| Year |
Citation |
Score |
| 2024 |
Xiong K, Zhang R, Ma J. Author Correction: scGHOST: identifying single-cell 3D genome subcompartments. Nature Methods. PMID 39284961 DOI: 10.1038/s41592-024-02462-9 |
0.31 |
|
| 2024 |
Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, ... ... Ma J, et al. Complete sequencing of ape genomes. Biorxiv : the Preprint Server For Biology. PMID 39131277 DOI: 10.1101/2024.07.31.605654 |
0.375 |
|
| 2024 |
Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z, Ma J. GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Nature Genetics. PMID 38744973 DOI: 10.1038/s41588-024-01745-3 |
0.365 |
|
| 2024 |
Gholamalamdari O, van Schaik T, Wang Y, Kumar P, Zhang L, Zhang Y, Hernandez Gonzalez GA, Vouzas AE, Zhao PA, Gilbert DM, Ma J, van Steensel B, Belmont AS. Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function. Biorxiv : the Preprint Server For Biology. PMID 38712201 DOI: 10.1101/2024.04.23.590809 |
0.321 |
|
| 2023 |
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, Belmont AS. Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin in different cell types. Biorxiv : the Preprint Server For Biology. PMID 37961445 DOI: 10.1101/2023.10.29.564613 |
0.304 |
|
| 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, ... ... Ma J, et al. Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells. Nature Communications. 14: 6519. PMID 37845234 DOI: 10.1038/s41467-023-42274-7 |
0.321 |
|
| 2023 |
Zhang Y, Boninsegna L, Yang M, Misteli T, Alber F, Ma J. Computational methods for analysing multiscale 3D genome organization. Nature Reviews. Genetics. PMID 37673975 DOI: 10.1038/s41576-023-00638-1 |
0.394 |
|
| 2023 |
Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z, Ma J. Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells. Biorxiv : the Preprint Server For Biology. PMID 37546900 DOI: 10.1101/2023.07.20.549578 |
0.352 |
|
| 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, ... ... Ma J, et al. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell. PMID 37419111 DOI: 10.1016/j.molcel.2023.06.018 |
0.34 |
|
| 2023 |
Yang M, Ma J. UNADON: transformer-based model to predict genome-wide chromosome spatial position. Bioinformatics (Oxford, England). 39: i553-i562. PMID 37387176 DOI: 10.1093/bioinformatics/btad246 |
0.343 |
|
| 2023 |
Yang M, Ma J. UNADON: Transformer-based model to predict genome-wide chromosome spatial position. Arxiv. PMID 37163136 |
0.31 |
|
| 2023 |
Kamat K, Lao Z, Qi Y, Wang Y, Ma J, Zhang B. Compartmentalization with nuclear landmarks yields random, yet precise, genome organization. Biophysical Journal. PMID 36871158 DOI: 10.1016/j.bpj.2023.03.003 |
0.325 |
|
| 2022 |
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, ... ... Ma J, et al. Author Correction: Comparative and demographic analysis of orang-utan genomes. Nature. PMID 35962045 DOI: 10.1038/s41586-022-04799-7 |
0.688 |
|
| 2022 |
Kuang W, Zhang L, Ye L, Ma J, Shi X, Lin Y, Sun X, Cui R. Genome and Transcriptome Sequencing Analysis of Fusarium Provides Insights into the Pathogenic Mechanisms of the Lotus Rhizome Rot. Microbiology Spectrum. e0017522. PMID 35867414 DOI: 10.1128/spectrum.00175-22 |
0.412 |
|
| 2022 |
Peng Y, Yan H, Guo L, Deng C, Wang C, Wang Y, Kang L, Zhou P, Yu K, Dong X, Liu X, Sun Z, Peng Y, Zhao J, Deng D, ... ... Ma J, et al. Reference genome assemblies reveal the origin and evolution of allohexaploid oat. Nature Genetics. PMID 35851189 DOI: 10.1038/s41588-022-01127-7 |
0.451 |
|
| 2022 |
Yang M, Ma J. Machine learning methods for exploring sequence determinants of 3D genome organization. Journal of Molecular Biology. 167666. PMID 35659533 DOI: 10.1016/j.jmb.2022.167666 |
0.377 |
|
| 2021 |
Li C, Wang G, Li H, Wang G, Ma J, Zhao X, Huo L, Zhang L, Jiang Y, Zhang J, Liu G, Liu G, Cheng R, Wei J, Yao L. High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. PMID 33566123 DOI: 10.1007/s00122-020-03760-4 |
0.33 |
|
| 2020 |
Tao Y, Lei H, Lee AV, Ma J, 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. 11: 1055. PMID 33013452 DOI: 10.3389/Fphys.2020.01055 |
0.359 |
|
| 2020 |
Tao Y, Lei H, Fu X, Lee AV, Ma J, Schwartz R. Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis. Bioinformatics (Oxford, England). 36: i407-i416. PMID 32657393 DOI: 10.1093/Bioinformatics/Btaa396 |
0.358 |
|
| 2020 |
Zhang R, Ma J. MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning. Cell Systems. 10: 397-407.e5. PMID 32550271 DOI: 10.1016/J.Cels.2020.04.004 |
0.363 |
|
| 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, ... ... Ma J, et al. CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity. Nature Biotechnology. PMID 32541958 DOI: 10.1038/S41587-020-0555-7 |
0.421 |
|
| 2020 |
Tian D, Zhang R, Zhang Y, Zhu X, Ma J. MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. Genome Research. PMID 31907193 DOI: 10.1101/Gr.250316.119 |
0.344 |
|
| 2019 |
Singh S, Yang Y, Póczos B, Ma J. Predicting enhancer-promoter interaction from genomic sequence with deep neural networks. Quantitative Biology (Beijing, China). 7: 122-137. PMID 34113473 DOI: 10.1007/s40484-019-0154-0 |
0.335 |
|
| 2019 |
Xiong K, Ma J. Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions. Nature Communications. 10: 5069. PMID 31699985 DOI: 10.1038/S41467-019-12954-4 |
0.413 |
|
| 2019 |
Farré 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 DM, Lewin HA. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi). Gigascience. 8. PMID 31367745 DOI: 10.1093/Gigascience/Giz090 |
0.447 |
|
| 2019 |
Yang Y, Zhang Y, Ren B, Dixon JR, Ma J. Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. Cell Systems. PMID 31229558 DOI: 10.1016/J.Cels.2019.05.011 |
0.439 |
|
| 2019 |
Farré M, Kim J, Proskuryakova AA, Zhang Y, Kulemzina AI, Li Q, Zhou Y, Xiong Y, Johnson JL, Perelman P, Johnson WE, Warren WC, Kukekova AV, Zhang G, O'Brien SJ, ... ... Ma J, et al. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. Genome Research. PMID 30760546 DOI: 10.1101/Gr.239863.118 |
0.366 |
|
| 2019 |
Ma J, Duan Z. Replication Timing Becomes Intertwined with 3D Genome Organization. Cell. 176: 681-684. PMID 30735630 DOI: 10.1016/J.Cell.2019.01.027 |
0.388 |
|
| 2019 |
Farré M, Li Q, Zhou Y, Damas J, Chemnick LG, Kim J, Ryder OA, Ma J, Zhang G, Larkin DM, Lewin HA. A Near-Chromosome-Scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari Desert. Gigascience. PMID 30649288 DOI: 10.1093/Gigascience/Giy162 |
0.414 |
|
| 2018 |
Jadaliha M, Gholamalamdari O, Tang W, Zhang Y, Petracovici A, Hao Q, Tariq A, Kim TG, Holton SE, Singh DK, Li XL, Freier SM, Ambs S, Bhargava R, Lal A, ... ... Ma J, et al. A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability. Plos Genetics. 14: e1007802. PMID 30496290 DOI: 10.1371/Journal.Pgen.1007802 |
0.325 |
|
| 2018 |
Chen Y, Zhang Y, Wang Y, Zhang L, Brinkman EK, Adam SA, Goldman R, van Steensel B, Ma J, Belmont AS. Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. The Journal of Cell Biology. PMID 30154186 DOI: 10.1083/Jcb.201807108 |
0.416 |
|
| 2018 |
Yang Y, Gu Q, Zhang Y, Sasaki T, Crivello J, O'Neill RJ, Gilbert DM, Ma J. Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. Cell Systems. PMID 29936186 DOI: 10.1016/J.Cels.2018.05.022 |
0.443 |
|
| 2018 |
Tasan I, Sustackova G, Zhang L, Kim J, Sivaguru M, HamediRad M, Wang Y, Genova J, Ma J, Belmont AS, Zhao H. CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. Nucleic Acids Research. PMID 29912475 DOI: 10.1093/Nar/Gky501 |
0.389 |
|
| 2018 |
Rajaraman A, Ma J. Toward Recovering Allele-specific Cancer Genome Graphs. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 29658776 DOI: 10.1089/cmb.2018.0022 |
0.334 |
|
| 2017 |
Shen H, Ma J. Privacy Challenges of Genomic Big Data. Advances in Experimental Medicine and Biology. 1028: 139-148. PMID 29058220 DOI: 10.1007/978-981-10-6041-0_8 |
0.426 |
|
| 2017 |
Yang Y, Zhang R, Singh S, Ma J. Exploiting sequence-based features for predicting enhancer-promoter interactions. Bioinformatics (Oxford, England). 33: i252-i260. PMID 28881991 DOI: 10.1093/Bioinformatics/Btx257 |
0.396 |
|
| 2017 |
Kim J, Farré M, Auvil L, Capitanu B, Larkin DM, Ma J, Lewin HA. Reconstruction and evolutionary history of eutherian chromosomes. Proceedings of the National Academy of Sciences of the United States of America. PMID 28630326 DOI: 10.1073/Pnas.1702012114 |
0.411 |
|
| 2016 |
Rajaraman A, Ma J. Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction. Bmc Bioinformatics. 17: 414. PMID 28185565 DOI: 10.1186/S12859-016-1262-8 |
0.4 |
|
| 2016 |
Bryan C, Guterman G, Ma KL, Lewin H, Larkin D, Kim J, Ma J, Farre M. Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution. Ieee Transactions On Visualization and Computer Graphics. PMID 27845661 DOI: 10.1109/Tvcg.2016.2598789 |
0.378 |
|
| 2016 |
Hou JP, Emad A, Puleo GJ, Ma J, Milenkovic O. A new correlation clustering method for cancer mutation analysis. Bioinformatics (Oxford, England). PMID 27540270 DOI: 10.1093/Bioinformatics/Btw546 |
0.322 |
|
| 2016 |
Bryan C, Guterman G, Ma KL, Lewin H, Larkin D, Kim J, Ma J, Farre M. Synteny Explorer: An Interactive Visualization Application for Teaching Genome Evolution. Ieee Transactions On Visualization and Computer Graphics. PMID 27514049 DOI: 10.1109/TVCG.2016.2598460 |
0.31 |
|
| 2016 |
Li Y, Zhou S, Schwartz DC, Ma J. Allele-Specific Quantification of Structural Variations in Cancer Genomes. Cell Systems. PMID 27453446 DOI: 10.1016/J.Cels.2016.05.007 |
0.506 |
|
| 2016 |
Ma J, Köster J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, Xu H, Liu XS. CRISPR-DO for genome-wide CRISPR design and optimization. Bioinformatics (Oxford, England). PMID 27402906 DOI: 10.1093/Bioinformatics/Btw476 |
0.328 |
|
| 2016 |
Heo Y, Ramachandran A, Hwu WM, Ma J, Chen D. BLESS 2: Accurate, memory-efficient, and fast error correction method. Bioinformatics (Oxford, England). PMID 27153708 DOI: 10.1093/Bioinformatics/Btw146 |
0.313 |
|
| 2016 |
He F, Li Y, Tang YH, Ma J, Zhu H. Identifying micro-inversions using high-throughput sequencing reads. Bmc Genomics. 17: 4. PMID 26818118 DOI: 10.1186/S12864-015-2305-7 |
0.441 |
|
| 2015 |
Qiao L, Zhang X, Han X, Zhang L, Li X, Zhan H, Ma J, Luo P, Zhang W, Cui L, Li X, Chang Z. A genome-wide analysis of the auxin/indole-3-acetic acid gene family in hexaploid bread wheat (Triticum aestivum L.). Frontiers in Plant Science. 6: 770. PMID 26483801 DOI: 10.3389/fpls.2015.00770 |
0.303 |
|
| 2015 |
Fang X, Nevo E, Han L, Levanon EY, Zhao J, Avivi A, Larkin D, Jiang X, Feranchuk S, Zhu Y, Fishman A, Feng Y, Sher N, Xiong Z, Hankeln T, ... ... Ma J, et al. Corrigendum: Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nature Communications. 6: 8051. PMID 26264976 DOI: 10.1038/Ncomms9051 |
0.351 |
|
| 2015 |
Silva GO, He X, Parker JS, Gatza ML, Carey LA, Hou JP, Moulder SL, Marcom PK, Ma J, Rosen JM, Perou CM. Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer. Breast Cancer Research and Treatment. PMID 26109346 DOI: 10.1007/S10549-015-3476-2 |
0.324 |
|
| 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, et al. Single-molecule analysis reveals widespread structural variation in multiple myeloma. Proceedings of the National Academy of Sciences of the United States of America. 112: 7689-94. PMID 26056298 DOI: 10.1073/Pnas.1418577112 |
0.446 |
|
| 2014 |
Rittschof CC, Bukhari SA, Sloofman LG, Troy JM, Caetano-Anollés D, Cash-Ahmed A, Kent M, Lu X, Sanogo YO, Weisner PA, Zhang H, Bell AM, Ma J, Sinha S, Robinson GE, et al. Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee. Proceedings of the National Academy of Sciences of the United States of America. 111: 17929-34. PMID 25453090 DOI: 10.1073/Pnas.1420369111 |
0.334 |
|
| 2014 |
Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, ... ... Ma J, et al. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Research. 24: 2077-89. PMID 25273068 DOI: 10.1101/Gr.174920.114 |
0.374 |
|
| 2014 |
Fang X, Nevo E, Han L, Levanon EY, Zhao J, Avivi A, Larkin D, Jiang X, Feranchuk S, Zhu Y, Fishman A, Feng Y, Sher N, Xiong Z, Hankeln T, ... ... Ma J, et al. Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nature Communications. 5: 3966. PMID 24892994 DOI: 10.1038/Ncomms4966 |
0.416 |
|
| 2014 |
Shen B, Ma J, Wang J, Wang J. Biomedical informatics and computational biology for high-throughput data analysis. Thescientificworldjournal. 2014: 398181. PMID 24688384 DOI: 10.1155/2014/398181 |
0.324 |
|
| 2014 |
Elsik CG, Worley KC, Bennett AK, Beye M, Camara F, Childers CP, de Graaf DC, Debyser G, Deng J, Devreese B, Elhaik E, Evans JD, Foster LJ, Graur D, Guigo R, ... ... Ma J, et al. Finding the missing honey bee genes: lessons learned from a genome upgrade. Bmc Genomics. 15: 86. PMID 24479613 DOI: 10.1186/1471-2164-15-86 |
0.48 |
|
| 2014 |
Heo Y, Wu XL, Chen D, Ma J, Hwu WM. BLESS: bloom filter-based error correction solution for high-throughput sequencing reads. Bioinformatics (Oxford, England). 30: 1354-62. PMID 24451628 DOI: 10.1093/Bioinformatics/Btu030 |
0.376 |
|
| 2014 |
Burns PD, Li Y, Ma J, Borodovsky M. UnSplicer: Mapping spliced RNA-seq reads in compact genomes and filtering noisy splicing Nucleic Acids Research. 42: e25. PMID 24259430 DOI: 10.1093/Nar/Gkt1141 |
0.397 |
|
| 2014 |
Kim J, Ma J. PSAR-Align: Improving multiple sequence alignment using probabilistic sampling Bioinformatics. 30: 1010-1012. PMID 24222208 DOI: 10.1093/Bioinformatics/Btt636 |
0.301 |
|
| 2014 |
Hou JP, Ma J. DawnRank: Discovering personalized driver genes in cancer Genome Medicine. 6. DOI: 10.1186/S13073-014-0056-8 |
0.373 |
|
| 2013 |
Li-Byarlay H, Li Y, Stroud H, Feng S, Newman TC, Kaneda M, Hou KK, Worley KC, Elsik CG, Wickline SA, Jacobsen SE, Ma J, 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 of the United States of America. 110: 12750-5. PMID 23852726 DOI: 10.1073/Pnas.1310735110 |
0.306 |
|
| 2013 |
Cui Y, Lindo J, Hughes CE, Johnson JW, Hernandez AG, Kemp BM, Ma J, Cunningham R, Petzelt B, Mitchell J, Archer D, Cybulski JS, 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: e66948. PMID 23843972 DOI: 10.1371/Journal.Pone.0066948 |
0.351 |
|
| 2013 |
Ge RL, Cai Q, Shen YY, San A, Ma L, Zhang Y, Yi X, Chen Y, Yang L, Huang Y, He R, Hui Y, Hao M, Li Y, Wang B, ... ... Ma J, et al. Draft genome sequence of the Tibetan antelope. Nature Communications. 4: 1858. PMID 23673643 DOI: 10.1038/Ncomms2860 |
0.404 |
|
| 2013 |
Kim J, Larkin DM, Cai Q, Asan, Zhang Y, Ge RL, Auvil L, Capitanu B, Zhang G, Lewin HA, Ma J. Reference-assisted chromosome assembly. Proceedings of the National Academy of Sciences of the United States of America. 110: 1785-90. PMID 23307812 DOI: 10.1073/Pnas.1220349110 |
0.424 |
|
| 2013 |
Li Y, Li-Byarlay H, Burns P, Borodovsky M, Robinson GE, Ma J. TrueSight: a new algorithm for splice junction detection using RNA-seq. Nucleic Acids Research. 41: e51. PMID 23254332 DOI: 10.1093/Nar/Gks1311 |
0.33 |
|
| 2012 |
Wu XL, Heo Y, El Hajj I, Hwu WM, Chen D, Ma J. TIGER: tiled iterative genome assembler. Bmc Bioinformatics. 13: S18. PMID 23281792 DOI: 10.1186/1471-2105-13-S19-S18 |
0.437 |
|
| 2012 |
Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, ... ... Ma J, et al. Analyses of pig genomes provide insight into porcine demography and evolution. Nature. 491: 393-8. PMID 23151582 DOI: 10.1038/Nature11622 |
0.473 |
|
| 2012 |
Qiu Q, Zhang G, Ma T, Qian W, Wang J, Ye Z, Cao C, Hu Q, Kim J, Larkin DM, Auvil L, Capitanu B, Ma J, Lewin HA, Qian X, et al. The yak genome and adaptation to life at high altitude. Nature Genetics. 44: 946-9. PMID 22751099 DOI: 10.1038/Ng.2343 |
0.409 |
|
| 2012 |
Wang VW, Laborde RR, Asmann YW, Li Y, Ma J, Eckloff BW, Tombers NM, Olsen SM, Moore EJ, Olsen KD, Smith DI. Abstract 3100: Identifying novel chromosomal fusions out of RNAseq data from oropharyngeal cancers Cancer Research. 72: 3100-3100. DOI: 10.1158/1538-7445.Am2012-3100 |
0.356 |
|
| 2011 |
Kim J, Ma J. PSAR: Measuring multiple sequence alignment reliability by probabilistic sampling Nucleic Acids Research. 39: 6359-6368. PMID 21576232 DOI: 10.1093/Nar/Gkr334 |
0.352 |
|
| 2011 |
Ma J. Reconstructing the history of large-scale genomic changes: Biological questions and computational challenges Journal of Computational Biology. 18: 879-893. PMID 21563973 DOI: 10.1089/Cmb.2010.0189 |
0.455 |
|
| 2011 |
Li Y, Chien J, Smith DI, Ma J. FusionHunter: Identifying fusion transcripts in cancer using paired-end RNA-seq Bioinformatics. 27: 1708-1710. PMID 21546395 DOI: 10.1093/Bioinformatics/Btr265 |
0.395 |
|
| 2011 |
Paten B, Diekhans M, Earl D, John JS, Ma J, Suh B, Haussler D. Cactus graphs for genome comparisons Journal of Computational Biology. 18: 469-481. PMID 21385048 DOI: 10.1089/Cmb.2010.0252 |
0.357 |
|
| 2011 |
Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, ... ... Ma J, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 469: 529-33. PMID 21270892 DOI: 10.1038/Nature09687 |
0.716 |
|
| 2010 |
Li G, Ma J, Zhang L. Greedy selection of species for ancestral state reconstruction on phylogenies: Elimination is better than insertion Plos One. 5. PMID 20140213 DOI: 10.1371/Journal.Pone.0008985 |
0.381 |
|
| 2008 |
Ma J, Ratan A, Raney BJ, Suh BB, Miller W, Haussler D. The infinite sites model of genome evolution. Proceedings of the National Academy of Sciences of the United States of America. 105: 14254-61. PMID 18787111 DOI: 10.1073/Pnas.0805217105 |
0.702 |
|
| 2008 |
Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, Haussler D. DUPCAR: reconstructing contiguous ancestral regions with duplications. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 1007-27. PMID 18774902 DOI: 10.1089/Cmb.2008.0069 |
0.688 |
|
| 2007 |
Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, ... ... Ma J, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science (New York, N.Y.). 316: 222-34. PMID 17431167 DOI: 10.1126/Science.1139247 |
0.707 |
|
| 2006 |
Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W. Reconstructing contiguous regions of an ancestral genome. Genome Research. 16: 1557-65. PMID 16983148 DOI: 10.1101/Gr.5383506 |
0.642 |
|
| 2005 |
Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W. Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Research. 15: 184-94. PMID 15590941 DOI: 10.1101/Gr.3007205 |
0.597 |
|
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