The effectiveness of position- and composition-specific gap costs for protein similarity searches

door Stojmirović, Aleksandar, Gertz, E. Michael, Altschul, Stephen F., Yu, Yi-Kuo
Gepubliceerd in 2008

Comparative analysis of genome sequences of the Th2 cytokine region of rabbit (Oryctolagus cuniculus) with those of nine different species

door Gertz, E. Michael, Agarwala, Richa, Mage, Rose G., Schäffer, Alejandro A.
Gepubliceerd in 2011

Evaluating annotations of an Agilent expression chip suggests that many features cannot be interpreted

door Gertz, E Michael, Sengupta, Kundan, Difilippantonio, Michael J, Ried, Thomas, Schäffer, Alejandro A
Gepubliceerd in 2009

Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches

door Yu, Yi-Kuo, Gertz, E. Michael, Agarwala, Richa, Schäffer, Alejandro A., Altschul, Stephen F.
Gepubliceerd in 2006

Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST

door Gertz, E Michael, Yu, Yi-Kuo, Agarwala, Richa, Schäffer, Alejandro A, Altschul, Stephen F
Gepubliceerd in 2006

PSI-BLAST pseudocounts and the minimum description length principle

door Altschul, Stephen F., Gertz, E. Michael, Agarwala, Richa, Schäffer, Alejandro A., Yu, Yi-Kuo
Gepubliceerd in 2009

Genome-Wide Changes in Protein Translation Efficiency Are Associated with Autism

door Rogozin, Igor B, Gertz, E Michael, Baranov, Pasha V, Poliakov, Eugenia, Schaffer, Alejandro A
Gepubliceerd in Genome Biol Evol (2018)

Linkage analysis of a large African family segregating stuttering suggests polygenic inheritance

door Raza, M. Hashim, Gertz, E. Michael, Mundorff, Jennifer, Lukong, Joseph, Kuster, Judith, Schäffer, Alejandro A., Drayna, Dennis
Gepubliceerd in 2012

Inferring models of multiscale copy number evolution for single-tumor phylogenetics

door Chowdhury, Salim Akhter, Gertz, E. Michael, Wangsa, Darawalee, Heselmeyer-Haddad, Kerstin, Ried, Thomas, Schäffer, Alejandro A., Schwartz, Russell
Gepubliceerd in Bioinformatics (2015)

Protein Database Searches Using Compositionally Adjusted Substitution Matrices

door Altschul, Stephen F., Wootton, John C., Gertz, E. Michael, Agarwala, Richa, Morgulis, Aleksandr, Schäffer, Alejandro A., Yu, Yi-Kuo
Gepubliceerd in 2005

Accuracy and coverage assessment of Oryctolagus cuniculus (Rabbit) Genes Encoding Immunoglobulins in the Whole Genome Sequence Assembly (OryCun2.0) and Localization of the IGH Locu...

door Gertz, E. Michael, Schäffer, Alejandro A., Agarwala, Richa, Bonnet-Garnier, Amélie, Rogel-Gaillard, Claire, Hayes, Hélène, Mage, Rose G.
Gepubliceerd in 2013

Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation

door Du, Xiangjun, Gertz, E. Michael, Wojtowicz, Damian, Zhabinskaya, Dina, Levens, David, Benham, Craig J., Schäffer, Alejandro A., Przytycka, Teresa M.
Gepubliceerd in Nucleic Acids Res (2014)

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe

door Gertz, E. Michael, Chowdhury, Salim Akhter, Lee, Woei-Jyh, Wangsa, Darawalee, Heselmeyer-Haddad, Kerstin, Ried, Thomas, Schwartz, Russell, Schäffer, Alejandro A.
Gepubliceerd in PLoS One (2016)

Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data

door Lei, Haoyun, Lyu, Bochuan, Gertz, E. Michael, Schäffer, Alejandro A., Shi, Xulian, Wu, Kui, Li, Guibo, Xu, Liqin, Hou, Yong, Dean, Michael, Schwartz, Russell
Gepubliceerd in J Comput Biol (2020)

Phylogenetic Analysis of Multiple FISH Markers in Oral Tongue Squamous Cell Carcinoma Suggests that a Diverse Distribution of Copy Number Changes Is Associated with Poor Prognosis

door Wangsa, Darawalee, Chowdhury, Salim Akhter, Ryott, Michael, Gertz, E. Michael, Elmberger, Göran, Auer, Gert, Lundqvist, Elisabeth Åvall, Küffer, Stefan, Ströbel, Philipp, Schäffer, Alejandro A., Schwartz, Russell, Munck-Wikland, Eva, Ried, Thomas, Heselmeyer-Haddad, Kerstin
Gepubliceerd in Int J Cancer (2015)

A common SLC26A4-linked haplotype underlying non-syndromic hearing loss with enlargement of the vestibular aqueduct

door Chattaraj, Parna, Munjal, Tina, Honda, Keiji, Rendtorff, Nanna D, Ratay, Jessica S, Muskett, Julie A, Risso, Davide S, Roux, Isabelle, Gertz, E Michael, Schäffer, Alejandro A, Friedman, Thomas B, Morell, Robert J, Tranebjærg, Lisbeth, Griffith, Andrew J
Gepubliceerd in J Med Genet (2017)

The phenotype of human STK4 deficiency

door Abdollahpour, Hengameh, Appaswamy, Giridharan, Kotlarz, Daniel, Diestelhorst, Jana, Beier, Rita, Schäffer, Alejandro A., Gertz, E. Michael, Schambach, Axel, Kreipe, Hans H., Pfeifer, Dietmar, Engelhardt, Karin R., Rezaei, Nima, Grimbacher, Bodo, Lohrmann, Sabine, Sherkat, Roya, Klein, Christoph
Gepubliceerd in 2012

High Levels of Chromosomal Copy Number Alterations and TP53 Mutations Correlate with Poor Outcome in Younger Breast Cancer Patients

door Koçak, Ayla, Heselmeyer-Haddad, Kerstin, Lischka, Annette, Hirsch, Daniela, Fiedler, David, Hu, Yue, Doberstein, Natalie, Torres, Irianna, Chen, Wei-Dong, Gertz, E. Michael, Schäffer, Alejandro A., Freitag-Wolf, Sandra, Kirfel, Jutta, Auer, Gert, Habermann, Jens K., Ried, Thomas
Gepubliceerd in Am J Pathol (2020)

Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patients

door Oltmann, Johanna, Heselmeyer-Haddad, Kerstin, Hernandez, Leanora S., Meyer, Rüdiger, Torres, Irianna, Hu, Yue, Doberstein, Natalie, Killian, J. Keith, Petersen, David, Zhu, Y. Jack, Edelman, Daniel C., Meltzer, Paul S., Schwartz, Russell, Gertz, E. Michael, Schäffer, Alejandro A., Auer, Gert, Habermann, Jens K., Ried, Thomas
Gepubliceerd in Genes Chromosomes Cancer (2018)

PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem

door Sadeqi Azer, Erfan, Rashidi Mehrabadi, Farid, Malikić, Salem, Li, Xuan Cindy, Bartok, Osnat, Litchfield, Kevin, Levy, Ronen, Samuels, Yardena, Schäffer, Alejandro A, Gertz, E Michael, Day, Chi-Ping, Pérez-Guijarro, Eva, Marie, Kerrie, Lee, Maxwell P, Merlino, Glenn, Ergun, Funda, Sahinalp, S Cenk
Gepubliceerd in Bioinformatics (2020)