Hastriter, M.W., S.E. Bush, K. Dittmar, S.S. Hla Bu and M.F. Whiting.  "Nycteridopsylla quadrispina Lu and Wu, a junior synonym of Nycteridopsyla iae Beaucournu and Kock (Siphonaptera: Ischnopsyllidae) as determined by morphological and DNA analyses."  Proceedings of the Entomological Society of Washington.  111 (2009): 598-602. 

Ogden, T.H., J. L. Gattolliat, M. Sartori, A. Staniczek, T. Soldan, and M. F. Whiting.  "Towards a new paradigm in mayfly phylogeny (Ephemeroptera): combined analysis of morphological and molecular data."  Systematic Entomology.  34 (2009): 616-634. 

Svenson. G. and M. F. Whiting.  "Tracing the Origins of the Praying Mantises (Dictyoptera: Mantodea): the emergence of modern Gondwanan mantises and their ecomorphic convergences."  Cladistics.  25 (2009): 468-514. 

Dowton, M., S. L. Cameron, J. I. Dowavic, A. D. Austin, and M. F. Whiting.  "Analysis of 67 rearrangments suggests that mitochondrial gene position is selectively neutral."  Molecular Biology and Evolution.  26 (2009): 1607-1617. 

Sheffield, N. C., H. Song, S. L. Cameron, and M. F. Whiting.  "Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics."  Systematic Biology.  58 (2009): 381-394. 

Cameron, S. L., J. Sullivan, H. Song, K. B. Miller, and M. F. Whiting.  "A mitochondrial genome phylogeny of the Neuropterida (lace-wings, alderflies and snakeflies) and their relationship to the other holometabolous insect orders."  Zoologica Scripta.  38 (2009): 575-590. 

Beutel, R. G., F. Friedrich, and M. F. Whiting.  "Head morphology of Caurinus (Boreidae, Mecoptera) and its phylogenetic implications."  Arthropod Structure and Development.  37 (2008): 418-433. 

Legendre, F., T. Robillard, L. Desutter-Grandcolas, M. F. Whiting, and P. Grandcolas.  "Phylogenetic analysis of non-stereotyped behavioral sequences with a successive event-pairing method."  Biological Journal of the Linnaean Society.  94 (2008): 853-867. 

Song, H., J. E. Buhay. M. F. Whiting, and K. A. Crandall.  "Many species in one?: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified."  Proceedings of the National Academy of Science.  105 (2008): 13486-13491. 

Robertson, J. A., J. V. McHugh, and M. F. Whiting.  "Searching for natural lineages within the Cerylonid Series (Coleoptera: Cucujoidea) using a molecular phylogenetic analysis."  Molecular Phylogenetics and Evolution.  46 (2008): 193-205. 

Ogden, T. H., M. Sartori, and M. F. Whiting.  "Pisciforma, Setisura, and Furcatergalia (Order: Ephemeroptera) are not monophyletic based on 18S rDNA sequences: A Reply to Sun et al. (2006)."  Annals of the Entomological Society of America.  101 (2008): 1-6. 

Cameron, S. L., C. L. Lambkin, S. C. Barker, and M. F. Whiting.  "A mitochondrial genome phylogeny of the Diptera: Whole genome sequence data successfully resolves relationships over broad timescales with high precision."  Systematic Entomology.  32 (2007): 40-59. 

Fenn, J. D., S. Cameron, and M. F. Whiting.  "Mitochondrial genomics of the Mormon cricket (Anabrus simplex) with a comparison of the control region throughout Orthoptera."  Insect Molecular Biology.  16 (2007): 239-252. 

Miller, K. B., J. Bergsten, and M. F. Whiting.  "Phylogeny and classification of diving beetles in the tribe Cybistrini (Coleoptera, Dystiscidae, Dytiscinae)."  Zoologica Scripta.  36 (2007): 41-59. 

Cameron, S. L. and M. F. Whiting.  "Mitochondrial genomic comparisons of the subterranean termites from the Genus Reticulitermes (Insecta: Isoptera: Rhinotermitidae)."  Genome.  50 (2007): 188-202. 

Cameron, S. L., K. P. Johnson, and M F. Whiting.  "The mitochondrial genome of the screamer louse Bothriometopus (Phthiraptera: Ischnocera): Effects of extensive gene rearrangements on the evolution of the genome as a whole."  Journal of Molecular Evolution.  65 (2007): 589-604. 

Hastriter, M.W. and M.F. Whiting.  "Records of fleas (Siphonaptera) of carnivores from Idaho."  Proceedings of the Entomological Society of Washington.  107 (2006): 417-427. 

Trowbridge, R. E., K. Dittmar, and M. F. Whiting.  "Identification and phylogenetic analysis of Arsenophorus and Photorhabdus-type bacteria from adult Hippoboscidae and Streblidae (Hippoboscoidea)."  Journal of Invertebrate Pathology.  91 (2006): 64-68. 

Dittmar, K., M. L. Porter, S. Murray, and M. F. Whiting.  "Molecular phylogenetic analysis of nycteribiid and streblid batflies (Diptera: Brachycera, Calyptratae): Implications for host association and phylogeographic origins."  Molecular Phylogenetics and Evolution.  38 (2006): 155-170. 

Hastriter, M.W., K. Dittmar, and M. F. Whiting.  "Investigation of Taxonomically Important Morphological Features of Endoparasitic Bat Flies of the Subfamily Ascodipterinae (Streblidae) by Scanning Electron Microscopy."  Zootaxa.  1122 (2006): 57-68. 

Jarvis, K. J. and M. F. Whiting.  "Phylogeny of Ice Crawlers (Insecta: Grylloblattodea) based on six loci."  Molecular Phylogenetics and Evolution.  41 (2006): 222-237. 

Cameron, S. L., A. T. Beckenbach, M. A. Dowton, and M. F. Whiting.  "Evidence from mitochondrial genomics on interordinal relationships in insects."  Arthropod Systematics and Phylogeny.  64 (2006): 27-34. 

Cameron, S. L., S. Barker, and M. F. Whiting.  "Mitochondrial genomics and the new insect order Mantophasmatodea."  Molecular Phylogenetics and Evolution.  38 (2006): 274-279. 

Jarvis, K. J., F. Haas, and M. F. Whiting.  "A phylogeny of Dermaptera (Insecta) based on molecular and morphological evidence: reconsidering the classification of earwigs."  Systematic Entomology.  30 (2005): 442-453. 

Taylor, S. D., K. Dittmar de la Cruz, M. L. Porter, and M. F. Whiting.  "Characterization of the long-wavelength opsin from Mecoptera and Siphonaptera: Does a flea see?."  Molecular Biology and Evolution.  22 (2005): 1165-1174. 

Ogden, H., M. F. Whiting, and W. Wheeler.  "Poor Taxon Sampling, Poor Character Sampling, and Non-Repeatable Analyses of a Contrived Dataset do not Provide a More Credible Estimate of Insect Phylogeny: A Reply to Kjer."  Cladistics.  21 (2005): 295-302. 

Terry, M. D., and M. F. Whiting.  "Behavior of POY versus CLUSTALL across a broad parameter landscape."  Cladistics.  21 (2005): 272-281. 

Terry, M. D., and M. F. Whiting.  "Phylogeny of polyneopterous insect orders: Is Mantophasmatodea a new order?."  Cladistics.  21 (2005): 240-257. 

Miller, K. B., Y. Alarie, G. W. Wolfe, and M. F. Whiting.  "Association of insect life stages using DNA sequences: The larvae of Philodytes umbrinus (Motschulsky) (Coleoptera: Dytiscidae)."  Systematic Entomology.  30 (2005): 499-509. 

Ogden, T. H. and M. F. Whiting.  "Phylogeny of Ephemeroptera (mayflies) based on molecular evidence."  Molecular Phylogenetic and Evolution.  37 (2005): 625-643. 

Trowbridge, R. E., K. Dittmar, and M. F. Whiting.  "Identification and phylogenetic analysis of Arsenophorus and Photorhabdus-type bacteria from adult Hippoboscidae and Streblidae (Hippoboscoidea)."  Journal of Invertebrate Pathology.  91.1 (2005): 64-68. 

Dittmar, K., M. L. Porter, S. Murray, and M. F. Whiting.  "Molecular phylogenetic analysis of nycteribiid and streblid batflies (Diptera: Brachycera, Calyptratae): Implications for host association and phylogeographic origins."  Molecular Phylogenetics and Evolution.  38 (2005): 155-170. 

Robertson, J. A., J. V. McHugh, and M. F. Whiting.  "A molecular phylogenetic analysis of the pleasing fungus beetles (Coleoptera: Erotylidae): evolution of colour patterns, gregariousness, and mycophagy."  Systematic Entomology.  29 (2004): 359-370. 

Bybee, S., S. Taylor, C.R. Nelson, and M.F. Whiting.  "A Phylogeny of Robberflies (Diptera: Asilidae) at the subfamilial level: Molecular Evidence."  Molecular Phylogenetics and Evolution.  30 (2004): 789-797. 

Svenson, G. J. and M. F. Whiting.  "Phylogeny of Mantodea based on Molecular Data: Evolution of a Charismatic Predator."  Systematic Entomology.  29 (2004): 359-370. 

Whiting, M. F. and A. S. Whiting.  "Is wing recurrence really impossible?: a reply to Trueman et al."  Systematic Entomology.  29 (2004): 140-141. 

Cryan, J. R., B. M. Wiegmann, L. L. Dietz, C. H. Dietrich, and M. F. Whiting.  "Treehopper trees: Phylogeny of Membracidae (Hemiptera: Cicadomorpha: Membracoidea) Based on Molecules and Morphology."  Systematic Entomology.  29 (2004): 441-454. 

Dittmar K, and M. F. Whiting.  "New Wolbachia endosymbionts from nearctic and neotropical fleas (Siphonaptera)."  Journal of Parasitology.  90 (2004): 953-957. 

Hastriter, M.W., K. Frafjord, and M.F. Whiting.  "A collection of Norwegian fleas (Siphonaptera) north of the Arctic Circle."  Proceedings of the Entomological Society of Washington.  106 (2004): 876-882. 

Cameron, S. L., K. B. Millar, C. A. DHease, M. F. Whiting, and S. C. Barker.  "Mitochondrial genome data alone is not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda)."  Cladistics.  20 (2004): 534-537. 

K. Dittmar, M. L. Porter, L. Price, G. Svenson, and M. F. Whiting.  "Invertebrates of caves of peninsular Malaysia."  Malaysian Nature Journal.  57 (2004): 1-12. 

Dittmar, K., U. Mamat, M. F. Whiting, T. Goldmann, K. Reinhard, and S. Guillen.  "Techniques of DNA-studies on prehispanic ectoparasites (Pulex sp., Pulicidae, Siphonaptera) from animal mummies of the Chiribaya."  Mem. Inst. Oswaldo Cruz, Rio De Janeiro.  98 (2003): 53-58. 

Whiting, M. F., S. Bradler, and T. Maxwell.  "Loss and recovery of wings in stick insects."  Nature.  421 (2003): 264-267. 

M. F. Whiting.  "DNA and The Book of Mormon: A Phylogenetic Perspective."  Journal of Book of Mormon Studies.  12 (2003): 24-35. 

Ogden, T. H. and M. F. Whiting.  "The problem with the Paleoptera Problem: Sense and sensitivity."  Cladistics.  19 (2003): 432-442. 

Dittmar de la Cruz, K. and M. F. Whiting.  "Genetic and phylogeographic structure of populations of Pulex simulans (Siphonaptera) from domesticated guinea pigs (Cavia aperea f. porcellus) in Peru inferred from two genes (Cyt B and Co II)."  Parasitol. Res.  91 (2003): 55-59. 

Barker, S. C., M. F. Whiting, K. P Johnson, and A. Murrell.  "Phylogeny of the lice (Insecta: Phthiraptera) inferred from small subunit rRNA."  Zoologica Scripta.  32 (2003): 407-414. 

Whiting, M. F., A. S. Whiting, and M. W. Hastriter.  "A comprehensive phylogeny of Mecoptera and Siphonaptera."  Entomologische Abhandlungen.  61 (2003): 169. 

Jarvis, K. J. and M. F. Whiting.  "New insights in grylloblattodean phylogeny."  Entomologische Abhandlungen.  61 (2003): 146. 

Svenson, G. J. and M. F. Whiting.  "Phylogeny of Mantodea based on molecular data: evolution of a charismatic predator."  Entomologische Abhandlungen.  61 (2003): 138. 

Bradler, S., M. F. Whiting, and R. Klug.  "Basal diversification and evolution of wings within stick insects (Phasmatodea)."  Entomologische Abhandlungen.  61 (2003): 132-133. 

Dittmar De La Cruz, K., M. F. Whiting, A. S. Whiting, and M. W. Hastriter.  "Preliminary phylogeny of the Siphonaptera."  Entomologische Abhandlungen.  61 (2003): 169. 

Terry, M. D. and M. F. Whiting.  "Phylogeny of Plecoptera: molecular evidence and evolutionary trends."  Entomologische Abhandlungen.  61 (2003): 130. 

Ogden, T. H. and M. F. Whiting.  "Phylogeny of Ephemeroptera: molecular evidence."  Entomologische Abhandlungen.  61 (2003): 126. 

Hastriter, M. W. , M. D. Zyzak, R. Soto, R. Fernandez, N. Solorzano, and M. F. Whiting.  "Fleas (Siphonaptera) from Ancash Department, Peru, with the description of a new species, Ectinorus alejoi (Rhopalopsyllidae), and the description of the male of Plocopsylla pallas (Rothschild, 1914) (Stephanocircidae)."  Annals of the Carnegie.  71 (2002): 87-106. 

Hastriter, M. W. and M. F. Whiting.  "Macropsylla novaehollandiae (Hystrichopsyllidae), a new species of flea from Tasmania."  Proc. Entomol. Soc. Washington.  104 (2002): 663-671. 

M. F. Whiting.  "Mecoptera is paraphyletic: multiple genes and phylogeny of Mecoptera and Siphonaptera."  Zoologica Scripta.  31 (2002): 93-105. 

M. F. Whiting.  "Phylogeny of the holometabolous insect orders: molecular evidence."  Zoologica Scripta.  31 (2002): 3-17. 

M. F. Whiting.  "Phylogeny of Holometabola: state of the art."  Zoologica Scripta.  31 (2002): 1-2. 

Ogden, T.H. W. P. McCafferty, and M. F. Whiting.  "Phylogeny of the Ephemeroptera of the world: a call for specimens."  The Mayfly Newsletter.  12 (2002): 5-6. 

Wheeler, W.C., M. F. Whiting, Q. D. Wheeler, and J. Carpenter.  "Phylogeny of the extant hexapod orders."  Cladistics.  17 (2001): 1-89. 

Hastriter, M. W., M. E. Alarcon, and M. F. Whiting.  "A collection of fleas from the San Martin reserve, Valdivia Province, Chile."  Proc. Entomol. Soc. Wash.  103 (2001): 437 443. 

Cryan, J.R., J.K. Liebherr, J.W. Fetzner, Jr., and M.F. Whiting.  "Evaluation of relationships within the endemic Hawaiian Platynini (Coleoptera: Carabidae) based on molecular and morphological evidence."  Molecular Phylogenetics and Evolution.  21 (2001): 72-85. 

Johnson, K. P. and M. F. Whiting.  "Multiple genes and the phylogeny of Ischnocera (Insecta: Phthiraptera)."  Molecular Phylogenetics and Evolution.  21 (2001): 282-292. 

Snell, Q., M. Whiting, M. Clement, and D. McLaughlin.  "Parallel Phylogenetic Inference."  Proceedings of Supercomputing.  2000. 

Clement, M., Q. Snell, M. Whiting. and G. Judd.  "High performance phylogenetic inference."  Proceedings of the Eighth IEEE International Symposium on High Performance Distributed Computing.  1999: 335 336. 

Siddall, M. E. and M. F. Whiting.  "Long branch abstractions."  Cladistics.  1999. 

Whiting, M. F.  "Long Branch Distraction and the Strepsiptera."  Systematic Biology.  1998. 

Whiting, M. F.  "Phylogenetic position of Strepsiptera: Review of molecular and morphological evidence."  Int. J. Insect Morphol. & Embryol.  1998. 

Whiting, M. F., J. M. Carpenter, Q. D. Wheeler, and W. C. Wheeler.  "The Strepsiptera problem: Phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology."  Systematic Biology.  46 (1997). 

DeSalle, R., B. Perez-Sweeney, M. F. Whiting, D. Agosti, R. Bang, J. Remsen, and J. Bonacum.  "Crossroads, Milestones and Landmarks in Insect Development and Evolution: Implications for Systematics."  Aliso.  14 (1996). 

Whiting, M. F.  "Strepsiptera."  Encyclopedia of Insects.  Ed. V. H. Resh and R. Carde.  2nd ed.  Academic Press, Dec. 2008. 

M. F. Whiting.  "Phylogenetic position of Diptera: A review of the evidence."  The Evolutionary Biology of Flies.  Ed. B.M. Wiegmann and D.K. Yeates.  Columbia University Press, Apr. 2005. 

Whiting, M. F.  "Phylogeny of Holometabolous Insects: The most successful group of terrestrial organisms."  Assembling the Tree of Life.  Ed. J. Cracraft and M. Donoghue.  Oxford University Press, 2004. 

Hastriter, M. W. and M. F. Whiting.  "Siphonaptera (fleas)."  Encyclopedia of Insects.  Ed. V. H. Resh and R. Carde.  Academic Press, 2003. 

M. F. Whiting.  "Strepsiptera."  Encyclopedia of Insects.  Ed. V. H. Resh and R. Carde.  Academic Press, 2003. 

M. F. Whiting.  "High throughput DNA sequencing for Systematic Applications."  Techniques in Molecular Systematics and Evolution.  Ed. R. DeSalle, G. Giribet, and W. C. Wheeler.  Birkhauser Press, 2002. 

M. F. Whiting.  "Phylogeny of the holometabolous insect orders based on 18S ribosomal data: when bad things happen to good data."  Molecular Systematics and Evolution: Theory and Practice.  Ed. R. DeSalle, G. Giribet and W. Wheeler.  Birkhauser press, 2002.