Lab Web Site: Biomedical Cybernetics Lab

Researcher Services


Publications powered by Harvard Catalyst Profiles

  1. Wang W, Li S, Li Z, Zhang J, Fan K, Tan G, Ai G, Lam SM, Shui G, Yang Z, Lu H, Jin P, Li Y, Chen X, Xia X, Liu X, Dannelly HK, Yang C, Yang Y, Zhang S, Alterovitz G, Xiang W, Zhang L. Publisher Correction: Harnessing the intracellular triacylglycerols for titer improvement of polyketides in Streptomyces. Nat Biotechnol. 2020 Jan; 38(1):109. View abstract
  2. Wang W, Li S, Li Z, Zhang J, Fan K, Tan G, Ai G, Lam SM, Shui G, Yang Z, Lu H, Jin P, Li Y, Chen X, Xia X, Liu X, Dannelly HK, Yang C, Yang Y, Zhang S, Alterovitz G, Xiang W, Zhang L. Harnessing the intracellular triacylglycerols for titer improvement of polyketides in Streptomyces. Nat Biotechnol. 2020 Jan; 38(1):76-83. View abstract
  3. An N, Xiao Y, Yuan J, Yang J, Alterovitz G. Extracting causal relations from the literature with word vector mapping. Comput Biol Med. 2019 Dec; 115:103524. View abstract
  4. Kim MY, Na I, Kim JS, Son SH, Choi S, Lee SE, Kim JH, Jang K, Alterovitz G, Chen Y, van der Vaart A, Won HS, Uversky VN, Kim CG. Rational discovery of antimetastatic agents targeting the intrinsically disordered region of MBD2. Sci Adv. 2019 11; 5(11):eaav9810. View abstract
  5. Li H, Wang X, Lu X, Zhu H, Li S, Duan S, Zhao X, Zhang F, Alterovitz G, Wang F, Li Q, Tian XL, Xu M. Co-expression network analysis identified hub genes critical to triglyceride and free fatty acid metabolism as key regulators of age-related vascular dysfunction in mice. Aging (Albany NY). 2019 Sep 12; 11(18):7620-7638. View abstract
  6. Liang M, Li Z, Wang W, Liu J, Liu L, Zhu G, Karthik L, Wang M, Wang KF, Wang Z, Yu J, Shuai Y, Yu J, Zhang L, Yang Z, Li C, Zhang Q, Shi T, Zhou L, Xie F, Dai H, Liu X, Zhang J, Liu G, Zhuo Y, Zhang B, Liu C, Li S, Xia X, Tong Y, Liu Y, Alterovitz G, Tan GY, Zhang LX. A CRISPR-Cas12a-derived biosensing platform for the highly sensitive detection of diverse small molecules. Nat Commun. 2019 08 14; 10(1):3672. View abstract
  7. Liao M, Tong T, Zong Y, Zhou X, Cheng L, Huang R, Ren B, Alterovitz G. Application of Omics and Bioinformatics Tools in Streptococcus Research. Curr Issues Mol Biol. 2019 Jun 05; 32:327-376. View abstract
  8. Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, Hayes A, Suresh A, Purkayastha A, King CH, Taylor D, Johanson E, Thompson EE, Donaldson E, Morizono H, Tsang H, Vora JK, Goecks J, Yao J, Almeida JS, Keeney J, Addepalli K, Krampis K, Smith KM, Guo L, Walderhaug M, Schito M, Ezewudo M, Guimera N, Walsh P, Kahsay R, Gottipati S, Rodwell TC, Bloom T, Lai Y, Simonyan V, Mazumder R. Enabling precision medicine via standard communication of HTS provenance, analysis, and results. PLoS Biol. 2018 12; 16(12):e3000099. View abstract
  9. Warner JL, Prasad I, Bennett M, Arniella M, Beeghly-Fadiel A, Mandl KD, Alterovitz G. SMART Cancer Navigator: A Framework for Implementing ASCO Workshop Recommendations to Enable Precision Cancer Medicine. JCO Precis Oncol. 2018; 2018. View abstract
  10. Zhou Y, Yang H, Zhou X, Luo H, Tang F, Yang J, Alterovitz G, Cheng L, Ren B. Lovastatin synergizes with itraconazole against planktonic cells and biofilms of Candida albicans through the regulation on ergosterol biosynthesis pathway. Appl Microbiol Biotechnol. 2018 Jun; 102(12):5255-5264. View abstract
  11. Warner JL, Yang PC, Alterovitz G. Overcoming the Straw Man Effect in Oncology: Visualization and Ranking of Chemotherapy Regimens Using an Information Theoretic Approach. JCO Clin Cancer Inform. 2017 11; 1:1-9. View abstract
  12. Barlow SM, Maron JL, Alterovitz G, Song D, Wilson BJ, Jegatheesan P, Govindaswami B, Lee J, Rosner AO. Somatosensory Modulation of Salivary Gene Expression and Oral Feeding in Preterm Infants: Randomized Controlled Trial. JMIR Res Protoc. 2017 Jun 14; 6(6):e113. View abstract
  13. Yang J, Yu S, Gong B, An N, Alterovitz G. Biobrick chain recommendations for genetic circuit design. Comput Biol Med. 2017 07 01; 86:31-39. View abstract
  14. Zollanvari A, Alterovitz G. SNP by SNP by environment interaction network of alcoholism. BMC Syst Biol. 2017 03 14; 11(Suppl 3):19. View abstract
  15. Yang J, Wang H, Ding H, An N, Alterovitz G. Nonlinear dimensionality reduction methods for synthetic biology biobricks' visualization. BMC Bioinformatics. 2017 Jan 19; 18(1):47. View abstract
  16. Wang A, An N, Yang J, Chen G, Li L, Alterovitz G. Wrapper-based gene selection with Markov blanket. Comput Biol Med. 2017 02 01; 81:11-23. View abstract
  17. Yang Y, Chen S, Yang F, Zhang L, Alterovitz G, Zhu H, Xuan J, Yang X, Luo H, Mu J, He L, Luo X, Xing Q. HLA-B*51:01 is strongly associated with clindamycin-related cutaneous adverse drug reactions. Pharmacogenomics J. 2017 12; 17(6):501-505. View abstract
  18. Kapur A, Marwah K, Alterovitz G. Gene expression prediction using low-rank matrix completion. BMC Bioinformatics. 2016 Jun 17; 17(1):243. View abstract
  19. Warner JL, Rioth MJ, Mandl KD, Mandel JC, Kreda DA, Kohane IS, Carbone D, Oreto R, Wang L, Zhu S, Yao H, Alterovitz G. SMART precision cancer medicine: a FHIR-based app to provide genomic information at the point of care. J Am Med Inform Assoc. 2016 07; 23(4):701-10. View abstract
  20. Warner JL, Zhang P, Liu J, Alterovitz G. Classification of hospital acquired complications using temporal clinical information from a large electronic health record. J Biomed Inform. 2016 Feb; 59:209-17. View abstract
  21. Lawler M, Siu LL, Rehm HL, Chanock SJ, Alterovitz G, Burn J, Calvo F, Lacombe D, Teh BT, North KN, Sawyers CL. All the World's a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health. Cancer Discov. 2015 Nov; 5(11):1133-6. View abstract
  22. Alterovitz G, Warner J, Zhang P, Chen Y, Ullman-Cullere M, Kreda D, Kohane IS. SMART on FHIR Genomics: facilitating standardized clinico-genomic apps. J Am Med Inform Assoc. 2015 Nov; 22(6):1173-8. View abstract
  23. Wang A, An N, Chen G, Li L, Alterovitz G. Improving PLS-RFE based gene selection for microarray data classification. Comput Biol Med. 2015 Jul; 62:14-24. View abstract
  24. Maron JL, Hwang JS, Pathak S, Ruthazer R, Russell RL, Alterovitz G. Computational gene expression modeling identifies salivary biomarker analysis that predict oral feeding readiness in the newborn. J Pediatr. 2015 Feb; 166(2):282-8.e5. View abstract
  25. Warner JL, Denny JC, Kreda DA, Alterovitz G. Seeing the forest through the trees: uncovering phenomic complexity through interactive network visualization. J Am Med Inform Assoc. 2015 Mar; 22(2):324-9. View abstract
  26. Li Y, Wei Y, Li B, Alterovitz G. Modified Anderson-Darling test-based target detector in non-homogenous environments. Sensors (Basel). 2014 Aug 29; 14(9):16046-61. View abstract
  27. Gao M, Warner J, Yang P, Alterovitz G. On the Bayesian Derivation of a Treatment-based Cancer Ontology. AMIA Jt Summits Transl Sci Proc. 2014; 2014:209-17. View abstract
  28. Villa A, Zollanvari A, Alterovitz G, Cagetti MG, Strohmenger L, Abati S. Prevalence of halitosis in children considering oral hygiene, gender and age. Int J Dent Hyg. 2014 Aug; 12(3):208-12. View abstract
  29. Warner JL, Yang P, Alterovitz G. Reversal of medical practices. Mayo Clin Proc. 2013 Oct; 88(10):1182-3. View abstract
  30. Warner JL, Zollanvari A, Ding Q, Zhang P, Snyder GM, Alterovitz G. Temporal phenome analysis of a large electronic health record cohort enables identification of hospital-acquired complications. J Am Med Inform Assoc. 2013 Dec; 20(e2):e281-7. View abstract
  31. Sonis S, Antin J, Tedaldi M, Alterovitz G. SNP-based Bayesian networks can predict oral mucositis risk in autologous stem cell transplant recipients. Oral Dis. 2013 Oct; 19(7):721-7. View abstract
  32. Warner JL, Alterovitz G, Bodio K, Joyce RM. External phenome analysis enables a rational federated query strategy to detect changing rates of treatment-related complications associated with multiple myeloma. J Am Med Inform Assoc. 2013 Jul-Aug; 20(4):696-9. View abstract
  33. Kallenbach J, Hsu WL, Dunker AK, Alterovitz G. Order-disorder interface characterization reveals critical factors for disease and drug targets. AMIA Jt Summits Transl Sci Proc. 2013; 2013:101. View abstract
  34. K Koppula S, Zollanvari A, An N, Alterovitz G. Robust prediction-based analysis for genome-wide association and expression studies. AMIA Jt Summits Transl Sci Proc. 2013; 2013:104. View abstract
  35. Warner J, Denny J, Kreda D, Alterovitz G. Analytic approaches to phenotypic complexity. Stud Health Technol Inform. 2013; 192:1267. View abstract
  36. Warner J, Yang P, Alterovitz G. Automated synthesis and visualization of a chemotherapy treatment regimen network. Stud Health Technol Inform. 2013; 192:62-6. View abstract
  37. Warner JL, Alterovitz G. Phenome based analysis as a means for discovering context dependent clinical reference ranges. AMIA Annu Symp Proc. 2012; 2012:1441-9. View abstract
  38. Yu YH, Chiou GY, Huang PI, Lo WL, Wang CY, Lu KH, Yu CC, Alterovitz G, Huang WC, Lo JF, Hsu HS, Chiou SH. Network biology of tumor stem-like cells identified a regulatory role of CBX5 in lung cancer. Sci Rep. 2012; 2:584. View abstract
  39. Quo CF, Kaddi C, Phan JH, Zollanvari A, Xu M, Wang MD, Alterovitz G. Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities. Brief Bioinform. 2012 Jul; 13(4):430-45. View abstract
  40. Parikh N, Zollanvari A, Alterovitz G. An automated bayesian framework for integrative gene expression analysis and predictive medicine. AMIA Jt Summits Transl Sci Proc. 2012; 2012:95-104. View abstract
  41. Deng M, Zollanvari A, Alterovitz G. A bayesian translational framework for knowledge propagation, discovery, and integration under specific contexts. AMIA Jt Summits Transl Sci Proc. 2012; 2012:25-34. View abstract
  42. Marwah K, Katzin D, Zollanvari A, Noy NF, Ramoni M, Alterovitz G. Context-specific ontology integration: a bayesian approach. AMIA Jt Summits Transl Sci Proc. 2012; 2012:79-86. View abstract
  43. Ting C, Alterovitz G, Merlob A, Abdi R. Genomic studies of GVHD-lessons learned thus far. Bone Marrow Transplant. 2013 Jan; 48(1):4-9. View abstract
  44. Alterovitz G, Tuthill C, Rios I, Modelska K, Sonis S. Personalized medicine for mucositis: Bayesian networks identify unique gene clusters which predict the response to gamma-D-glutamyl-L-tryptophan (SCV-07) for the attenuation of chemoradiation-induced oral mucositis. Oral Oncol. 2011 Oct; 47(10):951-5. View abstract
  45. Alterovitz G, Cavalcanti S, Muso TM, Ramoni MF, Wang M. REVERSE ENGINEERING AND SYNTHESIS OF BIOMOLECULAR SYSTEMS - Session Introduction. Pac Symp Biocomput. 2011; 300-1. View abstract
  46. Zollanvari A, Saccone NL, Bierut LJ, Ramoni MF, Alterovitz G. Is the reduction of dimensionality to a small number of features always necessary in constructing predictive models for analysis of complex diseases or behaviours? Conf Proc IEEE Eng Med Biol Soc. 2011; 2011:3573-6. View abstract
  47. Chang HH, McGeachie M, Alterovitz G, Ramoni MF. Mapping transcription mechanisms from multimodal genomic data. BMC Bioinformatics. 2010 Oct 28; 11 Suppl 9:S2. View abstract
  48. Hartwig S, Ho J, Pandey P, Macisaac K, Taglienti M, Xiang M, Alterovitz G, Ramoni M, Fraenkel E, Kreidberg JA. Genomic characterization of Wilms' tumor suppressor 1 targets in nephron progenitor cells during kidney development. Development. 2010 Apr; 137(7):1189-203. View abstract
  49. Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Dreyfuss J, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. Ontology engineering. Nat Biotechnol. 2010 Feb; 28(2):128-30. View abstract
  50. Alterovitz G, Cavalcanti S, Muso TM, Ramoni MF, Wang M. REVERSE ENGINEERING AND SYNTHESIS OF BIOMOLECULAR SYSTEMS - Session Introduction. Pac Symp Biocomput. 2010; 383-4. View abstract
  51. Maron JL, Alterovitz G, Ramoni M, Johnson KL, Bianchi DW. High-throughput discovery and characterization of fetal protein trafficking in the blood of pregnant women. Proteomics Clin Appl. 2009 Dec; 3(12):1389-96. View abstract
  52. Alterovitz G, Muso T, Ramoni MF. The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. Brief Bioinform. 2010 Jan; 11(1):80-95. View abstract
  53. Celi LA, Hinske LC, Alterovitz G, Szolovits P. An artificial intelligence tool to predict fluid requirement in the intensive care unit: a proof-of-concept study. Crit Care. 2008; 12(6):R151. View abstract
  54. Alterovitz G, Jiwaji A, Ramoni MF. Automated programming for bioinformatics algorithm deployment. Bioinformatics. 2008 Feb 01; 24(3):450-1. View abstract
  55. Alterovitz G, Xiang M, Liu J, Chang A, Ramoni MF. System-wide peripheral biomarker discovery using information theory. Pac Symp Biocomput. 2008; 231-42. View abstract
  56. Maron JL, Johnson KL, Slonim D, Lai CQ, Ramoni M, Alterovitz G, Jarrah Z, Yang Z, Bianchi DW. Gene expression analysis in pregnant women and their infants identifies unique fetal biomarkers that circulate in maternal blood. J Clin Invest. 2007 Oct; 117(10):3007-19. View abstract
  57. Alterovitz G, Liu J, Afkhami E, Ramoni MF. Bayesian methods for proteomics. Proteomics. 2007 Aug; 7(16):2843-55. View abstract
  58. Aivado M, Spentzos D, Germing U, Alterovitz G, Meng XY, Grall F, Giagounidis AA, Klement G, Steidl U, Otu HH, Czibere A, Prall WC, Iking-Konert C, Shayne M, Ramoni MF, Gattermann N, Haas R, Mitsiades CS, Fung ET, Libermann TA. Serum proteome profiling detects myelodysplastic syndromes and identifies CXC chemokine ligands 4 and 7 as markers for advanced disease. Proc Natl Acad Sci U S A. 2007 Jan 23; 104(4):1307-12. View abstract
  59. Alterovitz G, Xiang M, Mohan M, Ramoni MF. GO PaD: the Gene Ontology Partition Database. Nucleic Acids Res. 2007 Jan; 35(Database issue):D322-7. View abstract
  60. Alterovitz G, Liu J, Chow J, Ramoni MF. Automation, parallelism, and robotics for proteomics. Proteomics. 2006 Jul; 6(14):4016-22. View abstract
  61. Alterovitz G, Ramoni MF. Discovering biological guilds through topological abstraction. AMIA Annu Symp Proc. 2006; 1-5. View abstract
  62. Aivado M, Spentzos D, Alterovitz G, Otu HH, Grall F, Giagounidis AA, Wells M, Cho JY, Germing U, Czibere A, Prall WC, Porter C, Ramoni MF, Libermann TA. Optimization and evaluation of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) with reversed-phase protein arrays for protein profiling. Clin Chem Lab Med. 2005; 43(2):133-40. View abstract
  63. Alterovitz G, Aivado M, Spentzos D, Libermann TA, Ramoni M, Kohane IS. Analysis and robot pipelined automation for SELDI-TOF mass spectrometry. Conf Proc IEEE Eng Med Biol Soc. 2004; 4:3068-71. View abstract
  64. Alterovitz G. Electrical engineering and nontechnical design variables of multiple inductive loop systems for auditoriums. J Deaf Stud Deaf Educ. 2004; 9(2):202-9. View abstract
  65. Alterovitz G, Staelin DH, Philip JH. Temporal patient state characterization using Iterative Order and Noise (ION) estimation: applications to anesthesia patient monitoring. J Clin Monit Comput. 2002 Aug; 17(6):351-9. View abstract