Bejerano Lab

Publications

In descending chronological order.

Refereed journal papers and preprints

62. J. Birgmeier, M. Haeussler, C.A. Deisseroth, K.A. Jagadeesh, A.J. Ratner, H. Guturu, A.M. Wenger, P.D. Stenson, D.N. Cooper, C. Re, J.A. Bernstein and G. Bejerano. AMELIE accelerates Mendelian patient diagnosis directly from the primary literature. bioRxiv, https://doi.org/10.1101/171322, 2017. [link]

61. J.M. Paggi and G. Bejerano. A sequence-based, deep learning model accurately predicts RNA splicing branchpoints. bioRxiv, https://doi.org/10.1101/185868, 2017. [link]

60. M.J. Berger and G. Bejerano. Comment on "A genetic signature of the evolution of loss of flight in the Galapagos cormorant". bioRxiv, https://doi.org/10.1101/181826, 2017. [link]

59. R. Madelaine, S.A. Sloan, N. Huber, J.H. Notwell, L.C. Leung, G. Skariah, C. Halluin, S.P. Pasca, G. Bejerano, M.A. Krasnow, B.A. Barres and P. Mourrain MicroRNA-9 Couples Brain Neurogenesis and Angiogenesis. Cell Rep., 20(7):1533-1542, 2017. [link]

58. A.M. Marcovitz, Y. Turakhia, M. Gloudemans, B.A. Braun, H.I. Chen and G. Bejerano. A novel unbiased test for molecular convergent evolution and discoveries in echolocating, aquatic and high-altitude mammals. bioRxiv, https://doi.org/10.1101/170985, 2017. [link]

57. M. Balasubramanian, H. Lord, S. Levesque, H. Guturu, F. Thuriot, G. Sillon, A.M. Wenger, D.L. Sureka, T. Lester, D.S. Johnson, J. Bowen, A.R. Calhoun, D.H. Viskochil, DDD Study, G. Bejerano, J.A. Bernstein and D. Chitayat. Chitayat syndrome: hyperphalangism, characteristic facies, hallux valgus and bronchomalacia results from a recurrent c.266A>G p.(Tyr89Cys) variant in the ERF gene. J. Med. Gene., 54(3):157-165, 2017. [pubmed]

56. K.A. Jagadeesh*, D.J. Wu*, J.A. Birgmeier, D. Boneh and G. Bejerano. Deriving genomic diagnoses without revealing patient genomes. Science, 357(6352):692-695, 2017. [link]

55. Y. Turakhia, K.J. Zheng, G. Bejerano and W.J. Dally. Darwin: A Hardware-acceleration Framework for Genomic Sequence Alignment. bioRxiv, doi: http://dx.doi.org/10.1101/092171, 2017. [link]

54. A.M. Wenger*, H. Guturu*, J.A. Bernstein and G. Bejerano. Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers. Genet Med., 19(2):209-214, 2016. [pubmed]

53. K.A. Jagadeesh*, A.M. Wenger*, M.J. Berger, H. Guturu, P.D. Stenson, D.N. Cooper, J.A. Bernstein and G. Bejerano. M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity. Nature Genetics, 48(12):1581-1586, 2016. [pubmed]

52. J.H. Notwell, W. Heavner, S. Fazel Darbandi, S. Katzman, W.L. McKenna, C.F. Ortiz Londono, D. Tastad, M.J. Eckler, J.L. Rubenstein, S.K. McConnell, B. Chen and G. Bejerano. "TBR1 regulates autism risk genes in the developing neocortex. Genome Res., 26(8):1013-22, 2016. [pubmed]

51. A. Marcovitz, R. Jia and G. Bejerano. "Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements. Mol. Bio. & Evol., 33(5):1358-1369, 2016. [pubmed]

50. H. Guturu, S. Chinchali, S. L. Clarke and G. Bejerano. Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories. PLoS Comp. Bio., 12(2): e1004711, 2016. [pubmed]

49. G. Tuteja, T. Chung and G. Bejerano. Changes in the enhancer landscape during early placental development uncover a trophoblast invasion gene-enhancer network. Placenta, 37:45-55, 2016. [pubmed]

48. B.A. Braun, A. Marcovitz, J.G. Camp, R. Jia and G. Bejerano. Mx1 and Mx2 key antiviral proteins are surprisingly lost in toothed whales. Proc. Nat’l Acad. Sci. USA, 112(26):8036-8040, 2015. [pubmed]

47. O. Sazonova, Y. Zhao, S. Nürnberg, C. Miller, M. Pjanic, V.G. Castano, J.B. Kim, E.L. Salfati, A.B. Kundaje, G. Bejerano, T. Assimes, X. Yang and T. Quertermous. Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci. PLoS Genet., 11(5):e1005202, 2015. [pubmed]

46. J.H. Notwell, T. Chung, W. Heavner, and G. Bejerano. A family of transposable elements co-opted into developmental enhancers in the mouse neocortex. Nature communications, 6: 6444, 2015. [pubmed]

45. J.G. Camp, C.L. Frank, C.R. Lickwar, H. Guturu, T. Rube, A.M. Wenger, J. Chen, G. Bejerano, G.E. Crawford, and J.F. Rawls. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Res., 24(9):1504-1516, 2014. [pubmed]

44. G. Tuteja, K.B. Moreira, T. Chung, J. Chen, A.M. Wenger, and G. Bejerano. Automated Discovery of Tissue-Targeting Enhancers and Transcription Factors from Binding Motif and Gene Function Data . PLoS Comp. Bio., 10(1): e1003449, 2014. [pubmed]

43. P.L. Reno*, C.Y. McLean*, J.E. Hines, T.D. Capellini, G. Bejerano and D.M. Kingsley. A Penile Spine/Vibrissa Enhancer Sequence Is Missing in Modern and Extinct Humans but Is Retained in Multiple Primates with Penile Spines and Sensory Vibrissae. PLoS ONE, 8(12): e84258, 2013. [pubmed]

42. H. Guturu*, A.C. Doxey*, A.M. Wenger and G. Bejerano. Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements. Philos Trans R Soc Lond B Biol Sci., 368(1632):20130029, 2013. [pubmed]

41. A.M. Wenger*, S.L. Clarke*, J.H. Notwell*, T. Chung, G. Tuteja, H. Guturu, B.T. Schaar and G. Bejerano. The Enhancer Landscape during Early Neocortical Development Reveals Patterns of Dense Regulation and Co-option. PLoS Genet., 9(8):e1003728, 2013. [pubmed] [Nature Genetics feature]

40. M. Hiller, S. Agarwal, J.H. Notwell, R. Parikh, H. Guturu, A.M. Wenger and G. Bejerano. Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish. Nucleic Acids Res., 41(15):e151, 2013. [pubmed]

39. L.A. Pennacchio, W. Bickmore, A. Dean, M.A. Nobrega, G. Bejerano. Enhancers: five essential questions. Nat Rev Genet., 14(4):288-95, 2013. [pubmed]

38. A.M. Wenger, S.L. Clarke, H. Guturu, J. Chen, B.T. Schaar, C.Y. McLean and G. Bejerano. PRISM offers a comprehensive genomic approach to transcription factor function prediction. Genome Res., 23(5):889-904, 2013. [pubmed]

37. J.B. Losos, S.J. Arnold, G. Bejerano, E.D. Brodie 3rd, D. Hibbett, H.E. Hoekstra, D.P. Mindell, A. Monteiro, C. Moritz, H.A. Orr, D.A. Petrov, S.S. Renner, R.E. Ricklefs, P.S. Soltis, T.L. Turner. Evolutionary biology for the 21st century. PLoS Biol., 11(1):e1001466, 2013. [pubmed]

36. G. Tuteja G, E. Cheng, H. Papadakis, and G. Bejerano. PESNPdb: A comprehensive database of SNPs studied in association with pre-eclampsia. Placenta, 33(12):1055-7, 2012. [pubmed]

35. M. Hiller, B.T. Schaar, and G. Bejerano. Hundreds of conserved non-coding genomic regions are independently lost in mammals. Nucleic Acids Res., 40(22):11463-76, 2012. [pubmed]

34. M. Hiller, B.T. Schaar, V.B. Indjeian, D.M. Kingsley, L.R. Hagey, and G. Bejerano. A "Forward Genomics" Approach Links Genotype to Phenotype using Independent Phenotypic Losses among Related Species. Cell Rep., 2(4):817-23, 2012. [pubmed]

33. S.L. Clarke, J.E. Vandermeer, A.M. Wenger, B.T. Schaar, N. Ahituv and G. Bejerano. Human Developmental Enhancers Conserved between Deuterostomes and Protostomes. PLoS Genet., 8(8):e1002852, 2012. [pubmed]

32. T. Laurell, J.E. Vandermeer, A.M. Wenger, G. Grigelioniene, A. Nordenskjö M. Arner, A.G. Ekblom, G. Bejerano, N. Ahituv and A. Nordgren. A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb. Hum Mutat., 33(7):1063-6, 2012. [pubmed]

31. R.Y. Birnbaum, E.J. Clowney, O. Agamy, M.J. Kim, J. Zhao, T. Yamanaka, Z. Pappalardo, S.L. Clarke, A.M. Wenger, L. Nguyen, F. Gurrieri, D.B. Everman, C.E. Schwartz, O.S. Birk, G. Bejerano, S. Lomvardas and N. Ahituv. Coding exons function as tissue-specific enhancers of nearby genes. Genome Res., 22(6):1059-68, 2012. [pubmed]

30.  T.D. Capellini, K. Handschuh, L. Quintana, E. Ferretti, G. Di Giacomo, S. Fantini, G. Vaccari, S.L. Clarke, A.M. Wenger, G. Bejerano, J. Sharpe, V. Zappavigna and L. Selleri. Control of pelvic girdle development by genes of the Pbx family and Emx2. Dev Dyn., 240:1173-89 2011. [pubmed]

29.  C.Y. McLean*, P.L. Reno*, A.A. Pollen*, A.I. Bassan, T.D. Capellini, C. Guenther, V.B. Indjeian, X. Lim, D.B. Menke, B.T. Schaar, A.M. Wenger, G. Bejerano* and D.M. Kingsley*. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature, 471:216-219, 2011. [pdf] [suppl, lists]

28.  X. Fan, P. Ren, S. Dhal, G. Bejerano, S.B. Goodman, M.L. Druzin, S.S. Gambhir and N.R. Nayak. Noninvasive monitoring of placenta-specific transgene expression by bioluminescence imaging. PLoS One, 6(1):e16348, 2011. [pubmed]

27.  C.Y. McLean, D. Bristor, M. Hiller, S.L. Clarke, B.T. Schaar, C.B. Lowe, A.M. Wenger and G. Bejerano. GREAT improves functional interpretation of cis-regulatory regions. Nature Biotechnology, 28(5):495-501, 2010. [pdf] [suppl] [website]

26.  C.B. Lowe, G. Bejerano, S.R. Salama and D. Haussler. Endangered Species Hold Clues to Human Evolution. J Hered., 101(4):437-47, 2010. [pubmed]

25. C. McLean and G. Bejerano. Dispensability of mammalian DNA. Genome Research, 18(11):1743-1751, 2008.  [pdf ] [suppl]

24. D. Karolchik, G. Bejerano, A.S. Hinrichs, R.M. Kuhn, W. Miller, K.R. Rosenbloom, A.S Zweig, D. Haussler and W.J. Kent. Comparative Genomic Analysis Using the UCSC Genome Browser. Methods Mol Biol., 395:17-34, 2007. [pubmed]

23. S. Katzman, A.D. Kern, G. Bejerano, G. Fewell, L. Fulton, R.K. Wilson, S.R. Salama, and  D. Haussler. Human genome ultraconserved elements are ultraselected. Science, 317(5840):915, 2007. [pubmed]

22. C.B. Lowe, G. Bejerano and D. Haussler. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc. Nat’l Acad. Sci. USA, 104(19):8005-8010, 2007. [pdf] [suppl] [data]

21. UCSC Genomics Group. The UCSC genome browser database: update 2007. Nucleic Acids Research, 35:D668-73, 2007. [pubmed]

20. K.S. Pollard, S.R. Salama, B. King, A.D. Kern, T. Dreszer, S. Katzman, A.Siepel, J.S. Pedersen, G. Bejerano, R. Baertsch, K.R. Rosenbloom, J. Kent and D. Haussler. Forces Shaping the Fastest Evolving Regions in the Human Genome. PLoS Genetics, 2(10): e168, 2006. [pubmed]

19. G. Bejerano. Branch and bound computation of exact P-values, Bioinformatics, 22(17):2158-2159, 2006. [pdf] [code]

18. G. Bejerano, C.B. Lowe, N. Ahituv, B. King, A. Siepel, S.R. Salama, E.M. Rubin, W.J. Kent and D. Haussler. A Distal Enhancer and an Ultraconserved Exon are Derived From a Novel Retroposon. Nature, 441(7089):87-90, 2006. [pdf] [suppl] [website]

17. J.S. Pedersen, G. Bejerano, A. Siepel, K. Rosenbloom, K. Lindblad-Toh, E.S. Lander, W.J. Kent, W. Miller and D. Haussler. Identification and Classification of Conserved RNA Secondary Structures in the Human Genome. PLoS Computational Biology, 2(4):e33, 2006. [pubmed]

16. UCSC Genomics Group. The UCSC Genome Browser Database: Update 2006. Nucleic Acids Research, 34:D590-D598, 2006. [pubmed]

15. G. Bejerano, A.C. Siepel, W.J. Kent and D. Haussler. Computational screening of conserved genomic DNA in search of functional non-coding elements. Nature Methods, 2(7):535-545, 2005. [pdf]

14. A. Siepel, G. Bejerano, J.S. Pedersen, A. Hinrichs, M. Hou, K. Rosenbloom, H. Clawson, J. Spieth, L.W. Hillier, S. Richards, G.M. Weinstock, R.K. Wilson, R.A. Gibbs, W.J. Kent, W. Miller, and D. Haussler. Evolutionarily Conserved Elements in Vertebrate, Fly, Worm, and Yeast Genomes. Genome Research, 15(8):1034-1050, 2005. [pubmed]

13. E.A. Glazov, M. Pheasant, E.A. McGraw, G. Bejerano and J.S. Mattick. Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Research, 15(6):800-808, 2005. [pubmed]

12. G. Bejerano, N. Friedman and N. Tishby. Efficient exact p-value computation for small sample, sparse and surprising categorical data, J. Computational Biology, 11(5): 867-886, 2004. [pdf] [code]

11. International Chicken Genome Sequencing Consortium. Sequencing and comparative analysis of the chicken genome, Nature, 432(7018): 695-716, 2004. [pubmed]

10. G. Bejerano, D. Haussler and M. Blanchette. Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics, 20: I40-I48, 2004. [pdf] [website]

9. G. Bejerano, M. Pheasant, I.V. Makunin, S. Stephen, W.J. Kent, J.S. Mattick and D. Haussler. Ultraconserved elements in the human genome. Science, 304(5675): 1321-1325, 2004. Quoted by Science in Breakthrough of the Year, 5th runner up.[pdf] [suppl] [website]

8. G. Bejerano. Algorithms for variable length Markov chain modeling. Bioinformatics, 20(5): 788-789, 2004. [pdf] [code]

7. O. Lartillot, S. Dubnov, G. Assayag and G. Bejerano. A system for computer music generation by learning and improvisation in a particular style, IEEE Computer J., 36(10): 73-80, 2003. [pdf] [music]

6. N. Slonim, G. Bejerano, S. Fine and N. Tishby. Discriminative feature selection via multiclass variable memory Markov models, EURASIP J. Applied Signal Processing, 2:93-102, 2003. [pdf]

5. G. Bejerano, Y. Seldin, H. Margalit and N. Tishby. Markovian domain fingerprinting: Statistical segmentation of protein sequences, Bioinformatics, 17(10):927-934, 2001. [pdf] [poster]

4. L. Argaman, R. Hershberg, J. Vogel, G. Bejerano, G. Wagner, H. Margalit and S. Altuvia. Novel small RNA-encoding genes in Escherichia coli, Current Biology, 11(12): 941-950, 2001. [pubmed]

3. G. Bejerano and G. Yona. Variations on probabilistic suffix trees - a new tool for statistical modeling and prediction of protein families, Bioinformatics, 17(1): 23-43, 2001. [pdf] [code]

2. R. Hershberg, G. Bejerano, A. Santos-Zavaleta and H. Margalit. PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites, Nucleic Acids Research, 29(1):277, 2001. [pdf] [website]

1. A. Apostolico and G. Bejerano. Optimal amnesic probabilistic automata, or, how to learn and classify proteins in linear time and space, J. Computational Biology, 7(3-4):381-393, 2000. [pdf]


Refereed conference papers (8-12 pages)

9. I.V. Makunin, S. Stephen, M. Pheasant, G. Bejerano, W.J. Kent, D. Haussler and J.S. Mattick. Extremely conserved non-coding sequences in the vertebrate genomes. Proceedings of 4th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS), 2004.

8. G. Bejerano. Efficient exact p-value computation and applications to biosequence analysis. Proceedings of the 7th annual international conference on research in computational molecular biology (RECOMB), 2003. Best paper by a young scientist award. [pdf]

7. N. Slonim, G. Bejerano, S. Fine and N. Tishby. Discriminative feature selection via multiclass variable memory Markov models, Proceedings of 19th International Conference on Machine Learning (ICML), 2002.

6. O. Lartillot, S. Dubnov, G. Assayag, and G. Bejerano. Automated modeling of musical style, Proceedings of the International Computer Music Conference (ICMC), 2001.

5. Y. Barash, G. Bejerano and N. Friedman. A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites, 1st Workshop on Algorithms in Bioinformatics (WABI), 2001. Lecture Notes in Computer Science, 2149: 278-293.

4. Y. Seldin, G. Bejerano and N. Tishby. Unsupervised sequence segmentation by a mixture of switching variable memory Markov sources, Proceedings of 18th International Conference on Machine Learning (ICML), 2001.

3. Y. Seldin, G. Bejerano and N. Tishby. A variable memory Markovian modeling approach to unsupervised sequence segmentation, Proceedings of 33rd Symposium on the Interface of Computing Science and Statistics (Interface), 2001.

2. A. Apostolico and G. Bejerano. Optimal amnesic probabilistic automata, or, how to learn and classify proteins in linear time and space, Proceedings of the 4th annual international conference on research in computational molecular biology (RECOMB), 2000.

1. G. Bejerano and G. Yona. Modeling protein families using probabilistic suffix trees, Proceedings of the 3rd annual international conference on research in computational molecular biology (RECOMB), 1999. Best paper by a young scientist award. [pdf]


Book Chapters

1. D. Karolchik, G. Bejerano, A.S. Hinrichs, R.M. Kuhn, W. Miller, A.S. Zweig, D. Haussler, W.J. Kent. Comparative Genomics Analysis Using the UCSC Genome Browser. Methods in Molecular Biology series, ed. Nicholas Bergman, Comparative Genomics volume 1, Humana Press. [link]


Patents

1. N. Tishby, Y. Seldin, G. Bejerano and H. Margalit. Markovian Domain Fingerprinting In Statistical Segmentation Of Protein Sequences. [link]


Ph.D. Thesis

G. Bejerano. Automata learning and stochastic modeling for biosequence analysis. Hebrew University, Israel, 2003. [pdf]

      [last modified 2017/09/18 14:00] Bejerano LabDepartments of Computer Science, Developmental Biology and PediatricsStanford University