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Journal Articles

Wagner, S., Vlachogiannis, G., De Haven Brandon, A., Valenti, M., Box, G., Jenkins, L., Mancusi, C., Self, A., Manodoro, F., Assiotis, I., et al. (2019). Suppression of interferon gene expression overcomes resistance to MEK inhibition in KRAS-mutant colorectal cancer. Oncogene, Vol.38 (10), pp. 1717-1733.  show abstract

Dillon, M.T., Bergerhoff, K.F., Pedersen, M., Patin, E.C., Whittock, H., Crespo-Rodriguez, E., Pearson, A., Paget, J.T., Smith, H.G., Patel, R.R., et al. (2019). ATR inhibition potentiates the radiation induced inflammatory tumour microenvironment. Clin cancer res, .  show abstract

Smyth, E.C., Nyamundanda, G., Cunningham, D., Fontana, E., Ragulan, C., Tan, I.B., Lin, S.J., Wotherspoon, A., Nankivell, M., Fassan, M., et al. (2018). A seven-Gene Signature assay improves prognostic risk stratification of perioperative chemotherapy treated gastroesophageal cancer patients from the MAGIC trial. Ann oncol, Vol.29 (12), pp. 2356-2362.  show abstract

Neuzillet, C., Tijeras-Raballand, A., Ragulan, C., Cros, J., Patil, Y., Martinet, M., Erkan, M., Kleeff, J., Wilson, J., Apte, M., et al. (2018). Inter- and intra-tumoural heterogeneity in cancer-associated fibroblasts of human pancreatic ductal adenocarcinoma. J pathol, .  show abstract

Vlachogiannis, G., Hedayat, S., Vatsiou, A., Jamin, Y., Fernández-Mateos, J., Khan, K., Lampis, A., Eason, K., Huntingford, I., Burke, R., et al. (2018). Patient-derived organoids model treatment response of metastatic gastrointestinal cancers. Science, Vol.359 (6378), pp. 920-926.  show abstract

Heindl, A., Khan, A.M., Rodrigues, D.N., Eason, K., Sadanandam, A., Orbegoso, C., Punta, M., Sottoriva, A., Lise, S., Banerjee, S., et al. (2018). Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity. Nat commun, Vol.9 (1), p. 3917.  show abstract

Eason, K., Nyamundanda, G. & Sadanandam, A. (2018). polyClustR: defining communities of reconciled cancer subtypes with biological and prognostic significance. Bmc bioinformatics, Vol.19 (1), p. 182.  show abstract

Bijlsma, M.F., Sadanandam, A., Tan, P. & Vermeulen, L. (2017). Molecular subtypes in cancers of the gastrointestinal tract. Nat rev gastroenterol hepatol, Vol.14 (6), pp. 333-342.  show abstract

Nyamundanda, G., Poudel, P., Patil, Y. & Sadanandam, A. (2017). A Novel Statistical Method to Diagnose, Quantify and Correct Batch Effects in Genomic Studies. Sci rep, Vol.7 (1), p. 10849.  show abstract

Battersby, N.J., Dattani, M., Rao, S., Cunningham, D., Tait, D., Adams, R., Moran, B.J., Khakoo, S., Tekkis, P., Rasheed, S., et al. (2017). A rectal cancer feasibility study with an embedded phase III trial design assessing magnetic resonance tumour regression grade (mrTRG) as a novel biomarker to stratify management by good and poor response to chemoradiotherapy (TRIGGER): study protocol for a randomised controlled trial. Trials, Vol.18 (1), p. 394.  show abstract

Fontana, E., Homicsko, K., Eason, K. & Sadanandam, A. (2016). Molecular Classification of Colon Cancer: Perspectives for Personalized Adjuvant Therapy. Current colorectal cancer reports, Vol.12 (6), pp. 296-302.

Eason, K. & Sadanandam, A. (2016). Molecular or Metabolic Reprograming: What Triggers Tumor Subtypes?. Cancer res, Vol.76 (18), pp. 5195-5200.  show abstract

Guinney, J., Dienstmann, R., Wang, X., de Reyniès, A., Schlicker, A., Soneson, C., Marisa, L., Roepman, P., Nyamundanda, G., Angelino, P., et al. (2015). The consensus molecular subtypes of colorectal cancer. Nat med, Vol.21 (11), pp. 1350-1356.  show abstract

Sadanandam, A., Wullschleger, S., Lyssiotis, C.A., Grötzinger, C., Barbi, S., Bersani, S., Körner, J., Wafy, I., Mafficini, A., Lawlor, R.T., et al. (2015). A Cross-Species Analysis in Pancreatic Neuroendocrine Tumors Reveals Molecular Subtypes with Distinctive Clinical, Metastatic, Developmental, and Metabolic Characteristics. Cancer discov, Vol.5 (12), pp. 1296-1313.  show abstract

Kapoor, A., Yao, W., Ying, H., Hua, S., Liewen, A., Wang, Q., Zhong, Y., Wu, C.-., Sadanandam, A., Hu, B., et al. (2014). Yap1 activation enables bypass of oncogenic Kras addiction in pancreatic cancer. Cell, Vol.158 (1), pp. 185-197.  show abstract

Costello, J.C., Heiser, L.M., Georgii, E., Gönen, M., Menden, M.P., Wang, N.J., Bansal, M., Ammad-ud-din, M., Hintsanen, P., Khan, S.A., et al. (2014). A community effort to assess and improve drug sensitivity prediction algorithms. Nature biotechnology, Vol.32 (12), pp. 1202-1212.

Bansal, M., Yang, J., Karan, C., Menden, M.P., Costello, J.C., Tang, H., Xiao, G., Li, Y., Allen, J., Zhong, R., et al. (2014). A community computational challenge to predict the activity of pairs of compounds. Nature biotechnology, Vol.32 (12), pp. 1213-1222.

Purohit, A., Sadanandam, A., Myneni, P. & Singh, R.K. (2014). Semaphorin 5A mediated cellular navigation: connecting nervous system and cancer. Biochim biophys acta, Vol.1846 (2), pp. 485-493.  show abstract

Sadanandam, A., Wang, X., de Sousa E Melo, F., Gray, J.W., Vermeulen, L., Hanahan, D. & Medema, J.P. (2014). Reconciliation of classification systems defining molecular subtypes of colorectal cancer: interrelationships and clinical implications. Cell cycle, Vol.13 (3), pp. 353-357.  show abstract

Sadanandam, A., Lyssiotis, C.A., Homicsko, K., Collisson, E.A., Gibb, W.J., Wullschleger, S., Ostos, L.C., Lannon, W.A., Grotzinger, C., Del Rio, M., et al. (2013). A colorectal cancer classification system that associates cellular phenotype and responses to therapy. Nat med, Vol.19 (5), pp. 619-625.  show abstract

Hunter, K.E., Quick, M.L., Sadanandam, A., Hanahan, D. & Joyce, J.A. (2013). Identification and characterization of poorly differentiated invasive carcinomas in a mouse model of pancreatic neuroendocrine tumorigenesis. Plos one, Vol.8 (5), p. e64472.  show abstract

Sadanandam, A., Lal, A., Benz, S.C., Eppenberger-Castori, S., Scott, G., Gray, J.W., Spellman, P., Waldman, F. & Benz, C.C. (2012). Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells?. Breast cancer res treat, Vol.136 (3), pp. 693-703.  show abstract

Heiser, L.M., Sadanandam, A., Kuo, W.-., Benz, S.C., Goldstein, T.C., Ng, S., Gibb, W.J., Wang, N.J., Ziyad, S., Tong, F., et al. (2012). Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc natl acad sci u s a, Vol.109 (8), pp. 2724-2729.  show abstract

Sadanandam, A., Sidhu, S.S., Wullschleger, S., Singh, S., Varney, M.L., Yang, C.-., Ashour, A.E., Batra, S.K. & Singh, R.K. (2012). Secreted semaphorin 5A suppressed pancreatic tumour burden but increased metastasis and endothelial cell proliferation. Br j cancer, Vol.107 (3), pp. 501-507.  show abstract

Collisson, E.A., Sadanandam, A., Olson, P., Gibb, W.J., Truitt, M., Gu, S., Cooc, J., Weinkle, J., Kim, G.E., Jakkula, L., et al. (2011). Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat med, Vol.17 (4), pp. 500-503.  show abstract

Sadanandam, A., Futakuchi, M., Lyssiotis, C.A., Gibb, W.J. & Singh, R.K. (2011). A cross-species analysis of a mouse model of breast cancer-specific osteolysis and human bone metastases using gene expression profiling. Bmc cancer, Vol.11, p. 304.  show abstract

Sadanandam, A., Varney, M.L., Singh, S., Ashour, A.E., Moniaux, N., Deb, S., Lele, S.M., Batra, S.K. & Singh, R.K. (2010). High gene expression of semaphorin 5A in pancreatic cancer is associated with tumor growth, invasion and metastasis. Int j cancer, Vol.127 (6), pp. 1373-1383.  show abstract

Sadanandam, A., Rosenbaugh, E.G., Singh, S., Varney, M. & Singh, R.K. (2010). Semaphorin 5A promotes angiogenesis by increasing endothelial cell proliferation, migration, and decreasing apoptosis. Microvasc res, Vol.79 (1), pp. 1-9.  show abstract

Loss, L.A., Sadanandam, A., Durinck, S., Nautiyal, S., Flaucher, D., Carlton, V.E., Moorhead, M., Lu, Y., Gray, J.W., Faham, M., et al. (2010). Prediction of epigenetically regulated genes in breast cancer cell lines. Bmc bioinformatics, Vol.11, p. 305.  show abstract

Singh, S., Sadanandam, A., Varney, M.L., Nannuru, K.C. & Singh, R.K. (2010). Small interfering RNA-mediated CXCR1 or CXCR2 knock-down inhibits melanoma tumor growth and invasion. Int j cancer, Vol.126 (2), pp. 328-336.  show abstract

Hu, Z., Huang, G., Sadanandam, A., Gu, S., Lenburg, M.E., Pai, M., Bayani, N., Blakely, E.A., Gray, J.W. & Mao, J.-., et al. (2010). The expression level of HJURP has an independent prognostic impact and predicts the sensitivity to radiotherapy in breast cancer. Breast cancer res, Vol.12 (2), p. R18.  show abstract

Singh, S., Nannuru, K., Sadanandam, A., Varney, M. & Singh, R. (2009). Expression of CXCR1 and CXCR2 enhances human melanoma tumorigenesis, growth and invasion. Cancer research, Vol.69.

Futakuchi, M., Nannuru, K.C., Varney, M.L., Sadanandam, A., Nakao, K., Asai, K., Shirai, T., Sato, S.-. & Singh, R.K. (2009). Transforming growth factor-beta signaling at the tumor-bone interface promotes mammary tumor growth and osteoclast activation. Cancer sci, Vol.100 (1), pp. 71-81.  show abstract

Singh, S., Sadanandam, A., Nannuru, K.C., Varney, M.L., Mayer-Ezell, R., Bond, R. & Singh, R.K. (2009). Small-molecule antagonists for CXCR2 and CXCR1 inhibit human melanoma growth by decreasing tumor cell proliferation, survival, and angiogenesis. Clin cancer res, Vol.15 (7), pp. 2380-2386.  show abstract

Kuo, W.-., Das, D., Ziyad, S., Bhattacharya, S., Gibb, W.J., Heiser, L.M., Sadanandam, A., Fontenay, G.V., Hu, Z., Wang, N.J., et al. (2009). A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047. Bmc med, Vol.7, p. 77.  show abstract

Singh, S., Nannuru, K.C., Sadanandam, A., Varney, M.L. & Singh, R.K. (2009). CXCR1 and CXCR2 enhances human melanoma tumourigenesis, growth and invasion. Br j cancer, Vol.100 (10), pp. 1638-1646.  show abstract

Nannuru, K.C., Futakuchi, M., Sadanandam, A., Wilson, T.J., Varney, M.L., Myers, K.J., Li, X., Marcusson, E.G. & Singh, R.K. (2009). Enhanced expression and shedding of receptor activator of NF-kappaB ligand during tumor-bone interaction potentiates mammary tumor-induced osteolysis. Clin exp metastasis, Vol.26 (7), pp. 797-808.  show abstract

Sadanandam, A., Varney, M.L. & Singh, R.K. (2008). Identification of semaphorin 5A interacting protein by applying apriori knowledge and peptide complementarity related to protein evolution and structure. Genomics proteomics bioinformatics, Vol.6 (3-4), pp. 163-174.  show abstract

Wilson, T.J., Nannuru, K.C., Futakuchi, M., Sadanandam, A. & Singh, R.K. (2008). Cathepsin G enhances mammary tumor-induced osteolysis by generating soluble receptor activator of nuclear factor-kappaB ligand. Cancer res, Vol.68 (14), pp. 5803-5811.  show abstract

Sadanandam, A., Pal, S.N., Ziskovsky, J., Hegde, P. & Singh, R.K. (2008). MCAM: a database to accelerate the identification of functional cell adhesion molecules. Cancer inform, Vol.6, pp. 47-50.  show abstract

Ashour, A.E., Lin, X., Wang, X., Turnquist, H.R., Burns, N.M., Tuli, A., Sadanandam, A., Suleiman, K., Singh, R.K., Talmadge, J.E., et al. (2007). CCL21 is an effective surgical neoadjuvant for treatment of mammary tumors. Cancer biol ther, Vol.6 (8), pp. 1206-1210.  show abstract

Singh, S., Sadanandam, A. & Singh, R.K. (2007). Chemokines in tumor angiogenesis and metastasis. Cancer metastasis rev, Vol.26 (3-4), pp. 453-467.  show abstract

Sadanandam, A., Varney, M.L., Kinarsky, L., Ali, H., Mosley, R.L. & Singh, R.K. (2007). Identification of functional cell adhesion molecules with a potential role in metastasis by a combination of in vivo phage display and in silico analysis. Omics, Vol.11 (1), pp. 41-57.  show abstract

Sadanandam, A. Consensus gene expression subtypes of epithelial tumours. Biorxiv (the preprint server for biology), .

Sadanandam, A., Sadanandam, A., Collisson, E., Gibb, W., Hanahan, D. & Gray, J. Identification of Molecular Subtypes in Pancreatic Adenocarcinoma with Predictive and Prognostic Importance. Protocol exchange, .


Book Chapters

Collisson, E.A., Sadanandam, A., Spellman, P.T. & Gray, J.W. (2009). Cancer genome aberrations: measure, causes, and consequences. In Holland-Frei Cancer Medicine, (Ed.), . Eight (pp. 359-363). BC Decker Publications in collaboration with AACR.

Sadanandam, A., GIbb, W. & Singh, R.K. Bioinformatics analysis to identify cell adhesion molecules in cancer. In Preedy, V.R. (Ed.), Modern Insights into Disease from Molecules to Man. Science Publishers.


Conferences

Fontana, E., Nyamundanda, G., Cunningham, D., Ragulan, C., Sclafani, F., Eason, K., Bali, M.A., Vendrell, I., Patil, Y., Wilson, S.H., et al. (2018). Molecular subtype assay to reveal anti-EGFR response sub-clones in colorectal cancer (CRC)., JOURNAL OF CLINICAL ONCOLOGY, Vol.36 (4).

Sadanandam, A., Poudel, P., Fontana, E. & Ragulan, C. (2018). Characterizing heterogeneity in KRAS mutant colorectal cancers (CRC) using cellular, mutation, and immune profiles., JOURNAL OF CLINICAL ONCOLOGY, Vol.36 (4).

Sadanandam, A., Young, K., Nyamundanda, G., Ragulan, C., Lawlor, R. & Scarpa, A. (2018). Development of Multiplex Biomarker Assay to Subtype Pancreatic Neuroendocrine Tumors (PanNETs) with Distinct Prognosis and Mutations, NEUROENDOCRINOLOGY, Vol.106, p.164.

Cros, J., Bucau, M., Raffenne, J., Soukeur, M., Dumont, F., De Koning, L., de Mestier, L., Hentic, O., Sauvanet, A., Sadanandam, A., et al. (2018). Mitochondrial or Aerobic Glycolysis Oriented Metabolism May Define Pancreatic Neuroendocrine Tumors (PanNET) Resistance to mTOR-Targeting Therapies, NEUROENDOCRINOLOGY, Vol.106, p.27.

Fontana, E., Poudel, P., Nyamundanda, G., Patil, Y., Ragulan, C. & Sadanandam, A. (2017). Characterisation of heterogeneity in microsatellite instable (MSI) tumours associated with distinct cell types and immune phenotypes, ANNALS OF ONCOLOGY, Vol.28.

Sadanandam, A., Eason, K., Fontana, E., Nyamundanda, G., Del Rio, M., Si-Lin, K., Siew, T.W., Martineau, P., Tan, I.B. & Ragulan, C., et al. (2017). Development and validation of multiplex biomarker assay to stratify colorectal cancer (CRC) patient samples into subtypes, ANNALS OF ONCOLOGY, Vol.28.

Ragulan, C., Poudel, P., Young, K., Nyamundanda, G., Lawlor, R.T., Scarpa, A. & Sadanandam, A. (2017). Undiscovered immune heterogeneity in pancreatic adenocarcinoma (PDAC), ANNALS OF ONCOLOGY, Vol.28.

Fontana, E., Ragulan, C., Eason, K., Si-Lin, K., Siew, T.W., Nyamundanda, G., Patil, Y., Poudel, P., Chau, I., Tan, I.B., et al. (2017). Validated nCounter platform to stratify colorectal cancer (CRC) into Consensus Molecular Subtypes (CMS) and CRCassigner subtypes in Asian population, ANNALS OF ONCOLOGY, Vol.28, p.43.

Neuzillet, C., Tijeras-Raballand, A., Sadanandam, A., Bourgoin, P., Bourget, P., Poudel, P., Serova, M., De Gramont, A., Ruszniewski, P., Paradis, V., et al. (2016). Effects of MEK inhibition alone or in combination with PI3K-mTOR pathway inhibitors in pancreatic ductal adenocarcinoma in vitro and on an innovative ex vivo fresh tumor tissue culture model, CANCER RESEARCH, Vol.76.

Kapoor, A., Yao, W., Ying, H., Hua, S., Liewen, A., Sadanandam, A., Al-Khalil, R., Viale, A., Pettazzoni, P., Sanchez, N., et al. (2015). Yap1 activation enables bypass of oncogenic Kras addiction in pancreatic cancer, CANCER RESEARCH, Vol.75.

Guinney, J., Dienstmann, R., Wang, X., de Reynies, A., Schlicker, A., Soneson, C., Marisa, L., Roepman, P., Nyamundanda, G., Angelino, P., et al. (2015). Consensus molecular subtyping through a community of experts advances unsupervised gene expression-based disease classification and facilitates clinical translation, CANCER RESEARCH, Vol.75.

Damavandi, M.D., Braconi, C., Cascione, L., Lampis, A., Hahne, J., Murgia, C., Ghidini, M., Nyamundanda, G., Sadanandam, A., Croce, C., et al. (2015). Global gene expression profiling of mice tumor-derived organoids identifies key microRNAs and metabolic genes involved in CRC progression, CANCER RESEARCH, Vol.75.

Homicsko, K. & Sadanandam, A. (2014). NEW MOLECULAR CLASSIFICATION OF COLORECTAL CANCER, ANNALS OF ONCOLOGY, Vol.25.

Kapoor, A., Yao, W., Ying, H., Hua, S., Liewen, A., Wang, Q., Zhong, Y., Wu, C.-., Sadanandam, A., Hu, B., et al. (2014). Yap1 activation enables bypass of oncogenic Kras addiction in pancreatic cancer, MOLECULAR CANCER RESEARCH, Vol.12.

Dienstmann, R., Guinney, J., Delorenzi, M., De Reynies, A., Roepman, P., Sadanandam, A., Vermeulen, L., Schlicker, A., Missiaglia, E., Soneson, C., et al. (2014). Colorectal Cancer Subtyping Consortium (CRCSC) identification of a consensus of molecular subtypes., JOURNAL OF CLINICAL ONCOLOGY, Vol.32 (15).

Sadanandam, A. & Hanahan, D. (2013). Molecular genetic subtypes of pancreas and colon cancer: Phenotypes and potential therapeutic significance., CANCER RESEARCH, Vol.73 (8).

Sadanandam, A., Wullschleger, S., Spellman, P., Hanahan, D. & Gray, J.W. (2012). Recurrent fusion transcripts in breast cancer, CANCER RESEARCH, Vol.72.

Sadanandam, A., Collisson, E.A., Olson, P., Gibb, W.J., Truitt, M., Olshen, A., Tempero, M.A., Spellman, P.T., Hanahan, D. & Gray, J.W., et al. (2011). Molecular subtypes of pancreatic adenocarcinoma with different biological characteristics and therapeutical responses, CANCER RESEARCH, Vol.71.

Sadanandam, A., Gibb, W., Heiser, L., Kuo, W.-., Spellman, P. & Gray, J. (2009). Integrated omic analysis of breast cancer cell lines, CANCER RESEARCH, Vol.69.

Singh, R., Varney, M., Sadanandam, A., Solheim, J. & Talmadge, J. (2007). Vascular endothelial growth factor (VEGF)-C and VEGF receptor-3 signaling directly and indirectly modulates murine mammary tumor growth and metastasis, CLINICAL & EXPERIMENTAL METASTASIS, Vol.24 (4), p.232.

Sadanandam, A., Varney, M.L., Hollingsworth, M.A., Batra, S.K., Sretavan, D.W., Puschel, A.W. & Singh, R.K. (2007). Expression of semaphorin 5A in metastatic pancreatic cancer cells and modulates cellular proliferation, invasion and tumor growth and metastasis, CLINICAL & EXPERIMENTAL METASTASIS, Vol.24 (4), pp.256-257.

Sadanandam, A., Varney, M.L., Hollingsworth, M.A., Batra, S.K., Sretavan, D.W., Pueschel, A.W. & Singh, R.K. (2006). SEMA5A expression in pancreatic cancer is associated with metastases and regulates pancreatic cancer cell proliferation and their adherence in different microenvironment, CANCER RESEARCH, Vol.66 (8).

Futakuchi, M., Varney, M.L., Sadanandam, A., Nakao, K., Asai, K., Shirai, T. & Singh, R.K. (2006). TGF-beta directly and indirectly promote mammary tumor growth in the bone microenvironment by increasing osteoclastgenesis, CANCER RESEARCH, Vol.66 (8).

Varney, M.L., Sadanandam, A., Solheim, J.C., Talmadge, J.E. & Singh, R.K. (2006). VEGFR3 antagonist (MAZ51) directly and indirectly inhibits murine mammary tumor growth and metastasis, CANCER RESEARCH, Vol.66 (8).

Sadanandam, A., Futakuchi, M., Varney, M., Qiu, F. & Singh, R. (2006). Gene expression profiling using a unique murine mammary tumor model reveal role of novel genes regulating tumor-stromal interaction in mammary tumor-induced osteolysis, FASEB JOURNAL, Vol.20 (4), p.A222.

Huang, X., Ali, H.H., Sadanandam, A. & Singh, R.K. (2005). Protein Motif Searching Through Similar Enriched Parikh Vector Identification., BIBE, , pp.285-289.

Huang, X., Ali, H.H., Sadanandam, A. & Singh, R.K. (2004). SRPVS: A New Motif Searching Algorithm for Protein Analysis., CSB, , pp.674-675.

Sadanandam, A., Varney, M.L. & Singh, R.K. (2004). High-Throughput Computational and Experimental Biology Strategy in Identifying Tumor Expressing CAMs., CSB, , pp.450-451.