Alejandro A. Scha¨ffer Curriculum Vitae March 2015 Date of Birth: 1 July 1963 Place of Birth: Montevideo, Uruguay Citizenship: United States Family: married to Beth R. Sch¨affer, one son Office Address: National Center for Biotechnology Information National Library of Medicine/NIH Building 38A, Room 6S608 Bethesda, MD 20894 Office Phone: (301) 435-5884 E-mail: schaff[email protected] Education: B.S. Applied Mathematics (Computer Science), University Honors Carnegie-Mellon University, 1983 M.S. Mathematics, Honors Degree Program Carnegie-Mellon University, 1983 Ph.D. Computer Science, Stanford University, 1988 Honors: National Library of Medicine Regents Award for Scholarship or Technical Achievement, 2010 Part of a large group receiving an NIH Merit Award, 2008 Selected as a “Highly Cited Researcher” by ISI, 20006–2011 (service ended by ISI) National Center for Human Genome Research, Merit Award, 1996 Fannie and John Hertz Foundation Fellowship, 1986–1988 National Science Foundation Graduate Fellowship, 1983–1986 Andrew Carnegie Society Scholarship, 1982–83 National Merit Scholarship, 1980–83 Thesis Topic: Algorithmic Problems on Intersection Graphs Advisor: Prof. Christos H. Papadimitriou Employment Experience: 2006–present Clinical Investigator, National Center for Biotechnology Information, NIH (additional title assigned due to extensive human subjects research) 1998–present Computer Scientist, National Center for Biotechnology Information, NIH 1995–1998 Computer Scientist, National Center for Human Genome Research, NIH 1988–1996 Assistant Professor, Dept. of Computer Science, Rice University (on professional leave 1988–89, on family leave Autumn 1993) (on Intergovernment Personnel Assignment to NIH from August 1995) 1988–89 Postdoctoral Member of Technical Staff, AT&T Bell Laboratories, Murray Hill, NJ 1986–88 Research Student Associate, IBM Almad´en Research Center, San Jos´e, CA (summers: full-time, academic year: part-time) 1985 Summer Member of Technical Staff, AT&T Bell Laboratories, Murray Hill, NJ 1985 Winter, Spring Research Assistant, Stanford University 1984 Autumn Teaching Assistant, Stanford University 1984 Summer Member of Technical Staff, AT&T Bell Laboratories, Murray Hill NJ 1983–84 Research Assistant, Stanford University 1980–83 Part-time programmer, Computer Science Department, 1 Carnegie-Mellon University Areas of Interest: Computational Biology, Algorithms, Biological Sequence Analysis, Mammalian Genetics and Genomics, Primary Immunodeficiency Diseases Publications:(h-index = 53; g-index 184) 1. “LUCIFER: A Latent, UNIX-Compatible, Interfaced File Emulator and Retriever”, Alejandro A. Sch¨affer, Carnegie-Mellon University, SPICE Document D007, 1981. 2. “A Polynomial Time Algorithm for Finding the Prime Factors of Cartesian-Product Graphs”, JoanFeigenbaum,JohnHershberger,andAlejandroA.Sch¨affer,Discrete Applied Mathematics 12(1985), pp. 123–138. 3. “Recognizing Composite Graphs is Equivalent to Testing Graph Isomorphism”, Joan Feigen- baum and Alejandro A. Sch¨affer, SIAM Journal on Computing 15(1986), pp. 619–627. 4. “A Note on the Chromatic Number of the Alternative Negation of Two Graphs”, Alejandro A. Sch¨affer and Ashok Subramanian, Colloquium Mathematicum LV(1988), pp. 367–370. 5. “Convex Hulls of Piecewise-Smooth Jordan Curves”, Alejandro A. Sch¨affer and Christopher J. Van Wyk, Journal of Algorithms 8(1987), pp. 66–94. 6. “Shortest Prefix Strings Containing All Subset Permutations”, Alejandro A. Sch¨affer, Discrete Mathematics 64(1987), pp. 239–252. 7. “OnGossipingwithFaultyTelephoneLines”,RamseyW.Haddad,ShaibalRoy,andAlejandro A. Sch¨affer, SIAM Journal on Algebraic and Discrete Methods 8(1987) pp. 439–445. 8. “ATighterUpperBoundontheWorstCaseBehaviorofConway’sParallelSortingAlgorithm”, Alejandro A. Sch¨affer, Journal of Algorithms 9(1988) pp. 321–342. 9. “Fast Parallel Algorithms for Chordal Graphs”, Joseph Naor, Moni Naor, and Alejandro A. th Sch¨affer, (extended abstract) Proceedings of the 19 Annual ACM Symposium on Theory of Computing,1987,pp.355–364;(fullpaper)SIAMJournalonComputing18(1989)pp.327–349; more detailed version of full paper available as IBM Research Report RJ5629. 10. “Recognizing Bellman-Ford-Orderable Graphs”, Ramsey W. Haddad and Alejandro A. Sch¨af- fer, SIAM Journal on Discrete Mathematics 1(1988), pp. 447–471. 11. “Computing the Bump Number with Techniques from Two-Processor Scheduling”, Alejandro A. Sch¨affer and Barbara B. Simons, Order 5(1988), pp. 131–141. 12. “Time Bounds on Fault Tolerant Broadcasting”, David Peleg and Alejandro A. Sch¨affer, Net- works 19(1989), pp. 803–822. 13a. “Storing and Searching a Multikey Table”, Amos Fiat, Moni Naor, Alejandro A. Sch¨affer, th Jeanette P. Schmidt, and Alan Siegel, (extended abstract) Proceedings of the 20 Annual ACM Symposium on Theory of Computing, 1988, pp. 344–353. 13b. “An Implicit Data Structure for Searching a Multikey Table in Logarithmic Time”, Amos Fiat, J. Ian Munro, Moni Naor, Alejandro A. Sch¨affer, Jeanette P. Schmidt, and Alan Siegel, Journal of Computer and System Sciences 43(1991), pp. 406–424 (special issue for best papers th presented at the 20 ACM Symposium on Computing); this is a full version of 13a. 14. “Graph Spanners”, David Pelegand Alejandro A. Sch¨affer,Journal of Graph Theory13(1989), pp. 99–116. (cited > 150 times) 15. “A Faster Algorithm to Recognize Undirected Path Graphs”, Alejandro A. Sch¨affer, Discrete Applied Mathematics 43(1993), pp. 261–295. 16. “Recognizing Brittle Graphs: Remarks on a Paper of Ho`ang and Khouzam”, Alejandro A. Sch¨affer, Discrete Applied Mathematics 31(1991), pp. 29–35. 17. “Optimal Node Ranking of Trees in Linear Time”, Alejandro A. Sch¨affer, Information Pro- cessing Letters 33(1989), pp. 91–96. 2 18. “Finding the Prime Factors of Strong Direct Product Graphs in Polynomial Time”, Joan Feigenbaum and Alejandro A. Sch¨affer, invited paper for an International Conference on Alge- braicGraphTheory,Leibnitz,Austria,June1989;Discrete Mathematics109(1992),pp.77-102 (special volume devoted to this conference). 19. “A Note on Finding a Strict Saddlepoint”, Daniel Bienstock, Fan Chung, Michael Fredman, Alejandro A. Sch¨affer, Peter W. Shor, and Subhash Suri, American Mathematical Monthly 98(1991), pp. 418–419. 20a. “Simple Local Search Problems That Are Hard to Solve”, Alejandro A. Sch¨affer and Mihalis Yannakakis, SIAM Journal on Computing 20(1991), pp. 56–87. 20b. “On the Complexity of Local Search”, Christos H. Papadimitriou, Alejandro A. Sch¨affer, and nd Mihalis Yannakakis, (extended abstract) Proceedings of the 22 Annual ACM Symposium on Theory of Computing, 1990, pp. 438–445 (This is a combined summary of 20a. and a later paper by Papadimitriou) (20a and 20b cited a total of > 100 times). 21. “Parallel Batch Update of Minimum Spanning Trees”, Alejandro A. Sch¨affer and Peter J. Varman, Rice Univ. Comp. Sci. Tech. Rept. 90–140. 22. “FasterIsometricEmbeddinginProductsofCompleteGraphs”,FranzAurenhammer,Michael Formann,RamanaM.Idury,AlejandroA.Sch¨affer,andFrankWagner,Discrete Applied Math- ematics 52(1994), pp. 17–28. 23. “Markov Analysis of Multiple Disk Prefetching for External Mergesort”, Vinay Sadananda Pai, Alejandro A. Sch¨affer, and Peter J. Varman, (extended abstract) Proceedings of 21st InternationalConferenceonParallelProcessing,1992,pp.III-272–279;(fullpaperwithslightly altered title) Theoretical Computer Science 128(1994), pp. 211–239. 24. “Triangulating Three-Colored Graphs in Linear Time and Linear Space”, Ramana M. Idury and Alejandro A. Sch¨affer, SIAM Journal on Discrete Mathematics 6(1993), pp. 289–293. 25. “Dynamic Dictionary Matching with Failure Functions”, Ramana M. Idury and Alejandro A. Sch¨affer, (extended abstract) 3rd Combinatorial Pattern Matching Conference, 1992, Lec- ture Notes in Computer Science 644, pp. 276–287; (full paper) Theoretical Computer Science 131(1994), pp. 295–310. 26. “Optimal Edge Ranking of Trees in Polynomial Time”, Pilar de la Torre, Raymond Green- law, Alejandro A. Sch¨affer, (extended abstract) Proceedings of the 4th Annual ACM-SIAM SymposiumonDiscreteAlgorithms,1993,pp.138–144;(fullpaper)Algorithmica13(1995),pp. 592–618. 27. “ImprovedDynamicDictionaryMatching”,AmihoodAmir,MartinFarach,RamanaM.Idury, Johannes A. LaPoutr´e, Alejandro A. Sch¨affer, (extended abstract) Proceedings of the 4th An- nual ACM-SIAM Symposium on Discrete Algorithms, 1993, pp. 392–401; (full paper) Infor- mation and Computation 119(1995), pp. 258–282 (two versions cited a combined total of > 50 times). 28. “Faster Sequential Genetic Linkage Computations”, Robert W. Cottingham Jr., Ramana M. Idury, Alejandro A. Sch¨affer, American Journal of Human Genetics 53(1993), pp. 252–263. (cited > 1,200 times) 29. “Multiple Matching of Rectangular Patterns”, Ramana M. Idury, Alejandro A. Sch¨affer, (ex- th tended abstract) Proceedings of the 25 Annual ACM Symposium on Theory of Computing, 1993, pp. 81–90; (full paper) Information and Computation 117(1995), pp. 78–90. 30. “Multiple Matching of Parameterized Patterns”, Ramana M. Idury, Alejandro A. Sch¨affer, (extended abstract) 5th Combinatorial Pattern Matching Conference, 1994, Lecture Notes in Computer Science 807, pp. 226–239; (full paper) invited to Theoretical Computer Science 154(1996), pp. 203–224. 31. “Parallelization of General Linkage Analysis Problems”, Sandhya Dwarkadas, Alejandro A. Sch¨affer, Robert W. Cottingham Jr., Alan L. Cox, Peter Keleher, Willy Zwaenepoel, Human 3 Heredity 44(1994), pp. 127–141. 32. “Avoiding Recomputation in Linkage Analysis”, Alejandro A. Sch¨affer, Sandeep K. Gupta, K. Shriram, Robert W. Cottingham Jr., Human Heredity 44(1994), pp. 225–237. (cited > 700 times) 33. “Integrating Parallelization Strategies for Linkage Analysis”, Sandeep K. Gupta, Alejandro A. Sch¨affer, Alan L. Cox, Sandhya Dwarkadas, Willy Zwaenepoel, Computers and Biomedical Research 28(1995), pp. 116–139. 34a. “Making the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment More Space Efficient in Practice”, Sandeep K. Gupta, John Kececioglu, Alejandro A. Sch¨affer, (ex- tended abstract of 34b.) 6th Combinatorial Pattern Matching Conference, 1995, Lecture Notes in Computer Science 937, pp. 128–143. 34b. “Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum- of-Pairs Multiple Sequence Alignment”, Sandeep K. Gupta, John Kececioglu, Alejandro A. Sch¨affer, (full paper of 34a.) Journal of Computational Biology 2(1995), pp. 459–472. (cited > 75 times) 35. “Linkage Analyses in Type I Diabetes Using CASPAR, a Software and Statistical Program for Conditional Analysis of Polygenic Diseases”, Jeremy Buhler, David Owerbach, Alejandro A. Sch¨affer, Marek Kimmel, Kenneth H. Gabbay, Human Heredity 47(1997), pp. 211–222. 36. “FasterLinkageAnalysisComputationsforPedigreeswithLoopsorUnusedAlleles”,Alejandro A. Sch¨affer, Human Heredity 46(1996), pp. 226–235. (cited > 100 times) 37. “Automated Selection of STRP Markers for Whole Genome Screening for Segmental Aneu- somy”, Leslie G. Biesecker Alejandro A. Sch¨affer, Human Heredity 47(1997), pp. 76–85. 38. “ExclusionofCandidateLociandCholesterolBiosyntheticAbnormalitiesinFamilialPallister- HallSyndrome”,LeslieG.Biesecker,SeongmanKang,AlejandroA.Sch¨affer,MargaretAbbott, Richard I. Kelley, Jeffrey C. Allen, Carol Clericuzio, Theresa Grebe, Ann Olney, John M. Graham Jr., Journal of Medical Genetics 33(1996), pp. 947–951. 39. “Scanning the Genome with 1,772 Microsatellite Markers in Search for a Bipolar Disorder Susceptibility Gene”, Mihael H. Polymeropoulos, Alejandro A. Schaffer, Molecular Psychiatry 1(1996), pp. 404–407. 40. “Fine Mapping of the Nail-Patella Syndrome Locus at 9q34”, Iain McIntosh, Mark V. Clough, Alejandro A. Sch¨affer, Erik G. Puffenberger, V. Kim Horton, Kathryn Peters, Margaret H. Abbott, Carmen M. Roig, Steven Cutone, Laurie Ozelius, David J. Kwiatkowski, Reed E. Pyeritz, Laura J. Brown, Richard M. Pauli, Mary Kay McCormick, Clair A. Francomano, American Journal of Human Genetics 60(1997), pp. 133–142. 41. “Mapping of a Gene for Parkinson’s Disease to Chromosome 4q21-q23” Mihael H. Poly- meropoulos,JosephJ.Higgins,LawrenceI.Golbe,WilliamG.Johnson,SusanE.Ide,Giuseppe Di Iorio, Giuseppe Sanges, Edward S. Stenroos, Lana T. Pho, Alejandro A. Schaffer, Alice M. Lazzarini Robert L. Nussbaum, Roger C. Duvoisin, Science 274(1996), pp. 1197–1199. (cited > 400 times) 42. “GeneticHeterogeneityandClonalEvolutionUnderlyingDevelopmentofAsynchronousMetas- tasis in Human Breast Cancer”, Tuula Kuukasj¨arvi, Ritva Karhu, Minna Tanner, Merketta K¨ahk¨onen, Alejandro Sch¨affer, Nina Nupponnen, Sari Pennanen, Anne Kallioniemi, Olli-P. Kallioniemi, Jorma Isola, Cancer Research 57(1997), pp. 1597–1604. (cited > 250 times) 43. “Localization of a Gene for an Autosomal Recessive Form of Juvenile Parkinsonism to Chro- mosome 6q25.2-27”, Hiroto Matsumine, Masaaki Saito, Satoe Shimoda-Matsubayashi Hajime Tanaka, Atsushi Ishikawa, Yuko Nakagawa-Hattori, Masayuki Yokochi, Tomonori Kobayashi, ShuichiIgarashi,HirokiTakano,KazuhiroSanpei,RyokoKoike,HideoMori,TomoyoshiKondo, YoshihikoMizutani,AlejandroA.Sch¨affer,YasuhiroYamamura,ShigenobuNakamura,Shigeki 4 Kuzuhara, Shoji Tsuji, Yoshikuni Mizuno, American Journal of Human Genetics 60(1997), pp. 588–596. (cited > 200 times) 44. “LinkageMappingandPhenotypicAnalysisofAutosomalDominantPallister-HallSyndrome”, SeongmanKang,JeffreyAllen,JohnM.GrahamJr.,TheresaGrebe,CarolClericuzio,Nicholas Patronas,FrankOndrey,EricGreen,AlejandroSchaffer,MargaretAbbott,LeslieG.Biesecker, Journal of Medical Genetics 34(1997), pp. 441–446. 45. “Approximation Algorithms for a Genetic Diagnostics Problem”, S. Rao Kosaraju, Alejan- dro A. Sch¨affer, Leslie G. Biesecker, (invited paper) Proc. 5th International Workshop on Algorithms and Data Structures, 1997, Lecture Notes in Computer Science 1272, pp. 69–92. (refereed paper) Journal of Computational Biology 5(1998), pp. 9–26. 46. “AutomaticSelectionofLoopBreakersforGeneticLinkageAnalysis”,AnnBecker,DanGeiger, Alejandro A. Sch¨affer, Human Heredity 48(1998), pp. 49–60. 47. “GappedBLASTandPSI-BLAST–ANewGenerationofProteinDatabaseSearchPrograms”, Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch¨affer, Jinghui Zhang, Zheng Zhang, Webb Miller, David J. Lipman, Nucleic Acids Research 25(1997), pp. 3389-3402. (cited > 35,000 times) 48. “Genetic and Physical Mapping of the McKusick-Kaufman Syndrome”, Deborah Stone, Richa Agarwala,AlejandroA.Sch¨affer,JamesL.Weber,DavidVaske,TakayaOda,SettaraC.Chan- drasekharappa, Clair A. Francomano, Leslie G. Biesecker, Human Molecular Genetics 7(1998), pp. 475–481. 49. “Refinement of the Gene Locus for Autosomal Recessive Juvenile Parkinsonism (AR-JP) on Chromosome 6q25.2-27 and Identification of Markers Exhibiting Linkage Disequilibrium”, MasaakiSaito,HirotoMatsumine,HajimeTanaka,AtsushiIshikawa,SatoeShimoda-Matsubayashi, Alejandro A. Sch¨affer, Yoshikuni Mizuno, Shoji Tsuji, (Japanese) Journal of Human Genetics 43(1998), pp. 22–31. 50 “Computing Probabilities of Homozygosity by Descent” Alejandro A. Sch¨affer, Genetic Epi- demiology 16(1999), pp. 135–149. 51 “Coping with Complexity: Lessons from the Mathematical Sciences”, Alejandro A. Sch¨affer, Human Genetics 103(1998), pp. 5–10. (invited paper, only editorial review) 52. “Software for Constructing and Verifying Pedigrees Within Large Genealogies and an Appli- cation to the Old Order Amish of Lancaster County”, Richa Agarwala, Leslie G. Biesecker, KatherineA.Hopkins,ClairA.Francomano,AlejandroA.Sch¨affer,Genome Research8(1998), pp. 211–221. (cited > 50 times) 53. “Protein Sequence Similarity Searches Using Patterns as Seeds” Zheng Zhang, Alejandro A. Sch¨affer, Webb Miller, Thomas L. Madden, David J. Lipman, Eugene V. Koonin, Stephen F. Altschul, Nucleic Acids Research 26(1998), pp. 3986–3990. (cited > 150 times) 54. “Inverse Inbreeding Coefficient Problems with an Application to Linkage Analysis of Recessive Diseases in Inbred Populations”, Richa Agarwala, Leslie G. Biesecker, Alejandro A. Sch¨affer, (extended abstract) Proceedings of the 10th Annual ACM-SIAM Symposium on Discrete Al- gorithms, 1999, pp. 840–841; (full paper) Discrete Applied Mathematics 104(2000), pp. 3–44 (special issue on Computational Molecular Biology). 55. “InferringTreeModelsforOncogenesisfromComparativeGenomeHybridizationData”,Richard Desper, Feng Jiang, Olli-P. Kallioniemi, Holger Moch, Christos H. Papadimitriou, Alejandro A. Sch¨affer, Journal of Computational Biology6(1999), pp. 37–51. (actually published in 2000) (cited > 100 times) 56. “Evaluation of the Clonal Relationship Between Primary and Metastatic RCC by Compara- tive Genomic Hybridization”, Heidi Bissig, Jan Richter, Richard Desper, Verena Meier, Peter Schraml, Alejandro A. Sch¨affer, Guido Sauter, Michael J. Mihatsch, Holger Moch, American Journal of Pathology 155(1999), pp. 267–274. (cited > 75 times) 5 57. “A Genetic Map of Microsatellites in the Domestic Cat (Felis catus)”, Marilyn Menotti- Raymond, Victor A. David, Leslie A. Lyons, Alejandro A. Scha¨ffer, James F. Tomlin, Michelle K. Hutton, Stephen J. O’Brien, Genomics 57(1999), pp. 9–23. (cited > 200 times) 58. “Atm Haploinsufficiency Results in Increased Sensitivity to Sublethal Doses of Ionizing Radia- tioninMice”,CarroleeBarlow,MichaelA.Eckhaus,AlejandroA.Sch¨affer,AnthonyWynshaw- Boris, Nature Genetics 21(1999), pp. 359–360. (cited > 50 times) 59. “Towards a Complete North American Anabaptist Genealogy: A Systematic Approach to Merging Partially Overlapping Genealogy Resources”, Richa Agarwala, Leslie G. Biesecker, James F. Tomlin, Alejandro A. Sch¨affer, American Journal of Medical Genetics 86(1999), pp. 156–161. 60. “Genetic Linkage of Hyper-IgE Syndrome to Chromosome 4”, Bodo Grimbacher, Alejandro A. Sch¨affer,StevenM.Holland,JoieDavis,JohnI.Gallin,HarryL.Malech,T.PrescottAtkinson, Bernd H. Belohradsky, Rebecca H. Buckley, Fausto Cossu, Teresa Espan˜ol, Ben-Zion Garty, NuriaMatamoros,LaurieA.Myers,RobertP.Nelson,HansD.Ochs,EleonoreD.Renner,Nele Wellinghausen,JenniferM.Puck,AmericanJournalofHumanGenetics65(1999),pp.735–744. (cited > 150 times) 61. “IMPALA: Matching a Protein Sequence Against a Collection of PSI-BLAST-Constructed Position-SpecificScoreMatrices”,AlejandroA.Sch¨affer,YuriI.Wolf,ChrisP.Ponting,Eugene V. Koonin, L. Aravind, Stephen F. Altschul, Bioinformatics 15(1999), pp. 1000–1011. (cited > 200 times) 62. “Chromosome Abnormalities in Ovarian Adenocarcinoma III: Using Breakpoint Data to Infer and Test Mathematical Models for Oncogenesis”, Richard Simon, Richard Desper, Christos H. Papadimitriou, Amy Peng, Raymond Taetle, David S. Alberts, Jeffrey M. Trent, Alejandro A. Sch¨affer, Genes, Chromosomes & Cancer 28(2000), pp. 106–120. 63. “Genetic Modifiers of the Insulin-Resistance Phenotype in Mice”, Yoshiaki Kido, Neubert Philippe, Alejandro A. Sch¨affer, Domenico Accili, Diabetes 49(2000), pp. 589–596. (cited > 50 times) 64. “Distance-BasedReconstructionofTreeModelsforOncogenesis”,RichardDesper,FengJiang, Olli-P. Kallioniemi, Holger Moch, Christos H. Papadimitriou, Alejandro A. Sch¨affer, Journal of Computational Biology 7(2000), pp. 789–803. (cited > 50 times) 65. “A Fast and Scalable Radiation Hybrid Map Construction and Integration Strategy”, Richa Agarwala, David L. Applegate, Donna Maglott, Gregory D. Schuler, Alejandro A. Sch¨affer, Genome Research 10(2000), pp. 350–364. (cited > 75 times) 66. “Somatic Deletions in Hereditary Breast Cancers Implicate 13q21 as a Putative Novel Breast Cancer Susceptibility Locus”, Tommi Kainu, Suh-Hang Hank Juo, Richard Desper, Alejan- dro A. Sch¨affer, Elizabeth Gillanders, Ester Rozenblum, Diana Freas-Lutz, Don Weaver, Di- etrich Stephan, Joan Bailey-Wilson, Olli-P. Kallioniemi, Mika Tirkkonen, Kirsi Syryj¨akoski, Tuula Kuukasj¨arvi, Pasi Koivisto, Ritva Karhu, Kaija Holli, Adalgeir Arason, Gudrun Jo- hannesdottir, Jon Thor Bergthrosson, Hrefna Johannsdottir, Valgardur Egilsson, Rosa Bj¨ork Barkardottir, Oskar Johannsson, Karin Haraldsson, Therese Sandberg, Eva Holmberg, Henrik Gr¨onberg, H˚akan Olsson, ˚Ake Borg, Paula Vehmanen, Hannaleena Eerola, P¨aivi Heikkila, Seppo Pyrh¨onen, Heli Nevanlinna, Proceedings of the National Academy of Sciences USA 97(2000), pp. 9603–9608. (cited > 100 times) 67. “A Novel Nemaline Myopathy in the Amish Caused by a Mutation in Troponin T1”, Jennifer J. Johnston, Richard I. Kelley, Thomas O. Crawford, D. Holmes Morton, Richa Agarwala, Thorsten Koch, Alejandro A. Sch¨affer, Clair A. Francomano, Leslie G. Biesecker, American Journal of Human Genetics 67(2000), pp. 814–821. (cited > 100 times) 68. “Construction of Evolutionary Tree Models for Renal Cell Carcinoma from Comparative Ge- nomicHybridizationData”,FengJiang,RichardDesper,ChristosH.Papadimitriou,Alejandro 6 A.Sch¨affer,JanRichter,PeterSchraml,Olli-P.Kallioniemi,MichaelJ.Mihatsch,HolgerMoch, Cancer Research 60(2000), pp. 6503–6509. (cited > 75 times) 69. “TreeModelsforDependentCopyNumberChangesinBladderCancer”,AlejandroA.Sch¨affer, Ronald Simon, Richard Desper, Jan Richter, Guido Sauter, International Journal of Oncology 18(2001), pp. 349–354. 70. “TowardsaCompleteNorthAmericanAnabaptistGenealogyII:AnalysisofInbreeding”,Richa Agarwala, Alejandro A. Sch¨affer, James F. Tomlin, Human Biology 73(2001), pp. 533–545. 71. “Heritability of Life Span in the Old Order Amish”, Braxton D. Mitchell, Wen-Chi Hsueh, Terri M. King, Toni I. Pollin, John Sorkin, Richa Agarwala, Alejandro A. Sch¨affer, Alan R. Shuldiner, American Journal of Medical Genetics 102(2001), pp. 346–352. (cited > 50 times) 72. “Improving the Accuracy of PSI-BLAST Protein Database Searches with Composition-Based Statistics and Other Refinements”, Alejandro A. Sch¨affer, L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, Stephen F. Altschul, Nucleic Acids Research 29(2001), pp. 2994–3005. (cited > 600 times) 73. “Genomic Imbalances in the Progression of Pancreatic Endocrine Tumors”, Jianming Zhao, Holger Moch, Alexander F. Scheidweiler, Angela Baer, Alejandro A. Sch¨affer, Guido Sauter, Ernst J. M. Speel, Ju¨rgen Roth, Philipp U. Heitz, Paul Komminoth, Genes, Chromosomes & Cancer 32(2001), pp. 364–372. (cited 50 times) 74. “Graph Models of Oncogenesis with an Application to Melanoma, Michael D. Radmacher, Richard Simon, Richard Desper, Raymond Taetle, Alejandro A. Sch¨affer, Mark A. Nelson, Journal of Theoretical Biology 212(2001), pp. 535–548. 75. “An Immune Defect Causing Dominant Chronic Mucocutaneous Candidiasis and Thyroid Dis- easeMapstoChromosome2pinaSingleFamily”,T.PrescottAtkinson,AlejandroA.Sch¨affer, BodoGrimbacher,HarryW.SchroederJr.,CristinaWoellner,ChristaZerbe,JenniferM.Puck, American Journal of Human Genetics 69(2001), pp. 791–803. 76. “Stable Karyotypes in Epithelial Cancer Cell Lines Despite High Rates of Ongoing Structural and Numerical Chromosomal Instability”, Anna V. Roschke, Kristen Stover, Giovanni Tonon, Alejandro A. Sch¨affer, Ilan R. Kirsch, Neoplasia 4(2002), pp. 19–31. (cited 50 times) 77. “GeneticDifferencesDetectedbyComparativeGenomicHybridizationinHeadandNeckSqua- mous Cell Carcinomas from Different Tumor Sites: Construction of Oncogenetic Trees for Tu- mor Progression”, Qiang Huang, Guo Pei Yu, Steven A. McCormick, Juan Mo, Bhakti Datta, Manoj Mahimkar, Philip Lazarus, Alejandro A. Sch¨affer, Richard Desper, Stimson P. Schantz, Genes, Chromosomes & Cancer 34(2002), pp. 224–233. (cited > 100 times) 78. “Mutant Deoxynucleotide Carrier is Associated with Congenital Microcephaly”, Marjorie J. Rosenberg,RichaAgarwala,GerardBouffard,JoieDavis,GiuseppeFiermonte,MarkS.Hilliard, ThorstenKoch,LindaM.Kalikin,IzabelaMakalowska,D.HolmesMorton,ElizabethM.Petty, James L. Weber, Ferdinando Palmieri, Richard I. Kelley, Alejandro A. Sch¨affer, Leslie G. Biesecker, Nature Genetics 32(2002), pp. 175–179. (cited > 50 times) 79. “Second Generation Integrated Genetic Linkage/Radiation Hybrid Maps of the Domestic Cat (Felis Catus)”, M. Menotti-Raymond, V. A. David, Z. Q. Chen, K. A. Menotti, S. Sun, A. A. Sch¨affer,R.Agarwala,J.F.Tomlin,S.J.O’Brien,W.J.Murphy,Journal of Heredity94(2003), pp. 95–106. (special issue for papers presented at a symposium on Advances in Canine and Feline Genomics) (cited > 50 times) 80. “Linkage of Autosomal Dominant Common Variable Immunodeficiency to Chromosome 5p and Evidence for Locus Heterogeneity”, D. U. Braig, A. A. Sch¨affer, E. Glocker, U. Salzer, K. Warnatz, H. H. Peter, B. Grimbacher, Human Genetics 112(2003), pp. 369–378. 81. “A Genome-wide Scan for Open-Angle Glaucoma (POAG): The Barbados Family Study of Open-AngleGlaucoma”,BarbaraNemesure,XiaodongJiao,QimeiHe,M.CristinaLeske,Suh- Yuh Wu, Anselm Hennis, Nancy Mendell, Joy Redman, Henri-Jean Garchon, Richa Agarwala, 7 Alejandro A. Sch¨affer, Fielding Hejtmancik, for the Barbados Family Study Group, Human Genetics 112(2003), pp. 600–609. (cited > 50 times) 82. “Homozygous Loss of ICOS Is Associated with Adult-Onset Common Variable Immunodefi- ciency”, Bodo Grimbacher, Andreas Hutloff, Michael Schlesier, Erik Glocker, Klaus Warnatz, Ruth Dr¨ager, Hermann Eibel, Beate Fischer, Alejandro A. Sch¨affer, Hans W. Mages, Richard A. Kroczek, Hans H. Peter, Nature Immunology 4(2003), pp. 261–268. (cited > 300 times) 83. “AnabaptistGenealogyDatabase”,RichaAgarwala,LeslieG.Biesecker,AlejandroA.Sch¨affer, American Journal of Medical Genetics/Seminars in Medical Genetics 121C(2003), pp. 32–37. (special issue on Amish genetics) 84. “CanineImerslund-Gr¨asbeckSyndromeMapstoaRegionOrthologoustoHSA14q”,Qianchuan He, John C. Fyfe, Alejandro A. Sch¨affer, Adam Kilkenney, Petra Werner, Ewen F. Kirkness, Paula S. Henthorn, Mammalian Genome 14(2003), pp. 758–764. 85. “Radiation Hybrid Mapping of 304 Novel Microsatellites in the Domestic Cat Genome”, M. Menotti-Raymond, V. A. David, R. Agarwala, A. A. Sch¨affer, R. Stephens, S. J. O’Brien, W. J.Murphy,Cytogenetic and Genome Research102(2003),pp.272–276.(specialissueonanimal genomics) 86. “Reduced Incidence of Hip Fracture in the Old Order Amish”, Elizabeth A. Streeten, Daniel J. McBride, Amy L. Lodge, Toni I. Pollin, David G. Stinchcomb, Richa Agarwala, Alejandro A. Sch¨affer, Alan R. Shuldiner, Jay R. Shapiro, and Braxton D. Mitchell, Journal of Bone and Mineral Research 19(2004), pp. 308–313. 87. “A Microsatellite Polymorphism in Intron 2 of Human Toll-Like Receptor 2: Functional Impli- cations and Racial Differences”, Jae-Joon Yim, Li Ding, Alejandro A. Sch¨affer, Gye Young Park, Young-Soo Shim, Steven M. Holland, FEMS Immunology and Medical Microbiology 40(2004), pp. 163–169. 88. “Tumor Classification Using Phylogenetic Methods on Expression Data”, Richard Desper, Javed Khan, Alejandro A. Sch¨affer, Journal of Theoretical Biology 228(2004), pp. 477–496. 89. “ConstructionofTreeModelsforPathogenesisofNasopharyngealCarcinoma”,ZhongxiHuang, Richard Desper, Alejandro A. Sch¨affer, Zhihua Yin, Xin Li, Kaitai Yao, Genes, Chromosomes & Cancer 40(2004), pp. 307–315. 90. “Interferon–γ Receptor 1 Promoter Polymorphisms: Population Distribution and Functional Implications”, Sergio D. Rosenzweig, Alejandro A. Sch¨affer, Li Ding, Rachel Sullivan, Bal- asz Enyedi, Jae-Joon Yim, James L. Cook, James M. Musser, Steven M. Holland, Clinical Immunology 112(2004), pp. 113–119. 91. “The Genetics of Hypogammaglobulinemia”, Bodo Grimbacher, Alejandro A. Sch¨affer, Hans- Hartmut Peter, Current Allergy and Asthma Reports 4(2004), pp. 349–358. (invited review article, only editorial review) 92. “AStructure-basedMethodforProteinSequenceAlignment”MaricelG.Kann,PaulThiessen, Anna R. Panchenko, Alejandro A. Sch¨affer, Stephen F. Altschul, Steven H. Bryant, Bioinfor- matics 21(2005), pp. 1451–1456. 93. “Clinical and PET Evaluation of Two Families with Parkinson Disease Caused by Mutation in theKinaseDomainofDardarin,EncodedbyLRRK2”,DenaG.Hernandez,CoroPais´an-Ru´ız, Aideen McInerney-Leo, Shushant Jain, Andreas Meyer-Lindenberg, E. Whitney Evans, Karen F. Berman, Janel Johnson, Georg Auberger, Alejandro A. Scha¨ffer, Grisel Lopez, Robert L. Nussbaum, Andrew B. Singleton, Annals of Neurology 57(2005), pp. 453–456. (cited > 75 times) 94. “Amnionless Function Is Required for Cubilin Brush-Border Expression and Intrinsic Factor- Cobalamin (Vitamin B12) Absorption in vivo”, Qianchuan He, Mette Madsen, Adam Kilken- ney,BrittanyGregory,ErikI.Christensen,HenrikVorum,PeterHøjrup,AlejandroA.Sch¨affer, 8 EwenKirkness,StephanM.Tanner,AlbertdelaChapelle,UrsGiger,SørenK.Moestrup,John C. Fyfe, Blood 106(2005), pp. 1447–1453. (cited > 50 times) 95. “AHigh-ResolutionPhysicalMapofEquineHomologuesofHSA19ShowsDivergentEvolution Compared to Other Mammals”, Candice Brinkmeyer–Langford, Terje Raudsepp, Eun-Joon Lee, Glenda Goh, Alejandro A. Sch¨affer, Richa Agarwala, Michelle L. Wagner, Teruaki Tozaki, James R. Mickelson, James E. Womack, Loren C. Skow, Bhanu P. Chowdhary, Mammalian Genome 16(2005), pp. 631–649. 96. “Mutations in TNFRSF13B Encoding TACI Are Associated with Common Variable Immun- odeficiency in Humans”, U. Salzer, H. M. Chapel, A. D. B. Webster, Q. Pan-Hammarstr¨om, A. Schmitt-Graeff, M. Schlesier, H. H. Peter, J. K. Rockstroh, P. Schneider, A. A. Sch¨affer, L. Hammarstr¨om, B. Grimbacher, Nature Genetics 37(2005), pp. 820–828. (cited > 250 times) 97. “A Comprehensive Continuous-Time Model for the Appearance of CGH Signal Due to Chro- mosomal Missegregations During Mitosis”, Richard Desper, Michael Difilipantonio, Thomas Ried, Alejandro A. Sch¨affer, Mathematical Biosciences 197(2005), pp. 67–87. 98. “A Rhesus Macaque Radiation Hybrid Map and Comparative Analysis with the Human Genome”,WilliamJ.Murphy,RichaAgarwala,AlejandroA.Sch¨affer,RobertStephens,Clarence Smith Jr., Nicole J. Crumpler, Victor A. David, Stephen J. O’Brien, Genomics 86(2005), pp. 383–395. 99. “Protein Database Searches Using Compositionally Adjusted Substitution Matrices”, Stephen F. Altschul, John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Ale- jandro A. Sch¨affer, Yi-Kuo Yu, FEBS Journal 272(2005), pp. 5101–5109. (cited > 300 times) 100. “A 1.3-Mb Interval Map of Equine Homologs of HSA2”, Michelle L. Wagner, Terje Raud- sepp, Glenda Goh, Alejandro A. Sch¨affer, Richa Agarwala, Patricia K. Dranchak, Candice Brinkmeyer, Loren C. Skow, Bhanu P. Chowdhary, James R. Mickelson, Cytogenetic and Genome Research 112(2006), pp. 227–234. 101. “Does Having Children Extend Lifespan? A Genealogical Study of Parity and Longevity in the Amish”, P. F. McArdle, T. I. Pollin, J. R. O’Connell, J. D. Sorkin, R. Agarwala, A. A. Sch¨affer, E. A. Streeten, T. M. King, A. R. Shuldiner, B. D. Mitchell, Journal of Gerontology, Series A: Biological and Medical Sciences 61A(2006), pp. 190–195. 102. “HLA B44 is Associated with Decreased Severity of Autoimmune Lymphoproliferative Syn- drome in Patients with CD95 Mutations (ALPS Type Ia)”, Marla M. Vacek, Alejandro A. Sch¨affer, Joie Davis, Roxanne E. Fischer, Janet K. Dale, Sharon Adams, Stephen E. Straus, Jennifer M. Puck, Clinical Immunology 118(2006), pp. 59–65. 103. “Analysis of Families with Common Variable Immunodeficiency (CVID) and IgA Deficiency Suggests Linkage of CVID to Chromosome 16q”, Alejandro A. Sch¨affer, Jessica Pfannstiel, A. David B. Webster, Alessandro Plebani, Lennart Hammarstr¨om, Bodo Grimbacher, Human Genetics 118(2006), pp. 725–729. 104. “WindowMasker: Window-Based Masker for Sequenced Genomes”, Aleksander Morgulis, E. Michael Gertz, Alejandro A. Sch¨affer, Richa Agarwala, Bioinformatics 22(2006), pp. 134–141. (cited > 50 times) 105. “A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences”, Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Sch¨affer, Richa Agarwala, Journal of Computational Biology 13(2006), pp. 1028–1040. (cited > 50 times) 106. “Human Genetic Linkage Analysis”, Alejandro A. Sch¨affer, Chapter 17 of Handbook of Com- putational Molecular Biology, Srinivas Aluru (ed.), Chapman & Hall/CRC:Boca Raton, FL, 2006. 107. “Genetic Alterations in Caspase-10 May Be Causative or Protective in Autoimmune Lypho- proliferative Syndrome”, Shigui Zhu, Amy P. Hsu, Marla M. Vacek, Lixin Zheng, Alejandro A. Sch¨affer, Janet K. Dale, Joie Davis, Roxanne E. Fischer, Stephen E. Straus, Donna Boru- 9 chov, Frank T. Saulsbury, Michael J. Lenardo, Jennifer M. Puck, Human Genetics 119(2006), pp. 284–294. 108. “Novel Gene Acquisition on Carnivore Y Chromosomes”, William J. Murphy, Alison J. Pearks Wilkerson, Terje Raudespp, Richa Agarwala, Alejandro A. Sch¨affer, Roscoe Stanyon, Bhanu P. Chowdhary, PLoS Genetics 2(2006), pp. 0353-0363 (also labeled as article e43) 109. “Identification of a Genomic Deletion in the AP3B1 Gene Causing Hermansky-Pudlak Syn- drome, Type 2”, Johannes Jung, Georg Bohn, Anna Allroth, Kaan Boztug, Gudrun Brandes, IngaSandrock,AlejandroA.Sch¨affer,ChozhavendanRathiman,IngaK¨ollner,CarmelaBerger, Reinhard Schilke, Karl Welte, Bodo Grimbacher, Christoph Klein, Blood 108(2006), pp. 362– 369. (cited > 50 times) 110. “Linkage of Autosomal Dominant Common Variable Immunodeficiency to Chromosome 4q”, Anemone Finck, Jos W. M. van der Meer, Alejandro A. Sch¨affer, Jessica Pfannstiel, Claire Fieschi, Alessandro Plebani, A. David B. Webster, Lennart Hammarstr¨om, Bodo Grimbacher, European Journal of Human Genetics 14(2006), pp. 867–875. 111. “An ∼140kb Deletion Associated with Feline Spinal Muscular Atrophy Implies an Essential LIX1 Function for Motor Neuron Survival”, John C. Fyfe, Marilyn Menotti-Raymond, Victor A. David, Lars Brichta, Alejandro A. Sch¨affer, Richa Agarwala, William J. Murphy, William J. Wedemeyer, Brittany L. Gregory, Bethany G. Buzzell, Meghan C. Drummond, Brunhilde Wirth, Stephen J. O’Brien, Genome Research 16(2006), pp. 1084–1090. 112. “A Homozygous Single-base Deletion in MLPH Causes the Dilute Coat Color Phenotype in the Domestic Cat”, Yasuko Ishida, Victor A. David, Eduardo Eizirik, Alejandro A. Sch¨affer, Beena A. Neelam, Melody E. Roelke, Steven S. Hannah, StephenJ. O’Brien, Marilyn Menotti- Raymond, Genomics 88(2006), pp. 698–705. 113. “RetrievalAccuracy,StatisticalSignificanceandCompositionalSimilarityinProteinSequence Database Searches”, Yi-Kuo Yu, E. Michael Gertz, Richa Agarwala, Alejandro A. Sch¨affer, Stephen F. Altschul, Nucleic Acids Research 34(2006), pp. 5966–5973. 114. “High-Resolution Gene Maps of Horse Chromosomes 14 and 21: Additional Insights into Evo- lution and Rearrangements of HSA5 Homologues in Mammals”, Glenda Goh, Terje Raudsepp, Keith Durkin, Michelle L. Wagner, Alejandro A. Sch¨affer, Richa Agarwala, Teruaki Tozaki, James R. Mickelson, Bhanu P. Chowdhary, Genomics 89(2007), pp. 89–112. 115. “A 1.5 Megabase Resolution Radiation Hybrid Map of the Cat Genome and Comparative Analysis with the Canine and Human Genomes”, William J. Murphy, Brian Davis, Victor A. David, Richa Agarwala, Alejandro A. Sch¨affer, Alison J. Pearks Wilkerson, Beena Neelam, Stephen J. O’Brien, Marilyn Menotti-Raymond, Genomics 89(2007), pp. 189–196. 116. “ANovelHumanPrimaryImmunodeficiencySyndromeCausedbyDeficiencyoftheEndosomal Adaptor Protein p14”, Georg Bohn, Anna Allroth, Gudrun Brandes, Jens Thiel, Erik Glocker, Alejandro A. Sch¨affer, Chozhavendan Rathinam, Nicole Taub, David Teis, Cornelia Zeidler, Ricardo A. Dewey, Robert Geffers, Jan Buer, Lukas A. Huber, Karl Welte, Bodo Grimbacher, Christoph Klein, Nature Medicine 13(2007), pp. 38–45. (cited > 75 times) 117. “HAX1 Deficiency Causes Autosomal Recessive Severe Congenital Neutropenia (Kostmann Disease)”,ChristophKlein,MagdaGrudzien,GiridharanAppaswamy,ManuelaGermeshausen, Inga Sandrock, Alejandro A. Sch¨affer, Chozhavendan Rathinam, Kaan Boztug, Cornelia Zei- dler, Beate Schwinzer, Nima Rezaei, Georg Bohn, Malin Melin, G¨oran Carlsson, Bengt Fadeel, Niklas Dahl, Jan Palmblad, Jan-Inge Henter, Bodo Grimbacher, Karl Welte, Nature Genetics 39(2007), pp. 86–92. (cited > 200 times) 118. “Composition-Based Statistics and Translated Nucleotide Searches: Improving the TBLASTN Module of BLAST”, E. Michael Gertz, Yi-Kuo Yu, Richa Agarwala, Alejandro A. Sch¨affer, Stephen F. Altschul, BMC Biology 4(2006), article 41. (cited > 50 times) 119. “Construction of a River Buffalo (Bubalus bubalis) Whole-Genome Radiation Hybrid Panel 10