麻豆村

麻豆村
Joint Carnegie Mellon-University of Pittsburgh Ph.D. Program in Computational Biology  ›  Current Student Resources  ›  Student Publications

Student Publications

  1. Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I. (2021) ProDy 2.0: [Online ahead of print]. PMID: 33831302
  2. Pei F, Shi Q, Zhang H, Bahar I (2021) . J Chem Inf Model [Online ahead of print]. PMID: 33831302
  3. Wang H, Pei F, Vanyukov MM, Bahar I, Wu W, Xing EP. (2021) BMC Bioinformatics 22(1):50. PMID: 33546598
  4. Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T (2021) 22: 21. PMID: 33413539 PMCID: PMC7789082
  5. Wingert B, Krieger JM, Li H, Bahar I (2020)  Curr Opin Struct Biol 67:25-32. PMID: 33053463
  6. Cheng MH, Zhang S, Porritt RA, Rivas MN, Paschold L, Willscher E, Binder M, Arditi M*, Bahar I* (2020) . Proc Natl Acad Sci USA 117: 25254-25262 PMID: 32989130 PMCID: PMC7568239 

  7. Zhang Y, Krieger JM, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I (2020) . Prog Biophys Mol Biol S0079-6107(20)30082-1. PMID: 32866476 

  8. Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. (2020)  bioRxiv. PMID: 32587977 PMCID: PMC7310637
  9. Shi Q, Pei F, Silverman GA, Pak SC, Perlmutter DH, Liu B*, Bahar I*. (2020) . Int. J. Mol. Sci 21:2855. PMID: 32325894 PMCID: PMC7215584
  10. Li H, Taylor DL, Bahar I. (2020) . Bioinformatics 36:3935-3937. PMID: 32221612 PMCID: 
  11. Cheng MH, Ponzoni L, Sorkina T, Lee JY, Zhang S, Sorkin A, Bahar I. (2019) . Neuropharmacology 161:107676 PMID: 31228486 PMCID: 6917874 DOI: 10.1016/j.neuropharm.2019.107676
  12. Mikulska-Ruminska K, Shrivastava IH, Krieger JM, Zhang S, Li H, Bayir H, Wenzel SE, VanDemark AP, Kagan VE, Bahar I. (2019) . J Chem Inf Model 59: 2496-2508. PMID: 30762363 PMCID: 6541894
  13. Wang Y, Cobanoglu MC, Li J, Hidvegi T, Hale P, Ewing M, Chu AS, Gong Z, Muzumdar R, Pak SC, Silverman GA, Bahar I, Perlmutter DH (2019)  PloS One 14: e0209748. PMID: 30673724 PMCID: 6343872J281. Lee JY, Krieger J, Herguedas B, García-Nafría J, Dutta A, Shaikh SA, Greger IH, Bahar I. (2019) . Structure 27: 241-252. PMID: 30528594 PMCID: 6365164
  14. Shashank Singh, Yang Yang, Barnabás Póczos, Jian Ma. (2018) , Accepted , Vol to appear, Pgs to appear
  15. Xiangrui Zeng, Miguel Ricardo Leung, Tzviya Zeev-Ben-Mordehai, Min Xu. (2018). Journal of Structural Biology (202), 150-160
  16. Wingert, Bentley M., Rick Oerlemans, and Carlos J. Camacho. (2018) . Journal of computer-aided molecular design 32.1 (2018): 287-297.
  17. Bondarenko V, Wells MM, Xu Y, Tang P (2018) , in press
  18. Weiguang Mao, Ryan Hausler, Maria Chikina. (2018)  RECOME Satellite on Genetics (Abstract only)
  19. Natalie Sauerwald and Carl Kingsford.  (2018) Proceedings of Intelligent Systems for Molecular Biology (to appear in Bioinformatics)
  20. Chen Q, Wells MM, Arjunan P, Tillman TS, Adell D, Cohen AE, Xu Y, Tang P. (2018)  Biophysical Journal, 114(3): 299a. (abstract only)
  21. Marcus Thomas, Russell Schwartz (2018)  BMC Systems Biology
  22. Cong Ma, Mingfu Shao, Carl Kingsford. (2018)  Genome Biology, vol 19, pg 52
  23. Kaya C, Cheng MH, Block ER, Bartol TM, Sejnowski TJ, Sorkin A, Faeder JR, Bahar I. (2018)  eNeuro. 2018 Feb 5;5(1). pii: ENEURO.0298-17.2017. doi: 10.1523/ENEURO.0298-17.2017. eCollection 2018 Jan-Feb.
  24. Ruochi Zhang, Yuchuan Wang, Yang Yang, Yang Zhang, Jian Ma. (2018) . Bioinformatics, Accepted ISMB 2018, , Vol: to appear, Pgs: to appear
  25. Raghavendran Partha, Bharesh K Chauhan, Zelia Ferreira, Joseph D Robinson, Kira Lathrop, Ken K Nischal, Maria Chikina, Nathan L Clark. (2017) . eLife 2017;6:e25884
  26. Cheng MH, Kaya C, Bahar I. (2017) J Phys Chem B. 2017 Dec 26. doi: 10.1021/acs.jpcb.7b10340. [Epub ahead of print]
  27. Wells MM, Reinert N, Tang P, Xu Y. (2017) Biophysical Journal, 112(3): 556a. (abstract only)
  28. Tasan I, Sustackova G, Zhang L, Kim J, Sivaguru M, HamediRad M, Wang Y, Genova J, Ma J, Belmont AS, and Zhao H. (2017)  bioRxiv, doi
  29. Jingyu Zhang, Xiao-Jun Tian, Yi-Jiun Chen, Weikang Wang, Simon Watkins, Jianhua Xing. (2017) BioRxiv
  30. Wang Y, Wells MM, Dailey W, Eckenhoff R, Tang P, Xu Y. (2017) Biophysical Journal, 112(3): 18a. (abstract only)
  31. S Sant M Singh, XJ Tian, VS Donnenberg, AM Watson, J Zhang, LP Stabile, SC Watkins, J Xing. (2017) BioRxiv
  32. Daniel M Spagnolo, Yousef Al-Kofahi, Peihong Zhu, Timothy R Lezon, Albert Gough, Andrew M Stern, Adrian V Lee, Fiona Ginty, Brion Sarachan, D Lansing Taylor, S Chakra Chennubhotla. (2017)  Cancer Research, Vol 77, issue 21, Pgs e71-e74
  33. Sabrina Rashid, Darrell N. Kotton, and Ziv Bar-Joseph. (2017)  Bioinformatics, Volume: 33, Issue 16, Pages: 2504-2512
  34. Pellow D, Filippova D, Kingsford C.  Journal of Computational Biology. 2017;24(6):547-557.  
  35. Farrow DC, Brooks LC, Hyun S, Tibshirani RJ, Burke DS, Rosenfeld R. . Alizon S, ed. PLoS Computational Biology. 2017;13(3):e1005248. 
  36. Ion BF, Wells MM, Xu Y, Tang P. (2017) K Biophysical Journal, 113(3): 605-12.
  37. Marcus Thomas, Russell Schwartz (2017) Physical Biology, Vol 89, Pg 4123-4133
  38. Chen Q, Wells MM, Tillman TS, Kinde MN, Cohen AE, Xu Y, Tang P (2017) . Structure, 25(1): 180-7.
  39. F. Pei, H. Li, M. J. Henderson, S. A. Titus, A. Jadhav, A. Simeonov, M. Cobanoglu, S. H. Mousavi, T. Shun, L. McDermott, P. Iyer, M. Fioravanti, D. Carlisle, R. M. Friedlander, I. Bahar, D. Lansing Taylor, T. R. Lezon, A. M. Stern, M. E. Schurdak. (2017) Scientific reports, 7, 17803
  40. Q Zhang*, S Gupta*, DL Schipper, GJ Kowalczyk, AE Mancini, JR Faeder, REC Lee.  (2017) Cell systems 5 (6), 638-645. e5
  41. J Sunseri, DR Koes, P Roy, D Gau. (2017)  Biophysical Journal 112 (3), 287a (abstract only)
  42. Kleyman, M., Sefer, E., Nicola, T., Espinoza, C., Chhabra, D., Hagood, J.S., Kaminski, N., Ambalavanan, N. and Bar-Joseph, Z., (2017)  eLife, 6, p.e18541..
  43. M Ragoza, J Hochuli, E Idrobo, J Sunseri, DR Koes. (2017) . Journal of chemical information and modeling 57 (4), 942-957.
  44. Nicolas A. Pabon, Carlos J. Camacho. (2017) . eLife 2017: 10.7554/eLife.22889.
  45. R. Ambler, X. Ruan, R.F. Murphy, and C. Wülfing (2017) . The Immune Synapse: Methods and Protocols (C. T. Baldari and M. L. Dustin, eds.), Methods in Molecular Biology 1584:409-421.
  46. X. Ruan, C. Wülfing, and R. F. Murphy (2017)  Bioinformatics 33:i217-i224
  47. Natalie Sauerwald, She Zhang, Carl Kingsford, Ivet Bahar.  (2017)  Nucleic Acids Research.
  48. Emre Sefer, Michael Kleyman, Ziv Bar-Joseph. (2016) Cell Systems, Vol 3, Pgs 35-42
  49. Seojin Bang and Wei Wu. (2016) Bioinformatics and Biomedicine (BIBM), Vol N/A, Pages 460-465
  50. LA Harris, JS Hogg, JJ Tapia, JAP Sekar, S Gupta, I Korsunsky, A Arora, D Barua, RP sheehan, JR Faeder. (2016) . Bioinformatics 32 (21), 3366-3368
  51. A.W. Naik, J.D. Kangas, D. P. Sullivan, and R. F. Murphy (2016) , eLife 5:e10047. doi:10.7554/eLife.10047.
  52. K. T. Roybal, T. E. Buck, X. Ruan, B. H. Cho, D. J. Clark, R. Ambler, H. M. Tunbridge, J. Zhang, P. Verkade, C. Wülfing, and R. F. Murphy (2016) .  Science Signaling 9:rs3. doi: 10.1126/scisignal.aad4149.
  53. Y. Li, T. D. Majarian, A. W. Naik, G. R. Johnson, and R. F. Murphy (2016)  Cytometry Part A 89:633-643.  doi: 10.1002/cyto.a.22873.
  54. Sedgewick AJ, Shi I, Donovan RM, Benos PV.  BMC Bioinformatics. 2016;17(Suppl 5):175.  
  55. R. Ambler, X. Ruan, R.F. Murphy, and C. Wülfing (2016)   Methods Mol. Biol., in press.
  56. Spagnolo DM, Gyanchandani R, Al-Kofahi Y, Stern AM, Lezon TR, Gough A, Meyer DE, Ginty F, Sarachan B, Fine J, Lee AV, Taylor D L, Chennubhotla S C. J Pathol Inform 2016;7:47
  57. Zhiguang Huo, Ying Ding, Silvia Liu, Steffi Oesterreich*, George C. Tseng*. (2016)  Journal of the American Statistical Association. 2015.
  58. Silvia Liu^, Wei-Hsiang Tsai^, Ying Ding^, Rui Chen, Zhou Fang, SungHwan Kim, Tianzhou Ma, Ting-Yu Chang, Jianhua Luo, Hsei-Wei Wang*, I-Fang Chung* and George C. Tseng*. (2016)   Nucleic Acids Research 44, no. 5 : e47-e47.
  59. Erdem, C., Nagle, A.M., Casa, A.J., Litzenburger, B.C., Wang, Y., Taylor, D.L., Lee, A.V., and Lezon, T.R. (2016).  Molecular & Cellular Proteomics 15, 3045-3057. [Published ahead of print on June 30]
  60. Laura Tipton, Elodie Ghedin, and Alison Morris. (2016) Virulence 2016, 29 Sep 2016
  61. Alison Morris, Joselph N. Paulson, Hisham Talukder, Laura Tipton, Heather Kling, Lijia Cui, Adam Fitch, Mihai Pop, Karen A. Norris and Elodie Ghedin (2016)  Microbiome 2016 4:38, 8 Jul 2016
  62. Sushma K. Cribbs, Karan Uppal, Shuzhao Li, Dean P. Jones, Laurence Huang, Laura Tipton, Adam Fitch, Ruth M. Greenblatt, Lawrence Kingsley, David M. Guidot, Elodie Ghedin and Alison Morris (2016)  2016 4:3.
  63. Somayeh Pirhadi, Jocelyn Sunseri, David Ryan Koes . (2016)  Volume 69, September 2016, Pages 127–143
  64. J Sunseri, DR Koes (2016 ) Nucl. Acids Res. doi: 10.1093/nar/gkw287
  65. J Sunseri, M Ragoza, J Collins, (2016) DR Koes  Journal of Computer-Aided Molecular Design doi:10.1007/s10822-016-9960-x
  66. Xiao-Jun Tian, Hang Zhang, Jingyu Zhang, Jianhua Xing  (2016)  FEBS Letters
  67. J Zhang, XJ Tian, J Xing (2016)  Journal of clinical medicine 5 (4), 41
  68. Solomon B and Kingsford C. (2016)  Nature Biotechnology. doi:10.1038/nbt.3442
  69. Donovan RM, Tapia J-J, Sullivan DP, Faeder JR, Murphy RF, Dittrich M, and Zuckerman DM. (2016) . PLoS Comput Biol 12(2): e1004611. doi:10.1371/journal.pcbi.1004611
  70. Ye, Z., Baumgartner, M.P., Wingert, B.M. et al. (2015) .  J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9941-0
  71. Koes DR, Pabon NA, Deng X, Phillips MA, Camacho CJ. (2015) . PLoS ONE 10(8): e0134697
  72. Shirish Paranjpe, …, Silvia Liu, George C.Tseng, George K. Michalopoulos. (2015) . (accepted by Hepatology on Jun 2016)
  73. Farrow DC, Burke DS, Rosenfeld R.  Goldstein E, ed. PLoS ONE. 2015;10(5):e0125047.  
  74. G. R. Johnson, J. Li, A. Shariff, G.K.Rohde, and R.F. Murphy (2015) Automated Learning of Subcellular Pattern Variation among Punctate Proteins and of a Generative Model of their Distributions in Relation to Microtubules.  PLoS Computational Biology 11(12): e1004614. 
  75. Yan P. Yu^, Silvia Liu^, Zhigang Huo, Amantha Martin, Joel B. Nelson, George C. Tseng and Jian-Hua Luo*. Genomic copy number variations in the genomes of leukocytes predict prostate cancer clinical outcomes. PLoS ONE. 2015 Aug 21; 10(8): e0135982. (PubMed ID: 26295840)
  76. Chen Q, Kinde MN, Arjunan P, Wells MM, Cohen AE, Xu Y, Tang P. (2015). Scientific reports. 5:13833.
  77. Malkin AD, Sheehan RP, Mathew S, Federspiel WJ, Redl H, Clermont G. . 2015;11(10):e1004314. 
  78. Mao, W., Kaya, C., Dutta, A., Horovitz, A., & Bahar, I. (2015). . Bioinformatics, 31(12), 1929-1937.
  79. Bahar, I., Cheng, M. H., Lee, J. Y., Kaya, C., & Zhang, S. (2015).  Biophysical journal, 109(6), 1101-1109.
  80. Brooks LC, Farrow DC, Hyun S, Tibshirani RJ, Rosenfeld R. . Tanaka MM, ed. PLoS Computational Biology. 2015;11(8):e1004382. 
  81. Hawse WF, Sheehan RP, Miskov-Zivanov N, et al. . Journal of immunology (Baltimore, Md : 1950). 2015;194(10):4615-4619. 
  82. Roman, T., Xie, L., & Schwartz, R. (2016). . BMC Genomics, 17(1), 97.
  83. GR Johnson, TE Buck, DP Sullivan, GK Rohde, RF Murphy. (2015) . Mol. Biol. Cell. Published online 9/9/2015.
  84. Z-H Zuo, Y-P Yu, Y Ding, S Liu, A Michalopoulos, GC Tseng, J-H Luo. (2015)  Accepted, The American Journal of Pathology.
  85. Wells M, Tillman T, Mowrey D, Sun T, Xu Y, Tang P. (2015) . Journal of Medicinal Chemistry. 58(7):2958-66
  86. Mochan-Keef E, Swigon D, Ermentrout GB, Clermont G. (2015) PLoS One 10: e0134012.
  87. Price I, Mochan-Keef ED, Swigon D, Ermentrout GB, Lukens S, Toapanta FR, Ross T, Clermont G. (2015) . J Theor Biol. 374: 83–93.
  88. Ramanathan A, Pullum LL, Hobson TC, Quinn, SP et al. . Frontiers in Public Health. 2015;3:182. doi:10.3389/fpubh.2015.00182. 
  89. Matthew Patrick Baumgartner and Carlos J. Camacho. (2015) On  Just Accepted Manuscript DOI: 10.1021/acs.jcim.5b00338
  90. Quinn SP, Zahid MJ, Durkin JR, Francis RJ, Lo CW, Chennubhotla SC. Automated identification of abnormal respiratory ciliary motion in nasal biopsies. Science translational medicine. 2015;7(299):299ra124. doi:10.1126/scitranslmed.aaa1233
  91. Grover P, Shi H, Baumgartner M, Camacho CJ, Smithgall TE (2015). PLoS ONE 10(7): e0133590. doi: 10.1371/journal.pone.0133590
  92. J-H Luo, S Liu, Z-H Zuo, R Chen, GC Tseng, YP Yu. (2015) . Accepted, The American Journal of Pathology
  93. Wise A, Bar-Joseph Z.  Journal of Computational Biology. 2015;22(4):324-333. 
  94. Roman, T., Nayyeri, A., Fasy, B. T., & Schwartz, R. (2015). . BMC bioinformatics, *16*(1), 254.
  95. Wise A, Bar-Joseph Z.  Bioinformatics. 2015;31(8):1250-1257.  
  96. Raghavendran Partha, Karthik Raman. (2014) PLoS ONE 9(11): e112792.
  97. Kumar A, Rao A, Bhavani S, Newberg JY, and Murphy RF. (2014) . Proc. Natl. Acad. Sci. U.S.A. 111:18249-18254.
  98. Mochan E, Swigon D, Ermentrout GB, Lukens S, Clermont G.  J Theor Biol. Elsevier; 2014;353: 44–54.
  99. YP Yu, Y Ding, Z Chen, S Liu, R Chen, ZG Gulzar, B Yang, KM Cieply, A Luvison, B-G Ren, JD Brooks, D Jarrard, JB Nelson, GK Michalopoulos, GC Tseng, J-H Luo. (2014)  American Journal of Pathology 18:10, pp 2840-2849.
    PMCID: PMC4188871
  100. Moroco JA, Baumgartner MP, Rust HL, Choi HG, Hur W, Gray NS, Camacho CJ, Smithgall TE (2014)  Chem Biol Drug Des. [Epub ahead of print]
    PMID: 25376742
  101. Gardner CL, Hritz J, Sun C, Vanlandingham DL, Song TY, Ghedin E, Higgs S, Klimstra WB, Ryman KD (2014)  PLoS Negl Trop Dis 8(2):e2719.
  102. Mukherjee, S., Zheng, H., Derebe, M., Callenberg, K.M., Partch, C.L., Rollins, D., Propheter, D.C., Rizo, J., Grabe, M., Jiang, Q., Hooper, L.V. (2014). , Nature 505: 103-107. doi:10.1038/nature12729.
    PMCID: PMC4160023
  103. D. Filippova, R. Patro, G. Duggal, C. Kingsford (2014) “”, Algorithms Mol Biol. 9: 14. Published online May 3, 2014. doi: 10.1186.1748-7188-9-14
    PMCID: PMC4019371
  104.  Tan C, Smith RP, Tsai M-C, Schwartz R, You L. Przytycka TM, ed. PLoS Computational Biology. 2014;10(8):e1003751.
  105. J. S. Hogg, L. A. Harris, L. J. Stover, N. S. Nair, and J. R. Faeder (2014). “” PLOS Comp. Biol. doi:10.1371/journal.pcbi.1003335.
    PMCID: PMC3974646
  106. Kangas JD, Naik AW, Murphy RF,(2014) “”, BMC Bioinformatics. 2014 May 16;15:143
    PMCID: PMC4030446
  107. Latorraca, N.R.*, Callenberg, K.M.*, Boyle, J.P., Grabe, M. (2014). , J Membrane Biol 247 (5): 395-408. * co-first authors
  108. S. A. Chowdhury, S. E. Shackney, K. Heselmeyer-Haddad, T. Ried, A. A. Schäffer, R. Schwartz. (2014) “.“ PLoS Comput Biol. Jul 31;10(7):e1003740. doi: 10.1371/journal.pcbi.1003740. eCollection 2014. PMCID: PMC4117424
  109. Zhang L and Kim S (2014) “”, PLoS Comp. Biol. Feb 27;10(2):e1003420
    PMCID: PMC3937098
  110. G.R. Smith, L. Xie, B. Lee, and R. Schwartz. (2014) “.” Biophysical Journal, 106(1):310-320.
    PMCID: 3907212
  111.  (2013) C Kaya, A Armutlulu, S Ekesan, T Haliloglu Nucleic acids research 41(Web Server issue):W249-55.
    PMID: 23742907
  112. Price I, Ermentrout B, Zamora R, Wang B, Azhar N, Mi Q, Constantine G, Faeder JR, Luckhart S, Vodovotz Y (2013) . J Theor Biol pii: S0022-5193(13)00258-0.)
  113. Zinman GE, Naiman S, Kanfi Y, Cohen H, Bar-Joseph Z. (2013) “”, Nat Methods. 2013 Oct;10(10):925-6
  114. S. Quinn, M. Zahid, J. Durkin, R. Francis, C. Lo, and C. Chennubhotla. Dynamic texture analysis for automated clinical diagnosis of abnormal respiratory ciliary motion. 2013 Nature Biotechnology 
  115. Armaghan W Naik, Joshua D Kangas, Christopher J Langmead, Robert F Murphy.  2013 PLoS One Vol 8
  116. Duggal, G., Wang, H., Kingsford, C. (2013) “”, Nucleic Acids Research, 42 (1): 87-96.
    PMCID: PMC3874174
  117. Huang GT, Cunningham K, Benos PV, Chennubhotla C (2013) . Pac Symp Biocomput, 212-223.
    PMID: 23424126
  118. Darya Filippova, Rob Patro, Geet Duggal, Carl Kingsford.   Algorithms in Bioinformatics  Volume 8126, 2013, pp 300-312. 
  119. Luis Pedro Coelho, Joshua D Kangas, Armaghan W Naik, Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret Fuhrman, Ramanuja Simha, Peter B Berget, Jonathan W Jarvik, Robert F Murphy. 2013 Bioinformatics 29,18
  120. SA Chowdhury, S Shackney, K Heselmeyer-Haddad, T Ried, AA Schiffer and R Schwartz. (2013)  Bioinformatics, 29(13) i189-i198.
    PMCID: PMC3694640
  121. Duggal G, Patro R, Sefer E, Wang H, Filippova D, Khuller S, Kingsford C. (2013) . Algorithms Mol Biol. 8(1):8.
    PMCID: PMC3655033
  122. Sedgewick AJ, Benz SC, Rabizadeh S, Soon-Shiong P, Vaske CJ. (2013)  Bioinformatics 29: i62-i70.
    (Proceedings Issue for International Conference on Intelligent Systems for Molecular Biology (ISMB 2013))
    PMCID: PMC3694636
  123. Tsai MC, Blelloch G, Schwartz R, Ravi R. (2013)  IEEE/ACM Trans Comput Biol Bioinform. 10(5):1137-49.
    PMCID: PMC4019315
  124. Cobanoglu MC, Liu C, Hu F, Oltvai ZN, Bahar I (2013)  J Chem Inf Model 53 (12), pp 3399–3409
    PMCID: PMC3871285
  125. J. J. Tapia and J. R. Faeder (2013). “.” Proceedings of ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), September 2013.
  126. Zhou, Y., Vazquez, A., Wise, A., Warita, T., Warita, K., Bar-Joseph, Z., & Oltvai, Z. N. (2013) “”, BMC Systems Biology, 7(1), 138.
    PMCID: PMC3924228
  127. Donovan RM, Sedgewick AJ, Faeder JF, and Zuckerman DM. (2013)  J Chem Physics 139(11)
    PMCID: PMC3790806
  128. H. Wang, G. Duggal, R. Patro, M. Girvan, S. Hannenhalli, and C. Kingsford. (2013) “”, ACM BCB 2013.
  129. Rampey RA, Baldridge MT, Farrow DC, Bay SN, Bartel B. . G3: Genes|Genomes|Genetics. 2013;3(1):131-141.  
  130. Chang, K.N., Zhong, S., Weirauch, M.T., Hon, G., Pelizzola, M., Li, H., Huang, S.C., Schmitz, R.J., Urich, M.A., Kuo, D., Nery, J.R., Qiao, H., Yang, A., Jamali, A., Chen, H., Ideker, T. Ren, B., Bar-Joseph, Z., Hughes, T.R., Ecker, J.R. (2013)  “”, eLife 2013;2:e00675.
  131. Taylor DP, Wells JZ, Savol A, C. Chennubhotla C, and Wells A. (2013)  Clin. Cancer Res., vol. 19, no. 5, pp. 1063.1070, Mar. 2013.
    PMCID: PMC3594128
  132. Ramanathan A, Savol A, Burger V, Chennubhotla CS, Agarwal PK (2013)  Accounts Chem Res 47 (1), 149-156.
  133. Mowrey D, Chen Q, Liang Y, Liang J, Xu Y and Tang P. (2013) . PLoS ONE 8(5): e64326. doi:10.1371/journal.pone.0064326
    PMCID: PMC3648548
  134. Kang J, Puskar KM, Schwartz RS. LeDuc PR, 2013 Biophysical Journal 104, 2.
  135. Mowrey D, Cheng MH, Liu LT, Willenbring D, Wymore T, Xu Y, Tang P. (2013).  J Am Chem Soc. 35(6): 2172-2180.
    PMCID: PMC3582375
  136. Shao H, Travers T, Camacho CJ, Wells A. (2013) . Int J Biochem Cell Biol. 45(6):1051-63.PMCID: PMC3633689
  137. Ziraldo C, Mi Q, An G, Vodovotz Y. (2013)  Advanced Wound Care 2:527-537.
  138. Travers T, Shao H, Wells A, Camacho CJ. (2013)  Biophys J. 104(3):705-15.
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