Photo of Soares, Marcelo Bento

Marcelo Bento Soares, PhD

Professor and Department Head for Cancer Biology and Pharmacology, Senior Associate Dean for Research

Professor of Psychiatry & Behavioral Medicine, Professor of Neurosurgery

Cancer Biology and Pharmacology

Contact

Office Phone:

309-680-8628

Fax:

309-671-3442

Email:

mbsoares@uic.edu

Related Sites:

About

Dr. Soares’ laboratory has been working in collaboration with Dr. Sergey Malchenko to study the role of mitochondrial retrograde signaling in cancer development. In particular, they are investigating enhancement of tumor progression by reprogramming of neighboring cells upon mitochondrial transfer from cancer stem cells (CSCs). Intercellular mitochondrial transfer has been observed between different types of CSCs and neighboring cells, including brain CSCs and astrocytes. Dr. Soares’ interest also includes the development and assessment of educational interventions that promote compassion, resilience, inclusiveness and emotional intelligence on the well-being of medical students, residents, fellows and healthcare professionals at large.

Dr. Soares is course director for the C.R.E.A.T.E. (Compassion, Resilience and Emotional Awareness Training and Education) elective.

Selected Publications

Peer-reviewed Publications

  1. Palatnik, M., Coelho, M.P., Soares, M.B., Marques, M. & Mattos, N. (1980). ABO agglutinins from Biomphalaria straminea snails. Experientia 36: 543.
  2. Palatnik, M., Soares, M.B., Coelho, M.P., Marques, M. & Mattos, N. (1980). Agglutinins and haemolysins from Biomphalaria tenagophila snails. Experientia 36: 544.
  3. Palatnik, M., Soares, M.B., Junqueira,P.C., Corvelo, T.C., Soares, V.C.,& Faria, G.M. (1980). Weak reacting A antigen in an AB Brazilian donor. Brazilian J. Biol. 40: 721-727.
  4. Palatnik, M., Coelho, M.P., Soares, V.C., Soares, M.B. & Marques, M. (1980). Genetical and taxonomical aspects of Biomphalaria glabrata ABO agglutinins. Brazilian J. Genet. 3: 375-386.
  5. Palatnik, M., Soares, M.B., Junqueira, P.C., Corvelo, T.C., Soares, V.C., Faria, G.M. (1982). Phenotype A3B in two generations of a Brazilian negroid family. Brazilian J. Genet. 5: 165-174.
  6. Soares, M.B., Armada, J.L., Soares, V.C. & Seuanez, H. (1982). The Artocarpus integrifolia lectins: use and applications in chromosome studies of lymphocyte cultures. Cytobios 34: 165-174.
  7. Soares, M.B., Armada, J.L., da Silva, V.F. & Seuanez, H. (1982). Standardization of the karyotype of the rhesus monkey Macaca mulatta and interspecific homologies with human chromosomes. J. Human Evol. 11: 291-296.
  8. Soares, M.B. & Seuanez, H. (1982). Mitogenic and agglutinating activities in man and rhesus. Brazilian J. Genet. 5: 567-575.
  9. Soares, M.B. & Seuanez, H. (1982). Mitogenic and precipitating activities. Brazilian J. Genet. 5: 709-724.
  10. Soares, M.B., Ishii, D. & Efstratiadis, A. (1985). Developmental and tissue-specific expression of a family of transcripts related to rat insulin-like growth factor II mRNA. Nuc. Acids Res. 13: 1119-1134.
  11. Soares, M.B., Schon, E., Henderson, A., Karathanasis, S., Cate, R., Zeitlin,S. Chirgwin, J. & Efstratiadis, A. (1985). RNA-mediated gene duplication:the rat preproinsulin I gene is a functional retroposon. Mol. Cell Biol. 5: 2090-2103.
  12. Soares, M.B., Schon, E. & Efstratiadis, A. (1985). Rat LINE1: the origin and evolution of a family of long interspersed repetitive DNA elements. J. Mol. Evol. 22: 117-133.
  13. Soares, M.B., Turken, A., Ishii, D., Mills, L., Episkopou, V., Cotter, S., Zeitlin, S. & Efstratiadis, A. (1986). The rat insulin-like growth factor II gene: a single gene with two promoters expressing a multitranscript family. J. Mol. Biol. 192: 737-752.
  14. Stylianopoulou, F., Herbert, J., Soares, M.B. & Efstratiadis, A. (1988). Expression of the insulin-like growth factor II gene in the choroid plexus and the leptomeninges of the adult rat central nervous system. Proc. Natl. Acad. Sci. USA 85: 141-145.
  15. Dietrich, P., Dussan, M.P., Floeter-Winter, L.M., Affonso, M.H.T., Camargo, E.P. & Soares, M.B. (1990). Restriction fragment length polymorphisms in the ribosomal gene spacers of Trypanosoma cruzi and Trypanosoma conorhini. Mol. Biochem. Parasitol. 42 (1): 13-20.
  16. Camargo, E., Stravate, C., Teixeira, M.M.G., Uliana, S.R.B., Soares, M.B., Affonso, H.T. & Floeter-Winter, L. (1992). Ribosomal DNA restriction analysis and synthetic oligonucleotide probing in the identification of genera of lower trypanosomatids. J. Parasitol. 78 (1): 40-48.
  17. Dietrich, P., Soares, M.B., Affonso, M.H.T. & Floeter-Winter, L. (1993). The Trypanosoma cruzi ribosomal RNA encoding gene: analysis of promoter and upstream intergenic spacer sequences. Gene 125: 103-107.
  18. Petrukhin, K.E, Speer, M.C., Cayanis, E., Bonaldo, M.F., Tantravahi, U., Soares, M.B., Fischer, S.G., Warburton, D., Gilliam, T.C. & Ott, J. A (1993). Microsatellite Genetic Linkage Map of Human Chromosome 13. Genomics 15: 76-85.
  19. Adams, M.D., Soares, M.B., Kerlavage, A.R., Fields, C. and Craig Venter, J. (1993). Rapid cDNA Sequencing (Expressed Sequence Tags) from a Directionally Cloned Human Infant Brain cDNA Library. Nature Genetics 4: 373-380.
  20. Tanzi, R.E., Petrukhin, K., Chernov, I., Pellequer, J.L., Wasco, W., Ross, B., Romano, D.M., Brzustowicz, L.M., Devoto, M., Peppercorn, J., Bush, A.I., Sternlieb, I., Pirastu, M., Gusella, J.F., Evgrafov, O., Penchaszadeh, G.K., Honig, B., Edelman, I.S., Soares, M.B., Scheinberg, I.H. & Gilliam, T.C. (1993). Identification of the Wilson’s disease gene; A copper transporting ATPase with homology to the Menkes disease gene. Nature Genetics 5: 344-350.
  21. Bonaldo, M.F., Yu, M-T., Jelenc, P., Brown, S., Su, L., Lawton, L., Deaven, L., Efstratiadis, A., Warburton, D., & Soares, M.B (1994). Selection of cDNAs using chromosome-specific genomic clones: application to Human Chromosome 13. Hum. Mol. Genet. 3 (9): 1663-1673.
  22. Soares, M.B., Bonaldo, M.F., Su, L., Lawton, L. & Efstratiadis, A. (1994). Construction and characterization of a normalized cDNA library. Proc. Natl. Acad. Sci. USA 91(20): 9228-9232.
  23. Franco, G.R., Adams, M.D., Soares, M.B., Simpson, J.G., Venter, J.C. & Pena, S.D.J. (1995). Identification of new Schistosoma mansoni genes by the EST strategy using a directional cDNA library. Gene 152: 141-147.
  24. Stevens, T.J., Berry, R., Walter, N.A.R., Wilcox, A.S., Rubano, T., Hopkins, A., Weber, J. Goold, R., Soares, M.B. & Sikela, J.M. (1995). Gene-based sequence-tagged-sites (STSs) as the basis for a human gene map. Nature Genetics 10: 415-423.
  25. Ho, P.L., Soares, M.B., Yamane, T. and Raw, I (1995). Reverse biology applied to Micrurus corallinus, a South American coral snake. J. Toxicol. 14: 327-337.
  26. Polymeropoulos, M.H., Ide, Susan, Soares, M.B. & Lennon, G. (1995). Sequence characterization and genetic mapping of the human homologue to the rat visinin-like peptide 1 RNVP1. Genomics 29: 273-275.
  27. Fischer, S.G., Cayanis, E., Bonaldo, M.F., Bowcock, A.M., Deaven, L., Edelman, I., Gallardo, T., Kalachikov, S., Lawton, L., Longmire, J.L., Lovett, M., Osborne-Lawrence, S., Rothstein, R., Russo, J.J., Soares, M.B., Sunjevaric, I., Venkatraj, V.S., Warburton, D., Zhang, P. and Efstratiadis, A (1996). A high-resolution annotated physical map of the human chromosome 13q12-13 region containing the breast cancer susceptibility locus BRCA2. Proc. Natl. Acad. Sci. USA 93: 690-694.
  28. Bonaldo, M.F., Jelenc, P., Su, L., Lawton, L., Yu, M-T, Warburton, D. & Soares, M.B. (1996). Identification and characterization of three genes and two pseudogenes on chromosome 13. Hum. Genet. 97: 441-452.
  29. Lennon, G.G., Auffray, C., Polymeropoulos, M. & Soares, M.B.(1996). The I.M.A.G.E. Consortium: An integrated molecular analysis of genomes and their expression. Genomics 33:.151-152.
  30. Milosavljevic, A., Zeremski, M., Strezoska, Z., Grujic, D., Dyanov, H., Batus, S., Salbego, D., Paunesku, T., Soares, M.B. & Crkvenjakov, R. (1996). Discovering distinct genes represented in 29,570 clones from infant brain cDNA libraries by applying Sequencing By Hybridization methodology. Genome Research 6: 132-141.
  31. Hillier, L., Lennon, G., Becker, M., Bonaldo, M., Chiapelli, B., Chissoe, S., Dietrich, N., DuBuque, T., Favello, A., Gish, W., Hawkins, M., Hultman, M., Kucaba, T., Lacy, M., Le, M., Le, N., Mardis, E., Moore, B., Morris, M., Prange, C., Rifkin, L., Rohlfing, T., Schellenberg, K., Soares, M., Tan, F., Trevaskis, E., Underwood, K., Wohldmann, P., Waterston, R., Wilson, R. and Marra, M. (1996). Generation and analysis of 280,000 human expressed sequence tags. Genome Research 6, 807-828.
  32. Drmanac, S., Stavropoulos, N., Labat, I., Vonau, J., Hauser, B., Soares, M.B. and Drmanac, R. (1996). Gene-representing cDNA clusters defined by hybridization of 57,419 clones from infant brain libraries with short oligonucleotide probes. Genomics 37, 29-40.
  33. Bonaldo, M. F., Lennon, G. & Soares, M.B. (1996). Normalization and subtraction: two approaches to facilitate gene discovery. Genome Research 6, 791-806.
  34. Lawton, L.N., Bonaldo, M.F., Jelenc, P.C., Qiu, L., Baumes, S., Marcelino, R., de Jesus, G.M., Wellington, S., Knowles, J., Warburton, D., Brown, S. and Soares, M.B. (1997). Identification of a novel member of the TGF-beta superfamily highly expressed in human placenta. Gene 203, 17-26.
  35. Kalachikov, S., Migliazza, A., Cayanis, E., Fracchiolla, N.S., Bonaldo, M.F., Lawton, L., Jelenc, P., Ye, X., Qu, X., Chien, M., Hauptschein, R., Gaidano, G., Vitolo, U., Saglio, G., Resegotti, L., Brodjansky, V., Yankovsky, N., Zhang, P., Soares, M.B., Russo, J., Edelman, I.S., Efstratiadis, A., Dalla-Favera, R., and Fischer, S.G (1997). Cloning and gene mapping of the chromosome 13q14 region deleted in chronic lymphocytic leukemia. Genomics 42, 369-377.
  36. Ranta, S., Lehesjoki, A-E., Bonaldo, M.F., Knowles, J.A., Hirvasniemi, A., Ross, B., de Jong, P., Soares, M.B., de la Chapelle, A. and Gilliam, T.C. (1997). High resolution mapping and transcript identification at the progressive epilepsy with mental retardation (EPMR) locus on chromosome 8p. Genome Research 7:887-896.
  37. Ho, P.L., Soares, M.B., Maack, T., Gimenez, I., Puorto, G., Furtado, M.F. & Raw, I. (1997). Cloning of an unusual natriuretic peptide from the South American Coral Snake Micrurus corallinus. European Journal of Biochemistry 250, 144-149.
  38. Carter, T.A., Bonnemann, C.G., Wang, C.H., Obici, S., Parano, E., Bonaldo, M.F., Ross, B.M., Penchaszadeh, G.K., Mackenzie, A., Soares, M.B., Kunkel, L.M. and Gilliam, T.C. (1997). A multicopy transcription-repair gene, BTF2p44, maps to the SMA region and demonstrates SMA associated deletions. Human Molecular Genetics 6(2), 229-236.
  39. Cayanis, E., Russo, J.J., Kalachikov, S., Ye, X., Park, S.H., Sunjevaric, I., Bonaldo, M.F., Lawton, L., Venkatraj, V.S., Schon, E., Soares, M.B., Rothstein, R., Warburton, D., Edelman, I., Zhang, P., Efstratiadis, A. and Fischer, S.G (1998). High resolution YAC-Cosmid-STS map of human chromosome 13. Genomics 47, 26-43.
  40. Marra, M., Hillier, L., Kucaba, T, Allen, M., Barstead, R., Beck, C., Blistain, A., Bonaldo, M., Bowers, Y., Bowles, L., Cardenas M., Chamberlain, A., Chappell, J., Clifton, S., Favello, A., Geisel, S., Gibbons, M., Harvey, N., Hill, F., Jackson, Y., Kohn, S., Lennon, G., Mardis, E., Martin, J., Mila, L., McCann, R., Morales, R., Pape, D., Person, B., Prange, C., Ritter, E., Soares, M., Schurk, R., Shin, T., Steptoe, M., Swaller, T. Theising, B., Underwood, K., Wylie, T., Yount, T., Wilson, R. & Waterston, R. (1999). An encyclopedia of mouse genes. Nature Genetics 21, 191-194.
  41. Urmenyi, T.P., Bonaldo, M.F., Soares, M.B. and Rondinelli, E. (1999) Construction of a normalized cDNA library for the Trypanosoma cruzi genome project. J. Euk. Microbiol. 46(5): 542-544.
  42. Ranta, S., Zhang, Y., Ross, B., Lonka, L., Takkunen, E., Messer, A., Sharp, J., Wheeler, R., Kusumi, K., Mole, S., Liu, W., Soares, M.B., Bonaldo, M.F., Hirvasniemi, A., de la Chapelle, A., Gilliam, T.C. and Lehesjoki, A-E. (1999). The neuronal ceroid lipofuscinoses in human EPMR and mnd mutant mice are associated with mutations in CLN8. Nature Genetics 23: 233-236.
  43. Emmert-Buck, M.R., Strausberg, R.L., Krizman, D.B., Boguski, M.S., Bonaldo, M.F., Bonner, R.F., Bostwick, D.G., Buetow, K.H., Brown, M.R., Chuaqui, R.F., Cole, K.A., Duray, P.F., Englert, C.R., Gillespie, J.W., Greenhut, S., Grouse, G., Hillier, L.W., Katz, K.S., Klausner, R.D., Kuznetzov, V., Lash, A.E., Lennon, G., Linehan, W.M., Liotta, L.A., Lipman, D.L., Marra, M.A., Munson, P.J., Ornstein, D.K., Prabhu, V., Prange, C., Soares, M.B., Schuler, G.D., Tolstoshev, C.M., Trent, J.T., Vocke, C.D. & Waterston, R.H. (2000). Molecular Profiling of Clinical Tissue Specimens: Feasibility and Applications. American Journal of Pathology 156 (4): 1109-1115.
  44. Dimopoulos, G., Casavant, T.L., Chang, S., Scheetz, T., Roberts, C., Donohue, M., Schultz, J., Benes, V., Bork, P., Ansorge, W., Soares, M.B. & Kafatos, F.C. (2000). Anopheles gambiae pilot gene discovery project: identification of novel mosquito innate immunity genes from ESTs generated from immune competent cell lines. Proceedings of the National Academy of Sciences 97: 6619-6624.
  45. Silveira de Oliveira, J., Rossan de Brandao Prieto da Silva, A., Soares, M.B., Stephano, M.A., de Oliveira Dias, W., Raw, I. and Ho, P.L. (2000). Cloning and characterization of an alpha-neurotoxin-type protein specific for the coral snake Micrurus corallinus. Biochem. Biophys. Res. Commun. 267: 887-891.
  46. Grimmond, S., Hateren, N.V., Siggers, P., Arkell, R., Larder, R., Soares, M.B., Bonaldo, M., Smith, L., Tymowska-Lalanne, Z., Wells, C. & Greenfield, A. (2000). Sexually dimorphic expression of protease nexin-1 and vanin-1 in the developing mouse gonad prior to overt differentiation suggests a role in mammalian sexual development. Hum. Mol. Genet. 9: 233-236.
  47. Migliazza, A., Cayanis, E., Bosch-Albareda, F., Komatsu, H., Martinotti, S., Toniato, E., Kalachikov, S., Bonaldo, M.F., Jelenc, P., Ye, X., Rzhetsky, A., Qu, X., Chien, M., Inghirami, G., Gaidano, G., Vitolo, U., Saglio, G., Resegotti, L., Zhang, P., Soares, M.B., Russo, J., Fischer, S.G., Edelman, I.S., Efstratiadis, A., Dalla-Favera, R. (2000). Molecular pathogenesis of B-cell chronic lymphocytic leukemia: analysis of 13q14 chromosomal deletions. Curr. Top. Microbiol. Immunol. 252: 275-284.
  48. Netz, D.J.A., Sahl, H-G., Marcelino, R., Nascimento, J.S., Oliveira, S.S., Soares, M.B. & Bastos, M.C.F.(2001). Molecular characterization of Aureocin A70, a Multi-peptide Bacteriocin Isolated from Staphylococcus aureus. J. Mol. Biol. 311, 939-949.
  49. Blackshear, P.J., Lai, W.S., Thorn, J.M., Kennington, E., Staffa, N.G., Moore, D.T., Bouffard, G.G., Beckstrom-Sternberg, S.M., Touchman, J.W., Bonaldo, M.F. and Soares, M.B (2001). The NIEHS Xenopus Maternal EST Project: Interim Analysis of the First 13,879 ESTs from Unfertilized Eggs. Gene 267 (1): 71-87.
  50. Scheetz, T.E., Raymond, M.R., Nishimura, D.Y., McClain, A., Roberts, C., Birkett, C., Gardiner, J., Zhang, J., Butters, N., Sun, C., Casavant, T.L., Soares, M.B. & Sheffield, V.C. (2001) Generation of a high-density rat EST map. Genome Research 11: 497-502.
  51. Hartupee, J.C., Zhang, H., Bonaldo, M.F., Soares, M.B. & Dieckgraefe, B.K. (2001). Isolation and characterization of a cDNA encoding a novel member of the human regenerating protein family: Reg IV(1). Biochem. Biophys. Acta 1518 (3): 287-293.
  52. Kwitek-Black, A.E., Tonellato, P.J, Chen, D., Gullings-Handley, J., Cheng, Y.S., Twigger, S., Scheetz, T.E., Casavant, T.L., Stoll, M., Nobrega, M.A., Shiozawa, M., Soares, M.B., Sheffield, V.C., Jacob, H.J. (2001). Automated construction of high-density comparative maps between rat, human and mouse. Genome Research 11, 1935-1943.
  53. Reddy, A.R., Ramakrishna, W., Sekhar, A.C., Ithal, N., Babu, P.R., Bonaldo, M.F., Soares, M.B. & Bennetzen, J.L. (2002). Novel genes are enriched in normalized cDNA libraries from drought stressed seedlings of indica rice (Oryza sativa L. cv. Nagina 22). Genome 45: 204-211.
  54. Whitfield, C.W., Band, M.R., Bonaldo, M.F., Kumar, C.G., Liu, L., Pardinas, J.R., Robertson, H.M., Soares, M.B. and Robinson, G.E. (2002). Annotated Expressed Sequence Tags and cDNA Microarrays for Studies of Brain and Behavior in the Honey Bee. Genome Research 12, 555-566.
  55. Trivedi, N., Bischof, J., Davis, S., Pedretti, K., Scheetz, T.E., Braun, T.A., Roberts, C.A., Robinson, N.L., Sheffield, V.C., Soares, M.B. & Casavant, T.L. (2002). Parallel creation of non-redundant gene indices from partial mRNA transcripts. Future Generation Computer Systems 18, 863-870.
  56. Gavin, A.J., Scheetz, T.E., Roberts, C.A., O’Leary, B., Braun, T.A., Sheffield, V.C., Soares, M.B., Robinson, J.P. and Casavant, T.L. (2002). Pooled library tissue tags for EST-based gene discovery. Bioinformatics 18, 1162-1166.
  57. Morcuende, J.A., Huang, X.D, Stevens, J., Kucaba, T., Brown, B., Abdulkawy, H., Malchenko, S., Bonaldo, M.F., Casavant, T.L. & Soares, M.B. (2002). Identification and initial characterization of 6,000 Expressed Sequence Tags (ESTs) from rat normal-growing cartilage and Swarm rat chondrosarcoma cDNA libraries. The Iowa Orthopaedic Journal 22, 28-34.
  58. Strausberg, R.L, Feingold, E. A., Grouse, L. H., Derge, J. G., Klausner, R. D., Collins, F. S., Wagner, L., Shenmen, C. M., Schuler, G. D., Altschul, S. F., Zeeberg, B., Buetow, K. H., Schaefer, C. F., Bhat, N. K., Hopkins, R. F., Jordan, H., Moore, T., Max, S. I., Wang, J., Hsieh, F., Diatchenko, L., Marusina, K., Farmer, A. A., Rubin, G. M., Hong, L., Stapleton, M., Soares, M. B., Bonaldo, M. F., Casavant, T. L., Scheetz, T. E., Brownstein, M. J., Usdin, T. B., Toshiyuki, S., Carninci, P., Prange, C., Raha, S. S., Loquellano, N. A., Peters, G. J., Abramson, R. D., Mullahy, S. J., Bosak, S. A., McEwan, P. J., McKernan, K. J., Malek, J. A., Gunaratne, P. H., Richards, S., Worley, K. C., Hale, S., Garcia, A. M., Gay, L. J., Hulyk, S. W., Villalon, D. K., Muzny, D. M., Sodergren, E. J., Lu, X., Gibbs, R. A., Fahey, J., Helton, E., Ketteman, M., Madan, A., Rodrigues, S., Sanchez, A., Whiting, M., Young, A. C., Shevchenko, Y., Bouffard, G. G., Blakesley, R. W., Touchman, J. W., Green, E. D., Dickson, M. C., Rodriguez, A. C., Grimwood, J., Schmutz, J., Myers, R. M., Butterfield, Y. S., Krzywinski, M. I., Skalska, U., Smailus, D. E., Schnerch, A., Schein, J. E., Jones, S. J. and Marra, M. A. (2002). Generation and Initial Analysis of more than 15,000 Full-Length Human and Mouse cDNA Sequences. Proceedings of the National Academy of Science 99, 16899-16903.
  59. Scheetz, T.E., Trivedi, N., Roberts, C.A., Kucaba, T., Berger, B., Robinson, N.L., Birkett, C.L., Gavin, A.J., O’Leary, B., Braun, T.A., Bonaldo, M.F., Robinson, J.P., Sheffield, V.C., Soares, M.B. and Casavant, T.L. (2003). ESTprep: preprocessing cDNA sequence reads. Bioinformatics 19, 1-7.
  60. Tuggle, C. K., Green, J. A., Fitzsimmons, C., Woods, R., Prather, R. S., Malchenko, S., Soares, M. B., Kucaba, T., Crouch, K., Smith, C., Tack, D., Robinson, N., O’Leary, B., Scheetz, T., Casavant, T., Pomp, D., Edeal, B. J., Zhang, Y., Rothschild, M. F., Garwood, K., Beavis, W (2003). EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human. Mammalian Genome 14: 565-579.
  61. Verjovski-Almeida, S., DeMarco, R., Martins, E.A.L., Guimarães, P.E.M., Ojopi, E.P.B., Paquola, A.C.M., Piazza, J.P., Nishiyama Jr., M.Y., Kitajima, J.P., Adamson, R.E., Ashton, P.D., Bonaldo, M.F., Coulson, P.S., Dillon, G.P., Farias, L.P., Gregorio, S.P., Ho, P.L., Leite, R.A., Malaquias, L.C.C., Marques, R.C.P., Miyasato, P.A., Nascimento, A.L.T.O., Ohlweiler, F.P.O., Reis, E.M., Ribeiro, M.A., Sá, R.G., Stukart, G.C., Soares, M.B., Gargioni, C., Kawano, T., Rodrigues, V., Madeira, A.M.B.N., Wilson, R.A., Menck, C.F.M., Setubal, J.C., Leite, L.C.C. & Dias-Neto, E. (2003). Transcriptome analysis of the acoelomate human parasite Schistosoma mansoni. Nature Genetics 35(2):1-10.
  62. Lehane, M. J., Aksoy, S., Gibson, W., Kerhornou, A., Berriman, M., Hamilton, J., Soares, M. B., Bonaldo, M. F., Lehane, S., and Hall, N. (2003). Adult midgut expressed sequence tags from the tsetse fly Glossina morsitans morsitans and expression analysis of putative immune response genes. Genome Biol, 4(10): p. R63.
  63. Scheetz, T.E., Zabner, J., Welsh, M.J., Coco, J., Eyestone, M., Bonaldo, M.F., Kucaba, T., Casavant, T.C., Soares, M.B., and McCray, P.B. (2004). Large-scale gene discovery in human airway epithelia reveals novel transcripts. Physiol. Genomics 17: 69-77.
  64. Laffin, J.J.S., Scheetz, T.E., Bonaldo, M.F., Reiter, R.S., Chang, S., Eyestone, M., Abdulkawy, H., Brown, B., Roberts, C., Tack, D., Kucaba, T., Lin, J.J-C.,
    Sheffield, V.C., Casavant, T.C., and Soares, M.B. (2004). A Comprehensive non-redundant Expressed Sequence Tag collection for the developing Rattus norvegicus heart. Physiol. Genomics 17: 245–252.
  65. Hackett, J. D., Yoon, H. S., Soares, M. B., Bonaldo, M. F., Casavant, T. L., Scheetz, T. E., Nosenko, T., and Bhattacharya, D. (2004). Migration of the plastid genome to the nucleus in a peridinin dinoflagellate. Curr Biol 14, 213-218.
  66. DeMarco, R., Kowaltowski, A. T., Machado, A. A., Soares, M. B., Gargioni, C., Kawano, T., Rodrigues, V., Madeira, A. M., Wilson, R. A., Menck, C. F., Setubal, J.C., Dias-Neto, E., Leite, L.C. and Verjovski-Almeida, S. (2004). Saci-1, -2, and -3 and Perere, four novel retrotransposons with high transcriptional activities from the human parasite Schistosoma mansoni. Journal of Virology 78, 2967-2978.
  67. Scheetz, T.E., Laffin, J.J., Berger, B., Holte, S., Baumes, S.A., Brown, R., Chang, S., Coco, J., Conklin, J., Crouch, K., Donohue, M., Doonan, G., Estes, C., Eyestone, M., Fishler, K., Gardiner, J., Guo, L., Johnson, B., Keppel, C., Kreger, R., Lebeck, M., Marcelino, R., Miljkovich, V., Perdue, M., Qui, L., Rehmann, J., Reiter, R.S., Rhoads, B., Schaefer, K., Smith, C., Sunjevaric, I., Trout, K., Wu, N., Birkett, C.L., Bischof, J., Gackle, B., Gavin, A., Grundstad, A.J., Mokrzycki, B., Moressi, C., O’Leary, B., Pedretti, K., Roberts, C., Robinson, N.L., Smith, M., Tack, D., Trivedi, N., Kucaba, T., Freeman, T., Lin, J.J., Bonaldo, M.F., Casavant, T.C., Sheffield, V.C. and Soares, M.B. (2004). High-throughput gene discovery in the rat. Genome Research 14: 733-741.
  68. Imanishi, T., Itoh, T., Suzuki, Y., O’Donovan, C., Fukuchi, S., Koyanagi, K. O., Barrero, R. A., Tamura, T., Yamaguchi-Kabata, Y., Tanino, M., Yura, K., Miyazaki, S., Ikeo, K., Homma, K., Kasprzyk, A., Nishikawa, T., Hirakawa, M., Thierry-Mieg, J., Thierry-Mieg, D., Ashurst, J., Jia, L., Nakao, M., Thomas, M. A., Mulder, N., Karavidopoulou, Y., Jin, L., Kim, S., Yasuda, T., Lenhard, B., Eveno, E., Yamasaki, C., Takeda, J., Gough, C., Hilton, P., Fujii, Y., Sakai, H., Tanaka, S., Amid, C., Bellgard, M., Bonaldo Md Mde, F., Bono, H., Bromberg, S. K., Brookes, A. J., Bruford, E., Carninci, P., Chelala, C., Couillault, C., Souza, S. J., Debily, M. A., Devignes, M. D., Dubchak, I., Endo, T., Estreicher, A., Eyras, E., Fukami-Kobayashi, K., R. Gopinath G, Graudens, E., Hahn, Y., Han, M., Han, Z. G., Hanada, K., Hanaoka, H., Harada, E., Hashimoto, K., Hinz, U., Hirai, M., Hishiki, T., Hopkinson, I., Imbeaud, S., Inoko, H., Kanapin, A., Kaneko, Y., Kasukawa, T., Kelso, J., Kersey, P., Kikuno, R., Kimura, K., Korn, B., Kuryshev, V., Makalowska, I., Makino, T., Mano, S., Mariage-Samson, R., Mashima, J., Matsuda, H., Mewes, H. W., Minoshima, S., Nagai, K., Nagasaki, H., Nagata, N., Nigam, R., Ogasawara, O., Ohara, O., Ohtsubo, M., Okada, N., Okido, T., Oota, S., Ota, M., Ota, T., Otsuki, T., Piatier-Tonneau, D., Poustka, A., Ren, S. X., Saitou, N., Sakai, K., Sakamoto, S., Sakate, R., Schupp, I., Servant, F., Sherry, S., Shiba, R., Shimizu, N., Shimoyama, M., Simpson, A. J., Soares, B., Steward, C., Suwa, M., Suzuki, M., Takahashi, A., Tamiya, G., Tanaka, H., Taylor, T.,Terwilliger, J. D., Unneberg, P., Veeramachaneni, V., Watanabe, S., Wilming, L., Yasuda, N., Yoo, H. S., Stodolsky, M., Makalowski, W., Go, M., Nakai, K., Takagi, T., Kanehisa, M., Sakaki, Y., Quackenbush, J., Okazaki, Y., Hayashizaki, Y., Hide, W., Chakraborty, R., Nishikawa, K., Sugawara, H., Tateno, Y., Chen, Z., Oishi, M., Tonellato, P., Apweiler, R., Okubo, K., Wagner, L., Wiemann, S., Strausberg, R. L., Isogai, T., Auffray, C., Nomura, N., Gojobori, T., and Sugano, S. (2004). Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PloS Biol. 2(6): E162.
  69. Zhao, S.H., Simmons, D.G., Cross, J.C., Scheetz, T.E., Casavant, T.L., Soares, M.B., and Tuggle, C.K. (2004). PLET1 (C11orf34), a highly expressed and processed novel gene in pig and mouse placenta, is transcribed but poorly spliced in human. Genomics 84(1): 114-125.
  70. Kwitek, A.E., Gullings-Handley, J., Yu, J., Carlos, D.C., Orlebeke, K., Nie, J., Eckert, J., Lemke, A., Andrae, J.W., Bromberg, S., Pasko, D., Chen, D., Scheetz, T.E., Casavant, T.L., Soares, M.B., Sheffield, V.C., Tonellato, P.J., and Jacob, H.J. (2004). High Density Rat Radiation Hybrid Maps Containing Over 24,000 SSLPs, Genes, and ESTs Provide a Direct Link to the Rat Genome Sequence. Genome Research, 14 :750-757.
  71. Bonaldo, M.F., Bair, T.B., Scheetz, T.E., Snir, E., Akabogu, I., Bair, J.L., Berger, B., Crouch, K., Davis, A., Eyestone, M., Keppel, C., Kucaba, T., Lebeck, M., Lin, J.L., Melo, A.I.R., Rehmann, J., Reiter, R.S., Schaefer, K., Smith, C., Tack, D., Trout, K., Sheffield, V.C., Lin, J.J-C., Casavant, T.C. and Soares, M.B. (2004). 1,274 full-open reading frames of transcripts expressed in the developing mouse nervous system. Genome Research, 14: 2053-2063.
  72. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Buetow KH, Schaefer CF, Haussler D, Kent J, Diekhans M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MSH, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Krinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YSN, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morrin R, Pamquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJM, Holt RA, Baross A, Marra MA (2004). The Status, Quality and Expansion of the NIH Full-length cDNA project (MGC). Genome Research, 14: 2121-2127.
  73. Wang, D., Huang, J., Xie, H., Manzella, L. and Soares, M.B. (2005). A robust two-way semi-linear model for normalization of cDNA microarray data. BMC Bioinformatics, 6(1): 14.
  74. Zhang, S. S-M., Xu, X., Li, J., Liu, M-G., Zhao, H., Soares, M.B., Barnstable, C.J. and Fu, X-Y. (2005). Comprehensive in silico functional specification of mouse retina transcripts. BMC Genomics 6: 40.
  75. Segal, J. P., Stallings, N.R., Lee, C.E., Zhao, L., Socci, N.D., Viale, A., Harris, T.M., Soares, M.B., Childs, G., Elmquist, J., Parker, K.L. and Friedman, J.M. (2005). Use of laser-capture microdissection for the identification of marker genes for the ventromedial hypothalamic nucleus. Journal of Neuroscience 25(16): 4181-4188.
  76. McGlinn, E., van Bueren, K.L., Fiorenza, S., Mo, R., Poh, A.M., Forrest, A., Soares, M.B., Bonaldo, M.F., Grimmond, S., Hui, C., Wainwright, B. and Wicking, C. (2005). Pax9 and Jagged1 act downstream of Gli3 in vertebrate limb development. Mechanisms of Development 122 (11): 1218-1233.
  77. Hackett, J.D., Scheetz, T.E., Yoon, H.S., Soares, M.B., Bonaldo, M.F., Casavant, T.L. and Bhattacharya, D. (2005). Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics 6:80.
  78. Goodson, M.S., Kojadinovic, M., Troll, J.V., Scheetz, T.E., Casavant, T.L., Soares, M.B. and McFall-Ngai, M.J. (2005). Identifying components of the NF-kB pathway in the beneficial Euprymna scolopes-Vibrio fischeri light
    organ symbiosis. Applied Environmental Microbiology 71(11): 6934-6946.
  79. Morris, K.A., Snir, E., Pompeia, C., Koroleva, I.V., Kachar, B., Hayashizaki, Y., Carninci, P., Soares, M.B. and Beisel, K.W. (2005). Differential expression of genes wihin the cochlea as defined by a custom mouse inner ear microarray. J. Assoc. Res. Otolaryngol. 6(1): 75-89.
  80. Lorenzini, D.M., da Silva Jr., P.I., Soares, M.B., Arruda, P., Setubal, J. and Daffre, S. (2006). Discovery of immune-related genes expressed in hemocytes of the tarantula spider Acanthoscurria gomesiana. Developmental & Comparative Immunology 30(6): 545-556.
  81. Chun, C.K., Scheetz, T.E., Bonaldo, M.F., Brown, B., Clemens, A., Crookes-Goodson, W.J., Crouch, K., DeMartini, T., Eyestone, M., Goodson, M.S., Janssens, B., Kimbell, J.L., Koropatnick, T.A., Kucaba, T., Smith, C., Stewart, J.J., Tong, D., Troll, J.V., Webster, S., Winhall-Rice, J., Yap, C., Casavant, T., McFall-Ngai, M.J. and Soares, M.B. (2006). An annotated cDNA library of juvenile Euprymna scolopes with and without colonization by the symbiont Vibrio fischeri. BMC Genomics 7:154
  82. Dillon, R.J., Ivens, A.C., Churcher, C., Holroyd, N., Quail, M.A., Rogers, M.E., Soares, M.B., Bonaldo, M.F., Casavant, T., Lehane, M.J., Bates, P.A. (2006). Analysis of ESTs from Lutzomyia longipalpis sand flies and their contribution toward understanding the insect-parasite relationship. Genomics 88(6): 831-40.
  83. Ma, S., Kosorok, M.R., Huang, J., Xie, H., Manzella, L. and Soares, M.B. (2006). Robust semiparametric microarray normalization and significance analysis. Biometrics 62(2): 555-561.
  84. Attardo, G.M., Strickler-Dinglasan, P., Perkin, S.A., Caler, E., Bonaldo, M.F., Soares, M.B., El-Sayeed, N. and Aksoy, S. (2006). Analysis of fat body transcriptome from the adult tsetse fly, Glossina morsitans morsitans. Insect Mol. Biol. 15(4): 411-424.
  85. Dillon, R.J., Ivens, A.C., Churcher, C., Holroyd, N., Quail, M.A., Rogers, M.E., Soares, M.B., Bonaldo, M.F., Casavant, T.L., Lehane, M.J. and Bates, P.A. (2006). Analysis of ESTs from Lutzomyia longipalpis sand flies and their contribution toward understanding the insect-parasite relationship. Genomics 88:831-840.
  86. Reyes-Prieto, A., Hackett, J.D., Soares, M.B., Bonaldo, M.F. and Bhattacharya, D. (2006). Cyanobacterial contribution to algal nuclear genomes is primarily limited to plastid functions. Current Biology 16: 2320-2325.
  87. Zhang, S.S., Xu, X., Liu, M.G., Zhao, H., Soares, M.B., Barnstable, C.J. and Fu, X.Y. (2006). A biphasic pattern of gene expression during mouse retina development. BMC Dev. Biol. Oct 17; 6:48.
  88. Postovit, L-M., Costa, F.F., Bischof, J.M., Seftor, E.A., Wen, B., Seftor, R.E.B., Feinberg, A.P., Soares, M.B. and Hendrix, M.J.C. (2007). The commonality of plasticity underlying multipotent tumor cells and embryonic stem cells. J Cell Biochem 54:1-10.
  89. Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O’leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S,Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW. Genome sequence of Aedes aegypti, a major arbovirus vector. Science. 2007 Jun 22;316(5832):1718-23. Epub 2007 May 17.
  90. Koutsos, A.C., Blass, C., Meister, S., Schmidt, S., MacCallum, R.M., Soares, M.B., Collins, F.H., Benes, V., Zdobnov, E., Kafatos, F.C. and Christophides, G.K. (2007). Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster. Proc. Natl. Acad. Sci. 104(29): 11865-6.
  91. Wang, D., Zhang, C.-H., Soares, M.B. and Huang, J. Systematic approaches for incorporating control spots and data quality information to improve normalization of cDNA microarray data. Journal of Biopharmaceutical Statistics 17, 415-431 (2007).
  92. Bonnet, A., Iannuccelli, E., Hugot, K., Benne, F., Bonaldo, M.F., Soares, M.B., Hatey, F. and Tosser-Klopp, G. (2007). A pig multi-tissue normalised cDNA library: large-scale sequencing, cluster analysis and 9K micro-array resource generation. BMC Genomics 9, 17 (2008).
  93. Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O’Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo M, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares M, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, and Gojobori T. (2008). Yamasaki, C. et al. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res 36, D793-D799 (2008).. Nuc. Acids Res. 2008 Jan;36(Database issue):D793-9. Epub 2007 Dec 18.
  94. Gomulski LM, Dimopoulos G, Xi Z, Soares MB, Bonaldo MF, Malacrida AR, Gasperi G. (2008). Gene discovery in an invasive tephritid model pest species, the Mediterranean fruit fly, Ceratitis capitata. BMC Genomics 9:243.
  95. Chun, C.K., Troll, J.V., Koroleva, I., Brown, B., Manzella, L., Snir, E., Almabrazi, H., Scheetz, T.E., Bonaldo, M. F., Casavant, T.L., Soares, M.B., Ruby, E.G., McFall-Ngai, M.J. (2008). Proc Natl Acad Sci U S A 105, 11323-11328 (2008).
  96. Xie, H., Wang, M., Bischof, J., Bonaldo, M.F. and Soares, M.B. (2009). SNP-based prediction of the human germ cell methylation landscape. Genomics 93 (5): 434-440.
  97. Tange, Y., Kondo, A., Egorin, M.J., Mania-Farnell, B., Daneriallis, G.M., Nakazaki, H., Sredni, S.T., Rajaram, V., Goldman, S., Soares, M.B. and Tomita, T. (2009) Interstitial continuous infusion therapy in a malignant glioma model in rats. Childs Nerv Syst. 25(6): 655-662.
  98. Kondo, A., Goldman, S., Vanin, E.F., Sredni, S.T., Rajaram, V., Soares, M.B. and Tomita, T. (2009) An experimental brainstem tumor model using in vivo bioluminescence imaging in rat. Childs Nerv Syst. 25(5): 527-533.
  99. Xie, H., Wang, M., Bonaldo, M.F., Smith, C., Rajaram, V., Goldman, S., Tomita, T. and Soares, M.B. (2009). High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Research 37(13): 4331-4340.
  100. Kondo, A., Goldman, S., Lulla, R.R., Mania-Farnell, B., Vanin, E.F., Sredni, S.T., Rajaram, V., Soares, M.B. and Tomita, T. (2009). Longitudinal assessment of regional directed delivery in a rodent malignant glioma model. J. Neurosurg. Pediatr. 4(6):592-598, 2009.
  101. Helm, J.R., Hertz-Fowler, C., Aslett, M., Berriman, M., Sanders, M., Quail, M.A., Soares, M.B., Bonaldo, M.F., Sakurai, T., Inoue, N. and Donelson, J.E. (2009). Analysis of expressed sequence tags from the four main developmental stages of Trypanosoma congolense. Molecular and Biochemical Parasitology 168(1): 34-42.
  102. Yadav, A.K., Renfrow, J.J., Scholtens, D.M., Xie, H., Duran, G.E., Bredel, C., Vogel, H., Chandler, J.P., Chakravarti, A., Robe, P.A., Das, S., Scheck, A.C., Kessler, J.A., Soares, M.B., Sikic, B.I., Harsh, G.R. and Bredel, M. (2009). Monosomy of Chromosome 10 associated with dysregulation of Epidermal Growth Factor Signaling in glioblastomas. JAMA 302(3):276-289.
  103. Soares, M.B., Bonaldo, M.F., Hackett, J.D. and Bhattacharya, D. (2009). Expressed Sequence Tags: normalization and subtraction of cDNA libraries. Methods Mol Biol. 533: 109-122.
  104. Lewandowska, M.A., Costa, F.F., Bischof, J.M., Williams, S.H., Soares, M.B. and Harris, A. (2009). Multiple mechanisms influence regulation of the cystic fibrosis transmembrane conductance regulator gene promoter. Am J Respir Cell Mol Biol. 2010 Sep;43(3):334-41. Epub 2009 Oct 23.
  105. Costa FF, Seftor EA, Bischof JM, Kirschmann DA, Strizzi L, Arndt K, de Fatima Bonaldo M, Soares MB, Hendrix MJ. (2009). Epigenetically reprogramming metastatic tumor cells with an embryonic microenvironment. Epigenomics 1(2):387-398.
  106. Sredni ST, Bonaldo MF, Costa FF, Huang CC, Hamm CA, Rajaram V, Tomita T, Goldman S, Bischof J, Soares MB. (2009). Upregulation of mir-221 and mir-222 in atipical teratoid/rhabdoid tumors: Potential therapeutic targets. Childs Nerv Syst. 2010 Mar;26(3):279-83. Epub 2009 Dec 10.
  107. Hamm CA, Xie H, Costa FF, Vanin EF, Seftor EA, Sredni ST, Bischof J, Wang D, Bonaldo MF, Hendrix MJC and Soares MB. (2009). Global demethylation of rat chondrosarcoma cells after treatment with 5-Aza-2’-deoxycytidine results in increased tumorigenicity. Plos One 4(12): e8340, 2009.
  108. Wier, A.M., Nyholm, S.V., Mandel, M.J., Prisca Massengo-Tiassé, R., Schaefer, A.L., Koroleva, I., Splinter-BonDurant, S., Brown, B., Manzella, L., Snir, E., Almabrazi, H., Scheetz, T.E., Bonaldo, M.F., Casavant, T.L., Soares, M.B., Cronan, J.E., Reed, J.L., Ruby, E.G. and McFall-Ngai, M.J. (2010). Proc Natl Acad Sci U S A 107, 2259-2264 (2010).
  109. Xie, H., Wang, M., Bonaldo, M.F., Rajaram, V., Stellpflug, W., Smith, C., Arndt, K., Goldman, S., Tomita, T. and Soares, M.B. (2010). Epigenomic analysis of Alu repeats in human ependymomas. Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6952-7. Epub 2010 Mar 29.
  110. Alves-Silva J, Ribeiro JM, Van Den Abbeele J, Attardo G, Hao Z, Haines LR, Soares MB, Berriman M, Aksoy S, Lehane MJ. (2010). An insight into the sialome of Glossina morsitans morsitans. BMC Genomics. 2010 Mar 30;11:213.
  111. Macagno, E.R., Gaasterland, T., Edsall, L., Bafna, V., Soares, M.B., Scheetz, T., Casavant, T., Da Silva, C., Wincker, P., Tasiemski, A. and Salzet, M. (2010). Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. BMC Genomics 11: 407-419.
  112. Berkofsky-Fessler W, Buzzai M, Kim MK, Fruchtman S, Najfeld V, Min DJ, Costa FF, Bischoff JM, Soares MB, McConnell MJ, Zhang W, Levine R, Gilliland DG, Carogero R, Licht JD. (2010). Transcriptional Profiling of Polycythemia Vera Identifies Gene Expression Patterns Both Dependent and Independent From the Action of JAK2V617F. Clin Cancer Res. 2010 Sep 1;16(17):4339-52. Epub 2010 Jul 2.
  113. Hamm CA, Stevens JW, Xie H, Vanin EF, Morcuende JA, Abdulkawy H, Seftor EA, Sredni ST, Bischof JM, Wang D, Malchenko S, Bonaldo MD, Casavant TL, Hendrix MJ, Soares MB. (2010). Microenvironment alters epigenetic and gene expression profiles in Swarm rat chondrosarcoma tumors. BMC Cancer. 2010 Sep 1;10:471.
  114. Malchenko S, Galat V, Seftor EA, Vanin EF, Costa FF, Seftor RE, Soares MB, Hendrix MJ. (2010). Cancer hallmarks in induced pluripotent cells: new insights. J Cell Physiol. 2010 Nov;225(2):390-3.
  115. Ichi, S., Costa, F.F., Bischof, J.M., Nakazaki, H., Shen, Y-W., Boshnjaku, V., Sharma, S., Mania-Farnell, B., McLone, D.G., Tomita, T., Soares, M.B. and Mayanil, C.S.K. (2010). Folic acid remodels chromatin on HES1 and NEUROG2 promoters during caudal neural tube development. J Biol Chem. 2010 Nov 19;285(47):36922-32. Epub 2010 Sep 10.
  116. Wang, M., Xie, H., Stellpflug, W., Rajaram, V., Bonaldo, M.F., Goldman, S., Tomita, T. and Soares, M.B. (2011). BTECH: A Platform to Integrate Genomic, Transcriptomic and Epigenomic Alterations in Brain Tumors. Neuroinformatics. 2011 Jan 6. [Epub ahead of print].
  117. Xie, H., Wang, M., Andrade, A., Bonaldo, M.F., Galat, V., Arndt, K., Rajaram, V., Goldman, S., Tomita, T. and Soares, M.B. (2011). Genome-wide quantitative assessment of variation in DNA methylation patterns. Nuc. Acids Res. Jan 28. [Epub ahead of print] PMID: 21278160.
  118. Molognoni, F., Cruz, A.T., Meliso, F.B., Morais, A.S., Souza, C.F., Xander, P., Bischof, J.M., Costa, F.F., Soares, M.B., Liang, G., Jones, P.A. and Jasiulionis, M.G. (2011). Epigenetic reprogramming as a key contributor to melanocyte malignant transformation. Epigenetics 6 (4), April 2011.
  119. Lulla, R.R., Costa, F.C., Bischof, J.M., Chou, P.M., Bonaldo, M.F., Vanin, E.F. and Soares, M.B. (2011). Identification of differentially expressed microRNAs in osteosarcoma. Sarcoma Epub 2011 July 18.
  120. Bousquet, J., Anto, J.M., Sterk, P.J., Adcock, I.M., Chung, K.F., Roca, J., Agusti, A., Brightling, C., Cambon-Thomsen, A., Cesario, A., Abdelhak, S., Antonarakis, S.E., Avignon, A., Ballabio, A., Baraldi, E., Baranov, A., Bieber, T., Bockaert, J., Brahmachari, S., Brambilla, C., Bringer, J., Dauzat, M., Ernberg, I., Fabbri, L., Froguel, P., Galas, D., Gojobori, T., Hunter, P., Jorgensen, C., Kauffmann, F., Kourilsky, P., Kowalski, M., Lancet, D., Le Pen, C., Mallet, J., Mayosi, B., Mercier, J., Metspalu, A., Nadeau, J.H., Ninot, G., Noble, D., Ozturk, M., Palkonen, S., Préfaut, C., Rabe, K., Renard, E., Roberts, R.G., Samolinski, B., Schunemann, H.J., Simon, H-U., Soares, M.B., Superti-Furga, G., Tegner, J., Verjovski-Almeida, S., Wellstead, P., Wolkenhauer, O., Wouters, E., Balling, R., Brookes, A.J., Charron, D., Pison, C., Chen, Z., Hood, L., and Auffray, C. (2011). Systems medicine and integrated care to combat chronic noncommunicable diseases. Genome Medicine 2011 Jul 6;3(7):43.
  121. Galat, V., Malchenko, S., Galat, Y., Ishkin, A., Nikolsky, Y., Kosak, S. T., Soares, M.B., Iannaccone, P., Crispino, J. and Hendrix, M.J.C. (2011). A model of early human embryonic stem cell differentiation reveals inter- and intracellular changes upon transition to squamous epithelium. Stem Cells and Development 2012 May 20;21(8):1250-63. Epub 2011 Oct 19.
  122. Xi, G., Mania-Farnell, B., Rajaram, V., Mayanil, C.S., Soares, M.B., Tomita, T. and Goldman, S. (2011). Efficacy of interstitial continuous vincristine infusion in a bioluminescent rodent intracranial tumor model. J. Neurooncol. 2012 Jan;106(2):261-70. Epub 2011 Aug 14; PMID: 21842443.
  123. Costa FF, Bischof JM, Vanin EF, Lulla RR, Wang M, Sredni ST, Rajaram V, Bonaldo MF, Wang D, Goldman S, Tomita T, Soares MB. (2011). Identification of microRNAs as potential prognostic markers in ependymoma. PLoS ONE 6(10):e25114. Epub 2011 Oct 28.
  124. Malchenko, S., Seftor, E.A., Nikolsky, Y., Hasegawa, S.L., Kuo, S., Stevens, J.W., Poyarkov, S., Nikolskaya, T., Kucaba, T., Wang, M., Abdulkawy, H., Casavant, T., Morcuende, J., Buckwalter, J., Hohl, R., DeYoung, B., Kernstine, K., Bonaldo, M.F., Hendrix, M.J.C., Soares, M.B. and Soares, V.M.F.C. (2011). Putative multi-functional signature of lung metastases in dedifferentiated chondrosarcoma. Sarcoma 2012;2012:820254. Epub 2012 Feb 16.
  125. de Andrade, A., Wang, M., Bonaldo, M.F., Xie, H. and Soares, M.B. (2011). Genetic and epigenetic variations contributed by Alu retrotransposition. BMC Genomics 2011 Dec 20; 12:617.
  126. Xi, G., Rajaram, V., Mania-Farnell, B., Mayanil, C.S., Soares, M.B., Tomita, T., and Goldman, S. (2012). Efficacy of vincristine administered via convection-enhanced delivery in a rodent brainstem tumor model documented by bioluminescence imaging. Childs Nerv. Syst. April 28(4):565-74. Epub 2012 Jan 27; PMID: 22282078.
  127. Cowley AW Jr, Nadeau JH, Baccarelli A, Berecek K, Fornage M, Gibbons GH, Harrison DG, Liang M, Nathanielsz PW, O’Connor DT, Ordovas J, Peng W, Soares MB, Szyf M, Tolunay HE, Wood KC, Zhao K, Galis ZS. Report of the National Heart, Lung, and Blood Institute working group on epigenetics of hypertension. Hypertension 2012 May; 59(5): 899-905. Epub 2012 Mar 19.
  128. Zhang, X., Wallace, A.D., Du, P., Kibbe, W.A., Jafari, N., Xie, H., Lin, S., Baccarelli, A., Soares, M.B. and Hou, L. (2012). DNA methylation alterations in response to pesticide exposure in vitro. Environmental & Molecular Mutagenesis August 53(7):542-9. doi: 10.1002/em.21718. Epub 2012 Jul; PMID: 22847954.
  129. Zhang, X., Wallace, A.D., Du, P., Lin, S., Baccarelli, A., Jiang, H., Jafari, N., Zheng, Y., Xie, H., Soares, M.B., Kibbe, W.A. and Hou, L. (2012). Genome-wide study of DNA methylation alterations in response to Diazinon exposure in vitro. Environmental Toxicology and Pharmacology 2012 Aug 1 [Epub ahead of print] PMID: 22964155.
  130. Lin, X., Rice, K.L., Buzzai, M., Hexner, E., Costa, F.F., Kilpivaara, O., Mullally, A., Soares, M.B., Ebert, B.L., Levine, R., and Licht, J.D. (2012). miR-433 is aberrantly expressed in Myeloproliferative Neoplasms and suppresses hematopoietic cell growth and differentiation. Leukemia Aug 6. doi: 10.1038/leu.2012.224. [Epub ahead of print] PMID: 22864358.
  131. Hoxha, E., Lambers, E., Xie, H., de Andrade, A., Krishnamurthy, P., Wasserstrom, J.A., Ramirez, V., Thal, M., Verma, S.K., Soares, M.B. and Kishore, R. Histone deacetylase 1 deficiency impairs differentiation and electrophysiological properties of cardiomyocytes derived from induced pluripotent cells. Stem Cells 2012 Aug 22 doi: 10.1002/stem.1209 [Epub ahead of print] PMID: 22915496.
  132. Martin J, Bryar P, Mets M, Weinstein J, Jones A, Martin A, Vanin EF, Scholtens D, Costa FF, Soares MB, Laurie NA (2012). Differentially expressed miRNAs in retinoblastoma. Gene 2012 Oct 25. doi:pii:S0378-1119(12)01299-1. 10.1016/j.gene.2012.09.129. [Epub ahead of print]; PMID: 23103829.
  133. Chan CX, Soares MB, Bonaldo MF, Wisecaver JH, Hackett JD, Anderson DM, Erdner DL, Bhattacharya D. Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote. J. Phycol. 2012 Oct 1; 48(5):1130-1142. Epub 2012 Jun 19; PMID: 23066170.
  134. Xi G, Robinson E, Mainia-Farmell B, Vanin EF, Shim K-Y, Tsurubuchi T, Allender EV, Mayanil CS, Soares MB, Ho D, Tomita T. Convection-enhanced delivery of nanodiamond drug delivery platforms for intracranial tumor treatment. Nanomedicine: Nanotechnology, Biology, and Medicine (In Press) DOI: 10.1016/j.nano.2013.07.013, 2013.
  135. Malchenko, S., Xie, J., Bonaldo, M.F., Vanin, E., Bhattacharyya, B., Galat, V., Goossens, W., Seftor, R.E.B., Crispino, J., Miller, R., Bohn, M.C., Hendrix, M.J.C. and Soares, M.B. Onset of rosette formation during spontaneous neural differentiation of hESC and hiPSC colonies. Gene 2013 Aug 15. pii: S0378-1119(13)01009-3. doi: 10.1016/j.gene.2013.07.101. [Epub ahead of print].
  136. Lee, C., Zhang, Q., Kozlowski, J., Brendler, C., Soares, M.B., Dash, A., McClelland, M., and Mercola, D. Natural products and transforming growth factor-beta (TGF-beta) signaling in cancer development and progression. Curr Cancer Drug Targets 13, 500-505 (2013).
  137. Reindel, R., Bischof, J., Kim, K-Y., Orenstein, J., Soares, M., Baker, S., Shulman, S., Perlman, E., Lingen, M., Pink, A., Trevenen, C. and Rowley, A.H. CD84 is markedly upregulated in Kawasaki disease arteriopathy. Clinical and Experimental Immunology 2014 Jul;177(1):203-11. doi: 10.1111/cei.12327.
  138. McErlean P, Favoreto S Jr, Costa FF, Shen J, Quraishi J, Biyasheva A, Cooper JJ, Scholtens DM, Vanin EF, de Bonaldo MF, Xie H, Soares MB, Avila PC. Human rhinovirus infection causes different DNA methylation changes in nasal epithelial cells from healthy and asthmatic subjects. BMC Med Genomics. 2014 Jun 19; 7:37. doi: 10.1186/1755-8794-7-37.
  139. Malchenko, S., Sredni, S.T., Hashimoto, H., Kasai, A., Nagayasu, K., Xie, J., Margaryan, N., Seiriki, K., Lulla, R., Seftor, R.E.B., Pachman, L.M., Meltzer, H.Y., Hendrix, M.J.C. and Soares, M.B. A mouse model of human primitive neuroectodermal tumors resulting from microenvironmentally-driven malignant transformation of orthotopically transplanted radial glial cells. PLoS ONE, 2015 Mar 31;10(3):e0121707. doi: 10.1371/journal.pone.0121707. eCollection 2015.
  140. Soares, M.B. Collaborative Research in Light of the Prevailing Criteria for Promotion and Tenure In Academia. Genomics 106(4): 193-195, 2015.
  141. Xu, D., Huang, C.C., Kachaochana, A., Morgan, G.A., Bonaldo, M.F., Soares, M.B., Costa, F., Sarwark, J., Sredni, S.T., and Pachman, L.M. MicroRNA-10a Regulation of Proinflammatory Mediators: An Important Component of Untreated Juvenile Dermatomyositis. J. Rheumatol. 43(1): 161-168, 2016
  142. Samis, J., Vanin, E.F., Sredni, S.T., Bonaldo, M.F., Costa, F.F., Tomita, T., Habiby, R., Zimmerman, D., Soares, M.B. (2016). Extensive miRNA expression analysis in craniopharyngiomas. Childs Nerv Syst 32: 1617-1624.
  143. Shidfar, A., Costa, F.F., Scholtens, D., Bischof, J., Sullivan, M.E., Ivancic, D.Z., Vanin, E.F., Soares, M.B., Wang, J., and Khan, S.A. (2016). Expression of miR-18a and miR-210 In normal breast tissue as candidate biomarkers of breast cancer risk. Cancer Prev Res (Phila) October 27 2016 DOI:10.1158/1940-6207.CAPR-16-0177
  144. Malchenko, S., Sredni, S.T., Bi, Y., Margaryan, N.V., Boyineni, J., Mohanam, I., Tomita, T., Davuluri, R.V., Soares, M.B. (2017). Stabilization of HIF-1alpha and HIF-2alpha, up-regulation of MYCC and accumulation of stabilized p53 constitute hallmarks of CBN-PNET animal model. PLOS ONE DOI:10.1371/journal.pone.0173106 March 1, 2017.
  145. Sagner, M., McNeil, A., Puska, P., Auffray, C., Price, N.D., Hood, L., Lavie, C.J., Han, Z-G., Chen, Z., Brahmachari, S.K., McEwen, B.S., Soares, M.B., Balling, R., Epel, E., Arena, R. (2017). The P4 Health Spectrum – A Predictive, Preventive, Personalized and Participatory Continuum for Promoting Healthspan. Progress in Cardiovascular Diseases 59: 506-521.
  146. Malchenko, S., Sredni, S.T., Boyineni, J., Bi, Y., Margaryan, N.V., Guda, M.R., Kostenko, Y., Tomita, T., Davuluri, R.V., Velpula, K., Hendrix, M.J.C. and Soares, M.B. (2018). Characterization of brain tumor Initiating cells isolated from an animal model of CNS primitive neuroectodermal tumors. Oncotarget 9(17): 13733-13747.
  147. Lewis R, Li YD, Hoffman L, Hashizume R, Gravohac G, Rice G, Wadhwani NR, Jie C, Pundy T, Mania-Farnell B, Mayanil CS, Soares MB, Lei T, James CD, Foreman NK, Tomita T, Xi G. (2019). Global Reduction of H3K4me3 Improves Chemotherapeutic Efficacy for Pediatric Ependymomas. Neoplasia 21 (6): 505–515. doi:10.1016/j.neo.2019.03.012. [Epub ahead of print]
  148. Boyineni, J., Sredni, S., Margaryan, N., Demirkhanyan, L., Tye, M., Johnson, R., Gonzalez-Nilo, F., Hendrix, M., Pavlov, E., Soares, M., Zakharian, E., and Malchenko, S. (2020). Inorganic polyphosphate as an energy source in tumorigenesis. Oncotarget 11 (50):4613-4624.
  149. Auffray, C., Balling, R., Blomberg, N., Bonaldo, M.C, Boutron, B., Brahmachari, S., Bréchot, C., Cesario, A., Chen, S-J., Clément, K., Danilenko, D., Alberto Di Meglio, A.Di, Gelemanović, A., Goble, C., Gojobori, T., Goldman, J.D., Goldman, M., Guo, Y-K., Heath, J., Hood, L., Hunter, P., Jin, L., Kitano, H., Knoppers, B., Lancet, D., Larue, C., Lathrop, M., Laville, M., Lindner, A.B., Magnan, A., Metspalu, A., Morin, E., Ng, L.F.P., Nicod, L., Noble, D., Nottale, L., Nowotny, H., Ochoa, T., Okeke, I.N., Oni, T., Openshaw, P., Oztürk, M., Palkonen, S., Paweska, J.T., Pison, D., Polymeropoulos, M.H., Pristipino, C., Protzer, U., Roca, J., Rozman, D., Santolini, M., Sanz, F., Scambia, G., Segal, E., Serageldin, I., Soares, M.B., Sterk, P., Sugano, S., Superti-Furga, G., Supple, D., Tegner, J., Uhlen, M., Urbani, A., Valencia, A., Valentini, V., Werf, S.V.D, Vinciguerra, M., Wolkenhauer, O., and Wouters, E. (2020). COVID-19 and beyond: a call for action and audacious solidarity to all the citizens and nations, it is humanity’s fight. F1000Research 2020, 9:1130.

Book Chapters

  1. Soares, M.B. (1994). Construction of directionally cloned cDNA libraries in phagemid vectors. In Automated DNA Sequencing and Analysis Techniques. J. Craig Venter (Ed.). Academic Press, London, pp. 110-114.Soares, M.B. & Bonaldo, M.F. (1998). Construction and screening of normalized cDNA libraries. In Genome Analysis volume II: A Laboratory Manual, vol. 2, pp. 49-157. B. Birren, E. D. Green, S. Klapholz, R. Myers, J. Roskams, Eds. Cold Spring Harbor Laboratory Press, New York.
  2. Soares, M.B. & Bonaldo, M.F. (2003). cDNA Libraries. In Nature Encyclopedia of the Human Genome. D.N. Cooper, Ed. Nature Publishing Group ©2002 Macmillan Publishers Ltd.
  3. Soares, M.B. & Bonaldo, M.F. (2005). Manufacturing EST libraries. In Nature Online Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons, Ltd. Published Online: 15 Nov 2005.

Review Articles

  1. Soares, M.B. (1997). Identification and cloning of differentially expressed genes. Current Opinion in Biotechnology 8: 542-546.
  2. Severson, D.W., Knudson, D.L., Soares, M.B. and Loftus, B.J. (2004). Aedes aegypti genomics. Insect Biochemistry and Molecular Biology 34: 715-721.
  3. Lee, C., Zhang, Q., Zi, X., Dash, A., Soares, M.B., Rahmatpanah, F., Jia, Z., McClelland, M. and Mercola, D. (2012). TGF-β mediated DNA methylation in prostate cancer. Translational Andrology and Urology (in press).
  4. Lee, C., Zhang, Q., Kozlowski, J., Brendler, C., Soares, M.B., Dash, A., McClelland, M., and Mercola, D. (2012). Natural products and transforming growth factor-beta (TGF-β) signaling in cancer development and progression. Current Cancer Drug Targets.

Proceedings

  1. Auffray, C., Chen, Z., Hood, L., Soares, B., and Sugano, S. (2003). Foreword: From the TRANSCRIPTOME conferences to the SYSTEMOSCOPE international consortium. C. R. Biol. 326(10-11): 867-875.
  2. Xie, H., Wang, M., Tange, Y., Bonaldo, M.F. and Soares, M.B. (2009). A primer design algorithm for global analysis of CpG methylation. Proceedings of the 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, Editors: Zhang J, Li G, Yang JY. IEEE Computer Society, Los Alamitos, CA, pp 126-130.

Contribution to Public Databases

A total of 5,311,053 Expressed Sequence Tag (EST) entries in the dbEST subdivision of GenBank [http://www.ncbi.nlm.nih.gov/dbEST/], as of December 21st, 2014. These ESTs were derived from cDNA clones generated in my laboratory. Sequences were either produced in my laboratory or at the laboratory of a collaborator. At that time, this represented approximately 26.5% of all human ESTs (2,770,390 out of a total of 10,464,028), 18% of all mouse ESTs (924,147 out of a total of 5,143,558), and 31% of all rat ESTs (383,762 out of a total of 1,243,364). I have also contributed to gene discovery/EST projects of numerous other species, including – but not limited to – Sus scrofa (pig), Xenopus, Aedes, Schistosoma, Anopheles, Glossina, Apis melifera. Altogether, my laboratory has contributed to a significant fraction of all EST data available in the dbEST database.

Patents

  1. A Method for Normalization of cDNA Libraries. M. Bento Soares (inventor), A. Efstratiadis (co-inventor), M.F. Bonaldo (co-inventor). U.S. Patent # 08126594.