Alexander D. Diehl PhD
Alexander D. Diehl
PhD
Associate Professor
Department of Biomedical Informatics
Jacobs School of Medicine & Biomedical Sciences
Specialty/Research Focus
Autoimmunity; Bioinformatics; Genomics and proteomics; Immunology; Infectious Disease; Molecular and Cellular Biology; Molecular genetics; Neurobiology
Professional Summary:
My primary research is in the field of biomedical ontology development. An ontology is a controlled, structured vocabulary intended to represent knowledge within a particular domain. Terms in an ontology have logical relationships to each other and to terms in other ontologies, to allow for reasoning and inference across the ontology. Biomedical ontologies allow annotation and integration of scientific data within particular fields of science and medicine, and their careful curation and logical structure facilitate data analysis. My work in biomedical ontology is strongly informed by my earlier experience in laboratory research in immunology, genetics, molecular biology and virology.
My research group works on ontologies for both basic and clinical applications, in collaboration with researchers both at UB and other institutions. I led efforts to revise and extend the Cell Ontology, which is intended to represent in vivo cell types from across biology. We worked extensively to bring it up to community-accepted standards in ontology development, placing particular emphasis on improving the representation of hematopoietic cells and neurons. We are developing the Cell Ontology as a metadata standard for annotation and analysis of experimental data in immunology in support of the National Institute of Allergy and Infectious Diseases (NIAID) ImmPort Immunology Database and Analysis Portal and Human Immunology Project Consortium. We have also developed ways to use the Cell Ontology in support of the analysis of gene expression data linked to cell types and have contributed to the Functional Annotation of the Mammalian Genome (FANTOM) 5 Consortium‘s work on identifying gene transcription start sites across multiple cell types and tissues.
My research team is also developing the Neurological Disease Ontology to represent clinical and basic aspects of neurological diseases in order to support translational research in this area. In collaboration with clinical colleagues at UB, we are initially focusing on Alzheimer’s disease and dementia, multiple sclerosis and stroke. We have as well developed a companion ontology, the Neuropsychological Testing Ontology, to aid in the annotation and analysis of neuropsychological testing results used as part of the diagnosis of Alzheimer‘s disease and other neurological diseases.
I am a long-term member of the Gene Ontology (GO) Consortium and have a particular interest in the representation of immunology and neuroscience in the GO. I am also involved in UB’s contribution to the Protein Ontology and contribute as well to the work of the Infectious Disease Ontology Consortium, Immunology Ontology Consortium and Vaccine Ontology Consortium.
I teach and mentor students at the master’s and doctoral levels, and advise undergraduate, graduate, and medical students in summer research projects as well.
Education and Training:
- PhD, Molecular Cell Biology, Washington University (1995)
- BS, Molecular Biophysics and Biochemistry, Yale University (1986)
Employment:
- Associate Professor, Biomedical Informatics, University at Buffalo Jacobs School of Medicine & Biomedical Sciences (2017-present)
- Assistant Professor, Biomedical Informatics, University at Buffalo Jacobs School of Medicine & Biomedical Sciences (2017)
- Research Assistant Professor, Biomedical Informatics, University at Buffalo Jacobs School of Medicine & Biomedical Sciences (2014–2016)
- Assistant Professor, Neurology, University at Buffalo Jacobs School of Medicine & Biomedical Sciences (2010–2016)
- Research Scientist, Mouse Genome Informatics, The Jackson Laboratory (2009–2010)
- Senior Scientific Curator, The Jackson Laboratory (2006–2009)
- Scientific Curator, The Jackson Laboratory (2003–2006)
- Research Scientist, Decode Genetics (2000–2002)
- Post Doctoral Fellow, Microbiology and Tumor Biology Center, Karolinska Institute (1996–2000)
Awards and Honors:
- Wenner-Gren Samfundet Post-Doctoral Fellowship (1997)
- Howard Hughes Medical Institute Pre-Doctoral Fellowship (1990)
- Associate Member of Sigma Xi Scientific Honor Society (1986)
Research Expertise:
- Biomedical ontology development: Experienced biomedical ontology developer for the Gene Ontology, Cell Ontology, Protein Ontology, Vaccine Ontology, Infectious Disease Ontology, and Neurological Disease Ontology.
Research Centers:
- Center of Excellence in Bioinformatics and Life Sciences
- Jacobs Neurological Institute
UB 2020 Strategic Strengths:
- Health and Wellness Across the Lifespan
Grants and Sponsored Research:
- September 2011–June 2015
PRO: A Protein Ontology in OBO Foundry for Integration of Biomedical Knowledge
NIGMS
Role: Co-Investigator - December 2010–August 2011
ARRA: Revision and Extension of the Cell Ontology
The Jackson Laboratory
Role: Principal Investigator
$35,649 - June 2010–August 2010
Importation of Neuron Types from the BAMS and NeuronDB Resources to the Cell Ontology
International Neuroinformatics Coordinating Facility
Role: Principal Investigator
$3,200
Journal Articles:
- Ceusters W, Jensen M, Diehl AD. (2017) Ontological Realism for the Research Domain Criteria for Mental Disorders. Stud Health Technol Inform (Jan), 235: 431-435.
- Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH. (2017) Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res (Jan), 45(D1): 339-346.
- Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH. (2016) Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res (Nov).
- Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ. (2016) The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J Biomed Semantics (Jul), 7(1): 44-44.
- Ray PL, Cox AP, Jensen M, Allen T, Duncan W, Diehl AD. (2016) Representing vision and blindness. J Biomed Semantics (Mar), 7: 15-15.
- Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR, Ruttenberg AH. (2015) flowCL: ontology-based cell population labelling in flow cytometry. Bioinformatics (Apr), 31(8): 1337-1339.
- Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y. (2015) Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (Feb), 347(6225): 1010-1014.
- Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y. (2015) Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (Feb), 347(6225): 1010-1014.
- Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, Bertin N, Bono H, de Hoon M, Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T, Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, 't Hoen PA, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P, Hayashizaki Y, Forrest AR, Kawaji H. (2015) Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol (Jan), 16: 22-22.
- Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR. (2014) flowCL: ontology-based cell population labelling in flow cytometry. Bioinformatics (Dec).
- Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. (2014) CLO: The cell line ontology. J Biomed Semantics (Aug), 5: 37-37.
- Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest AR, Carninci P, Rehli M, Sandelin A, Kawaji H, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmid C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple CA, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furuno M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Nozaki T, Ogishima S, Ohkura N, Ohmiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Satoh H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyoda H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verardo R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Hume DA, Hayashizaki Y. (2014) An atlas of active enhancers across human cell types and tissues. Nature (Mar), 507(7493): 455-461.
- Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassman T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y. (2014) A promoter-level mammalian expression atlas. Nature (Mar), 507(7493): 462-470.
- Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, AlJanahi A, Çelen I, Gan C, Lv M, Schuster-Lezell E, Wu CH. (2014) Protein Ontology: a controlled structured network of protein entities. Nucleic Acids Res (Jan), 42(Datab): 415-421.
- Jensen M, Cox AP, Chaudhry N, Ng M, Sule D, Duncan W, Ray P, Weinstock-Guttman B, Smith B, Ruttenberg A, Szigeti K, Diehl AD. (2013) The neurological disease ontology. J Biomed Semantics (Dec), 4(1): 42-42.
- Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, Aljanahi A, Celen I, Gan C, Lv M, Schuster-Lezell E, Wu CH. (2013) Protein Ontology: a controlled structured network of protein entities. Nucleic Acids Res (Nov).
- Meehan TF, Vasilevsky NA, Mungall CJ, Dougall DS, Haendel MA, Blake JA, Diehl AD. (2013) Ontology based molecular signatures for immune cell types via gene expression analysis. BMC Bioinformatics (Aug), 14: 263-263.
- Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall CJ, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM. (2012) A unified anatomy ontology of the vertebrate skeletal system. PLoS One (Dec), 7(12): 51070-51070.
- Leonelli S, Diehl AD, Christie KR, Harris MA, Lomax J. (2011) How the gene ontology evolves. BMC Bioinformatics (Aug), 12: 325-325.
- Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. (2011) Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform (Feb), 44(1): 75-79.
- Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD. (2011) Logical development of the cell ontology. BMC Bioinformatics (Jan), 12: 6-6.
- Karp DR, Marthandan N, Marsh SG, Ahn C, Arnett FC, Deluca DS, Diehl AD, Dunivin R, Eilbeck K, Feolo M, Guidry PA, Helmberg W, Lewis S, Mayes MD, Mungall C, Natale DA, Peters B, Petersdorf E, Reveille JD, Smith B, Thomson G, Waller MJ, Scheuermann RH. (2010) Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis. Hum Mol Genet (Feb), 19(4): 707-719.
- Gene Ontology Consortium. (2010) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. (Jan), 38: D331-D335.
- Reference Genome Group of the Gene Ontology Consortium. (2009) The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Comput Biol. (Jul), 5(7).
- Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG. (2009) An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinformatics (Feb), 10: 70-70.
- Feltrin E, Campanaro S, Diehl AD, Ehler E, Faulkner G, Fordham J, Gardin C, Harris M, Hill D, Knoell R, Laveder P, Mittempergher L, Nori A, Reggiani C, Sorrentino V, Volpe P, Zara I, Valle G, Deegan J. (2009) Muscle Research and Gene Ontology: New standards for improved data integration. BMC Med Genomics (Jan), 2: 6-6.
- Lovering RC, Camon EB, Blake JA, Diehl AD. (2008) Access to immunology through the Gene Ontology. Immunology (Oct), 125(2): 154-160.
- Diehl AD, Lee JA, Scheuermann RH, Blake JA. (2007) Ontology development for biological systems: immunology. Bioinformatics (Apr), 23(7): 913-915.
- Eppig JT, Bult CJ, Kadin JA, Richardson JE, Blake JA, Anagnostopoulos A, Baldarelli RM, Baya M, Beal JS, Bello SM, Boddy WJ, Bradt DW, Burkart DL, Butler NE, Campbell J, Cassell MA, Corbani LE, Cousins SL, Dahmen DJ, Dene H, Diehl AD, Drabkin HJ, Frazer KS, Frost P, Glass LH, Goldsmith CW, Grant PL, Lennon-Pierce M, Lewis J, Lu I, Maltais LJ, McAndrews-Hill M, McClellan L, Miers DB, Miller LA, Ni L, Ormsby JE, Qi D, Reddy TB, Reed DJ, Richards-Smith B, Shaw DR, Sinclair R, Smith CL, Szauter P, Walker MB, Walton DO, Washburn LL, Witham IT, Zhu Y. (2005) The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology. Nucleic Acids Res (Jan), 33(Datab): 471-475.
- Charo J, Geluk A, Sundbäck M, Mirzai B, Diehl AD, Malmberg KJ, Achour A, Huriguchi S, van Meijgaarden KE, Drijfhout JW, Beekman N, van Veelen P, Ossendorp F, Ottenhoff TH, Kiessling R. (2001) The identification of a common pathogen-specific HLA class I A*0201-restricted cytotoxic T cell epitope encoded within the heat shock protein 65. Eur J Immunol (Dec), 31(12): 3602-3611.
- Kambayashi T, Assarsson E, Michaëlsson J, Berglund P, Diehl AD, Chambers BJ, Ljunggren HG. (2000) Emergence of CD8+ T cells expressing NK cell receptors in influenza A virus-infected mice. J Immunol (Nov), 165(9): 4964-4969.
- Garbi N, Tan P, Diehl AD, Chambers BJ, Ljunggren HG, Momburg F, Hämmerling GJ. (2000) Impaired immune responses and altered peptide repertoire in tapasin-deficient mice. Nat Immunol (Sep), 1(3): 234-238.
- Mori I, Diehl AD, Chauhan A, Ljunggren HG, Kristensson K. (1999) Selective targeting of habenular, thalamic midline and monoaminergic brainstem neurons by neurotropic influenza A virus in mice. J Neurovirol (Aug), 5(4): 355-362.
- Liu T, Chambers B, Diehl AD, Van Kaer L, Jondal M, Ljunggren HG. (1997) TAP peptide transporter-independent presentation of heat-killed Sendai virus antigen on MHC class I molecules by splenic antigen-presenting cells. J Immunol (Dec), 159(11): 5364-5371.
- Salcedo M, Diehl AD, Olsson-Alheim MY, Sundbäck J, Van Kaer L, Kärre K, Ljunggren HG. (1997) Altered expression of Ly49 inhibitory receptors on natural killer cells from MHC class I-deficient mice. J Immunol (Apr), 158(7): 3174-3180.
- Diehl A, Rea DW, Hass LF. (1986) MATCH-UP/MATRIX: a microcomputer program designed to search for protein primary structure homology. Comput Appl Biosci (Jun), 2(2): 95-98.
Professional Memberships:
- International Society for Biocuration (2014–present)
- International Association for Ontology and Its Applications (2014–present)
Presentations:
- "Principles of Ontology Development" ICBO: International Conference on Biomedical Ontology (2011)
- "The Neurological Disease Ontology" BFO 2011 (Basic Formal Ontology Editorial Meeting) (2011)
- "The Neurological Disease Ontology" Alzforum / Protein Ontology Kick-Off Meeting (2011)
- "Development of the Cell Ontology via Logical Definition of Cell Types" ; The Biocomplexity Institute, Indiana University (2011)
- "Comprehensive Annotation System for Infectious Disease Data" IDO (Infectious Disease Ontology) Workshop 2010 (2010)
- "Cross-Product Development of the Cell Ontology" Skeletal Anatomy Jamboree; NESCent (2010)
- "Restructuring of the Cell Ontology: Focus on Hematopoietic Cells" ; The Jackson Laboratory; Genetics Interest Group (2010)
- "Hematopoietic Cell Types: Prototype for a Revised Cell Ontology" International Conference on Biomedical Ontology (2009)
- "Introduction to the Gene Ontology" Cell Behavior Ontology Workshop (2009)
- "Improvements in the Representation of Immune Cells in the Cell Ontology" DAIT Bioinformatics Summit 2008 (2008)
- "Gene Ontology for Immunology: an Overview" 94th Annual Meeting of the American Association of Immunologists (2008)
- "Representing Immunology in the GO: Ontology Development and Annotation" DAIT Bioinformatics Summit 2007 (2007)
- "Representation of Immunology in the GO" Ontology Workshop: Focus on Immunology (NIAID) (2006)
- "Requirement for MHC Class II Expression for Influenza Infection of Mouse and Human Cell Lines" Keystone Symposium on the Cell Biology of Viral Entry, Replication, and Pathogenesis (2000)
- "Molecular Pathogenesis of Viral Infection" Keystone Symposium on Molecular Aspects of Viral Immunity (1995)
- "Generation and analysis of mutant cells deficient in expression of MHC Class II molecules" XXVth Annual Meeting of the Scandinavian Society for Immunology (1994)
Service Activities:
- Ad-hoc Journal Reviewer Bioinformatics, Database, Journal of Biomedical Semantics, Neuroinformatics, Trends in Microbiology; Peer Reviewer (2009–2012)
- The Broad Foundaiton; Inflammatory Bowel Disease; Ad-hoc reviewer for Inflammatory Bowel Disease Program of The Broad Foundation.;; Ad Hoc Reviewer (2007)