CHIP Publication

CHIP Publications in Medline (PubMed) and Elsewhere

Abstracts, book, and posters not included.

Medline publications

Schachter, AD, Ichimura, T, Kohane, IS. Chromosomes 18 and X are quantitative trait loci for nephrotic-range proteinuria in rats. Pediatr Nephrol. Aug, 2005
Brownstein, JS, Kleinman, KP, Mandl, KD. Identifying Pediatric Age Groups for Influenza Vaccination Using a Real-Time Regional Surveillance System. Am J Epidemiol. Aug, 2005
Lai, WR, Johnson, MD, Kucherlapati, R, Park, PJ. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics. Aug, 2005
Wang, L, Ramoni, MF, Mandl, KD, Sebastiani, P. Factors affecting automated syndromic surveillance. Artif Intell Med. Jul, 2005
Cassa, CA, Iancu, K, Olson, KL, Mandl, KD. A software tool for creating simulated outbreaks to benchmark surveillance systems. BMC Med Inform Decis Mak. Jul, 2005
Fraser, HS, Biondich, P, Moodley, D, Choi, S, Mamlin, BW, Szolovits, P. Implementing electronic medical record systems in developing countries. Inform Prim Care. 7, 2005
Turchin, A, Kohane, IS, Pendergrass, ML. Identification of patients with diabetes from the text of physician notes in the electronic medical record. Diabetes Care. Jul, 2005
Laserson, KF, Thorpe, LE, Leimane, V, Weyer, K, Mitnick, CD, Riekstina, V, Zarovska, E, Rich, ML, Fraser, HS, Alarcón, E, Cegielski, JP, Grzemska, M, Gupta, R, Espinal, M. Speaking the same language: treatment outcome definitions for multidrug-resistant tuberculosis. Int J Tuberc Lung Dis. Jun, 2005
Olson, KL, Bonetti, M, Pagano, M, Mandl, KD. Real time spatial cluster detection using interpoint distances among precise patient locations. BMC Med Inform Decis Mak. Jun, 2005
Kang, PB, Kho, AT, Sanoudou, D, Haslett, JN, Dow, CP, Han, M, Blasko, JM, Lidov, HG, Beggs, AH, Kunkel, LM. Variations in gene expression among different types of human skeletal muscle. Muscle Nerve. Jun, 2005
Tseng, YH, Butte, AJ, Kokkotou, E, Yechoor, VK, Taniguchi, CM, Kriauciunas, KM, Cypess, AM, Niinobe, M, Yoshikawa, K, Patti, ME, Kahn, CR. Prediction of preadipocyte differentiation by gene expression reveals role of insulin receptor substrates and necdin. Nat Cell Biol. Jun, 2005
Bosl, WJ, Li, R. Mitotic-exit control as an evolved complex system. Cell. May, 2005
Pollard, J, Butte, AJ, Hoberman, S, Joshi, M, Levy, J, Pappo, J. A computational model to define the molecular causes of type 2 diabetes mellitus. Diabetes Technol Ther. Apr, 2005
Greenberg, SA, Pinkus, JL, Pinkus, GS, Burleson, T, Sanoudou, D, Tawil, R, Barohn, RJ, Saperstein, DS, Briemberg, HR, Ericsson, M, Park, P, Amato, AA. Interferon-alpha/beta-mediated innate immune mechanisms in dermatomyositis. Ann Neurol. May, 2005
Carter, SL, Eklund, AC, Mecham, BH, Kohane, IS, Szallasi, Z. Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics. Apr, 2005
Aivado, M, Spentzos, D, Alterovitz, G, Otu, HH, Grall, F, Giagounidis, AA, Wells, M, Cho, JY, Germing, U, Czibere, A, Prall, WC, Porter, C, Ramoni, MF, Libermann, TA. Optimization and evaluation of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) with reversed-phase protein arrays for protein profiling. Clin Chem Lab Med. 4, 2005
Marinescu, VD, Kohane, IS, Riva, A. MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics. Mar, 2005
Sebastiani, P, Ramoni, MF, Nolan, V, Baldwin, CT, Steinberg, MH. Genetic dissection and prognostic modeling of overt stroke in sickle cell anemia. Nat Genet. Apr, 2005
Mandl, KD, Reis, B, Cassa, C. Measuring outbreak-detection performance by using controlled feature set simulations. MMWR Morb Mortal Wkly Rep. Sep, 2004
Greenberg, SA, Walsh, RJ. Molecular diagnosis of inheritable neuromuscular disorders. Part II: Application of genetic testing in neuromuscular disease. Muscle Nerve. Apr, 2005
Greenberg, SA, Walsh, RJ. Molecular diagnosis of inheritable neuromuscular disorders. Part I: Genetic determinants of inherited disease and their laboratory detection. Muscle Nerve. Apr, 2005
Kong, SW, Hwang, KB, Kim, RD, Zhang, BT, Greenberg, SA, Kohane, IS, Park, PJ. CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays. Bioinformatics. May, 2005
Sax, U, Kohane, I, Mandl, KD. Wireless technology infrastructures for authentication of patients: PKI that rings. J Am Med Inform Assoc. 01, 2005
Porter, SC, Kohane, IS, Goldmann, DA. Parents as partners in obtaining the medication history. J Am Med Inform Assoc. 01, 2005
Liadaki, K, Kho, AT, Sanoudou, D, Schienda, J, Flint, A, Beggs, AH, Kohane, IS, Kunkel, LM. Side population cells isolated from different tissues share transcriptome signatures and express tissue-specific markers. Exp Cell Res. Feb, 2005
Sebastiani, P, Abad, MM, Alpargu, G, Ramoni, MF. Robust transmission/disequilibrium test for incomplete family genotypes. Genetics. Dec, 2004
Marinescu, VD, Kohane, IS, Riva, A. The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res. Jan, 2005
Fraser, HS, Jazayeri, D, Nevil, P, Karacaoglu, Y, Farmer, PE, Lyon, E, Fawzi, MK, Leandre, F, Choi, SS, Mukherjee, JS. An information system and medical record to support HIV treatment in rural Haiti. BMJ. Nov, 2004
Madhav, NK, Brownstein, JS, Tsao, JI, Fish, D. A dispersal model for the range expansion of blacklegged tick (Acari: Ixodidae). J Med Entomol. Sep, 2004
Derdáková, M, Dudiòák, V, Brei, B, Brownstein, JS, Schwartz, I, Fish, D. Interaction and transmission of two Borrelia burgdorferi sensu stricto strains in a tick-rodent maintenance system. Appl Environ Microbiol. Nov, 2004
Spentzos, D, Levine, DA, Ramoni, MF, Joseph, M, Gu, X, Boyd, J, Libermann, TA, Cannistra, SA. Gene expression signature with independent prognostic significance in epithelial ovarian cancer. J Clin Oncol. Dec, 2004
Hwang, KB, Kong, SW, Greenberg, SA, Park, PJ. Combining gene expression data from different generations of oligonucleotide arrays. BMC Bioinformatics. Oct, 2004
Simons, WW, Mandl, KD, Kohane, IS. The PING personally controlled electronic medical record system: technical architecture. J Am Med Inform Assoc. 10, 2004
Greenberg, SA. Microarray analysis of human nervous system gene expression in neurological disease. Int Rev Neurobiol. 10, 2004
Adam, RM, Eaton, SH, Estrada, C, Nimgaonkar, A, Shih, SC, Smith, LE, Kohane, IS, Bägli, D, Freeman, MR. Mechanical stretch is a highly selective regulator of gene expression in human bladder smooth muscle cells. Physiol Genomics. Dec, 2004
Greenberg, SA. Henry Head (1861-1940). J Neurol. Sep, 2004
Stelling, J, Sauer, U, Szallasi, Z, Doyle, FJ, Doyle, J. Robustness of cellular functions. Cell. Sep, 2004
Voisine, P, Ruel, M, Khan, TA, Bianchi, C, Xu, SH, Kohane, I, Libermann, TA, Otu, H, Saltiel, AR, Sellke, FW. Differences in gene expression profiles of diabetic and nondiabetic patients undergoing cardiopulmonary bypass and cardioplegic arrest. Circulation. Sep, 2004
Namini, AH, Berkowicz, DA, Kohane, IS, Chueh, H. A submission model for use in the indexing, searching, and retrieval of distributed pathology case and tissue specimens. Medinfo. 9, 2004
Choi, SS, Jazayeri, DG, Mitnick, CD, Chalco, K, Bayona, J, Fraser, HS. Implementation and initial evaluation of a Web-based nurse order entry system for multidrug-resistant tuberculosis patients in Peru. Medinfo. 9, 2004
Kim, RD, Park, PJ. Improving identification of differentially expressed genes in microarray studies using information from public databases. Genome Biol. 08, 2004
Reis, BY, Mandl, KD. Syndromic surveillance: the effects of syndrome grouping on model accuracy and outbreak detection. Ann Emerg Med. Sep, 2004
Park, PJ, Cao, YA, Lee, SY, Kim, JW, Chang, MS, Hart, R, Choi, S. Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference. J Biotechnol. Sep, 2004
Porter, SC, Cai, Z, Gribbons, W, Goldmann, DA, Kohane, IS. The asthma kiosk: a patient-centered technology for collaborative decision support in the emergency department. J Am Med Inform Assoc. 08, 2004
Csoka, AB, English, SB, Simkevich, CP, Ginzinger, DG, Butte, AJ, Schatten, GP, Rothman, FG, Sedivy, JM. Genome-scale expression profiling of Hutchinson-Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis. Aging Cell. Aug, 2004
Cai, Z, Tsung, EF, Marinescu, VD, Ramoni, MF, Riva, A, Kohane, IS. Bayesian approach to discovering pathogenic SNPs in conserved protein domains. Hum Mutat. Aug, 2004
Brownstein, JS, Holford, TR, Fish, D. Enhancing West Nile virus surveillance, United States. Emerg Infect Dis. Jun, 2004
Ligon, KL, Alberta, JA, Kho, AT, Weiss, J, Kwaan, MR, Nutt, CL, Louis, DN, Stiles, CD, Rowitch, DH. The oligodendroglial lineage marker OLIG2 is universally expressed in diffuse gliomas. J Neuropathol Exp Neurol. May, 2004
Lu, T, Pan, Y, Kao, SY, Li, C, Kohane, I, Chan, J, Yankner, BA. Gene regulation and DNA damage in the ageing human brain. Nature. Jun, 2004
Beitel, AJ, Olson, KL, Reis, BY, Mandl, KD. Use of emergency department chief complaint and diagnostic codes for identifying respiratory illness in a pediatric population. Pediatr Emerg Care. Jun, 2004
Greenberg, SA, Amato, AA. Uncertainties in the pathogenesis of adult dermatomyositis. Curr Opin Neurol. Jun, 2004
Mecham, BH, Wetmore, DZ, Szallasi, Z, Sadovsky, Y, Kohane, I, Mariani, TJ. Increased measurement accuracy for sequence-verified microarray probes. Physiol Genomics. Aug, 2004
Mecham, BH, Klus, GT, Strovel, J, Augustus, M, Byrne, D, Bozso, P, Wetmore, DZ, Mariani, TJ, Kohane, IS, Szallasi, Z. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res. 05, 2004
Lader, AS, Ramoni, MF, Zetter, BR, Kohane, IS, Kwiatkowski, DJ. Identification of a transcriptional profile associated with in vitro invasion in non-small cell lung cancer cell lines. Cancer Biol Ther. Jul, 2004
Riva, A, Delorme, MO, Chevalier, T, Guilhot, N, Hénaut, C, Hénaut, A. The difficult interpretation of transcriptome data: the case of the GATC regulatory network. Comput Biol Chem. Apr, 2004
Sebastiani, P, Yu, YH, Ramoni, MF. Bayesian machine learning and its potential applications to the genomic study of oral oncology. Adv Dent Res. Dec, 2003
Kho, AT, Zhao, Q, Cai, Z, Butte, AJ, Kim, JY, Pomeroy, SL, Rowitch, DH, Kohane, IS. Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev. Mar, 2004
Sanoudou, D, Frieden, LA, Haslett, JN, Kho, AT, Greenberg, SA, Kohane, IS, Kunkel, LM, Beggs, AH. Molecular classification of nemaline myopathies: "nontyping" specimens exhibit unique patterns of gene expression. Neurobiol Dis. Apr, 2004
Tronick, EZ, Fetters, L, Olson, KL, Chen, Y. Similar and functionally typical kinematic reaching parameters in 7- and 15-month-old in utero cocaine-exposed and unexposed infants. Dev Psychobiol. Apr, 2004
Allocco, DJ, Kohane, IS, Butte, AJ. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics. Feb, 2004
Riva, A, Kohane, IS. A SNP-centric database for the investigation of the human genome. BMC Bioinformatics. Mar, 2004
Szot, A, Jacobson, FL, Munn, S, Jazayeri, D, Nardell, E, Harrison, D, Drosten, R, Ohno-Machado, L, Smeaton, LM, Fraser, HS. Diagnostic accuracy of chest X-rays acquired using a digital camera for low-cost teleradiology. Int J Med Inform. Feb, 2004
Greenberg, SA, Briemberg, HR. A neurological and hematological syndrome associated with zinc excess and copper deficiency. J Neurol. Jan, 2004
Fine, AM, Wong, JB, Fraser, HS, Fleisher, GR, Mandl, KD. Is it influenza or anthrax? A decision analytic approach to the treatment of patients with influenza-like illnesses. Ann Emerg Med. Mar, 2004
Pack, SD, Alper, OM, Stromberg, K, Augustus, M, Ozdemirli, M, Miermont, AM, Klus, G, Rusin, M, Slack, R, Hacker, NF, Ried, T, Szallasi, Z, Alper, O. Simultaneous suppression of epidermal growth factor receptor and c-erbB-2 reverses aneuploidy and malignant phenotype of a human ovarian carcinoma cell line. Cancer Res. Feb, 2004
Friedman, CP, Altman, RB, Kohane, IS, McCormick, KA, Miller, PL, Ozbolt, JG, Shortliffe, EH, Stormo, GD, Szczepaniak, MC, Tuck, D, Williamson, J. Training the next generation of informaticians: the impact of "BISTI" and bioinformatics--a report from the American College of Medical Informatics. J Am Med Inform Assoc. 02, 2004
Saluja, SK, Kohane, I. Localization and characterization of mouse-human alignments within the human genome. Does evolutionary conservation suggest functional importance? AMIA Annu Symp Proc. 1, 2003
Jazayeri, D, Farmer, P, Nevil, P, Mukherjee, JS, Leandre, F, Fraser, HS. An Electronic Medical Record system to support HIV treatment in rural Haiti. AMIA Annu Symp Proc. 1, 2003
Reis, BY, Mandl, KD. Integrating syndromic surveillance data across multiple locations: effects on outbreak detection performance. AMIA Annu Symp Proc. 1, 2003
Kuo, WP, Mendez, E, Chen, C, Whipple, ME, Farell, G, Agoff, N, Park, PJ. Functional relationships between gene pairs in oral squamous cell carcinoma. AMIA Annu Symp Proc. 1, 2003
Nimgaonkar, A, Karnad, DR, Sudarshan, S, Ohno-Machado, L, Kohane, I. Prediction of mortality in an Indian intensive care unit. Comparison between APACHE II and artificial neural networks. Intensive Care Med. Feb, 2004
Fukuoka, Y, Inaoka, H, Kohane, IS. Inter-species differences of co-expression of neighboring genes in eukaryotic genomes. BMC Genomics. Jan, 2004
Madden, JM, Soumerai, SB, Lieu, TA, Mandl, KD, Zhang, F, Ross-Degnan, D. Length-of-stay policies and ascertainment of postdischarge problems in newborns. Pediatrics. Jan, 2004
Greenberg, SA. Acquired rippling muscle disease with myasthenia gravis. Muscle Nerve. Jan, 2004
Tomczak, KK, Marinescu, VD, Ramoni, MF, Sanoudou, D, Montanaro, F, Han, M, Kunkel, LM, Kohane, IS, Beggs, AH. Expression profiling and identification of novel genes involved in myogenic differentiation. FASEB J. Feb, 2004
Ruel, M, Bianchi, C, Khan, TA, Xu, S, Liddicoat, JR, Voisine, P, Araujo, E, Lyon, H, Kohane, IS, Libermann, TA, Sellke, FW. Gene expression profile after cardiopulmonary bypass and cardioplegic arrest. J Thorac Cardiovasc Surg. Nov, 2003
Mandl, KD, Overhage, JM, Wagner, MM, Lober, WB, Sebastiani, P, Mostashari, F, Pavlin, JA, Gesteland, PH, Treadwell, T, Koski, E, Hutwagner, L, Buckeridge, DL, Aller, RD, Grannis, S. Implementing syndromic surveillance: a practical guide informed by the early experience. J Am Med Inform Assoc. 11, 2003
Koopman, LA, Kopcow, HD, Rybalov, B, Boyson, JE, Orange, JS, Schatz, F, Masch, R, Lockwood, CJ, Schachter, AD, Park, PJ, Strominger, JL. Human decidual natural killer cells are a unique NK cell subset with immunomodulatory potential. J Exp Med. Oct, 2003
Beeghly, M, Olson, KL, Weinberg, MK, Pierre, SC, Downey, N, Tronick, EZ. Prevalence, stability, and socio-demographic correlates of depressive symptoms in Black mothers during the first 18 months postpartum. Matern Child Health J. Sep, 2003
Sebastiani, P, Lazarus, R, Weiss, ST, Kunkel, LM, Kohane, IS, Ramoni, MF. Minimal haplotype tagging. Proc Natl Acad Sci U S A. Aug, 2003
Patti, ME, Butte, AJ, Crunkhorn, S, Cusi, K, Berria, R, Kashyap, S, Miyazaki, Y, Kohane, I, Costello, M, Saccone, R, Landaker, EJ, Goldfine, AB, Mun, E, DeFronzo, R, Finlayson, J, Kahn, CR, Mandarino, LJ. Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1. Proc Natl Acad Sci U S A. Jul, 2003
Nimgaonkar, A, Sanoudou, D, Butte, AJ, Haslett, JN, Kunkel, LM, Beggs, AH, Kohane, IS. Reproducibility of gene expression across generations of Affymetrix microarrays. BMC Bioinformatics. Jun, 2003
Kuo, WP, Whipple, ME, Jenssen, TK, Todd, R, Epstein, JB, Ohno-Machado, L, Sonis, ST, Park, PJ. Microarrays and clinical dentistry. J Am Dent Assoc. Apr, 2003
Haslett, JN, Sanoudou, D, Kho, AT, Han, M, Bennett, RR, Kohane, IS, Beggs, AH, Kunkel, LM. Gene expression profiling of Duchenne muscular dystrophy skeletal muscle. Neurogenetics. Aug, 2003
Lee, K, Kohane, IS, Butte, AJ. PGAGENE: integrating quantitative gene-specific results from the NHLBI programs for genomic applications. Bioinformatics. Apr, 2003
Sanoudou, D, Haslett, JN, Kho, AT, Guo, S, Gazda, HT, Greenberg, SA, Lidov, HG, Kohane, IS, Kunkel, LM, Beggs, AH. Expression profiling reveals altered satellite cell numbers and glycolytic enzyme transcription in nemaline myopathy muscle. Proc Natl Acad Sci U S A. Apr, 2003
Fraser, HS, Long, WJ, Naimi, S. Evaluation of a cardiac diagnostic program in a typical clinical setting. J Am Med Inform Assoc. 03, 2003
Blackshaw, S, Kuo, WP, Park, PJ, Tsujikawa, M, Gunnersen, JM, Scott, HS, Boon, WM, Tan, SS, Cepko, CL. MicroSAGE is highly representative and reproducible but reveals major differences in gene expression among samples obtained from similar tissues. Genome Biol. 02, 2003
Landrigan, CP, Muret-Wagstaff, S, Chiang, VW, Nigrin, DJ, Goldmann, DA, Finkelstein, JA. Senior resident autonomy in a pediatric hospitalist system. Arch Pediatr Adolesc Med. Feb, 2003
Cao, C, McIntosh, N, Kohane, IS, Wang, K. Artifact detection in the PO2 and PCO2 time series monitoring data from preterm infants. J Clin Monit Comput. Aug, 1999
Reis, BY, Pagano, M, Mandl, KD. Using temporal context to improve biosurveillance. Proc Natl Acad Sci U S A. Feb, 2003
Weiner, DL, Butte, AJ, Hibberd, PL, Fleisher, GR. Computerized recruiting for clinical trials in real time. Ann Emerg Med. Feb, 2003
Porter, SC, Fleisher, GR, Kohane, IS, Mandl, KD. The value of parental report for diagnosis and management of dehydration in the emergency department. Ann Emerg Med. Feb, 2003
Reis, BY, Mandl, KD. Time series modeling for syndromic surveillance. BMC Med Inform Decis Mak. Jan, 2003
Greenberg, SA. The history of dermatome mapping. Arch Neurol. Jan, 2003
Lazarus, R, Vercelli, D, Palmer, LJ, Klimecki, WJ, Silverman, EK, Richter, B, Riva, A, Ramoni, M, Martinez, FD, Weiss, ST, Kwiatkowski, DJ. Single nucleotide polymorphisms in innate immunity genes: abundant variation and potential role in complex human disease. Immunol Rev. Dec, 2002
Riva, A, Kohane, IS. SNPper: retrieval and analysis of human SNPs. Bioinformatics. Dec, 2002
Park, PJ, Butte, AJ, Kohane, IS. Comparing expression profiles of genes with similar promoter regions. Bioinformatics. Dec, 2002
Kuo, WP, Jenssen, TK, Park, PJ, Lingen, MW, Hasina, R, Ohno-Machado, L. Gene expression levels in different stages of progression in oral squamous cell carcinoma. Proc AMIA Symp. 12, 2002
Turchin, A, Kohane, IS. Gene homology resources on the World Wide Web. Physiol Genomics. Dec, 2002
Tsien, CL, Libermann, TA, Gu, X, Kho, A, Kohane, IS. CHIP TUNER: a web tool for evidence-based noise reduction in gene discovery. Proc AMIA Symp. 12, 2002
Schachter, AD, Kohane, IS. An unsupervised self-optimizing gene clustering algorithm. Proc AMIA Symp. 12, 2002
Riva, A, Kohane, IS. Accessing genomic data through XML-based remote procedure calls. Proc AMIA Symp. 12, 2002
Fraser, HS, Jazayeri, D, Mitnick, CD, Mukherjee, JS, Bayona, J. Informatics tools to monitor progress and outcomes of patients with drug resistant tuberculosis in Peru. Proc AMIA Symp. 12, 2002
Cai, Z, Kohane, I, Fleisher, GR, Greenes, DS. Computerized reminders to physicians in the emergency department: a web-based system to report late-arriving abnormal laboratory results. Proc AMIA Symp. 12, 2002
Greenberg, SA. P-ANCA vasculitic neuropathy with 12-year latency between onset of neuropathy and systemic symptoms. BMC Neurol. Oct, 2002
Kim, JH, Kohane, IS, Ohno-Machado, L. Visualization and evaluation of clusters for exploratory analysis of gene expression data. J Biomed Inform. Feb, 2002
Haslett, JN, Sanoudou, D, Kho, AT, Bennett, RR, Greenberg, SA, Kohane, IS, Beggs, AH, Kunkel, LM. Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) and normal skeletal muscle. Proc Natl Acad Sci U S A. Nov, 2002
Greenberg, SA, Sanoudou, D, Haslett, JN, Kohane, IS, Kunkel, LM, Beggs, AH, Amato, AA. Molecular profiles of inflammatory myopathies. Neurology. Oct, 2002
Butte, AJ, Bao, L, Reis, BY, Watkins, TW, Kohane, IS. Comparing the similarity of time-series gene expression using signal processing metrics. J Biomed Inform. Dec, 2001
Landrigan, CP, Muret-Wagstaff, S, Chiang, VW, Nigrin, DJ, Goldmann, DA, Finkelstein, JA. Effect of a pediatric hospitalist system on housestaff education and experience. Arch Pediatr Adolesc Med. Sep, 2002
Park, PJ, Tian, L, Kohane, IS. Linking gene expression data with patient survival times using partial least squares. Bioinformatics. 8, 2002
Beeghly, M, Weinberg, MK, Olson, KL, Kernan, H, Riley, J, Tronick, EZ. Stability and change in level of maternal depressive symptomatology during the first postpartum year. J Affect Disord. Sep, 2002
Ramoni, MF, Sebastiani, P, Kohane, IS. Cluster analysis of gene expression dynamics. Proc Natl Acad Sci U S A. Jul, 2002
Zhao, Q, Kho, A, Kenney, AM, Kohane, I, Rowitch, DH. Identification of genes expressed with temporal-spatial restriction to developing cerebellar neuron precursors by a functional genomic approach. Proc Natl Acad Sci U S A. Apr, 2002
Kuo, WP, Jenssen, TK, Butte, AJ, Ohno-Machado, L, Kohane, IS. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics. Mar, 2002
Wahde, M, Klus, GT, Bittner, ML, Chen, Y, Szallasi, Z. Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matrices. Bioinformatics. Mar, 2002
Szallasi, Z. Build your own (virtual) cell. Trends Pharmacol Sci. Apr, 2002
Periwal, V, Szallasi, Z. Trading "wet-work" for network. Nat Biotechnol. Apr, 2002
Kuruvilla, FG, Park, PJ, Schreiber, SL. Vector algebra in the analysis of genome-wide expression data. Genome Biol. 02, 2002
Porter, SC. Data acquisition in emergency medicine: electronic communication using free text. Pediatr Emerg Care. Feb, 2002
Mandl, KD, Lee, TH. Integrating medical informatics and health services research: the need for dual training at the clinical health systems and policy levels. J Am Med Inform Assoc. 2, 2002
Kohane, IS. The contributions of biomedical informatics to the fight against bioterrorism. J Am Med Inform Assoc. 2, 2002
Lober, WB, Karras, BT, Wagner, MM, Overhage, JM, Davidson, AJ, Fraser, H, Trigg, LJ, Mandl, KD, Espino, JU, Tsui, FC. Roundtable on bioterrorism detection: information system-based surveillance. J Am Med Inform Assoc. 2, 2002
Mandl, KD, Feit, S, Larson, C, Kohane, IS. Newborn screening program practices in the United States: notification, research, and consent. Pediatrics. Feb, 2002
Tsien, CL, Kohane, IS, McIntosh, N. Building ICU artifact detection models with more data in less time. Proc AMIA Symp. 2, 2001
Riva, A, Kohane, IS. A web-based tool to retrieve human genome polymorphisms from public databases. Proc AMIA Symp. 2, 2001
Butte, AJ, Dzau, VJ, Glueck, SB. Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues". Physiol Genomics. Dec, 2001
Greenberg, SA, Amato, AA. Inflammatory myopathy associated with mixed connective tissue disease and scleroderma renal crisis. Muscle Nerve. Nov, 2001
Gonzalez-Heydrich, J, Steingard, RJ, Putnam, FW, Beardslee, W, Kohane, IS. Corticotropin releasing hormone increases apparent potency of adrenocorticotropic hormone stimulation of cortisol secretion. Med Hypotheses. Nov, 2001
Fraser, HS, Jazayeri, D, Bannach, L, Szolovits, P, McGrath, SJ. TeleMedMail: free software to facilitate telemedicine in developing countries. Medinfo. 10, 2001
Porter, SC, Kohane, IS. Optimal data entry by patients: effects of interface structure and design. Medinfo. 10, 2001
Greenberg, SA. DNA microarray gene expression analysis technology and its application to neurological disorders. Neurology. Sep, 2001
Szallasi, Z. Scrapie-ing' together a signal from prions. Trends Pharmacol Sci. Sep, 2001
Tolkach, AB, Dolgikh, VT, Reĭs, BA, Shikunova, LG, Konvaĭ, VD, Malykhin, AG, Ktinidi, LI. [Use of plasmapheresis for correction of metabolic disorders in patients with surgical sepsis] Anesteziol Reanimatol. 8, 2001
Butte, AJ, Shaw, JS, Bernstein, H. Strict interpretation of vaccination guidelines with computerized algorithms and improper timing of administered doses. Pediatr Infect Dis J. Jun, 2001
Klus, GT, Rokaeus, N, Bittner, ML, Chen, Y, Korz, DM, Sukumar, S, Schick, A, Szallasi, Z. Down-regulation of the desmosomal cadherin desmocollin 3 in human breast cancer. Int J Oncol. Jul, 2001
Butte, AJ. Challenges in bioinformatics: infrastructure, models and analytics. Trends Biotechnol. May, 2001
Reis, BY, Butte, AS, Kohane, IS. Extracting knowledge from dynamics in gene expression. J Biomed Inform. Feb, 2001
Kohane, IS. The ever imminent electronic medical record. J Med Pract Manage. 5, 2001
Riva, A, Mandl, KD, Oh, DH, Nigrin, DJ, Butte, A, Szolovits, P, Kohane, IS. The personal internetworked notary and guardian. Int J Med Inform. Jun, 2001
Ramoni, M, Sebastiani, P, Dybowski, R. Robust outcome prediction for intensive-care patients. Methods Inf Med. Mar, 2001
Szallasi, Z. The grand design. Trends Pharmacol Sci. Apr, 2001
Weinberg, MK, Tronick, EZ, Beeghly, M, Olson, KL, Kernan, H, Riley, JM. Subsyndromal depressive symptoms and major depression in postpartum women. Am J Orthopsychiatry. Jan, 2001
Butte, AJ, Ye, J, Häring, HU, Stumvoll, M, White, MF, Kohane, IS. Determining significant fold differences in gene expression analysis. Pac Symp Biocomput. 3, 2001
Park, PJ, Pagano, M, Bonetti, M. A nonparametric scoring algorithm for identifying informative genes from microarray data. Pac Symp Biocomput. 3, 2001
Tsien, CL, Libermann, TA, Gu, X, Kohane, IS. On reporting fold differences. Pac Symp Biocomput. 3, 2001
Klus, GT, Song, A, Schick, A, Wahde, M, Szallasi, Z. Mutual information analysis as a tool to assess the role of aneuploidy in the generation of cancer-associated differential gene expression patterns. Pac Symp Biocomput. 3, 2001
Kim, JH, Ohno-Machado, L, Kohane, IS. Unsupervised learning from complex data: the matrix incision tree algorithm. Pac Symp Biocomput. 3, 2001
Szallasi, Z. To kill two birds with one stone: a general concept in gene regulation? Trends Pharmacol Sci. Mar, 2001
Mandl, KD, Szolovits, P, Kohane, IS. Public standards and patients' control: how to keep electronic medical records accessible but private. BMJ. Feb, 2001
Nigrin, DJ, Kohane, IS. Glucoweb: a case study of secure, remote biomonitoring and communication. Proc AMIA Symp. 11, 2000
Kohane, IS, Altman, RB. The new peer review. Proc AMIA Symp. 11, 2000
Butte, AJ, Weinstein, DA, Kohane, IS. Enrolling patients into clinical trials faster using RealTime Recuiting. Proc AMIA Symp. 11, 2000
Greenes, DS, Fleisher, GR, Kohane, I. Potential impact of a computerized system to report late-arriving laboratory results in the emergency department. Pediatr Emerg Care. Oct, 2000
Butte, AJ, Tamayo, P, Slonim, D, Golub, TR, Kohane, IS. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc Natl Acad Sci U S A. Oct, 2000
Kohane, IS. Bioinformatics and clinical informatics: the imperative to collaborate. J Am Med Inform Assoc. 9, 2000
Gonzalez-Heydrich, J, DeMaso, DR, Irwin, C, Steingard, RJ, Kohane, IS, Beardslee, WR. Implementation of an electronic medical record system in a pediatric psychopharmacology program. Int J Med Inform. Jul, 2000
Tsien, CL, Kohane, IS, McIntosh, N. Multiple signal integration by decision tree induction to detect artifacts in the neonatal intensive care unit. Artif Intell Med. Jul, 2000
Butte, AJ, Kohane, IS. Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput. 7, 2000
Huang, SA, Tu, HM, Harney, JW, Venihaki, M, Butte, AJ, Kozakewich, HP, Fishman, SJ, Larsen, PR. Severe hypothyroidism caused by type 3 iodothyronine deiodinase in infantile hemangiomas. N Engl J Med. Jul, 2000
Rhee, EK, Evangelista, JK, Nigrin, DJ, Erickson, LC. Impact of anatomic closure on somatic growth among small, asymptomatic children with secundum atrial septal defect. Am J Cardiol. Jun, 2000
Mandl, KD, Feit, S, Peña, BM, Kohane, IS. Growth and determinants of access in patient e-mail and Internet use. Arch Pediatr Adolesc Med. May, 2000
Porter, SC, Silvia, MT, Fleisher, GR, Kohane, IS, Homer, CJ, Mandl, KD. Parents as direct contributors to the medical record: validation of their electronic input. Ann Emerg Med. Apr, 2000
Nigrin, DJ, Kohane, IS. Temporal expressiveness in querying a time-stamp--based clinical database. J Am Med Inform Assoc. 3, 2000
Bellazzi, R, Riva, A, Montani, S, Larizza, C, Bestazza, M, Fiocchi, S, d'Annunzio, G, Lorini, R, Stefanelli, M. Application report: preliminary evaluation of the T-IDDM project in Pavia. Stud Health Technol Inform. 3, 1999
Nigrin, DJ, Kohane, IS. Scaling a data retrieval and mining application to the enterprise-wide level. Proc AMIA Symp. 11, 1999
Mandl, KD, Kohane, IS. Healthconnect: clinical grade patient-physician communication. Proc AMIA Symp. 11, 1999
Butte, AJ, Kohane, IS. Unsupervised knowledge discovery in medical databases using relevance networks. Proc AMIA Symp. 11, 1999
Porter, SC, Mandl, KD. Data quality and the electronic medical record: a role for direct parental data entry. Proc AMIA Symp. 11, 1999
Cao, C, Kohane, IS, McIntosh, N. Artifact detection in cardiovascular time series monitoring data from preterm infants. Proc AMIA Symp. 11, 1999
Mandl, KD, Tronick, EZ, Brennan, TA, Alpert, HR, Homer, CJ. Infant health care use and maternal depression. Arch Pediatr Adolesc Med. Aug, 1999
Nigrin, DJ. ATRAS: a decision support application layered on the W3-EMRS architecture. Medinfo. 6, 1998
Sun, Y, Kohane, IS, Harary, O, Mandl, KD, Salem-Schatz, SR, Homer, CJ. The challenges of automating a real-time clinical practice guideline. Clin Perform Qual Health Care. 6, 1999
Gonzalez-Heydrich, J, Steingard, RJ, Putnam, F, Beardslee, W, Kohane, IS. Using 'off the shelf', computer programs to mine additional insights from published data: diurnal variation in potency of ACTH stimulation of cortisol secretion revealed. Comput Methods Programs Biomed. Mar, 1999
Nigrin, DJ, Kohane, IS. Data mining by clinicians. Proc AMIA Symp. 2, 1998
Fraser, HS, Long, WJ, Naimi, S. Differential diagnoses of the heart disease program have better sensitivity than resident physicians. Proc AMIA Symp. 2, 1998
Sun, Y, Harary, O, Mandl, KD, Salem-Schatz, S, Homer, CJ, Kohane, IS. Linking multiple heterogeneous data sources to practice guidelines. Proc AMIA Symp. 2, 1998
Kohane, IS, Dong, H, Szolovits, P. Health information identification and de-identification toolkit. Proc AMIA Symp. 2, 1998
Mandl, KD, Katz, SB, Kohane, IS. Social equity and access to the World Wide Web and E-mail: implications for design and implementation of medical applications. Proc AMIA Symp. 2, 1998
Weinberg, MK, Tronick, EZ, Cohn, JF, Olson, KL. Gender differences in emotional expressivity and self-regulation during early infancy. Dev Psychol. Jan, 1999
Riva, A, Bellazzi, R, Lanzola, G, Stefanelli, M. A development environment for knowledge-based medical applications on the World-Wide Web. Artif Intell Med. Nov, 1998
Mandl, KD, Kohane, IS, Brandt, AM. Electronic patient-physician communication: problems and promise. Ann Intern Med. Sep, 1998
Sun, Y, Kohane, IS, Stark, AR. Computer-assisted adjustment of inspired oxygen concentration improves control of oxygen saturation in newborn infants requiring mechanical ventilation. J Pediatr. Nov, 1997
Wang, K, Bradshaw, K, Szolovits, P, Kohane, I. A Java-based multi-institutional medical information retrieval system. Proc AMIA Annu Fall Symp. 11, 1997
Rind, DM, Kohane, IS, Szolovits, P, Safran, C, Chueh, HC, Barnett, GO. Maintaining the confidentiality of medical records shared over the Internet and the World Wide Web. Ann Intern Med. Jul, 1997
Kohane, I. Physician pushes for the use of technology. Interview by Tyler L. Chin. Health Data Manag. Jul, 1997
Fraser, HS, Kohane, IS, Long, WJ. Using the technology of the World Wide Web to manage clinical information. BMJ. May, 1997
Nigrin, DJ. IT? Give me what I'll use. Healthc Inform. May, 1997
Kohane, IS. Patient assessment systems using the World Wide Web. Behav Healthc Tomorrow. Feb, 1997
Ionasescu, VV, Searby, C, Greenberg, SA. Dejerine-Sottas disease with sensorineural hearing loss, nystagmus, and peripheral facial nerve weakness: de novo dominant point mutation of the PMP22 gene. J Med Genet. Dec, 1996
Haimowitz, IJ, Kohane, IS. Managing temporal worlds for medical trend diagnosis. Artif Intell Med. Jul, 1996
Kohane, IS. Exploring the functions of World Wide Web-based electronic medical record systems. MD Comput. 7, 1996
Kohane, IS, Greenspun, P, Fackler, J, Cimino, C, Szolovits, P. Building national electronic medical record systems via the World Wide Web. J Am Med Inform Assoc. 5, 1996
Miller, D, Emans, SJ, Kohane, I. Follow-up study of adolescent girls with a history of premature pubarche. J Adolesc Health. Apr, 1996
Wang, K, Kohane, I, Bradshaw, KL, Fackler, J. A real time patient monitoring system on the World Wide Web. Proc AMIA Annu Fall Symp. 1, 1996
Schindler, J, Kilbridge, P, Szolovits, P, Safran, C, Rind, D, Murphy, S, Barnett, GO, Kohane, IS. Using HL7 and the World Wide Web for unifying patient data from remote databases. Proc AMIA Annu Fall Symp. 1, 1996
Kohane, IS, Fackler, JC, Cimino, C, Kilbridge, P, Murphy, S, Chueh, H, Rind, D, Safran, C, Barnett, O, Szolovits, P. Sharing electronic medical records across multiple heterogeneous and competing institutions. Proc AMIA Annu Fall Symp. 1, 1996
Riva, A. A Web-based architecture for the intelligent management of chronic patients. Proc AMIA Annu Fall Symp. 1, 1996
Haimowitz, IJ, Le, PP, Kohane, IS. Clinical monitoring using regression-based trend templates. Artif Intell Med. Dec, 1995
Kohane, IS. Editorial. Artif Intell Med. Dec, 1995
Gordon, CM, Rowitch, DH, Mitchell, ML, Kohane, IS. Topical iodine and neonatal hypothyroidism. Arch Pediatr Adolesc Med. Dec, 1995
Waisel, DB, Fackler, JC, Brunner, JX, Kohane, I. PEFIOS: an expert closed-loop oxygenation algorithm. Medinfo. 1, 1995
Le, PP, Kohane, IS, Weeks, JC. Using a pen-based computer to collect health-related quality of life and utilities information. Proc Annu Symp Comput Appl Med Care. 1, 1995
Hinds, A, Greenspun, P, Kohane, IS. WHAM!: a forms constructor for medical record access via the World Wide Web. Proc Annu Symp Comput Appl Med Care. 1, 1995

Non-medline publications

Katsoulakis MA, Kho AT*: Stochastic mean curvature flows: Asymptotic derivation, level set formulation and numerics. Interfaces and Free Boundaries. (3) 265-290, 2001.
Sebastiani P, Ramoni MF. On the use of Bayesian networks to analyze survey data. Res Official Stat 4(1):53-64, 2001.
Sebastiani P, Ramoni MF. Common trends in European school populations. Res Official Stat 4(1):169-183, 2001.
Sebastiani P, Ramoni MF. Bayesian inference with missing data using bound and collapse. J Comput Graph Stat 9(4):779-800, 2000.
Ramoni MF, Sebastiani P. Robust learning with missing data. Mach Learn 45(2):147-170, 2001
Sebastiani P, Ramoni MF. Bayesian selection of decomposable models with incomplete data. J Am Stat Assoc 96(456):1375-1386, 2001.
Ramoni MF, Sebastiani P, Cohen PR. Bayesian analysis of sensory inputs of a mobile robot. Lect Note Stat 162: 363-379, 2002.
Ramoni MF, Sebastiani P, Cohen PR. Bayesian clustering by dynamics. Mach Learn 47(1):91-121, 2002.
Sebastiani P, Gussoni E, Kohane IS, Ramoni MF. Statistical challenges in functional genomics (with discussion). Stat Science 18(1):33-70, 2003.
Sebastiani P, Kohane, IS, Ramoni MF. The role of machine learning in the post-genomic era. Mach Learn 52(1-2):5-9, 2003.
Sebastiani P, Ramoni MF. Normative selection of Bayesian networks. J Multivar Anal 93(2):340-357, 2005.
Sebastiani P, Ramoni MF, Kohane IS. Bayesian clustering of gene expression dynamics. In G Parmigiani, ES Garrett, RA Irizarry, SL Zeger, editors, The Analysis of Gene Expression Data: Methods and Software pp 400-427. Springer, New York, NY, 2003.
Ramoni MF, Sebastiani P. Bayesian methods for intelligent data analysis. In M Berthold, DJ Hand, editors, Intelligent Data Analysis: An Introduction pp 131-168. Springer, New York, NY, 2003, 2nd edition.
Ramoni MF, Sebastiani P, Cohen PR. Sequence learning via Bayesian clustering by dynamics. In L Giles, R Sun, editors, Sequence Learning: Paradigms, Algorithms and Applications pp 11-34. Springer, New York, NY, 2001.