Section of Computational Biology

2010

DNMT3A mutations in acute myeloid leukemia

Ley, T. J., Ding, L., Walter, M. J., McLellan, M. D., Lamprecht, T., Larson, D. E., Kandoth, C., Payton, J. E., Baty, J., Welch, J., Harris, C. C., Lichti, C. F., Townsend, R. R., Fulton, R. S., Dooling, D. J., Koboldt, D. C., Schmidt, H., Zhang, Q., Osborne, J. R. & Lin, L. & 28 others, O'Laughlin, M., McMichael, J. F., Delehaunty, K. D., McGrath, S. D., Fulton, L. A., Magrini, V. J., Vickery, T. L., Hundal, J., Cook, L. L., Conyers, J. J., Swift, G. W., Reed, J. P., Alldredge, P. A., Wylie, T., Walker, J., Kalicki, J., Watson, M. A., Heath, S., Shannon, W. D., Varghese, N., Nagarajan, R., Westervelt, P., Tomasson, M. H., Link, D. C., Graubert, T. A., DiPersio, J. F., Mardis, E. R. & Wilson, R. K., Dec 16 2010, In: New England Journal of Medicine. 363, 25, p. 2424-2433 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1650 Scopus citations

Folding kinetics for the conformational switch between alternative RNA structures

Cao, S., Fürtig, B., Schwalbe, H. & Chen, S. J., Oct 28 2010, In: Journal of Physical Chemistry B. 114, 42, p. 13609-13615 7 p.

Research output: Contribution to journal › Article › peer-review

7 Scopus citations

Genome remodelling in a basal-like breast cancer metastasis and xenograft

Ding, L., Ellis, M. J., Li, S., Larson, D. E., Chen, K., Wallis, J. W., Harris, C. C., McLellan, M. D., Fulton, R. S., Fulton, L. L., Abbott, R. M., Hoog, J., Dooling, D. J., Koboldt, D. C., Schmidt, H., Kalicki, J., Zhang, Q., Chen, L., Lin, L. & Wendl, M. C. & 49 others, McMichael, J. F., Magrini, V. J., Cook, L., McGrath, S. D., Vickery, T. L., Appelbaum, E., Deschryver, K., Davies, S., Guintoli, T., Lim, L., Crowder, R., Tao, Y., Snider, J. E., Smith, S. M., Dukes, A. F., Sanderson, G. E., Pohl, C. S., Delehaunty, K. D., Fronick, C. C., Pape, K. A., Reed, J. S., Robinson, J. S., Hodges, J. S., Schierding, W., Dees, N. D., Shen, D., Locke, D. P., Wiechert, M. E., Eldred, J. M., Peck, J. B., Oberkfell, B. J., Lolofie, J. T., Du, F., Hawkins, A. E., Oĝlaughlin, M. D., Bernard, K. E., Cunningham, M., Elliott, G., Mason, M. D., Thompson, D. M., Ivanovich, J. L., Goodfellow, P. J., Perou, C. M., Weinstock, G. M., Aft, R., Watson, M., Ley, T. J., Wilson, R. K. & Mardis, E. R., Apr 15 2010, In: Nature. 464, 7291, p. 999-1005 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1018 Scopus citations

Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

Noushmehr, H., Weisenberger, D. J., Diefes, K., Phillips, H. S., Pujara, K., Berman, B. P., Pan, F., Pelloski, C. E., Sulman, E. P., Bhat, K. P., Verhaak, R. G. W., Hoadley, K. A., Hayes, D. N., Perou, C. M., Schmidt, H. K., Ding, L., Wilson, R. K., Van Den Berg, D., Shen, H. & Bengtsson, H. & 7 others, Neuvial, P., Cope, L. M., Buckley, J., Herman, J. G., Baylin, S. B., Laird, P. W. & Aldape, K., May 18 2010, In: Cancer Cell. 17, 5, p. 510-522 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1921 Scopus citations

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

Verhaak, R. G. W., Hoadley, K. A., Purdom, E., Wang, V., Qi, Y., Wilkerson, M. D., Miller, C. R., Ding, L., Golub, T., Mesirov, J. P., Alexe, G., Lawrence, M., O'Kelly, M., Tamayo, P., Weir, B. A., Gabriel, S., Winckler, W., Gupta, S., Jakkula, L. & Feiler, H. S. & 13 others, Hodgson, J. G., James, C. D., Sarkaria, J. N., Brennan, C., Kahn, A., Spellman, P. T., Wilson, R. K., Speed, T. P., Gray, J. W., Meyerson, M., Getz, G., Perou, C. M. & Hayes, D. N., Jan 19 2010, In: Cancer Cell. 17, 1, p. 98-110 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

5634 Scopus citations

New estimators for calculating solvation entropy and enthalpy and comparative assessments of their accuracy and precision

Wyczalkowski, M. A., Vitalis, A. & Pappu, R. V., Jun 24 2010, In: Journal of Physical Chemistry B. 114, 24, p. 8166-8180 15 p.

Research output: Contribution to journal › Article › peer-review

22 Scopus citations

Niche construction through cooperation: A nonlinear dynamics contribution to modeling facets of the evolutionary history in the genus homo

Fuentes, A., Wyczalkowski, M. A. & MacKinnon, K. C., Jun 2010, In: Current Anthropology. 51, 3, p. 435-444 10 p.

Research output: Contribution to journal › Article › peer-review

44 Scopus citations

Predicting loop-helix tertiary structural contacts in RNA pseudoknots

Cao, S., Giedroc, D. P. & Chen, S. J., Mar 2010, In: RNA. 16, 3, p. 538-552 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

37 Scopus citations

2009

A new computational approach for mechanical folding kinetics of RNA hairpins

Cao, S. & Chen, S. J., 2009, In: Biophysical Journal. 96, 10, p. 4024-4034 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus citations

BreakDancer: An algorithm for high-resolution mapping of genomic structural variation

Chen, K., Wallis, J. W., McLellan, M. D., Larson, D. E., Kalicki, J. M., Pohl, C. S., McGrath, S. D., Wendl, M. C., Zhang, Q., Locke, D. P., Shi, X., Fulton, R. S., Ley, T. J., Wilson, R. K., Ding, L. & Mardis, E. R., 2009, In: Nature Methods. 6, 9, p. 677-681 5 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1122 Scopus citations

CMDS: A population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data

Zhang, Q., Ding, L., Larson, D. E., Koboldt, D. C., McLellan, M. D., Chen, K., Shi, X., Kraja, A., Mardis, E. R., Wilson, R. K., Borecki, I. B. & Province, M. A., Dec 23 2009, In: Bioinformatics. 26, 4, p. 464-469 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

55 Scopus citations

Predicting structures and stabilities for H-type pseudoknots with interhelix loops

Cao, S. & Chen, S. J., Apr 2009, In: RNA. 15, 4, p. 696-706 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

83 Scopus citations

Recurring mutations found by sequencing an acute myeloid leukemia genome

Mardis, E. R., Ding, L., Dooling, D. J., Larson, D. E., McLellan, M. D., Chen, K., Koboldt, D. C., Fulton, R. S., Delehaunty, K. D., McGrath, S. D., Fulton, L. A., Locke, D. P., Magrini, V. J., Abbott, R. M., Vickery, T. L., Reed, J. S., Robinson, J. S., Wylie, T., Smith, S. M. & Carmichael, L. & 38 others, Eldred, J. M., Harris, C. C., Walker, J., Peck, J. B., Du, F., Dukes, A. F., Sanderson, G. E., Brummett, A. M., Clark, E., McMichael, J. F., Meyer, R. J., Schindler, J. K., Pohl, C. S., Wallis, J. W., Shi, X., Lin, L., Schmidt, H., Tang, Y., Haipek, C., Wiechert, M. E., Ivy, J. V., Kalicki, J., Elliott, G., Ries, R. E., Payton, J. E., Westervelt, P., Tomasson, M. H., Watson, M. A., Baty, J., Heath, S., Shannon, W. D., Nagarajan, R., Link, D. C., Walter, M. J., Graubert, T. A., DiPersio, J. F., Wilson, R. K. & Ley, T. J., Sep 10 2009, In: New England Journal of Medicine. 361, 11, p. 1058-1066 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1911 Scopus citations

Statistical aspects of discerning indel-type structural variation via DNA sequence alignment

Wendl, M. C. & Wilson, R. K., Aug 5 2009, In: BMC genomics. 10, p. 359 1 p., 1471.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus citations

Technology takes on deadlines for fetal human rights

Wendl, M. C., Apr 16 2009, In: Nature. 458, 7240, p. 831 1 p.

Research output: Contribution to journal › Letter › peer-review

Open Access

The theory of discovering rare variants via DNA sequencing

Wendl, M. C. & Wilson, R. K., Oct 20 2009, In: BMC genomics. 10, p. 485 1 p., 1471.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus citations

VarScan: Variant detection in massively parallel sequencing of individual and pooled samples

Koboldt, D. C., Chen, K., Wylie, T., Larson, D. E., McLellan, M. D., Mardis, E. R., Weinstock, G. M., Wilson, R. K. & Ding, L., 2009, In: Bioinformatics. 25, 17, p. 2283-2285 3 p.

Research output: Contribution to journal › Article › peer-review

Open Access

993 Scopus citations

2008

Aspects of coverage in medical DNA sequencing

Wendl, M. C. & Wilson, R. K., May 16 2008, In: BMC bioinformatics. 9, 239.

Research output: Contribution to journal › Article › peer-review

Open Access

25 Scopus citations

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

McLendon, R., Friedman, A., Bigner, D., Van Meir, E. G., Brat, D. J., Mastrogianakis, G. M., Olson, J. J., Mikkelsen, T., Lehman, N., Aldape, K., Yung, W. K. A., Bogler, O., Weinstein, J. N., VandenBerg, S., Berger, M., Prados, M., Muzny, D., Morgan, M., Scherer, S. & Sabo, A. & 211 others, Nazareth, L., Lewis, L., Hall, O., Zhu, Y., Ren, Y., Alvi, O., Yao, J., Hawes, A., Jhangiani, S., Fowler, G., San Lucas, A., Kovar, C., Cree, A., Dinh, H., Santibanez, J., Joshi, V., Gonzalez-Garay, M. L., Miller, C. A., Milosavljevic, A., Donehower, L., Wheeler, D. A., Gibbs, R. A., Cibulskis, K., Sougnez, C., Fennell, T., Mahan, S., Wilkinson, J., Ziaugra, L., Onofrio, R., Bloom, T., Nicol, R., Ardlie, K., Baldwin, J., Gabriel, S., Lander, E. S., Ding, L., Fulton, R. S., McLellan, M. D., Wallis, J., Larson, D. E., Shi, X., Abbott, R., Fulton, L., Chen, K., Koboldt, D. C., Wendl, M. C., Meyer, R., Tang, Y., Lin, L., Osborne, J. R., Dunford-Shore, B. H., Miner, T. L., Delehaunty, K., Markovic, C., Swift, G., Courtney, W., Pohl, C., Abbott, S., Hawkins, A., Leong, S., Haipek, C., Schmidt, H., Wiechert, M., Vickery, T., Scott, S., Dooling, D. J., Chinwalla, A., Weinstock, G. M., Mardis, E. R., Wilson, R. K., Getz, G., Winckler, W., Verhaak, R. G. W., Lawrence, M. S., O'Kelly, M., Robinson, J., Alexe, G., Beroukhim, R., Carter, S., Chiang, D., Gould, J., Gupta, S., Korn, J., Mermel, C., Mesirov, J., Monti, S., Nguyen, H., Parkin, M., Reich, M., Stransky, N., Weir, B. A., Garraway, L., Golub, T., Meyerson, M., Chin, L., Protopopov, A., Zhang, J., Perna, I., Aronson, S., Sathiamoorthy, N., Ren, G., Yao, J., Wiedemeyer, W. R., Kim, H., Sek, W. K., Xiao, Y., Kohane, I. S., Seidman, J., Park, P. J., Kucherlapati, R., Laird, P. W., Cope, L., Herman, J. G., Weisenberger, D. J., Pan, F., Van Den Berg, D., Van Neste, L., Joo, M. Y., Schuebel, K. E., Baylin, S. B., Absher, D. M., Li, J. Z., Southwick, A., Brady, S., Aggarwal, A., Chung, T., Sherlock, G., Brooks, J. D., Myers, R. M., Spellman, P. T., Purdom, E., Jakkula, L. R., Lapuk, A. V., Marr, H., Dorton, S., Yoon, G. C., Han, J., Ray, A., Wang, V., Durinck, S., Robinson, M., Wang, N. J., Vranizan, K., Peng, V., Van Name, E., Fontenay, G. V., Ngai, J., Conboy, J. G., Parvin, B., Feiler, H. S., Speed, T. P., Gray, J. W., Brennan, C., Socci, N. D., Olshen, A., Taylor, B. S., Lash, A., Schultz, N., Reva, B., Antipin, Y., Stukalov, A., Gross, B., Cerami, E., Wei, Q. W., Qin, L. X., Seshan, V. E., Villafania, L., Cavatore, M., Borsu, L., Viale, A., Gerald, W., Sander, C., Ladanyi, M., Perou, C. M., Hayes, D. N., Topal, M. D., Hoadley, K. A., Qi, Y., Balu, S., Shi, Y., Wu, J., Penny, R., Bittner, M., Shelton, T., Lenkiewicz, E., Morris, S., Beasley, D., Sanders, S., Kahn, A., Sfeir, R., Chen, J., Nassau, D., Feng, L., Hickey, E., Barker, A., Gerhard, D. S., Vockley, J., Compton, C., Vaught, J., Fielding, P., Ferguson, M. L., Schaefer, C., Zhang, J., Madhavan, S., Buetow, K. H., Collins, F., Good, P., Guyer, M., Ozenberger, B., Peterson, J. & Thomson, E., Oct 23 2008, In: Nature. 455, 7216, p. 1061-1068 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

6256 Scopus citations

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

Ley, T. J., Mardis, E. R., Ding, L., Fulton, B., McLellan, M. D., Chen, K., Dooling, D., Dunford-Shore, B. H., McGrath, S., Hickenbotham, M., Cook, L., Abbott, R., Larson, D. E., Koboldt, D. C., Pohl, C., Smith, S., Hawkins, A., Abbott, S., Locke, D. & Hillier, L. W. & 28 others, Miner, T., Fulton, L., Magrini, V., Wylie, T., Glasscock, J., Conyers, J., Sander, N., Shi, X., Osborne, J. R., Minx, P., Gordon, D., Chinwalla, A., Zhao, Y., Ries, R. E., Payton, J. E., Westervelt, P., Tomasson, M. H., Watson, M., Baty, J., Ivanovich, J., Heath, S., Shannon, W. D., Nagarajan, R., Walter, M. J., Link, D. C., Graubert, T. A., DiPersio, J. F. & Wilson, R. K., Nov 6 2008, In: Nature. 456, 7218, p. 66-72 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1056 Scopus citations

Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma

Marks, J. L., Gong, Y., Chitale, D., Golas, B., McLellan, M. D., Kasai, Y., Ding, L., Mardis, E. R., Wilson, R. K., Solit, D., Levine, R., Michel, K., Thomas, R. K., Rusch, V. W., Ladanyi, M. & Pao, W., Jul 15 2008, In: Cancer research. 68, 14, p. 5524-5528 5 p.

Research output: Contribution to journal › Article › peer-review

Open Access

188 Scopus citations

Predicting ribosomal frameshifting efficiency

Cao, S. & Chen, S. J., Apr 8 2008, In: Physical Biology. 5, 1, 016002.

Research output: Contribution to journal › Article › peer-review

23 Scopus citations

Publisher's Note: Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange (Physical Review e (2008) 77 (026104))

Wyczalkowski, M. A. & Pappu, R. V., Feb 26 2008, In: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 77, 2, 029905.

Research output: Contribution to journal › Comment/debate

Open Access

Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange

Wyczalkowski, M. A. & Pappu, R. V., Feb 20 2008, In: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 77, 2, 026104.

Research output: Contribution to journal › Article › peer-review

10 Scopus citations

Somatic mutations affect key pathways in lung adenocarcinoma

Ding, L., Getz, G., Wheeler, D. A., Mardis, E. R., McLellan, M. D., Cibulskis, K., Sougnez, C., Greulich, H., Muzny, D. M., Morgan, M. B., Fulton, L., Fulton, R. S., Zhang, Q., Wendl, M. C., Lawrence, M. S., Larson, D. E., Chen, K., Dooling, D. J., Sabo, A. & Hawes, A. C. & 70 others, Shen, H., Jhangiani, S. N., Lewis, L. R., Hall, O., Zhu, Y., Mathew, T., Ren, Y., Yao, J., Scherer, S. E., Clerc, K., Metcalf, G. A., Ng, B., Milosavljevic, A., Gonzalez-Garay, M. L., Osborne, J. R., Meyer, R., Shi, X., Tang, Y., Koboldt, D. C., Lin, L., Abbott, R., Miner, T. L., Pohl, C., Fewell, G., Haipek, C., Schmidt, H., Dunford-Shore, B. H., Kraja, A., Crosby, S. D., Sawyer, C. S., Vickery, T., Sander, S., Robinson, J., Winckler, W., Baldwin, J., Chirieac, L. R., Dutt, A., Fennell, T., Hanna, M., Johnson, B. E., Onofrio, R. C., Thomas, R. K., Tonon, G., Weir, B. A., Zhao, X., Ziaugra, L., Zody, M. C., Giordano, T., Orringer, M. B., Roth, J. A., Spitz, M. R., Wistuba, I. I., Ozenberger, B., Good, P. J., Chang, A. C., Beer, D. G., Watson, M. A., Ladanyi, M., Broderick, S., Yoshizawa, A., Travis, W. D., Pao, W., Province, M. A., Weinstock, G. M., Varmus, H. E., Gabriel, S. B., Lander, E. S., Gibbs, R. A., Meyerson, M. & Wilson, R. K., Oct 23 2008, In: Nature. 455, 7216, p. 1069-1075 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2291 Scopus citations

The chromosome 3p21.3-encoded gene, LIMD1, is a critical tumor suppressor involved in human lung cancer development

Sharp, T. V., Al-Attar, A., Foxler, D. E., Ding, L., Vallim, T. Q. D. A., Zhang, Y., Nijmeh, H. S., Webb, T. M., Nicholson, A. G., Zhang, Q., Kraja, A., Spendlove, I., Osborne, J., Mardis, E. & Longmore, G. D., Dec 16 2008, In: Proceedings of the National Academy of Sciences of the United States of America. 105, 50, p. 19932-19937 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

53 Scopus citations

2007

Algebraic correction methods for computational assessment of clone overlaps in DNA fingerprint mapping

Wendl, M. C., Apr 18 2007, In: BMC bioinformatics. 8, 127.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

Biphasic Folding Kinetics of RNA Pseudoknots and Telomerase RNA Activity

Cao, S. & Chen, S. J., Mar 30 2007, In: Journal of Molecular Biology. 367, 3, p. 909-924 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

35 Scopus citations

Calcineurin-NFATc signaling pathway regulates AQP2 expression in response to calcium signals and osmotic stress

Li, S. Z., McDill, B. W., Kovach, P. A., Ding, L., Go, W. Y., Ho, S. N. & Chen, F., May 2007, In: American Journal of Physiology - Cell Physiology. 292, 5, p. C1606-C1616

Research output: Contribution to journal › Article › peer-review

77 Scopus citations

Characterizing the cancer genome in lung adenocarcinoma

Weir, B. A., Woo, M. S., Getz, G., Perner, S., Ding, L., Beroukhim, R., Lin, W. M., Province, M. A., Kraja, A., Johnson, L. A., Shah, K., Sato, M., Thomas, R. K., Barletta, J. A., Borecki, I. B., Broderick, S., Chang, A. C., Chiang, D. Y., Chirieac, L. R. & Cho, J. & 50 others, Fujii, Y., Gazdar, A. F., Giordano, T., Greulich, H., Hanna, M., Johnson, B. E., Kris, M. G., Lash, A., Lin, L., Lindeman, N., Mardis, E. R., McPherson, J. D., Minna, J. D., Morgan, M. B., Nadel, M., Orringer, M. B., Osborne, J. R., Ozenberger, B., Ramos, A. H., Robinson, J., Roth, J. A., Rusch, V., Sasaki, H., Shepherd, F., Sougnez, C., Spitz, M. R., Tsao, M. S., Twomey, D., Verhaak, R. G. W., Weinstock, G. M., Wheeler, D. A., Winckler, W., Yoshizawa, A., Yu, S., Zakowski, M. F., Zhang, Q., Beer, D. G., Wistuba, I. I., Watson, M. A., Garraway, L. A., Ladanyi, M., Travis, W. D., Pao, W., Rubin, M. A., Gabriel, S. B., Gibbs, R. A., Varmus, H. E., Wilson, R. K., Lander, E. S. & Meyerson, M., Dec 6 2007, In: Nature. 450, 7171, p. 893-898 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

955 Scopus citations

Design and implementation of a generalized laboratory data model

Wendl, M. C., Smith, S., Pohl, C. S., Dooling, D. J., Chinwalla, A. T., Crouse, K., Hepler, T., Leong, S., Carmichael, L., Nhan, M., Oberkfell, B. J., Mardis, E. R., Hillier, L. D. W. & Wilson, R. K., Sep 26 2007, In: BMC bioinformatics. 8, 362.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus citations

H-index: However ranked, citations need context [2]

Wendl, M. C., Sep 27 2007, In: Nature. 449, 7161, p. 403 1 p.

Research output: Contribution to journal › Letter › peer-review

Open Access

86 Scopus citations

PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data

Chen, K., McLellan, M. D., Ding, L., Wendl, M. C., Kasai, Y., Wilson, R. K. & Mardis, E. R., May 2007, In: Genome research. 17, 5, p. 659-666 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

69 Scopus citations

Random covering of multiple one-dimensional domains with an application to DNA sequencing

Wendl, M. C., 2007, In: SIAM Journal on Applied Mathematics. 68, 3, p. 890-905 16 p.

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

2006

A general coverage theory for shotgun DNA sequencing

Wendl, M. C., Jul 2006, In: Journal of Computational Biology. 13, 6, p. 1177-1196 20 p.

Research output: Contribution to journal › Review article › peer-review

14 Scopus citations

Characterizing the conformational ensemble of monomeric polyglutamine

Wang, X., Vitalis, A., Wyczalkowski, M. A. & Pappu, R. V., May 1 2006, In: Proteins: Structure, Function and Genetics. 63, 2, p. 297-311 15 p.

Research output: Contribution to journal › Article › peer-review

121 Scopus citations

Codon usage patterns in Nematoda: Analysis based on over 25 million codons in thirty-two species

Mitreva, M., Wendl, M. C., Martin, J., Wylie, T., Yin, Y., Larson, A., Parkinson, J., Waterston, R. H. & McCarter, J. P., Aug 14 2006, In: Genome biology. 7, 8, R75.

Research output: Contribution to journal › Article › peer-review

Open Access

55 Scopus citations

Congenital progressive hydronephrosis (cph) is caused by an S256L mutation in aquaporin-2 that affect its phosphorylation and apical membrane accumulation

McDill, B. W., Li, S. Z., Kovach, P. A., Ding, L. & Chen, F., May 2 2006, In: Proceedings of the National Academy of Sciences of the United States of America. 103, 18, p. 6952-6957 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

118 Scopus citations

Free energy landscapes of RNA/RNA complexes: With applications to snRNA complexes in spliceosomes

Cao, S. & Chen, S. J., Mar 17 2006, In: Journal of Molecular Biology. 357, 1, p. 292-312 21 p.

Research output: Contribution to journal › Article › peer-review

31 Scopus citations

Occupancy modeling of coverage distribution for whole genome shotgun DNA sequencing

Wendl, M. C., Jan 2006, In: Bulletin of Mathematical Biology. 68, 1, p. 179-196 18 p.

Research output: Contribution to journal › Article › peer-review

12 Scopus citations

Predicting RNA pseudoknot folding thermodynamics

Cao, S. & Chen, S. J., 2006, In: Nucleic acids research. 34, 9, p. 2634-2652 19 p.

Research output: Contribution to journal › Article › peer-review

Open Access

120 Scopus citations

2005

Bioweapons could kill more in one strike than guns [2]

Wendl, M. C., Sep 8 2005, In: Nature. 437, 7056, 1 p.

Research output: Contribution to journal › Letter › peer-review

Open Access

2 Scopus citations

Extension of Lander-Waterman theory for sequencing filtered DNA libraries

Wendl, M. C. & Barbazuk, W. B., Oct 10 2005, In: BMC bioinformatics. 6, 245.

Research output: Contribution to journal › Article › peer-review

Open Access

19 Scopus citations

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Hillier, L. D. W., Graves, T. A., Fulton, R. S., Fulton, L. A., Pepin, K. H., Minx, P., Wagner-McPherson, C., Layman, D., Wylie, K., Sekhon, M., Becker, M. C., Fewell, G. A., Delehaunty, K. D., Miner, T. L., Nash, W. E., Kremitzki, C., Oddy, L., Du, H., Sun, H. & Bradshaw-Cordum, H. & 102 others, Ali, J., Carter, J., Cordes, M., Harris, A., Isak, A., Van Brunt, A., Nguyen, C., Du, F., Courtney, L., Kalicki, J., Ozersky, P., Abbott, S., Armstrong, J., Belter, E. A., Caruso, L., Cedroni, M., Cotton, M., Davidson, T., Desai, A., Elliott, G., Erb, T., Fronick, C., Gaige, T., Haakenson, W., Haglund, K., Holmes, A., Harkins, R., Kim, K., Kruchowski, S. S., Strong, C. M., Grewal, N., Goyea, E., Hou, S., Levy, A., Martinka, S., Mead, K., McLellan, M. D., Meyer, R., Randall-Maher, J., Tomlinson, C., Dauphin-Kohlberg, S., Kozlowicz-Reilly, A., Shah, N., Swearengen-Shahid, S., Snider, J., Strong, J. T., Thompson, J., Yoakum, M., Leonard, S., Pearman, C., Trani, L., Radionenko, M., Waligorski, J. E., Wang, C., Rock, S. M., Tin-Wollam, A. M., Maupin, R., Latreille, P., Wendl, M. C., Yang, S. P., Pohl, C., Wallis, J. W., Spieth, J., Bieri, T. A., Berkowicz, N., Nelson, J. O., Osborne, J., Ding, L., Meyer, R., Sabo, A., Shotland, Y., Sinha, P., Wohldmann, P. E., Cook, L. L., Hickenbotham, M. T., Eldred, J., Williams, D., Jones, T. A., She, X., Ciccarelli, F. D., Izaurralde, E., Taylor, J., Schmutz, J., Myers, R. M., Cox, D. R., Huang, X., McPherson, J. D., Mardis, E. R., Clifton, S. W., Warren, W. C., Chinwalla, A. T., Eddy, S. R., Marra, M. A., Ovcharenko, I., Furey, T. S., Miller, W., Eichler, E. E., Bork, P., Suyama, M., Torrents, D., Waterston, R. H. & Wilson, R. K., Apr 7 2005, In: Nature. 434, 7034, p. 724-731 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

78 Scopus citations

Initial sequence of the chimpanzee genome and comparison with the human genome

The Chimpanzee Sequencing and Analysis Consortium, Sep 1 2005, In: Nature. 437, 7055, p. 69-87 19 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1826 Scopus citations

Predicting RNA folding thermodynamics with a reduced chain representation model

Cao, S. & Chen, S. J., Dec 2005, In: RNA. 11, 12, p. 1884-1897 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

108 Scopus citations

Probabilistic assessment of clone overlaps in DNA fingerprint mapping via a priori models

Wendl, M. C., 2005, In: Journal of Computational Biology. 12, 3, p. 283-297 15 p.

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

The question of forbidden knowledge [1] (multiple letters)

Wendl, M. C., Fish, J. M., Kempner, J., Perlis, C. S. & Merz, J. F., Jun 10 2005, In: Science. 308, 5728, p. 1549-1550 2 p.

Research output: Contribution to journal › Letter › peer-review

2004

EAnnot: A genome annotation tool using experimental evidence

Ding, L., Sabo, A., Berkowicz, N., Meyer, R. R., Shotland, Y., Johnson, M. R., Pepin, K. H., Wilson, R. K. & Spieth, J., Dec 2004, In: Genome research. 14, 12, p. 2503-2509 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

13 Scopus citations

Finishing the euchromatic sequence of the human genome

International Human Genome Sequencing Consortium, Oct 21 2004, In: Nature. 431, 7011, p. 931-945 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

3764 Scopus citations

Section of Computational Biology

Research output

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