring cell identity.
  RECOMB, 2021.
• Zhang R, Ma JZ*, and Ma J*.
  Towards the prediction of higher-order genetic interactions.
  RECOMB, 2021.
• Tao Y, Rajaraman A, Cui X, Cui Z, Eaton J, Kim H, Ma J*, and Schwartz R*.
  Assessing the contribution of tumor mutational phenotypes to cancer progression risk.
  PLOS Computational Biology, 17(3):e1008777, 2021.
• Zhou T^†, Zhang R^†, and Ma J.
  The 3D genome structure of single cells.
  Annual Review of Biomedical Data Science, Vol. 4, 2021 [e-link].
• Zhang L, Zhang Y, Chen Y, Gholamalamdari O, Wang Y, Ma J, and Belmont AS.
  TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes.
  Genome Research, 31(2):251-264, 2021.
  

• Zhang R and Ma J.
  MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning.
  Cell Systems, 10(5):397-407.E5, 2020.
  
  • RECOMB, early version appeared in Proceedings of the 24th Annual Conference on Research in Computational Molecular Biology, 2020.
• Tian D^†, Zhang R^†, Zhang Y, Zhu X, and Ma J.
  MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome.
  Genome Research, 30(2):227-238, 2020.
  [Cover Article] [CMU News]
• Zhang R, Zou Y, and Ma J.
  Hyper-SAGNN: a self-attention based graph neural network for hypergraphs.
  ICLR, 8th International Conference on Learning Representations, 2020.
  arXiv, arXiv:1911.02613 [cs.LG]
• Zhang Y, Xiao Y, Yang M, and Ma J.
  Cancer mutational signatures representation by large-scale context embedding.
  ISMB, in Proceedings of the 28th Conference on Intelligent Systems for Molecular Biology
  Bioinformatics, 36(Supplement_1):i309-i316, 2020.
• Tao Y, Lei H, Fu X, Lee A, Ma J, and Schwartz R.
  Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis.
  ISMB, in Proceedings of the 28th Conference on Intelligent Systems for Molecular Biology
  Bioinformatics, 36(Supplement_1):i407-i416, 2020.
• Tao Y, Lei H, Lee AV, Ma J, and Schwartz R.
  Neural network deconvolution method for resolving pathway-Level progression of tumor clonal expression programs with application to breast cancer brain metastases.
  Frontiers in Physiology, doi:10.3389/fphys.2020.01055, 2020.
• Sun Q, Hao Q, Lin YC, Song YJ, Bangru S, Arif W, Tripathi V, Zhang Y, Cho JH, Freier SM, Jenkins L, Ma J, Yoon JH, Kalsotra A, Lal A, Prasanth SG, and Prasanth KV.
  Antagonism between splicing and microprocessor complex dictates the serum-induced processing of lnc-MIRHG for efficient cell cycle re-entry.
  RNA, 26(11):1603-1620, 2020.
• Byun S, Seok S, Kim Y-C, Zhang Y, Yau P, Iwamori N, Xu HE, Ma J, Kemper B, and Kemper JK.
  Fasting-induced FGF21 signaling activates hepatic autophagy and lipid degradation via JMJD3 histone demethylase.
  Nature Communications, 11, 807, 2020.
• Kim Y-C, Seok S, Zhang Y, Ma J, Kong B, Guo G, Kemper B, and Kemper JK.
  Intestinal FGF15/19 physiologically repress hepatic lipogenesis in the late fed-state by activating SHP and DNMT3A.
  Nature Communications, 11, 5969, 2020.
• Lazzarotto CR, Malinin NL, Li Y, Zhang R, Yang Y, Lee G, Cowley E, He Y, Lan X, Jividen K, Katta V, Kolmakova NG, Petersen CT, Qi Q, Strelcov E, Maragh S, Krenciute G, Ma J, Cheng Y, and Tsai SQ.
  CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity.
  Nature Biotechnology, 38(11):1317-1327, 2020.

• Xiong K and Ma J.
  Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions.
  Nature Communications, 10, 5069, 2019.
  [CMU News]
• Yang Y, Zhang Y, Ren B, Dixon J, and Ma J.
  Comparing 3D genome organization in multiple species using Phylo-HMRF.
  Cell Systems, 8(6):494-505.e14, 2019.
  • RECOMB, early version appeared in Proceedings of the 23rd Annual Conference on Research in Computational Molecular Biology, 2019.
• Ma J and Duan Z.
  Replication timing becomes intertwined with 3D genome organization.
  Cell, 176(4):681-684, 2019 (Preview).
• Chidester B, Zhou T, Do MN, and Ma J.
  Rotation equivariant and invariant neural networks for microscopy image analysis.
  ISMB, in Proceedings of the 27th Conference on Intelligent Systems for Molecular Biology
  Bioinformatics, 35(14):i530-i537, 2019.
• HuBMAP Consortium.
  The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.
  Nature, 574, 187–192, 2019.
• Chidester B, Ton T-V, Tran M-T, Ma J, and Do MN.
  Enhanced rotation-equivariant U-Net for nuclear segmentation.
  CVMI, workshop on Computer Vision for Microscopy Image analysis at CVPR, 2019.
• Singh S, Yang Y, Poczos B, and Ma J.
  Predicting enhancer-promoter interaction from genomic sequence with deep neural networks.
  Quantitative Biology, 7(2):122-137, 2019.
  • Preliminary version presented in 2016 NIPS Workshop on Machine Learning in Computational Biology.
• Tao Y, Lei H, Lee A, Ma J, and Schwartz R.
  Phylogenies derived from matched transcriptome reveal the evolution of cell populations and temporal order of perturbed pathways in breast cancer brain metastases.
  ISMCO, International Symposium on Mathematical and Computational Oncology, 2019.
• Kim YC, Jung H, Seok S, Zhang Y, Ma J, Li T, Kemper B, and Kemper JK.
  MicroRNA-210 promotes bile acid-induced cholestatic liver injury by targeting mixed-lineage leukemia-4 methyltransferase in mice.
  Hepatology, doi: 10.1002/hep.30966, 2019.
• Tariq A, Hao Q, Sun Q, Singh DK, Jadaliha M, Zhang Y, Chetlangia N, Ma J, Holton S, Bhargava R, Lal A, Prasanth SG, and Prasanth KV.
  LncRNA-mediated regulation of SOX9 expression in basal sub-type breast cancer cells.
  RNA, doi: 10.1261/rna.073254.119, 2019.
• Kumar N et al. (including Chidester B and Ma J)
  A multi-organ nucleus segmentation challenge.
  IEEE Trans Med Imaging, doi: 10.1109/TMI.2019.2947628, 2019.
• Farre M, Li Q, Zhou Y, Damas J, Chemnick LG, Kim J, Ryder OA, Ma J, Zhang G, Larkin DM, and Lewin HA.
  A near-chromosome scale genome assembly of the Gemsbok (Oryx gazella): An iconic antelope of the Kalahari Desert.
  GigaScience, 8(2). doi: 10.1093/gigascience/giy162, 2019.
• Farre M, Li Q, Darolti I, Zhou Y, Damas J, Proskuryakova AA, Kulemzina AI, Chemnick LG, Kim J, Ryder OA, Ma J, Graphodatsky AS, Zhang G, Larkin D, and Lewin HA.
  An integrated chromosome-scale genome assembly of the Masai Giraffe (Giraffa camelopardalis tippelskirchi).
  GigaScience, 8(8). doi: 10.1093/gigascience/giz090, 2019.
• Farre M, Kim J, Proskuryakova AA, Zhang Y, Kulemzina AI, Li Q, Zhou Y, Xiong Y, Johnson JL, Perelman P, Johnson WE, Warren W, Kukekova AV, Zhang G, O'Brien SJ, Ryder OA, Graphodatsky AS, Ma J, Lewin HA, and Larkin DM.
  Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks.
  Genome Research, 29(4):576-589, 2019.
• Kannan K, Shook M, Li Y, Robinson GE*, and Ma J*.
  Comparative analysis of brain and fat body gene splicing patterns in the honey bee, Apis mellifera.
  G3: Genes, Genomes, Genetics, 9(4):1055-1063, 2019.

• Yang Y, Gu Q, Zhang Y, 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, 7(2):208-218.e11, 2018.
  [CMU News] [NSF News] [ACM TechNews]
  • RECOMB, early version appeared in Proceedings of the 22nd Annual Conference on Research in Computational Molecular Biology, 2018.
  • Preliminary version presented in 2017 NIPS Workshop on Machine Learning in Computational Biology.
• Chen Y, Zhang Y, Wang Y, Zhang L, Brinkman EK, Adam SA, Goldman R, van Steensel B, Ma J, and Belmont AS.
  Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler.
  Journal of Cell Biology, 217(11):4025-4048, 2018.
  [Rockefeller Univ Press News] [NIH Director's Blog]
• 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, PMLR, 80:922-931, 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.
  • Early version presented at the 55th Annual Allerton Conference (2017).
• 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, 245-253, 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, 25(7):624-636, 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, 46(17):e100, 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, 128(7):3144-3159, 2018.
• Jadaliha M, Gholamalamdari O, Tang W, Zhang Y, Petracovici A, Hao Q, Tariq A, Kim T-G, Holton SE, Singh DK, Li X-L, Freier SM, Ambs S, Bhargava R, Lal A, Prasanth SG, Ma J, and Prasanth KV.
  A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability.
  PLOS Genetics, 14(11):e1007802, 2018.

• 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 21st 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.
• Shen H and Ma J.
  Privacy challenges of genomic big data.
  Adv Exp Med Biol, 1028:139-148, 2017.
• Dekker J et al. (as part of the 4D Nucleome Network).
  The 4D nucleome project.
  Nature, 549(7671):219-226, 2017.

• 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]
  • RECOMB, early version appeared in Proceedings of the 20th Annual International Conference on Research in Computational Molecular Biology, 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.

• 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.

• 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.

• 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.
  • RECOMB, 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, 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.

• 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.

• Kim J and Ma J.
  PSAR: Measuring multiple sequence alignment reliability by probabilistic sampling.
  Nucleic Acids Research, 39(15):6359-68, 2011.
  • RECOMB, early version appeared in Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, 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.
  • RECOMB, early version appeared in Proceedings of the 14th Annual International Conference on Research in Computational Molecular Biology, 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.

• 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