Research Output

2020

A multi-disciplinary clinic for SCN8A-related epilepsy

Schreiber, J. M., Tochen, L., Brown, M., Evans, S., Ball, L. J., Bumbut, A., Thewamit, R., Whitehead, M. T., Black, C., Boutzoukas, E., Fanto, E., Suslovic, W., Berl, M., Hammer, M. & Gaillard, W. D., Jan 2020, In : Epilepsy Research. 159, 106261.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Deep Learning Classification of Chest X-Ray Images

Majdi, M. S., Salman, K. N., Morris, M. F., Merchant, N. C. & Rodriguez, J. J., Mar 2020, 2020 IEEE Southwest Symposium on Image Analysis and Interpretation, SSIAI 2020 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 116-119 4 p. 9094612. (Proceedings of the IEEE Southwest Symposium on Image Analysis and Interpretation; vol. 2020-March).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Rare tumor-normal matched whole exome sequencing identifies novel genomic pathogenic germline and somatic aberrations

Sprissler, R., Perkins, B., Johnstone, L., Babiker, H. M., Chalasani, P., Lau, B., Hammer, M. & Mahadevan, D., Jun 2020, In : Cancers. 12, 6, p. 1-22 22 p., 1618.

Research output: Contribution to journalArticle

Open Access
2019

Altered expression of signaling pathways regulating neuronal excitability in hippocampal tissue of temporal lobe epilepsy patients with low and high seizure frequency

Hammer, M. F., Sprissler, R., Bina, R. W., Lau, B., Johnstone, L., Walter, C. M., Labiner, D. M. & Weinand, M. E., Sep 2019, In : Epilepsy Research. 155, 106145.

Research output: Contribution to journalArticle

Genomic evidence of local adaptation to climate and diet in indigenous Siberians

Hallmark, B., Karafet, T. M., Hsieh, P. H., Osipova, L. P., Watkins, J. C. & Hammer, M. F., 2019, In : Molecular biology and evolution. 36, 2, p. 315-327 13 p.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Identification of African-Specific Admixture between Modern and Archaic Humans

the GenomeAsia 100K Consortium, Dec 5 2019, In : American Journal of Human Genetics. 105, 6, p. 1254-1261 8 p.

Research output: Contribution to journalArticle

2 Scopus citations

Influence of age at seizure onset on the acquisition of neurodevelopmental skills in an SCN8A cohort

Encinas, A. C., Moore, I. K. M., Watkins, J. C. & Hammer, M. F., 2019, In : Epilepsia. 60, 8, p. 1711-1720 10 p.

Research output: Contribution to journalArticle

2 Scopus citations
1 Scopus citations

Stephen L. Zegura (2 July 1943-26 May 2019)

Ackermann, R. R., Bezanson, M., Hammer, M. & Raichlen, D., Feb 17 2019, In : Human biology. 91, 1, p. 49-52 4 p.

Research output: Contribution to journalArticle

Substructured population growth in the Ashkenazi Jews inferred with approximate Bayesian computation

Gladstein, A. L. & Hammer, M. F., Jun 1 2019, In : Molecular biology and evolution. 36, 6, p. 1162-1171 10 p.

Research output: Contribution to journalArticle

4 Scopus citations

The GenomeAsia 100K Project enables genetic discoveries across Asia

GenomeAsia100K Consortium, Dec 5 2019, In : Nature. 576, 7785, p. 106-111 6 p.

Research output: Contribution to journalArticle

Open Access
11 Scopus citations

The spectrum of intermediate SCN8A-related epilepsy

Johannesen, K. M., Gardella, E., Encinas, A. C., Lehesjoki, A. E., Linnankivi, T., Petersen, M. B., Lund, I. C. B., Blichfeldt, S., Miranda, M. J., Pal, D. K., Lascelles, K., Procopis, P., Orsini, A., Bonuccelli, A., Giacomini, T., Helbig, I., Fenger, C. D., Sisodiya, S. M., Hernandez-Hernandez, L., Krithika, S. & 25 others, Rumple, M., Masnada, S., Valente, M., Cereda, C., Giordano, L., Accorsi, P., Bürki, S. E., Mancardi, M., Korff, C., Guerrini, R., von Spiczak, S., Hoffman-Zacharska, D., Mazurczak, T., Coppola, A., Buono, S., Vecchi, M., Hammer, M. F., Varesio, C., Veggiotti, P., Lal, D., Brünger, T., Zara, F., Striano, P., Rubboli, G. & Møller, R. S., May 2019, In : Epilepsia. 60, 5, p. 830-844 15 p.

Research output: Contribution to journalArticle

22 Scopus citations
2018

GRAM: Global research activity map

Burd, R., Espy, K. A., Hossain, M. I., Kobourov, S., Merchant, N. & Purchase, H., May 29 2018, AVI 2018 - Proceedings of the 2018 International Conference on Advanced Visual Interfaces. Catarci, T., Marrella, A., Leotta, F. & Mecella, M. (eds.). Association for Computing Machinery, a31. (Proceedings of the Workshop on Advanced Visual Interfaces AVI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Human-centric programming in the large - Command languages to scalable cyber training

Dewan, P., Joyce, B. & Merchant, N. C., Oct 23 2018, Proceedings - 2018 IEEE Symposium on Visual Languages and Human-Centric Computing, VL/HCC 2018. Kelleher, C., Engels, G., Fernandes, J. P., Cunha, J. & Mendes, J. (eds.). IEEE Computer Society, Vol. 2018-October. p. 295-297 3 p. 8506564

Research output: Chapter in Book/Report/Conference proceedingConference contribution

MAKER as a service: Moving HPC applications to jetstream cloud

Hazekamp, N., Devisetty, U. K., Merchant, N. & Thain, D., May 16 2018, Proceedings - 2018 IEEE International Conference on Cloud Engineering, IC2E 2018. Li, J., Chandra, A., Guo, T. & Cai, Y. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 72-78 7 p. (Proceedings - 2018 IEEE International Conference on Cloud Engineering, IC2E 2018).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Modeling SNP array ascertainment with Approximate Bayesian Computation for demographic inference

Quinto-Cortés, C. D., Woerner, A. E., Watkins, J. C. & Hammer, M. F., Dec 1 2018, In : Scientific reports. 8, 1, 10209.

Research output: Contribution to journalArticle

5 Scopus citations

Siberian genetic diversity reveals complex origins of the Samoyedic-speaking populations

Karafet, T. M., Osipova, L. P., Savina, O. V., Hallmark, B. & Hammer, M. F., Nov 1 2018, In : American Journal of Human Biology. 30, 6, e23194.

Research output: Contribution to journalArticle

2 Scopus citations

The principles of tomorrow's university [version 1; referees: 2 approved]

Katz, D. S., Allen, G., Barba, L. A., Berg, D. R., Bik, H., Boettiger, C., Borgman, C. L., Brown, C. T., Buck, S., Burd, R., de Waard, A., Eve, M. P., Granger, B. E., Greenberg, J., Howe, A., Howe, B., Khanna, M., Killeen, T. L., Mayernik, M., McKiernan, E. & 12 others, Mentzel, C., Merchant, N., Niemeyer, K. E., Noren, L., Nusser, S. M., Reed, D. A., Seidel, E., Smith, M., Spies, J. R., Turk, M., Van Horn, J. D. & Walsh, J., 2018, In : F1000Research. 7, 1926.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

The role of phylogenetically conserved elements in shaping patterns of human genomic diversity

Woerner, A. E., Veeramah, K. R., Watkins, J. C. & Hammer, M. F., Jan 1 2018, In : Molecular Biology and Evolution. 35, 9, p. 2284-2295 12 p.

Research output: Contribution to journalArticle

3 Scopus citations
2017

Aboriginal Australian mitochondrial genome variation - An increased understanding of population antiquity and diversity

Nagle, N., Van Oven, M., Wilcox, S., Van Holst Pellekaan, S., Tyler-Smith, C., Xue, Y., Ballantyne, K. N., Wilcox, L., Papac, L., Cooke, K., Van Oorschot, R. A. H., McAllister, P., Williams, L., Kayser, M., Mitchell, R. J., Adhikarla, S., Adler, C. J., Balanovska, E., Balanovsky, O., Bertranpetit, J. & 36 others, Clarke, A. C., Comas, D., Cooper, A., Der Sarkissian, C. S. I., Dulik, M. C., Gaieski, J. B., Kumar, A., Prasad, G., Haak, W., Haber, M., Hobbs, A., Javed, A., Jin, L., Kaplan, M. E., Li, S., Martinez-Cruz, B., Matisoo-Smith, E. A., Mele, M., Merchant, N. C., Owings, A. C., Parida, L., Pitchappan, R., Platt, D. E., Quintana-Murci, L., Renfrew, C., Royyuru, A. K., Santhakumari, A. V., Santos, F. R., Schurr, T. G., Soodyall, H., Soria Hernanz, D. F., Swamikrishnan, P., Vilar, M. G., Wells, R. S., Zalloua, P. A. & Ziegle, J. S., Mar 13 2017, In : Scientific reports. 7, 43041.

Research output: Contribution to journalArticle

16 Scopus citations

Additive Damage Models for Cellular Pharmacodynamics of Radiation–Chemotherapy Combinations

Williams, K. S., Secomb, T. W. & Fox, A. E-K., Aug 28 2017, (Accepted/In press) In : Bulletin of Mathematical Biology. p. 1-23 23 p.

Research output: Contribution to journalArticle

2 Scopus citations

Altered gene expression profile in a mouse model of SCN8A encephalopathy

Sprissler, R. S., Wagnon, J. L., Bunton-Stasyshyn, R. K., Meisler, M. H. & Hammer, M. F., Feb 1 2017, In : Experimental Neurology. 288, p. 134-141 8 p.

Research output: Contribution to journalArticle

11 Scopus citations

An ALMA and MagAO Study of the Substellar Companion GQ Lup B

Wu, Y. L., Sheehan, P. D., Males, J. R., Close, L. M., Morzinski, K. M., Teske, J. K., Haug-Baltzell, A., Merchant, N. & Lyons, E., Feb 20 2017, In : Astrophysical Journal. 836, 2, 223.

Research output: Contribution to journalArticle

14 Scopus citations

Clinical implications of SCN1A missense and truncation variants in a large Japanese cohort with Dravet syndrome

Ishii, A., Watkins, J. C., Chen, D., Hirose, S. & Hammer, M. F., Feb 1 2017, In : Epilepsia. 58, 2, p. 282-290 9 p.

Research output: Contribution to journalArticle

23 Scopus citations

Complex Patterns of Admixture across the Indonesian Archipelago

Hudjashov, G., Karafet, T. M., Lawson, D. J., Downey, S., Savina, O., Sudoyo, H., Lansing, J. S., Hammer, M. F. & Cox, M. P., Oct 1 2017, In : Molecular biology and evolution. 34, 10, p. 2439-2452 14 p.

Research output: Contribution to journalArticle

25 Scopus citations

Exome Sequencing Provides Evidence of Polygenic Adaptation to a Fat-Rich Animal Diet in Indigenous Siberian Populations

Hsieh, P. H., Hallmark, B., Watkins, J. C., Karafet, T., Osipova, L. P., Gutenkunst, R. N. & Hammer, M. F., Nov 1 2017, In : Molecular Biology and Evolution. 34, 11, p. 2913-2926 14 p.

Research output: Contribution to journalArticle

9 Scopus citations

Overcoming the Law of the Hidden in Cyberinfrastructures

Bucksch, A., Das, A., Schneider, H., Merchant, N. C. & Weitz, J. S., Feb 1 2017, In : Trends in Plant Science. 22, 2, p. 117-123 7 p.

Research output: Contribution to journalReview article

3 Scopus citations

Rare variants of small effect size in neuronal excitability genes influence clinical outcome in Japanese cases of SCN1A truncation-positive Dravet syndrome

Hammer, M. F., Ishii, A., Johnstone, L., Tchourbanov, A., Lau, B., Sprissler, R., Hallmark, B., Zhang, M., Zhou, J., Watkins, J. & Hirose, S., Jul 2017, In : PloS one. 12, 7, e0180485.

Research output: Contribution to journalArticle

7 Scopus citations
2016

Bringing your tools to CyVerse Discovery Environment using Docker [version 1; referees: 3 approved]

Devisetty, U. K., Kennedy, K., Sarando, P., Merchant, N. C. & Lyons, E. H., 2016, In : F1000Research. 5, 1442.

Research output: Contribution to journalArticle

13 Scopus citations

Coevolution of genes and languages and high levels of population structure among the highland populations of Daghestan

Karafet, T. M., Bulayeva, K. B., Nichols, J., Bulayev, O. A., Gurgenova, F., Omarova, J., Yepiskoposyan, L., Savina, O. V., Rodrigue, B. H. & Hammer, M. F., Mar 1 2016, In : Journal of human genetics. 61, 3, p. 181-191 11 p.

Research output: Contribution to journalArticle

10 Scopus citations

Erratum: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies (Genome Research (2016) 26 (291-300))

Hsieh, P., Woerner, A. E., Wall, J. D., Lachance, J., Tishkoff, S. A., Gutenkunst, R. N. & Hammer, M. F., May 2016, In : Genome Research. 26, 5, 1 p.

Research output: Contribution to journalComment/debate

High-contrast imaging in the cloud with klipReduce and findr

Haug-Baltzell, A., Males, J. R., Morzinski, K. M., Wu, Y. L., Merchant, N., Lyons, E. & Close, L. M., Jan 1 2016, Software and Cyberinfrastructure for Astronomy IV. Chiozzi, G. & Guzman, J. C. (eds.). SPIE, 99130F. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 9913).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations

Jetstream - Performance, early experiences, and early results

Stewart, C. A., Fischer, J., Merchant, N. C., Stanzione, D. C., Hancock, D. Y., Cockerill, T., Miller, T., Taylor, J., Vaughn, M., Liming, L., Lowe, J. M. & Skidmore, E., Jul 17 2016, Proceedings of XSEDE 2016: Diversity, Big Data, and Science at Scale. Association for Computing Machinery, Vol. 17-21-July-2016. a22

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

Hsieh, P. H., Woerner, A. E., Wall, J. D., Lachance, J., Tishkoff, S. A., Gutenkunst, R. N. & Hammer, M. F., Mar 2016, In : Genome Research. 26, 3, p. 291-300 10 p.

Research output: Contribution to journalArticle

46 Scopus citations

PGen: Large-scale genomic variations analysis workflow and browser in SoyKB

Liu, Y., Khan, S. M., Wang, J., Rynge, M., Zhang, Y., Zeng, S., Chen, S., Maldonado dos Santos, J. V., Valliyodan, B., Calyam, P. P., Merchant, N., Nguyen, H. T., Xu, D. & Joshi, T., Oct 6 2016, In : BMC bioinformatics. 17, 337.

Research output: Contribution to journalArticle

11 Scopus citations

Scaling GIS analysis tasks from the desktop to the cloud utilizing contemporary distributed computing and data management approaches: A case study of project-based learning and cyberinfrastructure concepts

Swetnam, T. L., Pelletier, J. D., Rasmussen, C., Callahan, N. R., Merchant, N., Lyons, E., Rynge, M., Liu, Y., Nandigam, V. & Crosby, C., Jul 17 2016, Proceedings of XSEDE 2016: Diversity, Big Data, and Science at Scale. Association for Computing Machinery, a21. (ACM International Conference Proceeding Series; vol. 17-21-July-2016).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

SCN8A encephalopathy: Research progress and prospects

Meisler, M. H., Helman, G., Hammer, M. F., Fureman, B. E., Gaillard, W. D., Goldin, A. L., Hirose, S., Ishii, A., Kroner, B. L., Lossin, C., Mefford, H. C., Parent, J. M., Patel, M., Schreiber, J., Stewart, R., Whittemore, V., Wilcox, K., Wagnon, J. L., Pearl, P. L., Vanderver, A. & 1 others, Scheffer, I. E., Jul 1 2016, In : Epilepsia. 57, 7, p. 1027-1035 9 p.

Research output: Contribution to journalArticle

63 Scopus citations

Small Traditional Human Communities Sustain Genomic Diversity over Microgeographic Scales despite Linguistic Isolation

Cox, M. P., Hudjashov, G., Sim, A., Savina, O., Karafet, T. M., Sudoyo, H. & Lansing, J. S., Sep 1 2016, In : Molecular biology and evolution. 33, 9, p. 2273-2284 12 p.

Research output: Contribution to journalArticle

7 Scopus citations

The Genetic History of Peruvian Quechua-Lamistas and Chankas: Uniparental DNA Patterns among Autochthonous Amazonian and Andean Populations

The Genographic Project Consortium, Mar 1 2016, In : Annals of Human Genetics. 80, 2, p. 88-101 14 p.

Research output: Contribution to journalArticle

14 Scopus citations

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

Merchant, N., Lyons, E., Goff, S., Vaughn, M., Ware, D., Micklos, D. & Antin, P., Jan 11 2016, In : PLoS biology. 14, 1, e1002342.

Research output: Contribution to journalArticle

114 Scopus citations

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., Skoglund, P., Lazaridis, I., Sankararaman, S., Fu, Q., Rohland, N., Renaud, G., Erlich, Y., Willems, T., Gallo, C., Spence, J. P. & 59 others, Song, Y. S., Poletti, G., Balloux, F., Van Driem, G., De Knijff, P., Romero, I. G., Jha, A. R., Behar, D. M., Bravi, C. M., Capelli, C., Hervig, T., Moreno-Estrada, A., Posukh, O. L., Balanovska, E., Balanovsky, O., Karachanak-Yankova, S., Sahakyan, H., Toncheva, D., Yepiskoposyan, L., Tyler-Smith, C., Xue, Y., Abdullah, M. S., Ruiz-Linares, A., Beall, C. M., Di Rienzo, A., Jeong, C., Starikovskaya, E. B., Metspalu, E., Parik, J., Villems, R., Henn, B. M., Hodoglugil, U., Mahley, R., Sajantila, A., Stamatoyannopoulos, G., Wee, J. T. S., Khusainova, R., Khusnutdinova, E., Litvinov, S., Ayodo, G., Comas, D., Hammer, M. F., Kivisild, T., Klitz, W., Winkler, C. A., Labuda, D., Bamshad, M., Jorde, L. B., Tishkoff, S. A., Watkins, W. S., Metspalu, M., Dryomov, S., Sukernik, R., Singh, L., Thangaraj, K., Paäbo, S., Kelso, J., Patterson, N. & Reich, D., 2016, In : Nature. 538, 7624, p. 201-206 6 p.

Research output: Contribution to journalArticle

359 Scopus citations

The time scale of recombination rate evolution in great apes

Great Ape Genome Project, Apr 1 2016, In : Molecular biology and evolution. 33, 4, p. 928-945 18 p.

Research output: Contribution to journalArticle

38 Scopus citations

Whole exome sequencing reveals homozygous mutations in RAI1, OTOF, and SLC26A4 genes associated with nonsyndromic hearing loss in Altaian families (South Siberia)

Churbanov, A. Y., Karafet, T. M., Morozov, I. V., Mikhalskaia, V. Y., Zytsar, M. V., Bondar, A. A. & Posukh, O. L., Apr 1 2016, In : PloS one. 11, 4, e0153841.

Research output: Contribution to journalArticle

5 Scopus citations

Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

Hsieh, P. H., Veeramah, K. R., Lachance, J., Tishkoff, S. A., Wall, J. D., Hammer, M. F. & Gutenkunst, R. N., Mar 2016, In : Genome Research. 26, 3, p. 279-290 12 p.

Research output: Contribution to journalArticle

29 Scopus citations

xGDBvm: A web GUI-driven workflow for annotating eukaryotic genomes in the cloud

Duvick, J., Standage, D. S., Merchant, N. C. & Brendeld, V. P., Apr 1 2016, In : Plant Cell. 28, 4, p. 840-854 15 p.

Research output: Contribution to journalArticle

1 Scopus citations
2015

A genome-wide association study platform built on iPlant cyber-infrastructure

Wang, L., Ware, D., Lushbough, C., Merchant, N. C. & Stein, L., Feb 1 2015, In : Concurrency Computation. 27, 2, p. 420-432 13 p.

Research output: Contribution to journalArticle

4 Scopus citations

A model for effects of adaptive immunity on tumor response to chemotherapy and chemoimmunotherapy

Robertson-Tessi, M., Fox, A. E-K. & Goriely, A., Sep 7 2015, In : Journal of Theoretical Biology. 380, p. 569-584 16 p.

Research output: Contribution to journalArticle

12 Scopus citations

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Karmin, M., Saag, L., Vicente, M., Wilson Sayres, M. A., Järve, M., Talas, U. G., Rootsi, S., Ilumäe, A. M., Mägi, R., Mitt, M., Pagani, L., Puurand, T., Faltyskova, Z., Clemente, F., Cardona, A., Metspalu, E., Sahakyan, H., Yunusbayev, B., Hudjashov, G., DeGiorgio, M. & 80 others, Loogväli, E. L., Eichstaedt, C., Eelmets, M., Chaubey, G., Tambets, K., Litvinov, S., Mormina, M., Xue, Y., Ayub, Q., Zoraqi, G., Korneliussen, T. S., Akhatova, F., Lachance, J., Tishkoff, S., Momynaliev, K., Ricaut, F. X., Kusuma, P., Razafindrazaka, H., Pierron, D., Cox, M. P., Sultana, G. N. N., Willerslev, R., Muller, C., Westaway, M., Lambert, D., Skaro, V., Kovačević, L., Turdikulova, S., Dalimova, D., Khusainova, R., Trofimova, N., Akhmetova, V., Khidiyatova, I., Lichman, D. V., Isakova, J., Pocheshkhova, E., Sabitov, Z., Barashkov, N. A., Nymadawa, P., Mihailov, E., Seng, J. W. T., Evseeva, I., Migliano, A. B., Abdullah, S., Andriadze, G., Primorac, D., Atramentova, L., Utevska, O., Yepiskoposyan, L., Marjanović, D., Kushniarevich, A., Behar, D. M., Gilissen, C., Vissers, L., Veltman, J. A., Balanovska, E., Derenko, M., Malyarchuk, B., Metspalu, A., Fedorova, S., Eriksson, A., Manica, A., Mendez, F. L., Karafet, T. M., Veeramah, K. R., Bradman, N., Hammer, M. F., Osipova, L. P., Balanovsky, O., Khusnutdinova, E. K., Johnsen, K., Remm, M., Thomas, M. G., Tyler-Smith, C., Underhill, P. A., Willerslev, E., Nielsen, R., Metspalu, M., Villems, R. & Kivisild, T., Apr 1 2015, In : Genome Research. 25, 4, p. 459-466 8 p.

Research output: Contribution to journalArticle

151 Scopus citations