Nexus Copy Number

A new molecular assay and genomic complexity predict outcome in conventional and leukemic non-nodal mantle cell lymphoma

Guillem Clot, Pedro Jares, Eva Giné, Alba Navarro, Cristina Royo, Magda Pinyol, David Martín-Garcia, Santiago Demajo, Blanca Espinet, Antonio Salar, Ana Ferrer, Ana Muntañola, Marta Aymerich, Hilka Rauert-Wunderlich, Elaine S. Jaffe, Joseph M. Connors, Randy D. Gascoyne, Jan Delabie, Armando López-Guillermo, German Ott, George W. Wright, Louis M. Staudt, Andreas Rosenwald, David W. Scott, Lisa M. Rimsza, Sílvia Beà and Elías Campo. Blood 2018 :blood-2018-03-838136. May 10, 2018.

Expanded Genomic Profiling of Circulating Tumor Cells in Metastatic Breast Cancer Patients to Assess Biomarker Status and Biology Over Time (CALGB 40502 and CALGB 40503, Alliance)

Mark Jesus M. Magbanua, Hope S. Rugo, Denise M. Wolf, Louai Hauranieh, Ritu Roy, Praveen Pendyala, Eduardo V. Sosa, Janet H. Scott, Jin Sun Lee, Brandelyn Pitcher, Terry Hyslop, William T. Barry, Steven J. Isakoff, Maura Dickler, Laura van't Veer and John W. Park.Clinical Cancer Research; Biology of Human Tumors; AACR Publications. March 2018.

Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma.

Casuscelli J, Weinhold N, Gundem G, Wang L, Zabor EC, Drill E, Wang PI, Nanjangud GJ, Redzematovic A, Nargund AM, Manley BJ, Arcila ME, Donin NM, Cheville JC, Thompson RH, Pantuck AJ, Russo P, Cheng EH, Lee W, Tickoo SK, Ostrovnaya I, Creighton CJ, Papaemmanuil E, Seshan VE, Hakimi AA, Hsieh JJ. JCI Insight. 2017 Jun 15;2(12). [Epub ahead of print]


Microarray analysis to identifiy novel copy number alterations in acute myeloid leukemia.

Maria Chiara Fontana, Giovanni Marconi, Cristina Papayannidis, Eugenio Fonzi, Emanuela Ottaviani, Eugenia Franchini, Anna Ferrari, Giorgia Simonetti, Antonella Padella, Samantha Bruno, Nicoletta Testoni, Carmen Baldazzi, Andrea Ghelli Luserna di Rorà, Valentina Robustell†, Maria Chiara Abbenante, Stefania Paolini, Jacopo Nanni, Luca Bertamini, Giovanni Martinelli. Journal of Clinical Oncology. 2017 May;35(15_suppl):11622-11622.

Precision Medicine Analysis Of 203 Pediatric Brain Tumors Reveals Clinically Relevant Genomic Alterations

Pratiti Bandopadhayay Shakti Ramkissoon Jaeho Hwang Lori Ramkissoon Noah Greenwald Steven Schumacher Ryan O’Rourke Nathan Pinches Patricia Ho Hayley Malkin Claire Sinai Mariella Filbin Ashley Plant Wenya Bi Michael Chang Edward Yang Karen Wright Peter Manley Matthew Ducar Sanda Alexandrescu Hart Lidov Ivana Delalle Liliana Goumnerova Alanna Church Katherine Janeway Marian Harris Laura MacConaill Rebecca Folkerth Neal Lindeman Charles Stiles Mark Kieran Azra Ligon Sandro Santagata Adrian Dubuc Susan Chi Rameen Beroukhim Keith Ligon. Neuro Oncol (2017) 19 (suppl_4): iv20.

Genomic imbalances in syndromic congenital heart disease.

Coelho Molck M, Simioni M, Paiva Vieira T, Sgardioli IC, Paoli Monteiro F, Souza J, Fett-Conte AC, Félix TM, Lopes Monlléo I, Gil-da-Silva-Lopes VL. J Pediatr (Rio J). 2017 Mar 21. pii: S0021-7557(17)30218-8. doi: 10.1016/j.jped.2016.11.007. [Epub ahead of print]

Loss of LMOD1 impairs smooth muscle cytocontractility and causes megacystis microcolon intestinal hypoperistalsis syndrome in humans and mice.

Halim D, Wilson MP, Oliver D, Brosens E, Verheij JB, Han Y, Nanda V, Lyu Q, Doukas M, Stoop H, Brouwer RW, van IJcken WF, Slivano OJ, Burns AJ, Christie CK, de Mesy Bentley KL, Brooks AS, Tibboel D, Xu S, Jin ZG, Djuwantono T, Yan W, Alves MM, Hofstra RM, Miano JM. Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):E2739-E2747. doi: 10.1073/pnas.1620507114. Epub 2017 Mar 14.

Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes.

Gui H, Schriemer D, Cheng WW, Chauhan RK, Antiňolo G, Berrios C, Bleda M, Brooks AS, Brouwer RW, Burns AJ, Cherny SS, Dopazo J, Eggen BJ, Griseri P, Jalloh B, Le TL, Lui VC, Luzón-Toro B, Matera I, Ngan ES, Pelet A, Ruiz-Ferrer M, Sham PC, Shepherd IT, So MT, Sribudiani Y, Tang CS, van den Hout MC, van der Linde HC, van Ham TJ, van IJcken WF, Verheij JB, Amiel J, Borrego S, Ceccherini I, Chakravarti A, Lyonnet S, Tam PK, Garcia-Barceló MM, Hofstra RM. Genome Biol. 2017 Mar 8;18(1):48. doi: 10.1186/s13059-017-1174-6.

Germline BRCA2 mutations drive prostate cancers with distinct evolutionary trajectories

Taylor RA, Fraser M, Livingstone J, Espiritu SM, Thorne H, Huang V, Lo W, Shiah YJ, Yamaguchi TN, Sliwinski A, Horsburgh S, Meng A, Heisler LE, Yu N, Yousif F, Papargiris M, Lawrence MG, Timms L, Murphy DG, Frydenberg M, Hopkins JF, Bolton D, Clouston D, McPherson JD, van der Kwast T, Boutros PC, Risbridger GP, Bristow RG. Nat Commun. 2017 Jan 9;8:13671.


Genomic hallmarks of localized, non-indolent prostate cancer

Michael Fraser, Veronica Y. Sabelnykova, Takafumi N. Yamaguchi, Lawrence E. Heisler, Julie Livingstone, Vincent Huang, Yu-Jia Shiah, Fouad Yousif, Xihui Lin, Andre P. Masella, Natalie S. Fox, Michael Xie, Stephenie D. Prokopec, Alejandro Berlin, Emilie Lalonde, Musaddeque Ahmed, Dominique Trudel, Xuemei Luo, Timothy A. Beck, Alice Meng, Junyan Zhang, Alister D’Costa, Robert E. Denroche, Haiying Kong, Shadrielle Melijah G. Espiritu, Melvin L. K. Chua, Ada Wong, Taryne Chong, Michelle Sam, Jeremy Johns, Lee Timms, Nicholas B. Buchner, Michèle Orain, Valérie Picard, Helène Hovington, Alexander Murison, Ken Kron, Nicholas J. Harding, Christine P’ng, Kathleen E. Houlahan, Kenneth C. Chu, Bryan Lo, Francis Nguyen, Constance H. Li, Ren X. Sun, Richard de Borja, Christopher I. Cooper, Julia F. Hopkins, Shaylan K. Govind, Clement Fung, Daryl Waggott, Jeffrey Green, Syed Haider, Michelle A. Chan-Seng-Yue, Esther Jung, Zhiyuan Wang, Alain Bergeron, Alan Dal Pra, Louis Lacombe, Colin C. Collins, Cenk Sahinalp, Mathieu Lupien, Neil E. Fleshner, Housheng H. He, Yves Fradet, Bernard Tetu, Theodorus van der Kwast, John D. McPherson, Robert G. Bristow & Paul C. Boutros. Nature. 2017 Jan 9. [Epub ahead of print]

Complex Mosaic Ring Chromosome 11 Associated with Hemizygous Loss of 8.6 Mb of 11q24.2qter in Atypical Jacobsen Syndrome

Galvão Gomes A. Paiva Grangeiro C.H. Silva L.R. Oliveira-Gennaro F.G. Pereira C.S. Joaquim T.M. Panepucci R.A. Squire J.A. Martelli L. Mol Syndromol 2017;8:45-49
(DOI:10.1159/000452681)

Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study.

Shi J, Hua X, Zhu B, Ravichandran S, Wang M, Nguyen C, Brodie SA, Palleschi A, Alloisio M, Pariscenti G, Jones K, Zhou W, Bouk AJ, Boland J, Hicks B, Risch A, Bennett H, Luke BT, Song L, Duan J, Liu P, Kohno T, Chen Q, Meerzaman D, Marconett C, Laird-Offringa I, Mills I, Caporaso NE, Gail MH, Pesatori AC, Consonni D, Bertazzi PA, Chanock SJ, Landi MT. PLoS Med. 2016 Dec 6;13(12):e1002162.



Gene copy number variation in male breast cancer by aCGH

Stefania Tommasi, Anita Mangia, Giuseppina Iannelli, Patrizia Chiarappa, Elena Rossi, Laura Ottini, Marcella Mottolese, Wainer Zoli, Orsetta Zuffardi, Angelo Paradiso. 2010 Nov. Analytical Cellular Pathology / Cellular Oncology.

Oligonucleotide-based array CGH analysis of diffuse large B-cell lymphomas identifies gain of 7q22 as the most common genomic alteration

Edward A. Medina, Aswani R Bolla, Rajya L Bandi and Ryan S Robetorye. FASEB J. 2010 24:954.11.

Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis.

Baranzini SE, Mudge J, van Velkinburgh JC, Khankhanian P, Khrebtukova I, Miller NA, Zhang L, Farmer AD, Bell CJ, Kim RW, May GD, Woodward JE, Caillier SJ, McElroy JP, Gomez R, Pando MJ, Clendenen LE, Ganusova EE, Schilkey FD, Ramaraj T, Khan OA, Huntley JJ, Luo S, Kwok PY, Wu TD, Schroth GP, Oksenberg JR, Hauser SL, Kingsmore SF. Nature. 2010 Apr 29;464(7293):1351-6.

Genetics of uveal melanoma

Hanneke W Mensink, Dion Paridaens, Annelies de Klein Expert Review of Ophthalmology, December 2009, Vol. 4, No. 6, Pages 607-616.

Genomic Landscape of Meningiomas.

Lee Y, Liu J, Patel S, Cloughesy T, Lai A, Farooqi H, Seligson D, Dong J, Liau L, Becker D, Mischel P, Shams S, Nelson S.Brain Pathol. 2009 Nov 20.

Challenges In Array CGH For the Analysis Of Cancer Samples

Nowak NJ, Miecznikowski J, Moore SR, Gaile D, Bobadilla D, Smith DD, Kernstine K, Forman SJ, Mwahech-Fauceglia P, Reid M, Stoler D, Loree T, Rigual N, Sullivan M, Weiss LM, Hicks D, Slovak ML. Challenges In Array CGH For the Analysis Of Cancer Samples. Genetics in Medicine, 9(9): 585-595, 2007.
[PubMed]

A highly annotated whole-genome sequence of a Korean individual.

Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Kim H, Yang KS, Park WY, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS. Nature. 2009 Jul 8.

Multiple sub-microscopic genomic lesions are a universal feature of chronic myeloid leukaemia at diagnosis

Khorashad JS, De Melo VA, Fiegler H, Gerrard G, Marin D, Apperley JF, Goldman JM, Foroni L, Reid AG. Leukemia. 2008 Sep;22(9):1806-7. Epub 2008 Jul 31.
[Abstract] [PubMed]

6.7 Mb interstitial duplication in chromosome band 11q24.2q25 associated with infertility, minor dysmorphic features and normal psychomotor development

Göhring Ina; Blümlein Hans-Martin; Hoyer Juliane; Ekici Arif B; Trautmann Udo; Rauch Anita. Eur J Med Genet. 2008 Nov-Dec;51(6):666-71. Epub 2008 Aug 12.
[PubMed]

Multiple sub-microscopic genomic lesions are a universal feature of chronic myeloid leukaemia at diagnosis

Khorashad JS, De Melo VA, Fiegler H, Gerrard G, Marin D, Apperley JF, Goldman JM, Foroni L, Reid AG. Leukemia. 2008 Sep;22(9):1806-7. Epub 2008 Jul 31.
[Abstract] [PubMed]

DNA Copy Number Stratification of Breast Cancer Samples Identifies Distinct Biological Mechanisms

S. Shams, R. Davis, B. Poirier, J. Gregg. Poster presentation at AACR Translational Cancer Medicine Conference, July 2008, San Diego, CA.

Detection of copy number alterations in metastatic melanoma by a DNA fluorescence in situ hybridization probe panel and array comparative genomic hybridization: a southwest oncology group study (S9431)

Moore SR, Persons DL, Sosman JA, Bobadilla D, Bedell V, Smith DD, Wolman SR, Tuthill RJ, Moon J, Sondak VK, Slovak ML. Detection of copy number alterations in metastatic melanoma by a DNA fluorescence in situ hybridization probe panel and array comparative genomic hybridization: a southwest oncology group study (S9431). Clin Cancer Res. 2008 May 15;14(10):2927-35. [PubMed]
[PubMed]

Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia

Tom Walsh, Jon M. McClellan, Shane E. McCarthy, Anjene M. Addington, Sarah B. Pierce, Greg M. Cooper, Alex S. Nord, Mary Kusenda, Dheeraj Malhotra, Abishek Bhandari, Sunday M. Stray, Caitlin F. Rippey, Patricia Roccanova, Vlad Makarov, B. Lakshmi, Robert L. Findling, Linmarie Sikich, Thomas Stromberg , Barry Merriman, Nitin Gogtay, Philip Butler, Kristen Eckstrand, Laila Noory, Peter Gochman, Robert Long, Zugen Chen, Sean Davis, Carl Baker, Evan E. Eichler, Paul S. Meltzer, Stanley F. Nelson, Andrew B. Singleton, Ming K. Lee, Judith L. Rapoport, Mary-Claire King, Jonathan Sebat. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science, 27 March 2008. (10.1126/science.1155174).
[Abstract]

A de-novo 7.6 Mb tandem duplication of 14q32.2-qter associated with primordial short stature with neurosecretory growth hormone dysfunction, distinct facial anomalies and mild developmental delay

Thiel CT, Dörr HG, Trautmann U, Hoyer J, Hofmann K, Kraus C, Ekici AB, Reis A, Rauch A. A de novo 7.6Mb tandem duplication of 14q32.2-qter associated with primordial short stature with neurosecretory growth hormone dysfunction, distinct facial anomalies and mild developmental delay. Eur J Med Genet. 2008 Jul-Aug; 51(4):362-7. Epub 2008 Mar 20.
[PubMed]

3.8 MB Deletion of Chromosome 5q in a Newborn Tracheal Agenesis Patient

Elisabeth de Jong, Hannie Douben, Bert Eussen, Dick Tibboel and Annelies de Klein. Poster presentation at ASHG 2008, Philadelphia, PA

Nexus Expression

Overexpression of Transcobalamin 1 is an Independent Negative Prognosticator in Rectal Cancers Receiving Concurrent Chemoradiotherapy.

Lee YY, Wei YC, Tian YF, Sun DP, Sheu MJ, Yang CC, Lin LC, Lin CY, Hsing CH, Li WS, Li CF, Hsieh PL, Lin CY. J Cancer. 2017 May 12;8(8):1330-1337.
[PubMed]

Downregulation of RNF128 Predicts Progression and Poor Prognosis in Patients with Urothelial Carcinoma of the Upper Tract and Urinary Bladder

Lee YY, Wang CT, Huang SK, Wu WJ, Huang CN, Li CC, Chan TC, Liang PI, Hsing CH, Li CF. J Cancer. 2016 Oct 25;7(15):2187-2196.

DNA Damage-Mediated c-Myc Degradation Requires 14-3-3 Sigma

Wen, Yu-Ye; Chou, Ping-Chieh; Phan, Liem; Su, Chun-Hui; Chen, Jian; Hsieh, Yun-Chi; Xue, Yu-Wen; Qu, Chang-Ju; Gully, Chris; Parreno, Ken; Teng, Chiehlin; Hsu, Shih-Lan; Yeung, Sai-Ching; Wang, Huamin; Lee, Mong-Hong Cancer Hallmarks, Volume 1, Number 1, March 2013 , pp. 3-17(15).

Human TCR-alpha beta+ CD4- CD8- T cells can derive from CD8+ T cells and display an inflammatory effector phenotype.

Crispín JC, Tsokos GC. J Immunol. 2009 Oct 1;183(7):4675-81. Epub 2009 Sep 4.
[PubMed]

Human TCR-alpha beta+ CD4- CD8- T cells can derive from CD8+ T cells and display an inflammatory effector phenotype.

Crispín JC, Tsokos GC. J Immunol. 2009 Oct 1;183(7):4675-81. Epub 2009 Sep 4. [PubMed]
[PubMed]

ImaGene

New methods to analyse microarray data that partially lack a reference signal.

Carpaij N, Fluit AC, Lindsay JA, Bonten MJ, Willems RJ. BMC Genomics. 2009 Nov 13;10:522. [PubMed]






































[PubMed]

New methods to analyse microarray data that partially lack a reference signal.

Carpaij N, Fluit AC, Lindsay JA, Bonten MJ, Willems RJ. BMC Genomics. 2009 Nov 13;10:522.
[PubMed]

Identification of a novel microRNA cluster miR-193b-365 in multiple myeloma.

Unno K, Zhou Y, Zimmerman T, Platanias LC, Wickrema A. Leuk Lymphoma. 2009 Nov;50(11):1865-71. [PubMed]





































[PubMed]

Loading-related regulation of gene expression in bone in the contexts of estrogen deficiency, lack of estrogen receptor alpha and disuse.

Zaman G, Saxon LK, Sunters A, Hilton H, Underhill P, Williams D, Price JS, Lanyon LE. Bone. 2009 Oct 24. [Epub ahead of print] [PubMed]




































[PubMed]

FOXP3 inhibits activation-induced NFAT2 expression in T cells thereby limiting effector cytokine expression.

Torgerson TR, Genin A, Chen C, Zhang M, Zhou B, Añover-Sombke S, Frank MB, Dozmorov I, Ocheltree E, Kulmala P, Centola M, Ochs HD, Wells AD, Cron RQ. J Immunol. 2009 Jul 15;183(2):907-15. Epub 2009 Jun 29. [PubMed]

































[PubMed]

Dicer-dependent microRNA pathway controls invariant NKT cell development.

Fedeli M, Napolitano A, Wong MP, Marcais A, de Lalla C, Colucci F, Merkenschlager M, Dellabona P, Casorati G. J Immunol. 2009 Aug 15;183(4):2506-12. Epub 2009 Jul 22. [PubMed]


































[PubMed]

Anti-carbohydrate antibodies of normal sera: findings, surprises and challenges.

Huflejt ME, Vuskovic M, Vasiliu D, Xu H, Obukhova P, Shilova N, Tuzikov A, Galanina O, Arun B, Lu K, Bovin N. Mol Immunol. 2009 Sep;46(15):3037-49. Epub 2009 Jul 15. [PubMed]



































[PubMed]

Use of spermatozoal mRNA profiles to study gene-environment interactions in human germ cells.

Linschooten JO, Van Schooten FJ, Baumgartner A, Cemeli E, Van Delft J, Anderson D, Godschalk RW. Mutat Res. 2009 Jul 10;667(1-2):70-6. [PubMed]
































[PubMed]

Genome-wide identification of long noncoding RNAs in CD8+ T cells.

Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chen W, Mattick JS. J Immunol. 2009 Jun 15;182(12):7738-48. [PubMed]






























[PubMed]

Transcriptomic analysis of aorta from a short-term high-fat diet fed mouse reveals changes in the expression of vessel structure genes.

Dejeans N, Auclair S, Chauvet S, Milenkovic D, Mazur A. J Physiol Pharmacol. 2009 May;60 Suppl 1:37-45. [PubMed]































[PubMed]

Consequences of perinatal treatment with L-arginine and antioxidants for the renal transcriptome in spontaneously hypertensive rats.

Wesseling S, Koeners MP, Kantouh F, Joles JA, Braam B. Pflugers Arch. 2009 Jul;458(3):513-24. Epub 2009 Feb 3. [PubMed]































[PubMed]

In vivo knockdown of the androgen receptor results in growth inhibition and regression of well-established, castration-resistant prostate tumors

Snoek R, Cheng H, Margiotti K, Wafa LA, Wong CA, Wong EC, Fazli L, Nelson CC, Gleave ME, Rennie PS. Clin Cancer Res. 2009 Jan 1;15(1):39-47. [PubMed]






























[PubMed]

Regulation of hepatic metabolic pathways by the orphan nuclear receptor SHP

Konstantinos Boulias, Nitsa Katrakili, Krister Bamberg, Peter Underhill, Andy Greenfield, Iannis Talianidis. Regulation of hepatic metabolic pathways by the orphan nuclear receptor SHP. The EMBO Journal 24, 2624-2633 (20 Jul 2005)

Gene expression in thyroid autonomous adenomas provides insight into their physiopathology.

Sandrine Wattel, Hortensia Mircescu, David Venet, Agnes Burniat, Brigitte Franc, Sandra Frank, Guy Andry, Jacqueline Van Sande, Pierre Rocmans, Jacques E Dumont, Vincent … Gene expression in thyroid autonomous adenomas provides insight into their physiopathology. Oncogene , (18 Jul 2005)

Variation in tissue-specific gene expression among natural populations

Andrew Whitehead, Douglas L Crawford. Variation in tissue-specific gene expression among natural populations Genome Biology 2005 6:R13 http://genomebiology.com/2005/6/2/r13

The transcriptome of HCV replicon expressing cell lines in the presence of alpha interferon

Junpei Hayashi, Radka Stoyanova and Christoph Seeger. The transcriptome of HCV replicon expressing cell lines in the presence of alpha interferon. Virology, Volume 335, Issue 2, 10 May 2005, Pages 264-275

Altered gene expression in phenotypically normal renal cells from carriers of tumor suppressor gene mutations

Stoyanova R, Clapper ML, Bellacosa A, Henske EP, Testa JR, Ross EA, Yeung AT, Nicolas E, Tsichlis N, Li YS, Linehan WM, Howard S, Campbell KS, Godwin AK, Boman BM, Crowell JA, Kopelovich L, Knudson AG. Altered gene expression in phenotypically normal renal cells from carriers of tumor suppressor gene mutations. Cancer Biol Ther. 2004 Dec;3(12):1313-21. Epub 2004 Dec 9. PMID: 15662135 [PubMed – indexed for MEDLINE]


Use of RNA amplification in the optimal characterization of global gene expression using cDNA microarrays

Stoyanova R, Upson JJ, Patriotis C, Ross EA, Henske EP, Datta K, Boman B, Clapper ML, Knudson AG, Bellacosa A. Use of RNA amplification in the optimal characterization of global gene expression using cDNA microarrays. J Cell Physiol. 2004 Dec;201(3):359-65. PMID: 15389558 [PubMed – indexed for MEDLINE]

Optimized procedures for microarray analysis of histological specimens processed by laser capture microdissection

Upson JJ, Stoyanova R, Cooper HS, Patriotis C, Ross EA, Boman B, Clapper ML, Knudson AG, Bellacosa A. Optimized procedures for microarray analysis of histological specimens processed by laser capture microdissection. J Cell Physiol. 2004 Dec;201(3):366-73. PMID: 15389559 [PubMed – indexed for MEDLINE]

Microarray Image Processing and Quality Control, The Journal of VLSI Signal Processing, scheduled to appear in special Microarray issue

Petrov, A., Shams, S., Microarray Image Processing and Quality Control, The Journal of VLSI Signal Processing, scheduled to appear in special Microarray issue (October, 2004).

The Global Error Assessment Model for the Selection of Differentially Expressed Genes in Microarray Data

Mansourian, R., Mutch, D., Antille, N., Aubert, J., Fogel, P., Goff, J., Moulin, J., Petrov, A., Rytz, A., Voegel, J., Roberts, M., The Global Error Assessment Model for the Selection of Differentially Expressed Genes in Microarray Data, scheduled to appear in Bioinformatics in September 2004.



Microarray analysis identified differentially expressed genes in keratocytes from keratoconus patients

Ha NT, Nakayasu K, Murakami A, Ishidoh K, Kanai A. Microarray analysis identified differentially expressed genes in keratocytes from keratoconus patients. Curr Eye Res. 2004 Jun;28(6):373-9. PMID: 15512944 [PubMed – indexed for MEDLINE]

Plakoglobin is a new target gene of histone deacetylase in human fibrosarcoma HT1080 cells

Joong Sup Shim, Dong Hoon Kim, Ho Jeong Kwon. Plakoglobin is a new target gene of histone deacetylase in human fibrosarcoma HT1080 cells. Oncogene 23, 1704-1711 (04 Mar 2004)

DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray.

Siew Loon Ooi, Daniel D Shoemaker, Jef D Boeke. DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. Nature Genetics 35, 277-286 (01 Nov 2003)

Disruption of the c-JUN-JNK Complex by a Cell-permeable Peptide Containing the c-JUN Domain Induces Apoptosis and Affects a Distinct Set of Interleukin-1-induced Inflammatory Genes.

Holzberg, David , C. Graham Knight, Oliver Dittrich-Breiholz, Heike Schneider, Anneke Dörrie, Elke Hoffmann, Klaus Resch, and Michael Kracht. Disruption of the c-JUN-JNK Complex by a Cell-permeable Peptide Containing the c-JUN Domain Induces Apoptosis and Affects a Distinct Set of Interleukin-1-induced Inflammatory Genes. J. Biol. Chem., Oct 2003; 278: 40213 – 40223.

















Structure-activity relationship of synthetic toll-like receptor 4 agonists.

Stöver, Axel G. , Jean Da Silva Correia, Jay T. Evans, Christopher W. Cluff, Mark W. Elliott, Eric W. Jeffery, David A. Johnson, Michael J. Lacy, Jory R. Baldridge, Peter Probst, Richard J. Ulevitch, David H. Persing, and Robert M. Hershberg. Structure-activity relationship of synthetic toll-like receptor 4 agonists. J. Biol. Chem., Oct 2003; 10.1074/jbc.M310760200

Screening for ovarian cancer-associated genes with cDNA microarrays

Zhang XY, Li XP, Lai J, Feng J. Screening for ovarian cancer-associated genes with cDNA microarrays. Ai Zheng. 2003 Sep;22(9):943-7. Chinese. PMID: 12969526 [PubMed – indexed for MEDLINE]

Adult midgut expressed sequence tags from the tsetse fly Glossina morsitans morsitans and expression analysis of putative immune response genes

Lehane MJ, Aksoy S, Gibson W, Kerhornou A, Berriman M, Hamilton J, Soares MB, Bonaldo MF, Lehane S, Hall N . Adult midgut expressed sequence tags from the tsetse fly Glossina morsitans morsitans and expression analysis of putative immune response genes. Genome Biology 2003, 4(10):R63 (11 September 2003) http://genomebiology.com/2003/4/10/R63

Computational Methods for Selection of Differentially Regulated Genes in Cell Immortalization

Draghici, S., Kulaeva, O., Hoff, B., Petrov, A., Shams, S., Tainsky, M. A. , Computational Methods for Selection of Differentially Regulated Genes in Cell Immortalization, Bioinformatics, September 2003


























Noise Sampling Method: an ANOVA Approach Allowing Robust Selection of Differentially Regulated Genes Measured by DNA Microarrays, Bioinformatics

Draghici S, Kulaeva O, Hoff B, Petrov A, Shams S, Tainsky MA (2003) Noise Sampling Method: an ANOVA Approach Allowing Robust Selection of Differentially Regulated Genes Measured by DNA Microarrays, Bioinformatics, 2003 Jul 22;19(11):1348-59






























Epigenetic silencing of multiple interferon pathway genes after cellular immortalization

Olga I Kulaeva, Sorin Draghici, Lin Tang, Janice M Kraniak, Susan J Land, Michael A Tainsky. . Epigenetic silencing of multiple interferon pathway genes after cellular immortalization. Oncogene 22, 4118-4127 (26 Jun 2003)

Genomic Expression Discovery Predicts Pathways and Opposing Functions behind Phenotypes

Fathallah-Shaykh, Hassan M., He, Bin, Zhao, Li-Juan, Engelhard, Herbert H., Cerullo, Leonard, Lichtor, Terry, Byrne, Richard, Munoz, Lorenzo, Von Roenn, Kelvin, Rosseau, Gail L., Glick, Roberta, Sherman, Chen, and Farooq, Khan . Genomic Expression Discovery Predicts Pathways and Opposing Functions behind Phenotypes. J. Biol. Chem., Jun 2003; 278: 23830 – 23833.
























Molecular network and functional implications of macromolecular tRNA synthetase complex

Han JM, Kim JY, Kim S. Molecular network and functional implications of macromolecular tRNA synthetase complex. Biochem Biophys Res Commun. 2003 Apr 18; 303(4): 985-93. Review. PMID: 12684031 [PubMed – indexed for MEDLINE]

Analysis of Gene Expression Profile of Pancreatic Carcinoma using cDNA Microarray.

Tan ZJ, Hu XG, Cao GS, Tang Y. Analysis of Gene Expression Profile of Pancreatic Carcinoma using cDNA Microarray. World J Gastroenterol. 2003 Apr;9(4):818-23.

Transcriptome analysis of Sinorhizobium meliloti during symbiosis.

Frederic Ampe, Ernö Kiss, Frédérique Sabourdy, Jacques Batut. Transcriptome analysis of Sinorhizobium meliloti during symbiosis. Genome Biology 2003 4:R15 http://genomebiology.com/2003/4/2/r15

Bikunin Target Genes in Ovarian Cancer Cells Identified by Microarray Analysis


Suzuki, Mika , Hiroshi Kobayashi, Yoshiko Tanaka, Yasuyuki Hirashima, Naohiro Kanayama, Yuji Takei, Yasushi Saga, Mitsuaki Suzuki, Hiroshi Itoh, and Toshihiko Terao. Bikunin Target Genes in Ovarian Cancer Cells Identified by Microarray Analysis. J. Biol. Chem., Apr 2003; 278: 14640 – 14646.

Difference of gene expression profiles between esophageal carcinoma and its pericancerous epithelium by gene chip

Xu SH, Qian LJ, Mou HZ, Zhu CH, Zhou XM, Liu XL, Chen Y, Bao WY. Difference of gene expression profiles between esophageal carcinoma and its pericancerous epithelium by gene chip. World J Gastroenterol. 2003 Mar; 9(3): 417-22. PMID: 12632488 [PubMed – indexed for MEDLINE]

Gene-engineered Rigidification of Membrane Lipids Enhances the Cold Inducibility of Gene Expression in Synechocystis

Inaba, Masami , Iwane Suzuki, Balázs Szalontai, Yu Kanesaki, Dmitry A. Los, Hidenori Hayashi, and Norio Murata. Gene-engineered Rigidification of Membrane Lipids Enhances the Cold Inducibility of Gene Expression in Synechocystis. J. Biol. Chem., Mar 2003; 278: 12191 – 12198.















Preadipocyte Conversion to Macrophage. EVIDENCE OF PLASTICITY.

Charrière, G., Cousin, B., Arnaud, E., André, M., Bacou, F., Pénicaud, L., and Casteilla, L. . Preadipocyte Conversion to Macrophage. EVIDENCE OF PLASTICITY. J. Biol. Chem., Mar 2003; 278: 9850 – 9855.































Up-regulated Smad5 Mediates Apoptosis of Gastric Epithelial Cells Induced by Helicobacter

Nagasako, Tomokazu , Toshiro Sugiyama, Takuji Mizushima, Yosuke Miura, Mototsugu Kato, and Masahiro Asaka. Up-regulated Smad5 Mediates Apoptosis of Gastric Epithelial Cells Induced by Helicobacter pylori Infection. J. Biol. Chem., Feb 2003; 278: 4821 – 4825.


Significance Testing Among Groups using GeneSight, in Data Analysis Tools for Microarrays,

Hoff B, Significance Testing Among Groups using GeneSight, in Data Analysis Tools for Microarrays, S. Draghici ed., Chapman and Hall/CRC Press, 2003.




















A Comprehensive Microarray Data Management Approach in Microarrays Methods and Applications: Nuts & Bolts

Kiyoko AF, Petrov, A., A Comprehensive Microarray Data Management Approach in Microarrays Methods and Applications: Nuts & Bolts, G. Hardimann (ed.), DNA Press (2003)











Image Analysis Issues and Solutions for High-Density Arrays in Protein Microarray Technology

Petrov, A., Shams, S., Image Analysis Issues and Solutions for High-Density Arrays in Protein Microarray Technology, Dev Kambhampati (ed.), Wiley Publishers (2003)

Gene Expression-Based Tumor Classification with GeneSight from BioDiscovery, Inc.

Hoff, B., Shams, S., Kuklin, A. Gene Expression-Based Tumor Classification with GeneSight from BioDiscovery, Inc., Dispatches from the Forefront of Array BioInformatics Vol. 1, No.,



















An Emerging Technology for the Characterization of Antibodies Biotechniques

Schwenk,Jochen M., Stroll, Dieter, Templin, Markus F., And Joos, Thomas O. Cell Microarrays : An Emerging Technology for the Characterization of Antibodies Biotechniques 33:S54-61 December 2002.







Pathway Confers Basement Membrane Dependence upon Endoderm Differentiation of Embryonic Carcinoma Cells.

Smedberg, Jennifer L., Smith, Elizabeth R., Capo-chichi, Callinice D., Frolov, Andrey, Yang, Dong-Hua, Godwin, Andrew K., and Xu, Xiang-Xi Ras/MAPK Pathway Confers Basement Membrane Dependence upon Endoderm Differentiation of Embryonic Carcinoma Cells. J. Biol. Chem., Oct 2002; 277: 40911 – 40918.


Global Expression Profiling of Acetate-grown Escherichia coli.

Oh, Min-Kyu , Lars Rohlin, Katy C. Kao, and James C. Liao. Global Expression Profiling of Acetate-grown Escherichia coli. J. Biol. Chem., Apr 2002; 277: 13175 – 13183.

Gene expression profile differences in high and low metastatic human ovarian cancer cell lines by gene chip

Xu S, Mou H, Lu G, Zhu C, Yang Z, Gao Y, Lou H, Liu X, Cheng Y, Yang W. Gene expression profile differences in high and low metastatic human ovarian cancer cell lines by gene chip. Chin Med J (Engl). 2002 Jan; 115(1): 36-41. PMID: 11930655 [PubMed – indexed for MEDLINE]

Microarray Image Processing and Quality Control, in DNA Array Image Analysis Nuts & Bolts

Petrov, A., Shah, S., Draghici, S.,Shams, S. , Microarray Image Processing and Quality Control, in DNA Array Image Analysis Nuts & Bolts, G. Kamberova, S. Shah (ed.), Ch. 6, DNA Press (2002)

Data Analysis and Visualization in DNA Microarrays,Introduction to Bioinformatics

Draghici, S. Data Analysis and Visualization in DNA Microarrays,Introduction to Bioinformatics, S.Krawetz and D. Womble (Eds.), Humana Press, 2002.





























Investigation of genotyping HLA DRB1 gene using oligoneucleotide arrays

Chen JN, Li Y, Li YL, Qin HY, Li RY, Cao HM, Xie Y, Mao YM. [Investigation of genotyping HLA DRB1 gene using oligoneucleotide arrays] Yi Chuan Xue Bao. 2001; 28(10): 887-94. Chinese. PMID: 11695259 [PubMed – indexed for MEDLINE]

Query Tools for Microarray Data Mining Applications

Groch, K., Kuklin A. Query Tools for Microarray Data Mining Applications. Lab Technology. PharmaGenomics pp 53-55, August, 2001.























Dna microarray analysis of cyanobacterial gene expression during acclimation to high light.

Hihara Y, Kamei A, Kanehisa M, Kaplan A, Ikeuchi M. Dna microarray analysis of cyanobacterial gene expression during acclimation to high light. Plant Cell. 2001 Apr;13(4):793-806.





















DNA Arrays: The Steam Engine of the 21st Century?

Draghici, S. DNA Arrays: The Steam Engine of the 21st Century?, ACM SIGBIO Newsletter, vol. 21, no. 1, pp. 2-9, April, 2001.



























Identification of differentially expressed genes in hepatocellular carcinoma with cDNA microarrays

Shirota Y, Kaneko S, Honda M, Kawai HF, Kobayashi K. Identification of differentially expressed genes in hepatocellular carcinoma with cDNA microarrays. Hepatology ;33(4):832-40, April 2001.



Quality Control in Mircroarray Image Analysis

Kuklin, A., Petrov A., Shams, S. Quality Control in Mircroarray Image Analysis. Imaging & Microscopy Research, Development, Production. GIT Volume 1, April, 2001.





Differential gene expression between chronic hepatitis B and C hepatic lesion

Honda M, Kaneko S, Kawai H, Shirota Y, Kobayashi K. Differential gene expression between chronic hepatitis B and C hepatic lesion. Gastroenterology ;120(4):955-66, March 2001.
















alpha-fetoprotein-producing hepatoma cell lines share common expression profiles of genes in various categories demonstrated by cDNA microarray analysis

Kawai HF, Kaneko S, Honda M, Shirota Y, Kobayashi K. alpha-fetoprotein-producing hepatoma cell lines share common expression profiles of genes in various categories demonstrated by cDNA microarray analysis. Hepatology ;33(3):676-91, March 2001.












Gene Expression Pattern Analysis with Clustering in the Data Mining System GeneSight

Hoff B., Kuklin, A., Shams, A. Gene Expression Pattern Analysis with Clustering in the Data Mining System GeneSight. BIOforum, International Life Sciences and Technology, February, 2001, Advanced Publication.


















DNA Microarray Production, Virtual Experimental Design, Databasing and Clone Tracking with CloneTracker

Kuklin, A. DNA Microarray Production, Virtual Experimental Design, Databasing and Clone Tracking with CloneTracker. SC&I Technology Notes, January 2001.





Quantitative assessment of DNA microarrays–comparison with Northern blot analyses

Taniguchi M, Miura K, Iwao H, Yamanaka S. Quantitative assessment of DNA microarrays–comparison with Northern blot analyses. Genomics. 2001 Jan 1;71(1):34-9.

Experimental Design, Analysis of Variance and Slide Quality Assessment in Gene Expression Arrays

Draghici, S., Kuklin A., Hoff, B., Shams S. Experimental Design, Analysis of Variance and Slide Quality Assessment in Gene Expression Arrays, Current Opinion in Drug Discovery & Development, vol. 4, no. 3, 2001.




























Data management in Microarray Fabrication, Image Processing, and Data Mining

Kuklin, A., S. Shah, B. Hoff, and S. Shams. (2001) Data management in Microarray Fabrication, Image Processing, and Data Mining. In: Grigorenko (Ed.) DNA Arrays – Technologies and Experimental Strategies. CRC Press, Boca Raton pp. 115-128.









Automation in Microarray Image Analysis with AutoGene Technical Report

Kuklin A., Shams S., Shah S. Automation in Microarray Image Analysis with AutoGene Technical Report, JALA Vol 5, No. 5, pp. 67-70, November, 2000.










Information Processing Issues and Solutions Associated with Microarray Technology

Kuklin, A., Shah, S., Hoff, B, Shams, S., Information Processing Issues and Solutions Associated with Microarray Technology. LRA, Vol 12,pp.317-327, September 2000.






recent advances and applications in gene expression profiling

Kawai H, Kaneko S. DNA chip; recent advances and applications in gene expression profiling. Tanpakushitsu Kakusan Koso ;45(11):1841-7. Review. Japanese. No abstract available, August 2000.













The Transcriptional Response of Yeast to Saline Stress

Posas, Francesc , James R. Chambers, John A. Heyman, James P. Hoeffler, Eulalia de Nadal, and Joaquín Ariño. The Transcriptional Response of Yeast to Saline Stress. J. Biol. Chem., Jun 2000; 275: 17249 – 17255.








Spot Checks

Kuklin, A. Spot Checks. Modern Drug Discovery pp 52-54. May, 2000.







Laboratory Automation in Microarray Image Processing

Kuklin, A. Laboratory Automation in Microarray Image Processing. International Laboratory pp 36-40. May, 2000.








Data Mining in the Exploration of Genomic Expression.

Shams, S., Kuklin, A. Data Mining in the Exploration of Genomic Expression. Bio/Medical Synergies. 22: 4-5 Summer 2000.





That’s The Spot!

That’s The Spot! The Scientist, Lab Consumer, Vol 14:5 March 6, 2000.

Sensitive Detection System for High- Density Microarrays Using Dendrimer Technology

Stears, R.L., Getts, R.C., and Gullans, S.R. A Novel, Sensitive Detection System for High- Density Microarrays Using Dendrimer Technology. Physiol. Genomics 3:93-99, 2000.

Automation In Microarray Image Processing and Data Mining

Kuklin, A. Automation In Microarray Image Processing and Data Mining. High Throughput Screening Supplement, BioMedical Products 1:4-8. 2000.








Information Processing Issues and Solutions Associated with Microarray Technology

Zhout, Y-X., Kalocsai, P., Chen, J-Y., and Shams, S. Information Processing Issues and Solutions Associated with Microarray Technology. Microarray Biochip Technology. Schena, M. (Ed.), Eaton Publishing, BioTechniques Books,. Natick, MA, U.S.A. pp. 167-200, 2000.

High Throughput Screening of Gene Expression Signatures

Shah, S., Kuklin, A., Shams, S. High Throughput Screening of Gene Expression Signatures. Genetica 108: 41-46, 2000.






Exploring Expression Data: Identification and Analysis of Co-Expressed Genes.

Heyer, L.J., Kruglyak, S., and Yooseph, S. Exploring Expression Data: Identification and Analysis of Co-Expressed Genes. Genome Research 9:1106-1115. 1999.






















Image Analysis and Data Management Issues Associated with Microarray Technology.

Shams, S., Park, J.D., Chen, J.Y., Kalocsai, P. and Zhou, Y.X. Image Analysis and Data Management Issues Associated with Microarray Technology. DNA Microarrays – The New Frontier in Gene Discovery and Gene Expression Analysis. Short Course Syllabus. Society for Neuroscience, Miami Beach, FL. pp. 43-56, 1999.




Gene Expression Profiles of Laser-Captured Adjacent Neuronal Subtypes

Luo, L., Salunga, R., Guo, H. et al. Gene Expression Profiles of Laser-Captured Adjacent Neuronal Subtypes. Nature Medicine, Vol. 5 No.1: pp117-122. 1999.




Visualization and Analysis of Gene Expression Data

Kaloscai, P. and Shams, S. Visualization and Analysis of Gene Expression Data. JALA Vol 4, No. 5:pp17-21. 1999.














Using Laser Capture Microdissection and cDNA Microarrays to Profile Expression Neuronal Subtypes

Erlander, M. Using Laser Capture Microdissection and cDNA Microarrays to Profile Expression Neuronal Subtypes. DNA Microarrays. The New Frontier in Gene Discovery and Gene Expression Analysis. Short Course Syllabus. Society for Neuroscience, Miami Beach, FL. pp. 67- 71, 1999.