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Alejandro A. Schäffer, PhD Contact Information
Building 38A, Room 6S608
8600 Rockville Pike
Bethesda, MD 20894-6075
Tel: 301-435-5884
Fax: 301-480-2288
schaffer@ncbi.nlm.nih.gov

Alejandro A. Schäffer, PhD

Staff Scientist
Bioinformatics in Medical Genetics Group
NCBI, NLM, NIH

Research Interests

  • Computational biology
  • Biological sequence comparison
  • Mammalian genetics
  • Design and analysis of algorithms
  • Parallel computing

Selected Publications

  • Jin Y, Schäffer AA, Sherry ST, Feolo M: Quickly identifying identical and closely related subjects in large databases using genotype data. PLoS One 2017; 12(6):e0179106. doi: 10.1371/journal.pone.0179106. [PubMed][PMC]

  • Witzel M, Petersheim D, Fan Y, Bahrami E, Racek T, Rohlfs M, Puchałka J, Mertes C, Gagneur J, Ziegenhain C, Enard W, Stray-Pedersen A, Arkwright PD, Abboud MR, Pazhakh V, Lieschke GJ, Krawitz PM, Dahlhoff M, Schneider MR, Wolf E, Horny HP, Schmidt H, Schäffer AA, Klein C: Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes. Nat Genet. 2017;49(5):742-752. doi: 10.1038/ng.3833. [PubMed][PMC]

  • Schwartz R, Schäffer AA: The evolution of tumour phylogenetics: principles and practice. Nat Rev Genet. 2017;18(4):213-229. doi: 10.1038/nrg.2016.170. Review. [PubMed][PMC]

  • Chowdhury SA, Gertz EM, Wangsa D, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R: Inferring models of multiscale copy number evolution for single-tumor phylogenetics. Bioinformatics. 2015;31(12):i258-67. doi: 10.1093/bioinformatics/btv233. [PubMed][PMC]

  • Sei Y, Zhao X, Forbes J, Szymczak S, Li Q, Trivedi A, Voellinger M, Joy G, Feng J, Whatley M, Jones MS, Harper UL, Marx SJ, Venkatesan AM, Chandrasekharappa SC, Raffeld M, Quezado MM, Louie A, Chen CC, Lim RM, Agarwala R, Schäffer AA, et al.: A Hereditary Form of Small Intestinal Carcinoid Associated With a Germline Mutation in Inositol Polyphosphate Multikinase. Gastroenterology. 2015;149(1):67-78. doi: 10.1053/j.gastro.2015.04.008. [PubMed][PMC]

  • Boztug K, Järvinen PM, Salzer E, Racek T, Mönch S, Garncarz W, Gertz EM, Schäffer AA, Antonopoulos A, Haslam SM, Schieck L, Puchałka J, Diestelhorst J, Appaswamy G, Lescoeur B, Giambruno R, Bigenzahn JW, Elling U, Pfeifer D, Conde CD, Albert MH, Welte K, et al.: JAGN1 deficiency causes aberrant myeloid cell homeostasis and congenital neutropenia. Nat Genet. 2014;46(9):1021-7. doi: 10.1038/ng.3069. [PubMed][PMC]

  • Chowdhury SA, Shackney SE, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R: Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics. PLoS Comput Biol. 2014; 10:e1003740[PubMed][PDF]

  • Triot A, Järvinen PM, Arostegui JI, Murugan D, Kohistani N, Dapena Díaz JL, Racek T, Puchałka J, Gertz EM, Schäffer AA, Kotlarz D, Pfeifer D, Díaz de Heredia Rubio C, Ozdemir MA, Patiroglu T, Karakukcu M, Sánchez de Toledo Codina J, Yagüe J, Touw IP, Unal E, Klein C: Inherited biallelic CSF3R mutations in severe congenital neutropenia. Blood 2014; 123:3811-3817[PubMed][PDF]

  • Sassi A, Lazaroski S, Wu G, Haslam SM, Fliegauf M, Mellouli F, Patiroglu T, Unal E, Ozdemir MA6, Jouhadi Z, Khadir K, Ben-Khemis L, Ben-Ali M, Ben-Mustapha I, Borchani L, Pfeifer D, Jakob T, Khemiri M, Asplund AC, Gustafsson MO, Lundin KE, Falk-Sörqvist E, Moens LN, Gungor HE, Engelhardt KR, Dziadzio M, Stauss H, Fleckenstein B, Meier R, Prayitno K, Maul-Pavicic A, Schaffer S, Rakhmanov M, Henneke P, Kraus H, Eibel H, Kölsch U, Nadifi S, Nilsson M, Bejaoui M, Schäffer AA, Smith CI, Dell A, Barbouche MR, Grimbacher B: Hypomorphic homozygous mutations in phosphoglucomutase 3 (PGM3) impair immunity and increase serum IgE levels. J Allergy Clin Immunol. 2014; 133:1410-1419. [PubMed][PDF]

  • Schäffer AA: Digenic inheritance in medical genetics. J Med Genet. 2013; 50:641-652[PubMed][PDF]

  • Lopez-Herrera G, Tampella G, Pan-Hammarström Q, Herholz P, Trujillo-Vargas CM, Phadwal K, Simon AK, Moutschen M, Etzioni A, Mory A, Srugo I, Melamed D, Hultenby K, Liu C, Baronio M, Vitali M, Philippet P, Dideberg V, Aghamohammadi A, Rezaei N, Enright V, Du L, Salzer U, Eibel H, Pfeifer D, Veelken H, Stauss H, Lougaris V, Plebani A, Gertz EM, Schäffer AA, Hammarström L, Grimbacher B: Deleterious mutations in LRBA are associated with a syndrome of immune deficiency and autoimmunity. Am J Hum Genet. 2012; 90:986-1001. [PubMed] [PDF]

  • Boratyn GM, Schäffer AA, Agarwala R, Altschul SF, Lipman DJ, Madden TL: Domain enhanced lookup time accelerated BLAST. Biol Direct. 2012; 7:12. [PubMed] [PDF]

  • Abdollahpour H, Appaswamy G, Kotlarz D, Diestelhorst J, Beier R, Schäffer AA, Gertz EM, Schambach A, Kreipe HH, Pfeifer D, Engelhardt KR, Rezaei N, Grimbacher B, Lohrmann S, Sherkat R, Klein C: The phenotype of STK4 deficiency. Blood. 2012; 119:3450-3457. [PubMed] [PDF]

  • Hiekkalinna T, Schäffer AA, Lambert B, Norrgrann P, Göring HHH, Terwilliger JD: PSEUDOMARKER: a powerful program for joint linkage and/or linkage disequilibrium analysis on mixtures of singletons and related individuals. Hum Hered. 2011; 71:256-266. [PubMed][PDF]

  • Glocker E-O, Kotlarz D, Boztug K, Gertz EM, Schäffer AA, Noyan F, Perro M, Diestelhorst J, Allroth A, Murugan D, Hätscher N, Pfeifer D, Sykora KW, Sauer M, Kreipe H, Lacher M, Nustede R, Woellner C, Baumann U, Salzer U, Koletzko S, Shah N, Segal AW, Sauerbrey A, Buderus S, Snapper SB, Grimbacher B, Klein C: Inflammatory bowel disease and mutations affecting the interleukin-10 receptor. New Engl J Med. 2009; 361:2033-2045. [PubMed][PDF]

  • Glocker E-O, Hennigs A, Nabavi M, Schäffer AA, Woellner C, Salzer U, Pfeifer D, Veelken H, Warnatz K, Tahami F, Jamal S, Manguiat A, Rezaei N, Amirzargar AA, Plebani A, Hannesschläger N, Gross O, Ruland J, Grimbacher B: A homozygous CARD9 mutation in a family with susceptibility to fungal infections. New Engl J Med. 2009; 361:1727-1735. [PubMed] [PDF]

  • Bohn G, Allroth A, Brandes G, Thiel J, Glocker E, Schäffer AA, Rathinam C, Taub N, Teis D, Zeidler C, Dewey RA, Geffers R, Buer J, Huber LA, Welte K, Grimbacher B, Klein C. A novel human primary immunodeficiency syndrome caused by deficiency of the endosomal adaptor protein p14. Nat Med. 2007; 13:38-45. [PubMed] [PDF]

  • Klein C, Grudzien M, Appaswamy G, Germeshausen M, Sandrock I, Schäffer AA, Rathinam C, Boztug K, Zeidler C, Schwinzer B, Rezaei N, Bohn G, Melin M, Carlsson G, Fadeel B, Dahl N, Palmblad J, Henter J-I, Grimbacher B, Welte K. Deficiency of HAX1 causes autosomal recessive severe congenital neutropenia (Kostmann disease). Nat Genet. 2007; 39:86-92. [PubMed] [PDF]

  • Fyfe JC, Menotti-Raymond M, David VA, Brichta L, Schäffer AA, Agarwala R, Murphy WJ, Wedemeyer WJ, Gregory BL, Buzzell BG, Drummond MC, Wirth B, O'Brien SJ. An ~140kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival. Genome Res. 2006; 16:1084-1090. [PubMed] [PDF]

  • Schäffer AA, Pfannsteil J, Webster ADB, Plebani A, Hammarström L, Grimbacher B. Analysis of familiies with common variable immunodeficiency (CVID) and IgA deficiency suggests linkage of CVID to chromosome 16q. Hum Genet. 2006; 118:725-729. [PubMed] [PDF]

  • Murphy WJ, Agarwala R, and Schäffer AA, Stephens R, Smith C Jr., Crumpler NJ, David VA, O'Brien SJ. A rhesus macaque radiation hybrid map and comparative analysis with the human genome. Genomics 2005; 86:383-395. [PubMed] [PDF]

  • Salzer U, Chapel HM, Webster ADB, Pan-Hammarström Q, Schmitt-Graeff A, Schlesier M, Peter HH, Rockstroh JK, Schneider P, Schäffer AA, Hammarström L, Grimbacher B Mutations in TNFRSF13B encoding TACI are associated with common variable immunodeficiency in humans. Nat Genet. 2005; 37:820-828. [PubMed] [PDF]

  • Desper R, Khan J, and Schäffer AA. Tumor classification using phylogenetic methods on expression data. J. Theor. Biol. 2004; 228:477-496. [PubMed] [PDF]

  • Menotti-Raymond M, David VA, Chen ZQ, Menotti KA, Sun S, Schäffer AA, Agarwala R, Tomlin JF, O'Brien SJ, Murphy WJ Second-Generation Integrated Genetic Linkage/Radiation Hybrid Maps of the Domestic Cat (Felis catus). J Hered. 2003; 94: 95-106. [PubMed] [PDF]

  • Rosenberg MJ, Agarwala R, Bouffard G, Davis J, Fiermonte G, Hilliard MS, Koch T, Kalikin LM, Makalowska I, Morton DH, Petty EM, Weber JL, Palmieri F, Kelley RI, Schäffer AA, Biesecker LG: Mutant deoxynucleotide carrier is associated with congenital microcephaly. Nat Genet. 2002; 32: 175-179. [PubMed] [PDF]

  • Schäffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 2001; 2994-3005. [PubMed] [PS]

  • Johnston JJ, Kelley RI, Crawford TO, Morton DH, Agarwala R, Koch T, Schäffer AA, Francomano CA, Biesecker LG: A novel nemaline myopathy in the Amish caused by a mutation in troponin T1. Am J Hum Genet. 2000; 67: 814-821. [PubMed] [PDF]

  • Agarwala R, Applegate DL, Maglott D, Schuler GD, Schäffer AA. A Fast and scalable radiation hybrid map construction and integration strategy. Genome Res. 2000; 10:350-364. [PubMed][PMC]

  • Simon R, Desper R, Papadimitriou, CH, Peng A, Taetle R, Alberts DS, Trent JM, Schäffer AA. Chromosome abnormalities in ovarian adenocarcinoma III: Using breakpoint data to infer and test mathematical models for oncogenesis. Genes Chromosomes Cancer. 2000; 28: 106-120. [PubMed] [ovar1026.ps]

  • Desper R, Jiang F, Kallioniemi O-P, Moch H, Papadimitriou CH, Schäffer AA. Distance-based reconstruction of tree models for oncogenesis. J Comput Biol. 2000; 7: 789-803. [PubMed] [PDF]

  • Schäffer AA, Wolf YI, Ponting CP, Koonin EV, Aravind L, Altschul SF. IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics 1999; 15:1000-1011. [PubMed] [PDF]

  • Desper R, Jiang F, Kallioniemi O-P, Moch H, Papadimitriou CH, Schäffer AA. Inferring tree models for oncogenesis from comparative genome hybridization data. J Comput Biol. 1999; 6: 37-51. [PubMed] [PDF]

  • Agarwala R, Biesecker LG, Hopkins KA, Francomano CA, Schäffer AA. Software for constructing and verifying pedigrees within large genealogies and an application to the Old Order Amish of Lancaster County. Genome Res. 1998; 8:211-221. [PubMed] [pedhunter.ps]

  • Becker A, Geiger D, Schäffer AA. Automatic selection of loop breakers for genetic linkage analysis. Hum Hered. 1998; 48:49-60. [PubMed] [paper6.ps]

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25: 3389-3402. [PubMed] [PDF]

  • Schäffer AA. Faster linkage analysis computations for pedigrees with loops or unused alleles. Hum Hered. 1996; 46:226-235. [PubMed] [paper5.ps]

  • Gupta SK, Kececioglu J, Schäffer AA. Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. J Comput Biol. 1995; 2:459-472. [PubMed] [paper.ps]

  • Schäffer AA, Gupta SK, Shriram K, Cottingham RW Jr. Avoiding recomputation in linkage analysis. Hum Hered. 1994; 44:225-237. [PubMed] [paper2.ps]

  • Cottingham RW Jr, Idury RM, Schäffer AA. Faster sequential genetic linkage computations. Am J Hum Genet. 1993; 53:252-263. [PubMed] [paper1.ps]

Publications in PubMed

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Last updated: 2018-06-05T15:24:41Z